bims-camemi 2023-07-16 papers

bims-camemi

Biomed News

on Mitochondrial metabolism in cancer

Issue of 2023‒07‒16
forty-six papers selected by
Christian Frezza, Universität zu Köln

Ribonucleotide synthesis by NME6 fuels mitochondrial gene expression.
Lysosomal cystine export regulates mTORC1 signaling to guide kidney epithelial cell fate specialization.
Mitochondrial respiratory complex I deficiency inhibits brown adipogenesis by limiting heme regulation of histone demethylation.
Disruption of testis-enriched cytochrome c oxidase subunit COX6B2 but not COX8C leads to subfertility.
TCA cycle deficiency in multiple sclerosis.
Mitochondria as intracellular signalling organelles. An update.
Succinate dehydrogenase variants in paraganglioma: why are B subunit variants 'bad'?
Metabolic reprogramming of cancer cells by JMJD6-mediated pre-mRNA splicing is associated with therapeutic response to splicing inhibitor.
Notch signaling regulates a metabolic switch through inhibiting PGC-1α and mitochondrial biogenesis in dedifferentiated liposarcoma.
Increased mitochondrial free Ca2+ during ischemia is suppressed, but not eliminated by, germline deletion of the mitochondrial Ca2+ uniporter.
MYC overrides HIF-1α to regulate proliferating primary cell metabolism in hypoxia.
Hypoxia-reprogramed megamitochondrion contacts and engulfs lysosome to mediate mitochondrial self-digestion.
Defining NAD(P)(H) Catabolism.
CRAT links cholesterol metabolism to innate immune responses in the heart.
Local coordination of mRNA storage and degradation near mitochondria modulates C. elegans ageing.
Succinate mediates inflammation-induced adrenocortical dysfunction.
Glutamine antagonist DRP-104 suppresses tumor growth and enhances response to checkpoint blockade in KEAP1 mutant lung cancer.
Capturing copper to inhibit inflammation.
IF1 ablation prevents ATP synthase oligomerization, enhances mitochondrial ATP turnover and promotes an adenosine-mediated pro-inflammatory phenotype.
NAD metabolism modulates inflammation and mitochondria function in diabetic kidney disease.
Cellular allostatic load is linked to increased energy expenditure and accelerated biological aging.
Inhibition of phosphodiesterase 4D suppresses mTORC1 signaling and pancreatic cancer growth.
Metabolic flux in the driver's seat during cardiac health and disease.
Divergent iron-regulatory states contribute to heterogeneity in breast cancer aggressiveness.
Fetal manipulation of maternal metabolism is a critical function of the imprinted Igf2 gene.
The glucose-to-acetate metabolic flux that drives endothelial-to-mesenchymal transition via TGF-β signaling.
Targeting the TCA cycle can ameliorate widespread axonal energy deficiency in neuroinflammatory lesions.
Cytochrome c lysine acetylation regulates cellular respiration and cell death in ischemic skeletal muscle.
Succinyl-CoA Synthetase Dysfunction as a Mechanism of Mitochondrial Encephalomyopathy: More than Just an Oxidative Energy Deficit.
Fumarate hydratase inhibition activates innate immunity via mitochondrial nucleic acid release.
Fluorescence microscopy imaging of mitochondrial metabolism in cancer cells.
LRP8-mediated selenocysteine uptake is a targetable vulnerability in MYCN-amplified neuroblastoma.
A critical role for heme synthesis and succinate in the regulation of pluripotent states transitions.
αKG-driven RNA polymerase II transcription of cyclin D1 licenses malic enzyme 2 to promote cell-cycle progression.
Lactate-dependent transcriptional regulation controls mammalian eye morphogenesis.
Functional decomposition of metabolism allows a system-level quantification of fluxes and protein allocation towards specific metabolic functions.
Immunoproteasome-specific subunit PSMB9 induction is required to regulate cellular proteostasis upon mitochondrial dysfunction.
Maintenance of cellular vitamin B6 levels and mitochondrial oxidative function depend on pyridoxal 5'-phosphate homeostasis protein (PLPHP).
NAD metabolism: Role in senescence regulation and aging.
An engineered biosensor enables dynamic aspartate measurements in living cells.
Hereditary leiomyomatosis and renal cell cancer (HLRCC) - linked with FH mutations.
STING is a cell-intrinsic metabolic checkpoint restricting aerobic glycolysis by targeting HK2.
Mitofusin-2 in nucleus accumbens D2-MSNs regulates social dominance and neuronal function.
Oxidative phosphorylation is a metabolic vulnerability of endocrine therapy and palbociclib resistant metastatic breast cancers.
Chemically induced reprogramming to reverse cellular aging.
ATPase activity of DFCP1 controls selective autophagy.

EMBO J. 2023 Jul 13. e113256

Ribonucleotide synthesis by NME6 fuels mitochondrial gene expression.

Nils Grotehans, Lynn McGarry, Hendrik Nolte, Vanessa Xavier, Moritz Kroker, Álvaro Jesús Narbona-Pérez, Soni Deshwal, Patrick Giavalisco, Thomas Langer, Thomas MacVicar.

  Replication of the mitochondrial genome and expression of the genes it encodes both depend on a sufficient supply of nucleotides to mitochondria. Accordingly, dysregulated nucleotide metabolism not only destabilises the mitochondrial genome, but also affects its transcription. Here, we report that a mitochondrial nucleoside diphosphate kinase, NME6, supplies mitochondria with pyrimidine ribonucleotides that are necessary for the transcription of mitochondrial genes. Loss of NME6 function leads to the depletion of mitochondrial transcripts, as well as destabilisation of the electron transport chain and impaired oxidative phosphorylation. These deficiencies are rescued by an exogenous supply of pyrimidine ribonucleosides. Moreover, NME6 is required for the maintenance of mitochondrial DNA when the access to cytosolic pyrimidine deoxyribonucleotides is limited. Our results therefore reveal an important role for ribonucleotide salvage in mitochondrial gene expression.

Keywords:  NME6; mitochondria; mitochondrial DNA; mitochondrial transcription; nucleotide metabolism

DOI:  https://doi.org/10.15252/embj.2022113256
Nat Commun. 2023 Jul 14. 14(1): 3994

Lysosomal cystine export regulates mTORC1 signaling to guide kidney epithelial cell fate specialization.

Marine Berquez, Zhiyong Chen, Beatrice Paola Festa, Patrick Krohn, Svenja Aline Keller, Silvia Parolo, Mikhail Korzinkin, Anna Gaponova, Endre Laczko, Enrico Domenici, Olivier Devuyst, Alessandro Luciani.

Differentiation is critical for cell fate decisions, but the signals involved remain unclear. The kidney proximal tubule (PT) cells reabsorb disulphide-rich proteins through endocytosis, generating cystine via lysosomal proteolysis. Here we report that defective cystine mobilization from lysosomes through cystinosin (CTNS), which is mutated in cystinosis, diverts PT cells towards growth and proliferation, disrupting their functions. Mechanistically, cystine storage stimulates Ragulator-Rag GTPase-dependent recruitment of mechanistic target of rapamycin complex 1 (mTORC1) and its constitutive activation. Re-introduction of CTNS restores nutrient-dependent regulation of mTORC1 in knockout cells, whereas cell-permeant analogues of L-cystine, accumulating within lysosomes, render wild-type cells resistant to nutrient withdrawal. Therapeutic mTORC1 inhibition corrects lysosome and differentiation downstream of cystine storage, and phenotypes in preclinical models of cystinosis. Thus, cystine serves as a lysosomal signal that tailors mTORC1 and metabolism to direct epithelial cell fate decisions. These results identify mechanisms and therapeutic targets for dysregulated homeostasis in cystinosis.

DOI: https://doi.org/10.1038/s41467-023-39261-3
Mitochondrion. 2023 Jul 12. pii: S1567-7249(23)00067-3. [Epub ahead of print]

Mitochondrial respiratory complex I deficiency inhibits brown adipogenesis by limiting heme regulation of histone demethylation.

Jingjing Liu, Wen Lu, Dongyue Yan, Junyuan Guo, Li Zhou, Bimin Shi, Xiong Su.

  Mitochondrial functions play a crucial role in determining the metabolic and thermogenic status of brown adipocytes. Increasing evidence reveals that the mitochondrial oxidative phosphorylation (OXPHOS) system plays an important role in brown adipogenesis, but the mechanistic insights are limited. Herein, we explored the potential metabolic mechanisms leading to OXPHOS regulation of brown adipogenesis in pharmacological and genetic models of mitochondrial respiratory complex I deficiency. OXPHOS deficiency inhibits brown adipogenesis through disruption of the brown adipogenic transcription circuit without affecting ATP levels. Neither blockage of calcium signaling nor antioxidant treatment can rescue the suppressed brown adipogenesis. Metabolomics analysis revealed a decrease in levels of tricarboxylic acid cycle intermediates and heme. Heme supplementation specifically enhances respiratory complex I activity without affecting complex II and partially reverses the inhibited brown adipogenesis by OXPHOS deficiency. Moreover, the regulation of brown adipogenesis by the OXPHOS-heme axis may be due to the suppressed histone methylation status by increasing histone demethylation. In summary, our findings identified a heme-sensing retrograde signaling pathway that connects mitochondrial OXPHOS to the regulation of brown adipocyte differentiation and metabolic functions.

Keywords:  brown adipocytes; differentiation; heme; histone methylation; oxidative phosphorylation

DOI:  https://doi.org/10.1016/j.mito.2023.07.004
Exp Anim. 2023 Jul 10.

Disruption of testis-enriched cytochrome c oxidase subunit COX6B2 but not COX8C leads to subfertility.

Keisuke Shimada, Yonggang Lu, Masahito Ikawa.

