bims-mibica 2022-12-11 papers

bims-mibica

Biomed News

on Mitochondrial bioenergetics in cancer

Issue of 2022–12–11
33 papers selected by
Kelsey Fisher-Wellman, East Carolina University

EIF4A inhibition targets bioenergetic homeostasis in AML MOLM-14 cells in vitro and in vivo and synergizes with cytarabine and venetoclax.
PINK1-mediated mitophagy promotes oxidative phosphorylation and redox homeostasis to induce drug-tolerant persister cancer cells.
Protein S-glutathionylation and sex dimorphic effects on hydrogen peroxide production by dihydroorotate dehydrogenase in liver mitochondria.
Contribution of metabolic abnormalities to acute myeloid leukemia pathogenesis.
Xenotopic expression of alternative oxidase (AOX) to study mechanisms of mitochondrial disease.
A multi-omics longitudinal aging dataset in primary human fibroblasts with mitochondrial perturbations.
Mitochondrial biology and dysfunction in secondary mitochondrial disease.
Mitochondrial PARP1 regulates NAD+-dependent poly ADP-ribosylation of mitochondrial nucleoids.
NAD precursors cycle between host tissues and the gut microbiome.
Targeting CRL4 suppresses chemoresistant ovarian cancer growth by inducing mitophagy.
PHGDH and cancer: new job for an old enzyme!
Mitochondrial cristae architecture protects against mtDNA release and inflammation.
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.
A library of base editors for the precise ablation of all protein-coding genes in the mouse mitochondrial genome.
Mitochondrial DNA mutations as natural barcodes for lineage tracing of murine tumor models.
The role of cholesterol and mitochondrial bioenergetics in activation of the inflammasome in IBD.
Cellular and metabolic characteristics of pre-leukemic hematopoietic progenitors with GATA2 haploinsuficiency.
Mitochondrial respiration inhibitor enhances the anti-tumor effect of high-dose ascorbic acid in castration-resistant prostate cancer.
Principles of mitoribosomal small subunit assembly in eukaryotes.
Uncoupling of energy production.
Hypoxic activation of PFKFB4 in breast tumor microenvironment shapes metabolic and cellular plasticity to accentuate metastatic competence.
Functional noninvasive detection of glycolytic pancreatic ductal adenocarcinoma.
Analysis of compound heterozygous and homozygous mutations found in peripheral subunits of human respiratory Complex I, NDUFS1, NDUFS2, NDUFS8 and NDUFV1, by modeling in the E. coli enzyme.
Retrograde response to mitochondrial dysfunctions associated to LOF variations in FLAD1 exon 2: unraveling the importance of RFVT2.
Structure of the mitoribosomal small subunit with streptomycin reveals Fe-S clusters and physiological molecules.
Age-associated remodeling of T cell immunity and metabolism.
Memory CD8+ T cells upregulate glycolysis and effector functions under limiting oxygen conditions.
Decreased propionyl-CoA metabolism facilitates metabolic reprogramming and promotes hepatocellular carcinoma.
PDK1- and PDK2-mediated metabolic reprogramming contributes to the TGFβ1-promoted stem-like properties in head and neck cancer.
FAM3A maintains metabolic homeostasis by interacting with F1-ATP synthase to regulate the activity and assembly of ATP synthase.
Teaching old drugs new tricks.
Preliminary study to classify mechanisms of mitochondrial toxicity by in vitro metabolomics and bioinformatics.
Nicotinamide Nucleotide Transhydrogenase (NNT) is essential for adrenal steroidogenesis: clinical and in vitro lessons.

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
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
Free Radic Biol Med. 2022 Nov 30. pii: S0891-5849(22)01025-5. [Epub ahead of print]194 123-130

Protein S-glutathionylation and sex dimorphic effects on hydrogen peroxide production by dihydroorotate dehydrogenase in liver mitochondria.

Olivia Koufos, Ryan J Mailloux.