  Mammalian sperm flagellum contains the midpiece characterized by a mitochondrial sheath that packs tightly around the axoneme and outer dense fibers. Mitochondria are known as the "powerhouse" of the cell, and produce ATP through the tricarboxylic acid (TCA) cycle and oxidative phosphorylation (OXPHOS). However, the contribution of the TCA cycle and OXPHOS to sperm motility and male fertility is less clear. Cytochrome c oxidase (COX) is an oligomeric complex localized within the mitochondrial inner membrane, and the terminal enzyme of the mitochondrial electron transport chain in eukaryotes. Both COX6B2 and COX8C are testis-enriched COX subunits whose functions in vivo are poorly studied. Here, we generated Cox6b2 and Cox8c knockout (KO) mice using the CRISPR/Cas9 system. We examined their fertility and sperm mitochondrial function to determine the significance of testis-enriched COX subunits in male fertility. The mating test revealed that disrupting COX6B2 induces male subfertility, while disrupting COX8C does not affect male fertility. Cox6b2 KO spermatozoa showed low sperm motility, but mitochondrial function was normal according to oxygen consumption rates. Therefore, low sperm motility seems to cause subfertility in Cox6b2 KO male mice. These results also indicate that testis-enriched COX, COX6B2 and COX8C, are not essential for OXPHOS in mouse spermatozoa.

Keywords:  CRISPR/Cas9; cytochrome c oxidase subunit; mitochondria; sperm motility; subfertility

DOI:  https://doi.org/10.1538/expanim.23-0055
Nat Metab. 2023 Jul 10.

TCA cycle deficiency in multiple sclerosis.

Swadha Mishra, Fabian den Brave, Thomas Becker.

DOI: https://doi.org/10.1038/s42255-023-00840-9
Cell Signal. 2023 Jul 06. pii: S0898-6568(23)00208-5. [Epub ahead of print]109 110794

Mitochondria as intracellular signalling organelles. An update.

Lucia-Doina Popov.

  Traditionally, mitochondria are known as "the powerhouse of the cell," responsible for energy (ATP) generation (by the electron transport chain, oxidative phosphorylation, the tricarboxylic acid cycle, and fatty acid ß-oxidation), and for the regulation of several metabolic processes, including redox homeostasis, calcium signalling, and cellular apoptosis. The extensive studies conducted in the last decades portray mitochondria as multifaceted signalling organelles that ultimately command cells' survival or death. Based on current knowledge, we'll outline the mitochondrial signalling to other intracellular compartments in homeostasis and pathology-related mitochondrial stress conditions here. The following topics are discussed: (i) oxidative stress and mtROS signalling in mitohormesis, (ii) mitochondrial Ca2+ signalling; (iii) the anterograde (nucleus-to-mitochondria) and retrograde (mitochondria-to-nucleus) signal transduction, (iv) the mtDNA role in immunity and inflammation, (v) the induction of mitophagy- and apoptosis - signalling cascades, (vi) the mitochondrial dysfunctions (mitochondriopathies) in cardiovascular, neurodegenerative, and malignant diseases. The novel insights into molecular mechanisms of mitochondria-mediated signalling can explain mitochondria adaptation to metabolic and environmental stresses to achieve cell survival.

Keywords:  Mitochondriopathies; Mitophagy; Oxidative stress; Signal transduction; mtDNA

DOI:  https://doi.org/10.1016/j.cellsig.2023.110794
Endocr Oncol. 2023 Jan 01. 3(1): e220093

Succinate dehydrogenase variants in paraganglioma: why are B subunit variants 'bad'?

Lucinda M Gruber, Steven N Hart, Louis James Maher Iii.

  Mutations that predispose to familial pheochromocytoma and paraganglioma include inherited variants in the four genes (SDHA, SDHB, SDHC and SDHD) encoding subunits of succinate dehydrogenase (SDH), an enzyme of the mitochondrial tricarboxylic acid cycle and complex II of the electron transport chain. In heterozygous variant carriers, somatic loss of heterozygosity is thought to result in tumorigenic accumulation of succinate and reactive oxygen species. Inexplicably, variants affecting the SDHB subunit predict worse clinical outcomes. Why? Here we consider two hypotheses. First, relative to SDH A, C and D subunits, the small SDHB subunit might be more intrinsically 'fragile' to missense mutations because of its relatively large fraction of amino acids contacting prosthetic groups and other SDH subunits. We show evidence that supports this hypothesis. Second, the natural pool of human SDHB variants might, by chance, be biased toward severe truncating variants and missense variants causing more disruptive amino acid substitutions. We tested this hypothesis by creating a database of known SDH variants and predicting their biochemical severities. Our data suggest that natural SDHB variants are more pathogenic. It is unclear if this bias is sufficient to explain clinical data. Other explanations include the possibility that SDH subcomplexes remaining after SDHB loss have unique tumorigenic gain-of-function characteristics, and/or that SDHB may have additional unknown tumor-suppressor functions.

Keywords:  missense variant; paraganglioma; pathogenicity; pheochromocytoma; succinate dehydrogenase

DOI:  https://doi.org/10.1530/EO-22-0093
bioRxiv. 2023 Jun 28. pii: 2023.06.26.546606. [Epub ahead of print]

Metabolic reprogramming of cancer cells by JMJD6-mediated pre-mRNA splicing is associated with therapeutic response to splicing inhibitor.

Carolyn Jablonowski, Waise Quarni, Shivendra Singh, Haiyan Tan, Dhanushka Hewa Bostanthirige, Hongjian Jin, Jie Fang, Ti-Cheng Chang, David Finkelstein, Ji-Hoon Cho, Dongli Hu, Vishwajeeth Pagala, Sadie Miki Sakurada, Shondra M Pruett-Miller, Ruoning Wang, Andrew Murphy, Kevin Freeman, Junmin Peng, Andrew M Davidoff, Gang Wu, Jun Yang.

Dysregulated pre-mRNA splicing and metabolism are two hallmarks of MYC-driven cancers. Pharmacological inhibition of both processes has been extensively investigated as potential therapeutic avenues in preclinical and clinical studies. However, how pre-mRNA splicing and metabolism are orchestrated in response to oncogenic stress and therapies is poorly understood. Here, we demonstrate that JMJD6 acts as a hub connecting splicing and metabolism in MYC-driven neuroblastoma. JMJD6 cooperates with MYC in cellular transformation by physically interacting with RNA binding proteins involved in pre-mRNA splicing and protein homeostasis. Notably, JMJD6 controls the alternative splicing of two isoforms of glutaminase (GLS), namely kidney-type glutaminase (KGA) and glutaminase C (GAC), which are rate-limiting enzymes of glutaminolysis in the central carbon metabolism in neuroblastoma. Further, we show that JMJD6 is correlated with the anti-cancer activity of indisulam, a "molecular glue" that degrades splicing factor RBM39, which complexes with JMJD6. The indisulam-mediated cancer cell killing is at least partly dependent on the glutamine-related metabolic pathway mediated by JMJD6. Our findings reveal a cancer-promoting metabolic program is coupled with alternative pre-mRNA splicing through JMJD6, providing a rationale to target JMJD6 as a therapeutic avenue for treating MYC-driven cancers.

DOI: https://doi.org/10.1101/2023.06.26.546606
Oncogene. 2023 Jul 11.

Notch signaling regulates a metabolic switch through inhibiting PGC-1α and mitochondrial biogenesis in dedifferentiated liposarcoma.

Pei-Chieh Tien, Xiyue Chen, Bennett D Elzey, Raphael E Pollock, Shihuan Kuang.

Human dedifferentiated liposarcoma (DDLPS) is a rare but lethal cancer with no driver mutations being identified, hampering the development of targeted therapies. We and others recently reported that constitutive activation of Notch signaling through overexpression of the Notch1 intracellular domain (NICDOE) in murine adipocytes leads to tumors resembling human DDLPS. However, the mechanisms underlying the oncogenic functions of Notch activation in DDLPS remains unclear. Here, we show that Notch signaling is activated in a subset of human DDLPS and correlates with poor prognosis and expression of MDM2, a defining marker of DDLPS. Metabolic analyses reveal that murine NICDOE DDLPS cells exhibit markedly reduced mitochondrial respiration and increased glycolysis, mimicking the Warburg effect. This metabolic switch is associated with diminished expression of peroxisome proliferator-activated receptor gamma coactivator 1α (Ppargc1a, encoding PGC-1α protein), a master regulator of mitochondrial biogenesis. Genetic ablation of the NICDOE cassette rescues the expression of PGC-1α and mitochondrial respiration. Similarly, overexpression of PGC-1α is sufficient to rescue mitochondria biogenesis, inhibit the growth and promote adipogenic differentiation of DDLPS cells. Together, these data demonstrate that Notch activation inhibits PGC-1α to suppress mitochondrial biogenesis and drive a metabolic switch in DDLPS.

DOI: https://doi.org/10.1038/s41388-023-02768-6
Cell Rep. 2023 Jul 07. pii: S2211-1247(23)00746-5. [Epub ahead of print]42(7): 112735

Increased mitochondrial free Ca2+ during ischemia is suppressed, but not eliminated by, germline deletion of the mitochondrial Ca2+ uniporter.

Courtney E Petersen, Junhui Sun, Kavisha Silva, Anna Kosmach, Robert S Balaban, Elizabeth Murphy.

  Mitochondrial Ca2+ overload is proposed to regulate cell death via opening of the mitochondrial permeability transition pore. It is hypothesized that inhibition of the mitochondrial Ca2+ uniporter (MCU) will prevent Ca2+ accumulation during ischemia/reperfusion and thereby reduce cell death. To address this, we evaluate mitochondrial Ca2+ in ex-vivo-perfused hearts from germline MCU-knockout (KO) and wild-type (WT) mice using transmural spectroscopy. Matrix Ca2+ levels are measured with a genetically encoded, red fluorescent Ca2+ indicator (R-GECO1) using an adeno-associated viral vector (AAV9) for delivery. Due to the pH sensitivity of R-GECO1 and the known fall in pH during ischemia, hearts are glycogen depleted to decrease the ischemic fall in pH. At 20 min of ischemia, there is significantly less mitochondrial Ca2+ in MCU-KO hearts compared with MCU-WT controls. However, an increase in mitochondrial Ca2+ is present in MCU-KO hearts, suggesting that mitochondrial Ca2+ overload during ischemia is not solely dependent on MCU.