Dihydroorotate dehydrogenase (DHODH) oxidizes dihydroorotate to orotate for pyrimidine biosynthesis, donating electrons to the ubiquinone (UQ) pool of mitochondria. DHODH has a measurable rate for hydrogen peroxide (H2O2) production and thus contributes to cellular changes in redox tone. Protein S-glutathionylation serves as a negative feedback loop for the inhibition of H2O2 by several α-keto acid dehydrogenases and respiratory complexes in mitochondria, as well as ROS sources in liver cytoplasm. Here, we report this redox signaling mechanism also inhibits H2O2 production by DHODH in liver mitochondria isolated from male and female C57BL6N mice. We discovered that low amounts of the glutathionylation catalyst, disulfiram (50-500 nM), almost abolished H2O2 production by DHODH in mitochondria from male mice. Similar results were collected with diamide, however, higher doses (1000-5000 μM) were required to elicit this effect. Disulfiram and diamide also significantly suppressed H2O2 production by DHODH in female liver mitochondria. However, liver mitochondria from female mice were more resistant to disulfiram or diamide-mediated inhibition of H2O2 genesis when compared to samples from males. Analysis of the impact of disulfiram and diamide on DHODH activity revealed that both compounds inhibited the dehydrogenase directly, however the effect was less in female mice. Additionally, disulfiram and diamide impeded the use of dihydroorotate fueled oxidative phosphorylation in mitochondria from males and females, although samples collected from female rodents displayed more resistance to this inhibition. Taken together, our findings demonstrate H2O2 production by DHODH can be inhibited by glutathionylation and sex can impact this redox modification.

DOI: https://doi.org/10.1016/j.freeradbiomed.2022.11.043
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
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
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
Open Biol. 2022 Dec;12(12): 220274

Mitochondrial biology and dysfunction in secondary mitochondrial disease.

Megan J Baker, Jordan J Crameri, David R Thorburn, Ann E Frazier, Diana Stojanovski.

  Mitochondrial diseases are a broad, genetically heterogeneous class of metabolic disorders characterized by deficits in oxidative phosphorylation (OXPHOS). Primary mitochondrial disease (PMD) defines pathologies resulting from mutation of mitochondrial DNA (mtDNA) or nuclear genes affecting either mtDNA expression or the biogenesis and function of the respiratory chain. Secondary mitochondrial disease (SMD) arises due to mutation of nuclear-encoded genes independent of, or indirectly influencing OXPHOS assembly and operation. Despite instances of novel SMD increasing year-on-year, PMD is much more widely discussed in the literature. Indeed, since the implementation of next generation sequencing (NGS) techniques in 2010, many novel mitochondrial disease genes have been identified, approximately half of which are linked to SMD. This review will consolidate existing knowledge of SMDs and outline discrete categories within which to better understand the diversity of SMD phenotypes. By providing context to the biochemical and molecular pathways perturbed in SMD, we hope to further demonstrate the intricacies of SMD pathologies outside of their indirect contribution to mitochondrial energy generation.

Keywords:  mitochondria; mitochondrial protein import; mitochondrial quality control; secondary mitochondrial disease

DOI:  https://doi.org/10.1098/rsob.220274
Exp Mol Med. 2022 Dec 06.

Mitochondrial PARP1 regulates NAD+-dependent poly ADP-ribosylation of mitochondrial nucleoids.

Jong-Hyuk Lee, Mansoor Hussain, Edward W Kim, Shang-Jung Cheng, Anthony K L Leung, Nima Borhan Fakouri, Deborah L Croteau, Vilhelm A Bohr.