Keywords:  CP: Developmental biology; MCU; calcium; cardioprotection; ischemia-reperfusion; mitochondria

DOI:  https://doi.org/10.1016/j.celrep.2023.112735
Elife. 2023 07 10. pii: e82597. [Epub ahead of print]12

MYC overrides HIF-1α to regulate proliferating primary cell metabolism in hypoxia.

Courtney A Copeland, Benjamin A Olenchock, David Ziehr, Sarah McGarrity, Kevin Leahy, Jamey D Young, Joseph Loscalzo, William M Oldham.

  Hypoxia requires metabolic adaptations to sustain energetically demanding cellular activities. While the metabolic consequences of hypoxia have been studied extensively in cancer cell models, comparatively little is known about how primary cell metabolism responds to hypoxia. Thus, we developed metabolic flux models for human lung fibroblast and pulmonary artery smooth muscle cells proliferating in hypoxia. Unexpectedly, we found that hypoxia decreased glycolysis despite activation of hypoxia-inducible factor 1α (HIF-1α) and increased glycolytic enzyme expression. While HIF-1α activation in normoxia by prolyl hydroxylase (PHD) inhibition did increase glycolysis, hypoxia blocked this effect. Multi-omic profiling revealed distinct molecular responses to hypoxia and PHD inhibition, and suggested a critical role for MYC in modulating HIF-1α responses to hypoxia. Consistent with this hypothesis, MYC knockdown in hypoxia increased glycolysis and MYC over-expression in normoxia decreased glycolysis stimulated by PHD inhibition. These data suggest that MYC signaling in hypoxia uncouples an increase in HIF-dependent glycolytic gene transcription from glycolytic flux.

Keywords:  MYC; biochemistry; cell biology; chemical biology; human; hypoxia; hypoxia-inducible factor; metabolic flux analysis; prolyl hydroxylase

DOI:  https://doi.org/10.7554/eLife.82597
Nat Commun. 2023 07 11. 14(1): 4105

Hypoxia-reprogramed megamitochondrion contacts and engulfs lysosome to mediate mitochondrial self-digestion.

Tianshu Hao, Jianglong Yu, Zhida Wu, Jie Jiang, Longlong Gong, Bingjun Wang, Hanze Guo, Huabin Zhao, Bin Lu, Simone Engelender, He He, Zhiyin Song.

Mitochondria are the key organelles for sensing oxygen, which is consumed by oxidative phosphorylation to generate ATP. Lysosomes contain hydrolytic enzymes that degrade misfolded proteins and damaged organelles to maintain cellular homeostasis. Mitochondria physically and functionally interact with lysosomes to regulate cellular metabolism. However, the mode and biological functions of mitochondria-lysosome communication remain largely unknown. Here, we show that hypoxia remodels normal tubular mitochondria into megamitochondria by inducing broad inter-mitochondria contacts and subsequent fusion. Importantly, under hypoxia, mitochondria-lysosome contacts are promoted, and certain lysosomes are engulfed by megamitochondria, in a process we term megamitochondria engulfing lysosome (MMEL). Both megamitochondria and mature lysosomes are required for MMEL. Moreover, the STX17-SNAP29-VAMP7 complex contributes to mitochondria-lysosome contacts and MMEL under hypoxia. Intriguingly, MMEL mediates a mode of mitochondrial degradation, which we termed mitochondrial self-digestion (MSD). Moreover, MSD increases mitochondrial ROS production. Our results reveal a mode of crosstalk between mitochondria and lysosomes and uncover an additional pathway for mitochondrial degradation.

DOI: https://doi.org/10.1038/s41467-023-39811-9
Nutrients. 2023 Jul 07. pii: 3064. [Epub ahead of print]15(13):

Defining NAD(P)(H) Catabolism.

Jyothi Dhuguru, Ryan W Dellinger, Marie E Migaud.

  Dietary vitamin B3 components, such as nicotinamide and nicotinic acid, are precursors to the ubiquitous redox cofactor nicotinamide adenine dinucleotide (NAD+). NAD+ levels are thought to decline with age and disease. While the drivers of this decline remain under intense investigation, strategies have emerged seeking to functionally maintain NAD+ levels through supplementation with NAD+ biosynthetic intermediates. These include marketed products, such as nicotinamide riboside (NR) and its phosphorylated form (NMN). More recent developments have shown that NRH (the reduced form of NR) and its phosphorylated form NMNH also increases NAD+ levels upon administration, although they initially generate NADH (the reduced form of NAD+). Other means to increase the combined levels of NAD+ and NADH, NAD(H), include the inhibition of NAD+-consuming enzymes or activation of biosynthetic pathways. Multiple studies have shown that supplementation with an NAD(H) precursor changes the profile of NAD(H) catabolism. Yet, the pharmacological significance of NAD(H) catabolites is rarely considered although the distribution and abundance of these catabolites differ depending on the NAD(H) precursor used, the species in which the study is conducted, and the tissues used for the quantification. Significantly, some of these metabolites have emerged as biomarkers in physiological disorders and might not be innocuous. Herein, we review the known and emerging catabolites of the NAD(H) metabolome and highlight their biochemical and physiological function as well as key chemical and biochemical reactions leading to their formation. Furthermore, we emphasize the need for analytical methods that inform on the full NAD(H) metabolome since the relative abundance of NAD(H) catabolites informs how NAD(H) precursors are used, recycled, and eliminated.

Keywords:  NAD(P)(H) catabolism; NAD+ metabolism; methyl-nicotinamide; niacin; nicotinamide; pyridone

DOI:  https://doi.org/10.3390/nu15133064
Nat Metab. 2023 Jul 13.

CRAT links cholesterol metabolism to innate immune responses in the heart.

Hua Mao, Aude Angelini, Shengyu Li, Guangyu Wang, Luge Li, Cam Patterson, Xinchun Pi, Liang Xie.

Chronic inflammation is associated with increased risk and poor prognosis of heart failure; however, the precise mechanism that provokes sustained inflammation in the failing heart remains elusive. Here we report that depletion of carnitine acetyltransferase (CRAT) promotes cholesterol catabolism through bile acid synthesis pathway in cardiomyocytes. Intracellular accumulation of bile acid or intermediate, 7α-hydroxyl-3-oxo-4-cholestenoic acid, induces mitochondrial DNA stress and triggers cGAS-STING-dependent type I interferon responses. Furthermore, type I interferon responses elicited by CRAT deficiency substantially increase AIM2 expression and AIM2-dependent inflammasome activation. Genetic deletion of cardiomyocyte CRAT in mice of both sexes results in myocardial inflammation and dilated cardiomyopathy, which can be reversed by combined depletion of caspase-1, cGAS or AIM2. Collectively, we identify a mechanism by which cardiac energy metabolism, cholesterol homeostasis and cardiomyocyte-intrinsic innate immune responses are interconnected via a CRAT-mediated bile acid synthesis pathway, which contributes to chronic myocardial inflammation and heart failure progression.

DOI: https://doi.org/10.1038/s42255-023-00844-5
EMBO J. 2023 Jul 10. e112446

Local coordination of mRNA storage and degradation near mitochondria modulates C. elegans ageing.

Ioanna Daskalaki, Maria Markaki, Ilias Gkikas, Nektarios Tavernarakis.

  Mitochondria are central regulators of healthspan and lifespan, yet the intricate choreography of multiple, tightly controlled steps regulating mitochondrial biogenesis remains poorly understood. Here, we uncover a pivotal role for specific elements of the 5'-3' mRNA degradation pathway in the regulation of mitochondrial abundance and function. We find that the mRNA degradation and the poly-A tail deadenylase CCR4-NOT complexes form distinct foci in somatic Caenorhabditis elegans cells that physically and functionally associate with mitochondria. Components of these two multi-subunit complexes bind transcripts of nuclear-encoded mitochondria-targeted proteins to regulate mitochondrial biogenesis during ageing in an opposite manner. In addition, we show that balanced degradation and storage of mitochondria-targeted protein mRNAs are critical for mitochondrial homeostasis, stress resistance and longevity. Our findings reveal a multifaceted role of mRNA metabolism in mitochondrial biogenesis and show that fine-tuning of mRNA turnover and local translation control mitochondrial abundance and promote longevity in response to stress and during ageing.

Keywords:  ageing; mRNA metabolism; mitochondria; protein synthesis; stress

DOI:  https://doi.org/10.15252/embj.2022112446
Elife. 2023 Jul 14. pii: e83064. [Epub ahead of print]12

Succinate mediates inflammation-induced adrenocortical dysfunction.

Ivona Mateska, Anke Witt, Eman Hagag, Anupam Sinha, Canelif Yilmaz, Evangelia Thanou, Na Sun, Ourania Kolliniati, Maria Patschin, Heba Abdelmegeed, Holger Henneicke, Waldemar Kanczkowski, Ben Wielockx, Christos Tsatsanis, Andreas Dahl, Axel Karl Walch, Ka Wan Li, Mirko Peitzsch, Triantafyllos Chavakis, Vasileia Ismini Alexaki.

  The hypothalamus-pituitary-adrenal (HPA) axis is activated in response to inflammation leading to increased production of anti-inflammatory glucocorticoids by the adrenal cortex, thereby representing an endogenous feedback loop. However, severe inflammation reduces the responsiveness of the adrenal gland to adrenocorticotropic hormone (ACTH), although the underlying mechanisms are poorly understood. Here, we show by transcriptomic, proteomic and metabolomic analyses that LPS-induced systemic inflammation triggers profound metabolic changes in steroidogenic adrenocortical cells, including downregulation of the TCA cycle and oxidative phosphorylation, in mice. Inflammation disrupts the TCA cycle at the level of succinate dehydrogenase (SDH), leading to succinate accumulation and disturbed steroidogenesis. Mechanistically, IL-1β reduces SDHB expression through upregulation of DNA methyltransferase 1 (DNMT1) and methylation of the SDHB promoter. Consequently, increased succinate levels impair oxidative phosphorylation and ATP synthesis and enhance ROS production, leading to reduced steroidogenesis. Together, we demonstrate that the IL-1β-DNMT1-SDHB-succinate axis disrupts steroidogenesis. Our findings not only provide a mechanistic explanation for the adrenal dysfunction in severe inflammation, but also offer a potential target for therapeutic intervention.

Keywords:  cell biology; immunology; inflammation; mouse

DOI:  https://doi.org/10.7554/eLife.83064
bioRxiv. 2023 Jun 28. pii: 2023.06.27.546750. [Epub ahead of print]

Glutamine antagonist DRP-104 suppresses tumor growth and enhances response to checkpoint blockade in KEAP1 mutant lung cancer.

Ray Pillai, Sarah E LeBoeuf, Yuan Hao, Connie New, Jenna L E Blum, Ali Rashidfarrokhi, Shih Ming Huang, Christian Bahamon, Warren L Wu, Burcu Karadal-Ferrena, Alberto Herrera, Ellie Ivanova, Michael Cross, Jozef P Bossowski, Hongyu Ding, Makiko Hayashi, Sahith Rajalingam, Triantafyllia Karakousi, Volkan I Sayin, Kamal M Khanna, Kwok-Kin Wong, Robert Wild, Aristotelis Tsirigos, John T Poirier, Charles M Rudin, Shawn M Davidson, Sergei B Koralov, Thales Papagiannakopoulos.

Loss-of-function mutations in KEAP1 frequently occur in lung cancer and are associated with resistance to standard of care treatment, highlighting the need for the development of targeted therapies. We have previously shown that KEAP1 mutant tumors have increased glutamine consumption to support the metabolic rewiring associated with NRF2 activation. Here, using patient-derived xenograft models and antigenic orthotopic lung cancer models, we show that the novel glutamine antagonist DRP-104 impairs the growth of KEAP1 mutant tumors. We find that DRP-104 suppresses KEAP1 mutant tumor growth by inhibiting glutamine-dependent nucleotide synthesis and promoting anti-tumor CD4 and CD8 T cell responses. Using multimodal single-cell sequencing and ex vivo functional assays, we discover that DRP-104 reverses T cell exhaustion and enhances the function of CD4 and CD8 T cells culminating in an improved response to anti-PD1 therapy. Our pre-clinical findings provide compelling evidence that DRP-104, currently in phase 1 clinical trials, offers a promising therapeutic approach for treating patients with KEAP1 mutant lung cancer. Furthermore, we demonstrate that by combining DRP-104 with checkpoint inhibition, we can achieve suppression of tumor intrinsic metabolism and augmentation of anti-tumor T cell responses.

DOI: https://doi.org/10.1101/2023.06.27.546750
Nat Chem Biol. 2023 Jul 13.

Capturing copper to inhibit inflammation.

Christopher J Chang, Donita C Brady.

DOI: https://doi.org/10.1038/s41589-023-01383-6
Cell Death Dis. 2023 Jul 12. 14(7): 413

IF1 ablation prevents ATP synthase oligomerization, enhances mitochondrial ATP turnover and promotes an adenosine-mediated pro-inflammatory phenotype.

Sonia Domínguez-Zorita, Inés Romero-Carramiñana, Fulvio Santacatterina, Pau B Esparza-Moltó, Carolina Simó, Araceli Del-Arco, Cristina Núñez de Arenas, Jorge Saiz, Coral Barbas, José M Cuezva.

ATPase Inhibitory Factor 1 (IF1) regulates the activity of mitochondrial ATP synthase. The expression of IF1 in differentiated human and mouse cells is highly variable. In intestinal cells, the overexpression of IF1 protects against colon inflammation. Herein, we have developed a conditional IF1-knockout mouse model in intestinal epithelium to investigate the role of IF1 in mitochondrial function and tissue homeostasis. The results show that IF1-ablated mice have increased ATP synthase/hydrolase activities, leading to profound mitochondrial dysfunction and a pro-inflammatory phenotype that impairs the permeability of the intestinal barrier compromising mouse survival upon inflammation. Deletion of IF1 prevents the formation of oligomeric assemblies of ATP synthase and alters cristae structure and the electron transport chain. Moreover, lack of IF1 promotes an intramitochondrial Ca2+ overload in vivo, minimizing the threshold to Ca2+-induced permeability transition (mPT). Removal of IF1 in cell lines also prevents the formation of oligomeric assemblies of ATP synthase, minimizing the threshold to Ca2+-induced mPT. Metabolomic analyses of mice serum and colon tissue highlight that IF1 ablation promotes the activation of de novo purine and salvage pathways. Mechanistically, lack of IF1 in cell lines increases ATP synthase/hydrolase activities and installs futile ATP hydrolysis in mitochondria, resulting in the activation of purine metabolism and in the accumulation of adenosine, both in culture medium and in mice serum. Adenosine, through ADORA2B receptors, promotes an autoimmune phenotype in mice, stressing the role of the IF1/ATP synthase axis in tissue immune responses. Overall, the results highlight that IF1 is required for ATP synthase oligomerization and that it acts as a brake to prevent ATP hydrolysis under in vivo phosphorylating conditions in intestinal cells.

DOI: https://doi.org/10.1038/s41419-023-05957-z
J Biol Chem. 2023 Jul 08. pii: S0021-9258(23)02003-3. [Epub ahead of print] 104975

NAD metabolism modulates inflammation and mitochondria function in diabetic kidney disease.

Komuraiah Myakala, Xiaoxin X Wang, Nataliia V Shults, Ewa Krawczyk, Bryce A Jones, Xiaoping Yang, Avi Z Rosenberg, Brandon Ginley, Pinaki Sarder, Leonid Brodsky, Yura Jang, Chan Hyun Na, Yue Qi, Xu Zhang, Udayan Guha, Ci Wu, Shivani Bansal, Junfeng Ma, Amrita Cheema, Chris Albanese, Matthew D Hirschey, Teruhiko Yoshida, Jeffrey B Kopp, Julia Panov, Moshe Levi.

Diabetes mellitus is the leading cause of cardiovascular and renal disease in the United -States. In spite of the beneficial interventions available for patients with diabetes, there remains a need for additional therapeutic targets and therapies in diabetic kidney disease (DKD). Inflammation and oxidative stress are increasingly recognized as important causes of renal diseases. Inflammation is closely associated with mitochondrial damage. The molecular connection between inflammation and mitochondrial metabolism remains to be elucidated. Recently, nicotinamide adenine nucleotide (NAD+) metabolism has been found to regulate immune function and inflammation. In the present studies we tested the hypothesis that enhancing NAD metabolism could prevent inflammation in and progression of DKD. We found that treatment of db/db mice with type 2 diabetes with nicotinamide riboside (NR) prevented several manifestations of kidney dysfunction (i.e., albuminuria, increased urinary kidney injury marker-1 (KIM1) excretion and pathologic changes). These effects were associated with decreased inflammation, at least in part via inhibiting the activation of the cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) signaling pathway. An antagonist of the serum stimulator of interferon genes (STING) and whole-body STING deletion in diabetic mice showed similar renoprotection. Further analysis found that NR increased SIRT3 activity and improved mitochondrial function, which led to decreased mitochondrial DNA damage, a trigger for mitochondrial DNA leakage which activates the cGAS-STING pathway. Overall, these data show that NR supplementation boosted NAD metabolism to augment mitochondrial function, reducing inflammation and thereby preventing progression of diabetic kidney disease.

DOI: https://doi.org/10.1016/j.jbc.2023.104975
Psychoneuroendocrinology. 2023 Jun 14. pii: S0306-4530(23)00300-1. [Epub ahead of print]155 106322

Cellular allostatic load is linked to increased energy expenditure and accelerated biological aging.

Natalia Bobba-Alves, Gabriel Sturm, Jue Lin, Sarah A Ware, Kalpita R Karan, Anna S Monzel, Céline Bris, Vincent Procaccio, Guy Lenaers, Albert Higgins-Chen, Morgan Levine, Steve Horvath, Balaji S Santhanam, Brett A Kaufman, Michio Hirano, Elissa Epel, Martin Picard.

  Stress triggers anticipatory physiological responses that promote survival, a phenomenon termed allostasis. However, the chronic activation of energy-dependent allostatic responses results in allostatic load, a dysregulated state that predicts functional decline, accelerates aging, and increases mortality in humans. The energetic cost and cellular basis for the damaging effects of allostatic load have not been defined. Here, by longitudinally profiling three unrelated primary human fibroblast lines across their lifespan, we find that chronic glucocorticoid exposure increases cellular energy expenditure by ∼60%, along with a metabolic shift from glycolysis to mitochondrial oxidative phosphorylation (OxPhos). This state of stress-induced hypermetabolism is linked to mtDNA instability, non-linearly affects age-related cytokines secretion, and accelerates cellular aging based on DNA methylation clocks, telomere shortening rate, and reduced lifespan. Pharmacologically normalizing OxPhos activity while further increasing energy expenditure exacerbates the accelerated aging phenotype, pointing to total energy expenditure as a potential driver of aging dynamics. Together, our findings define bioenergetic and multi-omic recalibrations of stress adaptation, underscoring increased energy expenditure and accelerated cellular aging as interrelated features of cellular allostatic load.