PARPs play fundamental roles in multiple DNA damage recognition and repair pathways. Persistent nuclear PARP activation causes cellular NAD+ depletion and exacerbates cellular aging. However, very little is known about mitochondrial PARP (mtPARP) and poly ADP-ribosylation (PARylation). The existence of mtPARP is controversial, and the biological roles of mtPARP-induced mitochondrial PARylation are unclear. Here, we demonstrate the presence of PARP1 and PARylation in purified mitochondria. The addition of the PARP1 substrate NAD+ to isolated mitochondria induced PARylation, which was suppressed by treatment with the inhibitor olaparib. Mitochondrial PARylation was also evaluated by enzymatic labeling of terminal ADP-ribose (ELTA). To further confirm the presence of mtPARP1, we evaluated mitochondrial nucleoid PARylation by ADP ribose-chromatin affinity purification (ADPr-ChAP) and PARP1 chromatin immunoprecipitation (ChIP). We observed that NAD+ stimulated PARylation and TFAM occupancy on the mtDNA regulatory region D-loop, inducing mtDNA transcription. These findings suggest that PARP1 is integrally involved in mitochondrial PARylation and that NAD+-dependent mtPARP1 activity contributes to mtDNA transcriptional regulation.

DOI: https://doi.org/10.1038/s12276-022-00894-x
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
Signal Transduct Target Ther. 2022 Dec 09. 7(1): 388

Targeting CRL4 suppresses chemoresistant ovarian cancer growth by inducing mitophagy.

Yang Meng, Lei Qiu, Xinyi Zeng, Xiaoyan Hu, Yaguang Zhang, Xiaowen Wan, Xiaobing Mao, Jian Wu, Yongfeng Xu, Qunli Xiong, Zhixin Chen, Bo Zhang, Junhong Han.

Chemoresistance has long been the bottleneck of ovarian cancer (OC) prognosis. It has been shown that mitochondria play a crucial role in cell response to chemotherapy and that dysregulated mitochondrial dynamics is intricately linked with diseases like OC, but the underlying mechanisms remain equivocal. Here, we demonstrate a new mechanism where CRL4CUL4A/DDB1 manipulates OC cell chemoresistance by regulating mitochondrial dynamics and mitophagy. CRL4CUL4A/DDB1 depletion enhanced mitochondrial fission by upregulating AMPKαThr172 and MFFSer172/Ser146 phosphorylation, which in turn recruited DRP1 to mitochondria. CRL4CUL4A/DDB1 loss stimulated mitophagy through the Parkin-PINK1 pathway to degrade the dysfunctional and fragmented mitochondria. Importantly, CRL4CUL4A/DDB1 loss inhibited OC cell proliferation, whereas inhibiting autophagy partially reversed this disruption. Our findings provide novel insight into the multifaceted function of the CRL4 E3 ubiquitin ligase complex in regulating mitochondrial fission, mitophagy, and OC chemoresistance. Disruption of CRL4CUL4A/DDB1 and mitophagy may be a promising therapeutic strategy to overcome chemoresistance in OC.

DOI: https://doi.org/10.1038/s41392-022-01253-y
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
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
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
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
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
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
Haematologica. 2022 Dec 07.

Cellular and metabolic characteristics of pre-leukemic hematopoietic progenitors with GATA2 haploinsuficiency.

Avigail Rein, Ifat Geron, Eitan Kugler, Hila Fishman, Eyal Gottlieb, Ifat Abramovich, Amir Giladi, Ido Amit, Roger Mulet-Lazaro, Ruud Delwel, Stefan Gröschel, Smadar Levin-Zaidman, Nili Dezorella, Vered Holdengreber, Tata Nageswara Rao, Joanne Yacobovich, Orna Steinberg-Shemer, Qiu-Hua Huang, Yun Tan, Sai-Juan Chen, Shai Izraeli, Yehudit Birger.