Keywords:  Aging; Allostatic load; Chronic stress; Epigenetic aging; Glucocorticoid; Hypermetabolism; Mitochondria; Telomere

DOI:  https://doi.org/10.1016/j.psyneuen.2023.106322
JCI Insight. 2023 07 10. pii: e158098. [Epub ahead of print]8(13):

Inhibition of phosphodiesterase 4D suppresses mTORC1 signaling and pancreatic cancer growth.

Mi-Hyeon Jeong, Greg Urquhart, Cheryl Lewis, Zhikai Chi, Jenna L Jewell.

  The mammalian target of rapamycin complex 1 (mTORC1) senses multiple upstream stimuli to orchestrate anabolic and catabolic events that regulate cell growth and metabolism. Hyperactivation of mTORC1 signaling is observed in multiple human diseases; thus, pathways that suppress mTORC1 signaling may help to identify new therapeutic targets. Here, we report that phosphodiesterase 4D (PDE4D) promotes pancreatic cancer tumor growth by increasing mTORC1 signaling. GPCRs paired to Gαs proteins activate adenylyl cyclase, which in turn elevates levels of 3',5'-cyclic adenosine monophosphate (cAMP), whereas PDEs catalyze the hydrolysis of cAMP to 5'-AMP. PDE4D forms a complex with mTORC1 and is required for mTORC1 lysosomal localization and activation. Inhibition of PDE4D and the elevation of cAMP levels block mTORC1 signaling via Raptor phosphorylation. Moreover, pancreatic cancer exhibits an upregulation of PDE4D expression, and high PDE4D levels predict the poor overall survival of patients with pancreatic cancer. Importantly, FDA-approved PDE4 inhibitors repress pancreatic cancer cell tumor growth in vivo by suppressing mTORC1 signaling. Our results identify PDE4D as an important activator of mTORC1 and suggest that targeting PDE4 with FDA-approved inhibitors may be beneficial for the treatment of human diseases with hyperactivated mTORC1 signaling.

Keywords:  Cancer; Cell Biology

DOI:  https://doi.org/10.1172/jci.insight.158098
J Mol Cell Cardiol. 2023 Jul 12. pii: S0022-2828(23)00110-4. [Epub ahead of print]182 15-24

Metabolic flux in the driver's seat during cardiac health and disease.

E Douglas Lewandowski.

  Cardiac function is a dynamic process that must adjust efficiently to the immediate demands of physical state and activity. So too, the metabolic support of cardiac function is a dynamic process that must respond, in time, to the demands of cardiac function and viability. Flux through metabolic pathways provides chemical energy and generates signaling molecules that regulate activity among intracellular compartments to meet these demands. Thus, flux through metabolic pathways provides a dynamic mode of support of cardiomyocytes during physiological and pathophysiological challenges. Any inability of metabolic flux to keep pace with the demands of the cardiomyocyte results in progressive dysfunction that contributes to cardiac disease. Thus, the priority in maintaining and regulating flux through metabolic pathways in the cardiomyocyte cannot be understated. Great potential exists in current efforts to elucidate metabolic mechanisms as therapeutic targets for the diseased heart. As a consequence, detecting metabolic flux in the functioning myocardium of the heart, under normal and diseased conditions, is essential in elucidating the metabolic basis of contractile dysfunction. As a companion to the 2022 ISHR Research Achievement Award lecture, this review examines the use and applications of stable isotope kinetics to quantify metabolic flux through intermediary pathways and the exchange and transport of intermediates across the mitochondrial membrane and sarcolemma of intact functioning hearts in determining how these intracellular events are coordinated to support cardiac function and health. Finally, this work reviews recently demonstrated metabolic defects in diseased hearts and the potential for metabolic alleviation of heart disease.

Keywords:  Fatty acids; Glucose; Heart failure; Ischemia/Reperfusion; Isotopes; Metabolism; Mitochondria

DOI:  https://doi.org/10.1016/j.yjmcc.2023.07.004
bioRxiv. 2023 Jun 26. pii: 2023.06.23.546216. [Epub ahead of print]

Divergent iron-regulatory states contribute to heterogeneity in breast cancer aggressiveness.

William D Leineweber, Ali Khalilimeybodi, Padmini Rangamani, Stephanie I Fraley.

Similar primary tumors can progress to vastly different outcomes, where transcriptional state rather than mutational profile predicts prognosis. A key challenge is to understand how such programs are induced and maintained to enable metastasis. In breast cancer cells, aggressive transcriptional signatures and migratory behaviors linked to poor patient prognosis can emerge as a result of contact with a collagen-rich microenvironment mimicking tumor stroma. Here, we leverage heterogeneity in this response to identify the programs that sustain invasive behaviors. Invasive responders are characterized by expression of specific iron uptake and utilization machinery, anapleurotic TCA cycle genes, actin polymerization promoters, and Rho GTPase activity and contractility regulators. Non-invasive responders are defined by actin and iron sequestration modules along with glycolysis gene expression. These two programs are evident in patient tumors and predict divergent outcomes, largely on the basis of ACO1. A signaling model predicts interventions and their dependence on iron availability. Mechanistically, invasiveness is initiated by transient HO-1 expression that increases intracellular iron, mediating MRCK-dependent cytoskeletal activity and increasing reliance on mitochondrial ATP production rather than glycolysis.

DOI: https://doi.org/10.1101/2023.06.23.546216
Cell Metab. 2023 Jul 11. pii: S1550-4131(23)00217-6. [Epub ahead of print]35(7): 1195-1208.e6

Fetal manipulation of maternal metabolism is a critical function of the imprinted Igf2 gene.

Jorge Lopez-Tello, Hannah E J Yong, Ionel Sandovici, Georgina K C Dowsett, Efthimia R Christoforou, Esteban Salazar-Petres, Rebecca Boyland, Tina Napso, Giles S H Yeo, Brian Y H Lam, Miguel Constancia, Amanda N Sferruzzi-Perri.

  Maternal-offspring interactions in mammals involve both cooperation and conflict. The fetus has evolved ways to manipulate maternal physiology to enhance placental nutrient transfer, but the mechanisms involved remain unclear. The imprinted Igf2 gene is highly expressed in murine placental endocrine cells. Here, we show that Igf2 deletion in these cells impairs placental endocrine signaling to the mother, without affecting placental morphology. Igf2 controls placental hormone production, including prolactins, and is crucial to establish pregnancy-related insulin resistance and to partition nutrients to the fetus. Consequently, fetuses lacking placental endocrine Igf2 are growth restricted and hypoglycemic. Mechanistically, Igf2 controls protein synthesis and cellular energy homeostasis, actions dependent on the placental endocrine cell type. Igf2 loss also has additional long-lasting effects on offspring metabolism in adulthood. Our study provides compelling evidence for an intrinsic fetal manipulation system operating in placenta that modifies maternal metabolism and fetal resource allocation, with long-term consequences for offspring metabolic health.

Keywords:  fetal programming; genomic imprinting; glucose; hormones; insulin-like growth factor 2; metabolism; placenta; pregnancy; prolactin

DOI:  https://doi.org/10.1016/j.cmet.2023.06.007
Cell Metab. 2023 Jul 11. pii: S1550-4131(23)00216-4. [Epub ahead of print]35(7): 1093-1095

The glucose-to-acetate metabolic flux that drives endothelial-to-mesenchymal transition via TGF-β signaling.

Cristina Arce Recatalá, Massimo M Santoro.

The metabolic mechanisms supporting the process of endothelial-to-mesenchymal transition (EndMT) remain largely unknown. Here, Zhu et al. describe a novel role for acetate and ACC2 in regulating EndMT and atherosclerosis via modulation of the TGF-β signaling. This study sheds light on the role of glucose-derived metabolites that drive endothelial pathophysiology.

DOI: https://doi.org/10.1016/j.cmet.2023.06.006
Nat Metab. 2023 Jul 10.

Targeting the TCA cycle can ameliorate widespread axonal energy deficiency in neuroinflammatory lesions.

Yi-Heng Tai, Daniel Engels, Giuseppe Locatelli, Ioanna Emmanouilidis, Caroline Fecher, Delphine Theodorou, Stephan A Müller, Simon Licht-Mayer, Mario Kreutzfeldt, Ingrid Wagner, Natalia Prudente de Mello, Sofia-Natsouko Gkotzamani, Laura Trovò, Arek Kendirli, Almir Aljović, Michael O Breckwoldt, Ronald Naumann, Florence M Bareyre, Fabiana Perocchi, Don Mahad, Doron Merkler, Stefan F Lichtenthaler, Martin Kerschensteiner, Thomas Misgeld.

Inflammation in the central nervous system can impair the function of neuronal mitochondria and contributes to axon degeneration in the common neuroinflammatory disease multiple sclerosis (MS). Here we combine cell-type-specific mitochondrial proteomics with in vivo biosensor imaging to dissect how inflammation alters the molecular composition and functional capacity of neuronal mitochondria. We show that neuroinflammatory lesions in the mouse spinal cord cause widespread and persisting axonal ATP deficiency, which precedes mitochondrial oxidation and calcium overload. This axonal energy deficiency is associated with impaired electron transport chain function, but also an upstream imbalance of tricarboxylic acid (TCA) cycle enzymes, with several, including key rate-limiting, enzymes being depleted in neuronal mitochondria in experimental models and in MS lesions. Notably, viral overexpression of individual TCA enzymes can ameliorate the axonal energy deficits in neuroinflammatory lesions, suggesting that TCA cycle dysfunction in MS may be amendable to therapy.

DOI: https://doi.org/10.1038/s42255-023-00838-3
Nat Commun. 2023 Jul 13. 14(1): 4166

Cytochrome c lysine acetylation regulates cellular respiration and cell death in ischemic skeletal muscle.

Paul T Morse, Gonzalo Pérez-Mejías, Junmei Wan, Alice A Turner, Inmaculada Márquez, Hasini A Kalpage, Asmita Vaishnav, Matthew P Zurek, Philipp P Huettemann, Katherine Kim, Tasnim Arroum, Miguel A De la Rosa, Dipanwita Dutta Chowdhury, Icksoo Lee, Joseph S Brunzelle, Thomas H Sanderson, Moh H Malek, David Meierhofer, Brian F P Edwards, Irene Díaz-Moreno, Maik Hüttemann.

Skeletal muscle is more resilient to ischemia-reperfusion injury than other organs. Tissue specific post-translational modifications of cytochrome c (Cytc) are involved in ischemia-reperfusion injury by regulating mitochondrial respiration and apoptosis. Here, we describe an acetylation site of Cytc, lysine 39 (K39), which was mapped in ischemic porcine skeletal muscle and removed by sirtuin5 in vitro. Using purified protein and cellular double knockout models, we show that K39 acetylation and acetylmimetic K39Q replacement increases cytochrome c oxidase (COX) activity and ROS scavenging while inhibiting apoptosis via decreased binding to Apaf-1, caspase cleavage and activity, and cardiolipin peroxidase activity. These results are discussed with X-ray crystallography structures of K39 acetylated (1.50 Å) and acetylmimetic K39Q Cytc (1.36 Å) and NMR dynamics. We propose that K39 acetylation is an adaptive response that controls electron transport chain flux, allowing skeletal muscle to meet heightened energy demand while simultaneously providing the tissue with robust resilience to ischemia-reperfusion injury.

DOI: https://doi.org/10.1038/s41467-023-39820-8
Int J Mol Sci. 2023 Jun 27. pii: 10725. [Epub ahead of print]24(13):

Succinyl-CoA Synthetase Dysfunction as a Mechanism of Mitochondrial Encephalomyopathy: More than Just an Oxidative Energy Deficit.

Makayla S Lancaster, Brett H Graham.

  Biallelic pathogenic variants in subunits of succinyl-CoA synthetase (SCS), a tricarboxylic acid (TCA) cycle enzyme, are associated with mitochondrial encephalomyopathy in humans. SCS catalyzes the interconversion of succinyl-CoA to succinate, coupled to substrate-level phosphorylation of either ADP or GDP, within the TCA cycle. SCS-deficient encephalomyopathy typically presents in infancy and early childhood, with many patients succumbing to the disease during childhood. Common symptoms include abnormal brain MRI, basal ganglia lesions and cerebral atrophy, severe hypotonia, dystonia, progressive psychomotor regression, and growth deficits. Although subunits of SCS were first identified as causal genes for progressive metabolic encephalomyopathy in the early 2000s, recent investigations are now beginning to unravel the pathomechanisms underlying this metabolic disorder. This article reviews the current understanding of SCS function within and outside the TCA cycle as it relates to the complex and multifactorial mechanisms underlying SCS-related mitochondrial encephalomyopathy.

Keywords:  encephalomyopathy; mitochondria; mitochondrial DNA; protein succinylation; succinyl-CoA synthetase; tricarboxylic acid cycle

DOI:  https://doi.org/10.3390/ijms241310725
MedComm (2020). 2023 Aug;4(4): e314

Fumarate hydratase inhibition activates innate immunity via mitochondrial nucleic acid release.

Xiang Li, Fangfang Zhou, Linghui Zeng.

DOI: https://doi.org/10.1002/mco2.314
Front Oncol. 2023 ;13 1152553

Fluorescence microscopy imaging of mitochondrial metabolism in cancer cells.

Monika Gooz, Eduardo N Maldonado.

  Mitochondrial metabolism is an important contributor to cancer cell survival and proliferation that coexists with enhanced glycolytic activity. Measuring mitochondrial activity is useful to characterize cancer metabolism patterns, to identify metabolic vulnerabilities and to identify new drug targets. Optical imaging, especially fluorescent microscopy, is one of the most valuable tools for studying mitochondrial bioenergetics because it provides semiquantitative and quantitative readouts as well as spatiotemporal resolution of mitochondrial metabolism. This review aims to acquaint the reader with microscopy imaging techniques currently used to determine mitochondrial membrane potential (ΔΨm), nicotinamide adenine dinucleotide (NADH), ATP and reactive oxygen species (ROS) that are major readouts of mitochondrial metabolism. We describe features, advantages, and limitations of the most used fluorescence imaging modalities: widefield, confocal and multiphoton microscopy, and fluorescent lifetime imaging (FLIM). We also discus relevant aspects of image processing. We briefly describe the role and production of NADH, NADHP, flavins and various ROS including superoxide and hydrogen peroxide and discuss how these parameters can be analyzed by fluorescent microscopy. We also explain the importance, value, and limitations of label-free autofluorescence imaging of NAD(P)H and FAD. Practical hints for the use of fluorescent probes and newly developed sensors for imaging ΔΨm, ATP and ROS are described. Overall, we provide updated information about the use of microscopy to study cancer metabolism that will be of interest to all investigators regardless of their level of expertise in the field.

Keywords:  FAD; NAD(P)H; ROS; fluorescence microscopy; mitochondrial membrane potential; mitochondrial metabolism

DOI:  https://doi.org/10.3389/fonc.2023.1152553
EMBO Mol Med. 2023 Jul 12. e18014

LRP8-mediated selenocysteine uptake is a targetable vulnerability in MYCN-amplified neuroblastoma.

Hamed Alborzinia, Zhiyi Chen, Umut Yildiz, Florencio Porto Freitas, Felix C E Vogel, Julianna Patricia Varga, Jasmin Batani, Christoph Bartenhagen, Werner Schmitz, Gabriele Büchel, Bernhard Michalke, Jashuo Zheng, Svenja Meierjohann, Enrico Girardi, Elisa Espinet, Andrés F Flórez, Ancely Ferreira Dos Santos, Nesrine Aroua, Tasneem Cheytan, Julie Haenlin, Lisa Schlicker, Thamara N Xavier da Silva, Adriana Przybylla, Petra Zeisberger, Giulio Superti-Furga, Martin Eilers, Marcus Conrad, Marietta Fabiano, Ulrich Schweizer, Matthias Fischer, Almut Schulze, Andreas Trumpp, José Pedro Friedmann Angeli.

  Ferroptosis has emerged as an attractive strategy in cancer therapy. Understanding the operational networks regulating ferroptosis may unravel vulnerabilities that could be harnessed for therapeutic benefit. Using CRISPR-activation screens in ferroptosis hypersensitive cells, we identify the selenoprotein P (SELENOP) receptor, LRP8, as a key determinant protecting MYCN-amplified neuroblastoma cells from ferroptosis. Genetic deletion of LRP8 leads to ferroptosis as a result of an insufficient supply of selenocysteine, which is required for the translation of the antiferroptotic selenoprotein GPX4. This dependency is caused by low expression of alternative selenium uptake pathways such as system Xc- . The identification of LRP8 as a specific vulnerability of MYCN-amplified neuroblastoma cells was confirmed in constitutive and inducible LRP8 knockout orthotopic xenografts. These findings disclose a yet-unaccounted mechanism of selective ferroptosis induction that might be explored as a therapeutic strategy for high-risk neuroblastoma and potentially other MYCN-amplified entities.

Keywords:  ferroptosis; neuroblastoma; selenocysteine; selenoprotein; synthetic lethality

DOI:  https://doi.org/10.15252/emmm.202318014
Elife. 2023 Jul 10. pii: e78546. [Epub ahead of print]12

A critical role for heme synthesis and succinate in the regulation of pluripotent states transitions.

Damien Detraux, Marino Caruso, Louise Feller, Maude Fransolet, Sébastien Meurant, Julie Mathieu, Thierry Arnould, Patricia Renard.

  Using embryonic stem cells (ESCs) in regenerative medicine or in disease modeling requires a complete understanding of these cells. Two main distinct developmental states of ESCs have been stabilized in vitro, a naïve pre-implantation stage and a primed post-implantation stage. Based on two recently published CRISPR-Cas9 knockout functional screens, we show here that the exit of the naïve state is impaired upon heme biosynthesis pathway blockade, linked in mESCs to the incapacity to activate MAPK- and TGFb-dependent signaling pathways after succinate accumulation. In addition, heme synthesis inhibition promotes the acquisition of 2 cell-like cells in a heme-independent manner caused by a mitochondrial succinate accumulation and leakage out of the cell. We further demonstrate that extracellular succinate acts as a paracrine/autocrine signal, able to trigger the 2C-like reprogramming through the activation of its plasma membrane receptor, SUCNR1. Overall, this study unveils a new mechanism underlying the maintenance of pluripotency under the control of heme synthesis.

Keywords:  developmental biology; human; mouse; regenerative medicine; stem cells

DOI:  https://doi.org/10.7554/eLife.78546
Cell Rep. 2023 Jul 07. pii: S2211-1247(23)00781-7. [Epub ahead of print]42(7): 112770

αKG-driven RNA polymerase II transcription of cyclin D1 licenses malic enzyme 2 to promote cell-cycle progression.

Yanting Yang, Zhenxi Zhang, Wei Li, Yufan Si, Li Li, Wenjing Du.

  Increased metabolic activity usually provides energy and nutrients for biomass synthesis and is indispensable for the progression of the cell cycle. Here, we find a role for α-ketoglutarate (αKG) generation in regulating cell-cycle gene transcription. A reduction in cellular αKG levels triggered by malic enzyme 2 (ME2) or isocitrate dehydrogenase 1 (IDH1) depletion leads to a pronounced arrest in G1 phase, while αKG supplementation promotes cell-cycle progression. Mechanistically, αKG directly binds to RNA polymerase II (RNAPII) and increases the level of RNAPII binding to the cyclin D1 gene promoter via promoting pre-initiation complex (PIC) assembly, consequently enhancing cyclin D1 transcription. Notably, αKG addition is sufficient to restore cyclin D1 expression in ME2- or IDH1-depleted cells, facilitating cell-cycle progression and proliferation in these cells. Therefore, our findings indicate a function of αKG in gene transcriptional regulation and cell-cycle control.