Mono-Allelic germline disruptions of the transcription factor GATA2 result in a propensity for developing myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) affecting more than 85% of carriers. How a partial loss of GATA2 functionality enables leukemic transformation occurring years later in life, is unclear. This question is unsolved mainly due to lack of informative models, as Gata2 heterozygote mice do not develop hematologic malignancies. Here we show that two different germline Gata2 mutations (tgERG/GATA2het and tgERG/Gata2L359V) accelerate AML in mice expressing the human hematopoietic stem cell regulator ERG. Analysis of ERG/Gata2het fetal liver and bone marrow derived hematopoietic cells revealed a distinct pre-leukemic phenotype. This was characterized by enhanced transition from stem to progenitor state, increased proliferation, and a striking mitochondrial phenotype, consisting of highly expressed Oxidative- Phosphorylation related gene-sets, elevated oxygen consumption rates, and notably, markedly distorted mitochondrial morphology. Importantly, the same mitochondrial gene-expression signature was observed in human AMLs harboring GATA2 aberrations. Similar to the observations in mice, non-leukemic bone marrows from children with germline GATA2 mutation demonstrated marked mitochondrial abnormalities. Thus, we observed the tumor suppressive effects of GATA2 in two germline Gata2 genetic mouse models. As oncogenic mutations often accumulate with age, Gata2 deficiency mediated priming of hematopoietic cells for oncogenic transformation may explain the earlier occurrence of MDS/AML in patients with GATA2 germline mutation. The mitochondrial phenotype is a potential therapeutic opportunity for prevention of leukemic transformation in these patients.

DOI: https://doi.org/10.3324/haematol.2022.279437
J Mol Med (Berl). 2022 Dec 07.

Mitochondrial respiration inhibitor enhances the anti-tumor effect of high-dose ascorbic acid in castration-resistant prostate cancer.

Jia Qiu, Tianhong Yang, Yali Long, Peng He, Wanqing Shen, Bing Zhang, Xinchong Shi, Lei Peng, Zhoulei Li, Xiangsong Zhang.

  Previous evidences have demonstrated that anti-tumor effect of high-dose ascorbic acid is associated with the generation of reactive oxygen species (ROS) via autoxidation. Hypoxia induces therapy resistance in castration-resistant prostate cancer. As a mitochondrial respiration inhibitor, metformin has the potential to improve tumor oxygenation. In this study, we evaluate the anti-tumor effect of ascorbic acid combined with metformin in prostate cancer. We demonstrated that ascorbic acid inhibits prostate cancer cells proliferation by generating ROS, and metformin enhances the anti-tumor effects of ascorbic acid. Mechanistically, metformin reduces oxygen consumption rate and NADP+/NADPH value in prostate cancer cells, thereby increases the ROS content induced by ascorbic acid. In addition, our data demonstrated that ascorbic acid inhibits p-AKT signaling in a ROS-dependent pathway, leading to inhibition of p-mTOR expression. And metformin inhibits the p-mTOR expression by activating the AMPK signaling pathway, exerting a synergistic effect on tumor suppression with ascorbic acid. Furthermore, metformin improves tumor oxygenation, and the combined treatment effect of ascorbic acid and metformin were demonstrated in a xenograft model of prostate cancer. Taken together, our data demonstrate that metformin enhances the anti-tumor proliferation effect of ascorbic acid by increasing ROS content in castration-resistant prostate cancer. This provides a new strategy for the clinical application of high-dose ascorbic acid as an anti-tumor drug. KEY MESSAGES: Ascorbic acid inhibits tumor growth by inducing ROS generation. As a mitochondrial respiration inhibitor, metformin inhibits cellular oxygen consumption rate to improve oxygenation of prostate cancer. Metformin enhances anti-tumor effect of ascorbic acid by increasing ROS content. Ascorbic acid inhibits the mTOR expression via PI3K-AKT pathway, and metformin inhibits the mTOR expression by inhibiting AMPK signaling in prostate cancer cells.

Keywords:  Ascorbic acid; Castration-resistant prostate cancer; Mitochondrial respiration inhibitor

DOI:  https://doi.org/10.1007/s00109-022-02273-5
Nature. 2022 Dec 08.

Principles of mitoribosomal small subunit assembly in eukaryotes.

Nathan J Harper, Chloe Burnside, Sebastian Klinge.