Keywords:  CP: Molecular biology; RNA polymerase II; cell cycle; cyclin D1; malic enzyme 2; α-ketoglutarate

DOI:  https://doi.org/10.1016/j.celrep.2023.112770
Nat Commun. 2023 Jul 14. 14(1): 4129

Lactate-dependent transcriptional regulation controls mammalian eye morphogenesis.

Nozomu Takata, Jason M Miska, Marc A Morgan, Priyam Patel, Leah K Billingham, Neha Joshi, Matthew J Schipma, Zachary J Dumar, Nikita R Joshi, Alexander V Misharin, Ryan B Embry, Luciano Fiore, Peng Gao, Lauren P Diebold, Gregory S McElroy, Ali Shilatifard, Navdeep S Chandel, Guillermo Oliver.

Mammalian retinal metabolism favors aerobic glycolysis. However, the role of glycolytic metabolism in retinal morphogenesis remains unknown. We report that aerobic glycolysis is necessary for the early stages of retinal development. Taking advantage of an unbiased approach that combines the use of eye organoids and single-cell RNA sequencing, we identify specific glucose transporters and glycolytic genes in retinal progenitors. Next, we determine that the optic vesicle territory of mouse embryos displays elevated levels of glycolytic activity. At the functional level, we show that removal of Glucose transporter 1 and Lactate dehydrogenase A gene activity from developing retinal progenitors arrests eye morphogenesis. Surprisingly, we uncover that lactate-mediated upregulation of key eye-field transcription factors is controlled by the epigenetic modification of histone H3 acetylation through histone deacetylase activity. Our results identify an unexpected bioenergetic independent role of lactate as a signaling molecule necessary for mammalian eye morphogenesis.

DOI: https://doi.org/10.1038/s41467-023-39672-2
Nat Commun. 2023 Jul 13. 14(1): 4161

Functional decomposition of metabolism allows a system-level quantification of fluxes and protein allocation towards specific metabolic functions.

Matteo Mori, Chuankai Cheng, Brian R Taylor, Hiroyuki Okano, Terence Hwa.

Quantifying the contribution of individual molecular components to complex cellular processes is a grand challenge in systems biology. Here we establish a general theoretical framework (Functional Decomposition of Metabolism, FDM) to quantify the contribution of every metabolic reaction to metabolic functions, e.g. the synthesis of biomass building blocks. FDM allowed for a detailed quantification of the energy and biosynthesis budget for growing Escherichia coli cells. Surprisingly, the ATP generated during the biosynthesis of building blocks from glucose almost balances the demand from protein synthesis, the largest energy expenditure known for growing cells. This leaves the bulk of the energy generated by fermentation and respiration unaccounted for, thus challenging the common notion that energy is a key growth-limiting resource. Moreover, FDM together with proteomics enables the quantification of enzymes contributing towards each metabolic function, allowing for a first-principle formulation of a coarse-grained model of global protein allocation based on the structure of the metabolic network.

DOI: https://doi.org/10.1038/s41467-023-39724-7
Nat Commun. 2023 07 11. 14(1): 4092

Immunoproteasome-specific subunit PSMB9 induction is required to regulate cellular proteostasis upon mitochondrial dysfunction.

Minji Kim, Remigiusz A Serwa, Lukasz Samluk, Ida Suppanz, Agata Kodroń, Tomasz M Stępkowski, Praveenraj Elancheliyan, Biniyam Tsegaye, Silke Oeljeklaus, Michal Wasilewski, Bettina Warscheid, Agnieszka Chacinska.

Perturbed cellular protein homeostasis (proteostasis) and mitochondrial dysfunction play an important role in neurodegenerative diseases, however, the interplay between these two phenomena remains unclear. Mitochondrial dysfunction leads to a delay in mitochondrial protein import, causing accumulation of non-imported mitochondrial proteins in the cytosol and challenging proteostasis. Cells respond by increasing proteasome activity and molecular chaperones in yeast and C. elegans. Here, we demonstrate that in human cells mitochondrial dysfunction leads to the upregulation of a chaperone HSPB1 and, interestingly, an immunoproteasome-specific subunit PSMB9. Moreover, PSMB9 expression is dependent on the translation elongation factor EEF1A2. These mechanisms constitute a defense response to preserve cellular proteostasis under mitochondrial stress. Our findings define a mode of proteasomal activation through the change in proteasome composition driven by EEF1A2 and its spatial regulation, and are useful to formulate therapies to prevent neurodegenerative diseases.

DOI: https://doi.org/10.1038/s41467-023-39642-8
J Biol Chem. 2023 Jul 12. pii: S0021-9258(23)02075-6. [Epub ahead of print] 105047

Maintenance of cellular vitamin B6 levels and mitochondrial oxidative function depend on pyridoxal 5'-phosphate homeostasis protein (PLPHP).

Jolita Ciapaite, Carlo W T van Roermund, Marjolein Bosma, Johan Gerrits, Sander M Houten, Lodewijk IJlst, Hans R Waterham, Clara D M van Karnebeek, Ronald J A Wanders, Fried J T Zwartkruis, Judith J Jans, Nanda M Verhoeven-Duif.

  Recently, biallelic variants in PLPBP coding for pyridoxal 5'-phosphate homeostasis protein (PLPHP) were identified as a novel cause of early-onset vitamin B6-dependent epilepsy. The molecular function and precise role of PLPHP in vitamin B6 metabolism are not well understood. To address these questions we used PLPHP deficient patient skin fibroblasts and HEK293 cells, and YBL036C (PLPHP ortholog) deficient yeast. We showed that independent of extracellular B6 vitamer type (pyridoxine, pyridoxamine or pyridoxal), intracellular PLP was lower in PLPHP deficient fibroblasts and HEK293 cells compared to controls. Culturing cells with pyridoxine or pyridoxamine led to the concentration-dependent accumulation of pyridoxine 5'-phosphate and pyridoxamine 5'-phosphate (PMP), respectively, suggesting insufficient pyridox(am)ine 5'-phosphate oxidase (PNPO) activity. Experiments utilizing 13C4-pyridoxine confirmed lower PNPO activity and revealed increased fractional turnovers of PLP and pyridoxal, indicating increased PLP hydrolysis to pyridoxal in PLPHP deficient cells. This effect could be partly counteracted by inactivation of pyridoxal phosphatase. PLPHP deficiency had a distinct effect on mitochondrial PLP and PMP, suggesting impaired activity of mitochondrial transaminases. Moreover, in YBL036C deficient yeast PLP was depleted and PMP accumulated only with carbon sources requiring mitochondrial metabolism. Lactate and pyruvate accumulation along with the decrease of tricarboxylic acid cycle intermediates downstream of α-ketoglutarate suggested impaired mitochondrial oxidative metabolism in PLPHP deficient HEK293 cells. We hypothesize that impaired activity of mitochondrial transaminases may contribute to this depletion. Taken together, our study provides new insights into the pathomechanisms of PLPBP deficiency and reinforces the link between PLPHP function, vitamin B6 metabolism and mitochondrial oxidative metabolism.

Keywords:  Pyridoxal 5’-phosphate homeostasis protein PLPHP (PROSC); mitochondrial dysfunction; pyridox(am)ine 5′-phosphate oxidase (PNPO); transaminases; vitamin B(6) metabolism; α-ketoglutarate

DOI:  https://doi.org/10.1016/j.jbc.2023.105047
Aging Cell. 2023 Jul 09. e13920

NAD metabolism: Role in senescence regulation and aging.

Claudia Christiano Silva Chini, Heidi Soares Cordeiro, Ngan Le Kim Tran, Eduardo Nunes Chini.

  The geroscience hypothesis proposes that addressing the biology of aging could directly prevent the onset or mitigate the severity of multiple chronic diseases. Understanding the interplay between key aspects of the biological hallmarks of aging is essential in delivering the promises of the geroscience hypothesis. Notably, the nucleotide nicotinamide adenine dinucleotide (NAD) interfaces with several biological hallmarks of aging, including cellular senescence, and changes in NAD metabolism have been shown to be involved in the aging process. The relationship between NAD metabolism and cellular senescence appears to be complex. On the one hand, the accumulation of DNA damage and mitochondrial dysfunction induced by low NAD+ can promote the development of senescence. On the other hand, the low NAD+ state that occurs during aging may inhibit SASP development as this secretory phenotype and the development of cellular senescence are both highly metabolically demanding. However, to date, the impact of NAD+ metabolism on the progression of the cellular senescence phenotype has not been fully characterized. Therefore, to explore the implications of NAD metabolism and NAD replacement therapies, it is essential to consider their interactions with other hallmarks of aging, including cellular senescence. We propose that a comprehensive understanding of the interplay between NAD boosting strategies and senolytic agents is necessary to advance the field.

Keywords:  NAD+ metabolism; SASP; aging; nicotinamide adenine dinucleotide; senescence

DOI:  https://doi.org/10.1111/acel.13920
bioRxiv. 2023 Jun 27. pii: 2023.06.27.546775. [Epub ahead of print]

An engineered biosensor enables dynamic aspartate measurements in living cells.

Kristian Davidsen, Jonathan S Marvin, Abhi Aggarwal, Timothy A Brown, Lucas B Sullivan.

Intracellular levels of the amino acid aspartate are responsive to changes in metabolism in mammalian cells and can correspondingly alter cell function, highlighting the need for robust tools to measure aspartate abundance. However, comprehensive understanding of aspartate metabolism has been limited by the throughput, cost, and static nature of the mass spectrometry based measurements that are typically employed to measure aspartate levels. To address these issues, we have developed a GFP-based sensor of aspartate (jAspSnFR3), where the fluorescence intensity corresponds to aspartate concentration. As a purified protein, the sensor has a 20-fold increase in fluorescence upon aspartate saturation, with dose dependent fluorescence changes covering a physiologically relevant aspartate concentration range and no significant off target binding. Expressed in mammalian cell lines, sensor intensity correlated with aspartate levels measured by mass spectrometry and could resolve temporal changes in intracellular aspartate from genetic, pharmacological, and nutritional manipulations. These data demonstrate the utility of jAspSnFR3 and highlight the opportunities it provides for temporally resolved and high throughput applications of variables that affect aspartate levels.

DOI: https://doi.org/10.1101/2023.06.27.546775
Clin Exp Dermatol. 2023 Jul 08. pii: llad234. [Epub ahead of print]

Hereditary leiomyomatosis and renal cell cancer (HLRCC) - linked with FH mutations.

George W M Millington.

DOI: https://doi.org/10.1093/ced/llad234
Nat Cell Biol. 2023 Jul 13.

STING is a cell-intrinsic metabolic checkpoint restricting aerobic glycolysis by targeting HK2.

Liting Zhang, Congqing Jiang, Yunhong Zhong, Kongliang Sun, Huiru Jing, Jiayu Song, Jun Xie, Yaru Zhou, Mao Tian, Chuchu Zhang, Xiaona Sun, Shaowei Wang, Xi Cheng, Yuelan Zhang, Wei Wei, Xiang Li, Bishi Fu, Pinghui Feng, Bing Wu, Hong-Bing Shu, Junjie Zhang.

Evasion of antitumour immunity is a hallmark of cancer. STING, a putative innate immune signalling adaptor, has a pivotal role in mounting antitumour immunity by coordinating innate sensing and adaptive immune surveillance in myeloid cells. STING is markedly silenced in various human malignancies and acts as a cell-intrinsic tumour suppressor. How STING exerts intrinsic antitumour activity remains unclear. Here, we report that STING restricts aerobic glycolysis independent of its innate immune function. Mechanistically, STING targets hexokinase II (HK2) to block its hexokinase activity. As such, STING inhibits HK2 to restrict tumour aerobic glycolysis and promote antitumour immunity in vivo. In human colorectal carcinoma samples, lactate, which can be used as a surrogate for aerobic glycolysis, is negatively correlated with STING expression level and antitumour immunity. Taken together, this study reveals that STING functions as a cell-intrinsic metabolic checkpoint that restricts aerobic glycolysis to promote antitumour immunity. These findings have important implications for the development of STING-based therapeutic modalities to improve antitumour immunotherapy.

DOI: https://doi.org/10.1038/s41556-023-01185-x
Cell Rep. 2023 Jul 11. pii: S2211-1247(23)00787-8. [Epub ahead of print]42(7): 112776

Mitofusin-2 in nucleus accumbens D2-MSNs regulates social dominance and neuronal function.

Sriparna Ghosal, Elias Gebara, Eva Ramos-Fernández, Alessandro Chioino, Jocelyn Grosse, Isabelle Guillot de Suduiraut, Olivia Zanoletti, Bernard Schneider, Antonio Zorzano, Simone Astori, Carmen Sandi.

  The nucleus accumbens (NAc) is a brain hub regulating motivated behaviors, including social competitiveness. Mitochondrial function in the NAc links anxiety with social competitiveness, and the mitochondrial fusion protein mitofusin 2 (Mfn2) in NAc neurons regulates anxiety-related behaviors. However, it remains unexplored whether accumbal Mfn2 levels also affect social behavior and whether Mfn2 actions in the emotional and social domain are driven by distinct cell types. Here, we found that subordinate-prone highly anxious rats show decreased accumbal Mfn2 levels and that Mfn2 overexpression promotes dominant behavior. In mice, selective Mfn2 downregulation in NAc dopamine D2 receptor-expressing medium spiny neurons (D2-MSNs) induced social subordination, accompanied by decreased accumbal mitochondrial functions and decreased excitability in D2-MSNs. Instead, D1-MSN-targeted Mfn2 downregulation affected competitive ability only transiently and likely because of an increase in anxiety-like behaviors. Our results assign dissociable cell-type specific roles to Mfn2 in the NAc in modulating social dominance and anxiety.

Keywords:  CP: Neuroscience; anxiety; medium spiny neurons; mitochondria; mitofusin 2; motivation; nucleus accumbens; social competition; social dominance; tube test

DOI:  https://doi.org/10.1016/j.celrep.2023.112776
Nat Commun. 2023 Jul 14. 14(1): 4221

Oxidative phosphorylation is a metabolic vulnerability of endocrine therapy and palbociclib resistant metastatic breast cancers.

Rania El-Botty, Ludivine Morriset, Elodie Montaudon, Zakia Tariq, Anne Schnitzler, Marina Bacci, Nicla Lorito, Laura Sourd, Léa Huguet, Ahmed Dahmani, Pierre Painsec, Heloise Derrien, Sophie Vacher, Julien Masliah-Planchon, Virginie Raynal, Sylvain Baulande, Thibaut Larcher, Anne Vincent-Salomon, Guillaume Dutertre, Paul Cottu, Géraldine Gentric, Fatima Mechta-Grigoriou, Scott Hutton, Keltouma Driouch, Ivan Bièche, Andrea Morandi, Elisabetta Marangoni.

Resistance to endocrine treatments and CDK4/6 inhibitors is considered a near-inevitability in most patients with estrogen receptor positive breast cancers (ER + BC). By genomic and metabolomics analyses of patients' tumours, metastasis-derived patient-derived xenografts (PDX) and isogenic cell lines we demonstrate that a fraction of metastatic ER + BC is highly reliant on oxidative phosphorylation (OXPHOS). Treatment by the OXPHOS inhibitor IACS-010759 strongly inhibits tumour growth in multiple endocrine and palbociclib resistant PDX. Mutations in the PIK3CA/AKT1 genes are significantly associated with response to IACS-010759. At the metabolic level, in vivo response to IACS-010759 is associated with decreased levels of metabolites of the glutathione, glycogen and pentose phosphate pathways in treated tumours. In vitro, endocrine and palbociclib resistant cells show increased OXPHOS dependency and increased ROS levels upon IACS-010759 treatment. Finally, in ER + BC patients, high expression of OXPHOS associated genes predict poor prognosis. In conclusion, these results identify OXPHOS as a promising target for treatment resistant ER + BC patients.

DOI: https://doi.org/10.1038/s41467-023-40022-5
Aging (Albany NY). 2023 Jul 12. 15

Chemically induced reprogramming to reverse cellular aging.

Jae-Hyun Yang, Christopher A Petty, Thomas Dixon-McDougall, Maria Vina Lopez, Alexander Tyshkovskiy, Sun Maybury-Lewis, Xiao Tian, Nabilah Ibrahim, Zhili Chen, Patrick T Griffin, Matthew Arnold, Jien Li, Oswaldo A Martinez, Alexander Behn, Ryan Rogers-Hammond, Suzanne Angeli, Vadim N Gladyshev, David A Sinclair.

  A hallmark of eukaryotic aging is a loss of epigenetic information, a process that can be reversed. We have previously shown that the ectopic induction of the Yamanaka factors OCT4, SOX2, and KLF4 (OSK) in mammals can restore youthful DNA methylation patterns, transcript profiles, and tissue function, without erasing cellular identity, a process that requires active DNA demethylation. To screen for molecules that reverse cellular aging and rejuvenate human cells without altering the genome, we developed high-throughput cell-based assays that distinguish young from old and senescent cells, including transcription-based aging clocks and a real-time nucleocytoplasmic compartmentalization (NCC) assay. We identify six chemical cocktails, which, in less than a week and without compromising cellular identity, restore a youthful genome-wide transcript profile and reverse transcriptomic age. Thus, rejuvenation by age reversal can be achieved, not only by genetic, but also chemical means.

Keywords:  epigenetics; information theory of aging; rejuvenation medicine; reprogramming; small molecules

DOI:  https://doi.org/10.18632/aging.204896
Nat Commun. 2023 Jul 08. 14(1): 4051

ATPase activity of DFCP1 controls selective autophagy.

Viola Nähse, Camilla Raiborg, Kia Wee Tan, Sissel Mørk, Maria Lyngaas Torgersen, Eva Maria Wenzel, Mireia Nager, Veijo T Salo, Terje Johansen, Elina Ikonen, Kay Oliver Schink, Harald Stenmark.

Cellular homeostasis is governed by removal of damaged organelles and protein aggregates by selective autophagy mediated by cargo adaptors such as p62/SQSTM1. Autophagosomes can assemble in specialized cup-shaped regions of the endoplasmic reticulum (ER) known as omegasomes, which are characterized by the presence of the ER protein DFCP1/ZFYVE1. The function of DFCP1 is unknown, as are the mechanisms of omegasome formation and constriction. Here, we demonstrate that DFCP1 is an ATPase that is activated by membrane binding and dimerizes in an ATP-dependent fashion. Whereas depletion of DFCP1 has a minor effect on bulk autophagic flux, DFCP1 is required to maintain the autophagic flux of p62 under both fed and starved conditions, and this is dependent on its ability to bind and hydrolyse ATP. While DFCP1 mutants defective in ATP binding or hydrolysis localize to forming omegasomes, these omegasomes fail to constrict properly in a size-dependent manner. Consequently, the release of nascent autophagosomes from large omegasomes is markedly delayed. While knockout of DFCP1 does not affect bulk autophagy, it inhibits selective autophagy, including aggrephagy, mitophagy and micronucleophagy. We conclude that DFCP1 mediates ATPase-driven constriction of large omegasomes to release autophagosomes for selective autophagy.

DOI: https://doi.org/10.1038/s41467-023-39641-9