Mitochondrial ribosomes (mitoribosomes) synthesize proteins encoded within the mitochondrial genome that are assembled into oxidative phosphorylation complexes. Thus, mitoribosome biogenesis is essential for ATP production and cellular metabolism1. Here we used cryo-electron microscopy to determine 9 structures of native yeast and human mitoribosomal small subunit assembly intermediates at resolutions from 2.4 to 3.8 Å, illuminating the mechanistic basis for how GTPases are employed to control early steps of decoding center formation, how initial rRNA folding and processing events are mediated, and how mitoribosomal proteins play active roles during assembly. Furthermore, this series of intermediates from two species with divergent mitoribosomal architecture uncovers both conserved principles and species-specific adaptations that govern the maturation of mitoribosomal small subunits in eukaryotes. By revealing the dynamic interplay between assembly factors, mitoribosomal proteins, and rRNA required to generate functional subunits, our structural analysis provides a vignette for how molecular complexity and diversity can evolve in large ribonucleoprotein assemblies.

DOI: https://doi.org/10.1038/s41586-022-05621-0
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
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
Cancer Metab. 2022 Dec 09. 10(1): 24

Functional noninvasive detection of glycolytic pancreatic ductal adenocarcinoma.

Irina Heid, Corinna Münch, Sinan Karakaya, Smiths S Lueong, Alina M Winkelkotte, Sven T Liffers, Laura Godfrey, Phyllis F Y Cheung, Konstantinos Savvatakis, Geoffrey J Topping, Florian Englert, Lukas Kritzner, Martin Grashei, Andrea Tannapfel, Richard Viebahn, Heiner Wolters, Waldemar Uhl, Deepak Vangala, Esther M M Smeets, Erik H J G Aarntzen, Daniel Rauh, Wilko Weichert, Jörg D Hoheisel, Stephan A Hahn, Franz Schilling, Rickmer Braren, Marija Trajkovic-Arsic, Jens T Siveke.

   BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) lacks effective treatment options beyond chemotherapy. Although molecular subtypes such as classical and QM (quasi-mesenchymal)/basal-like with transcriptome-based distinct signatures have been identified, deduced therapeutic strategies and targets remain elusive. Gene expression data show enrichment of glycolytic genes in the more aggressive and therapy-resistant QM subtype. However, whether the glycolytic transcripts are translated into functional glycolysis that could further be explored for metabolic targeting in QM subtype is still not known.
METHODS: We used different patient-derived PDAC model systems (conventional and primary patient-derived cells, patient-derived xenografts (PDX), and patient samples) and performed transcriptional and functional metabolic analysis. These included RNAseq and Illumina HT12 bead array, in vitro Seahorse metabolic flux assays and metabolic drug targeting, and in vivo hyperpolarized [1-13C]pyruvate and [1-13C]lactate magnetic resonance spectroscopy (HP-MRS) in PDAC xenografts.
RESULTS: We found that glycolytic metabolic dependencies are not unambiguously functionally exposed in all QM PDACs. Metabolic analysis demonstrated functional metabolic heterogeneity in patient-derived primary cells and less so in conventional cell lines independent of molecular subtype. Importantly, we observed that the glycolytic product lactate is actively imported into the PDAC cells and used in mitochondrial oxidation in both classical and QM PDAC cells, although more actively in the QM cell lines. By using HP-MRS, we were able to noninvasively identify highly glycolytic PDAC xenografts by detecting the last glycolytic enzymatic step and prominent intra-tumoral [1-13C]pyruvate and [1-13C]lactate interconversion in vivo.
CONCLUSION: Our study adds functional metabolic phenotyping to transcriptome-based analysis and proposes a functional approach to identify highly glycolytic PDACs as candidates for antimetabolic therapeutic avenues.

Keywords:  Glycolysis; Hyperpolarized magnetic resonance spectroscopy; Lactate; Molecular subtype; PDAC

DOI:  https://doi.org/10.1186/s40170-022-00298-5
Mitochondrion. 2022 Nov 30. pii: S1567-7249(22)00104-0. [Epub ahead of print]68 87-104

Analysis of compound heterozygous and homozygous mutations found in peripheral subunits of human respiratory Complex I, NDUFS1, NDUFS2, NDUFS8 and NDUFV1, by modeling in the E. coli enzyme.

Hind A Alkhaldi, Steven B Vik.

  Respiratory Complex I (NADH:ubiquinone oxidoreductase) is composed of 45 subunits, seven mitochondrially-encoded and 38 imported. Mutations in the nuclearly-encoded subunits have been regularly discovered in humans in recent years, and many lead to cardiomyopathy, Leigh Syndrome, and early death. From the literature, we have identified mutations at 17 different sites and constructed 31 mutants in a bacterial model system. Many of these mutations, found in NDUFS1, NDUFS2, NDUFS8, and NDUFV1, map to subunit interfaces, and we hypothesized that they would disrupt assembly of Complex I. The mutations were constructed in the homologous E. coli genes, nuoG, nuoCD, nuoI and nuoF, respectively, and expressed from a plasmid containing all Complex I genes. Membrane vesicles were prepared and rates of deamino-NADH oxidase activity measured, which indicated a range of reduced activity. Some mutants were also analyzed using recently developed assays of assembly, time-delayed expression, and co-immunoprecipitation, which showed that assembly was disrupted. With compound heterozygotes, we determined which mutation was more deleterious. Construction of alanine mutations allowed us to distinguish between phenotypes that were caused by loss of the original amino acid or introduction of the mutant residue.

Keywords:  Bioenergetics; Cardiomyopathy; Complex I; Mitochondria; Mutations; NADH dehydrogenase

DOI:  https://doi.org/10.1016/j.mito.2022.11.007
Free Radic Res. 2022 Dec 08. 1-15

Retrograde response to mitochondrial dysfunctions associated to LOF variations in FLAD1 exon 2: unraveling the importance of RFVT2.

Maria Tolomeo, Guglielmina Chimienti, Martina Lanza, Roberto Barbaro, Alessia Nisco, Tiziana Latronico, Piero Leone, Giuseppe Petrosillo, Grazia Maria Liuzzi, Bryony Ryder, Michal Inbar-Feigenberg, Matilde Colella, Angela M S Lezza, Rikke K J Olsen, Maria Barile.

  Flavin adenine dinucleotide (FAD) synthase (EC 2.7.7.2), encoded by human flavin adenine dinucleotide synthetase 1 (FLAD1), catalyzes the last step of the pathway converting riboflavin (Rf) into FAD. FLAD1 variations were identified as a cause of LSMFLAD (lipid storage myopathy due to FAD synthase deficiency, OMIM #255100), resembling Multiple Acyl-CoA Dehydrogenase Deficiency, sometimes treatable with high doses of Rf; no alternative therapeutic strategies are available. We describe here cell morphological and mitochondrial alterations in dermal fibroblasts derived from a LSMFLAD patient carrying a homozygous truncating FLAD1 variant (c.745C > T) in exon 2. Despite a severe decrease in FAD synthesis rate, the patient had decreased cellular levels of Rf and flavin mononucleotide and responded to Rf treatment.We hypothesized that disturbed flavin homeostasis and Rf-responsiveness could be due to a secondary impairment in the expression of the Rf transporter 2 (RFVT2), encoded by SLC52A2, in the frame of an adaptive retrograde signaling to mitochondrial dysfunction. Interestingly, an antioxidant response element (ARE) is found in the region upstream of the transcriptional start site of SLC52A2. Accordingly, we found that abnormal mitochondrial morphology and impairments in bioenergetics were accompanied by increased cellular reactive oxygen species content and mtDNA oxidative damage. Concomitantly, an active response to mitochondrial stress is suggested by increased levels of PPARγ-co-activator-1α and Peroxiredoxin III. In this scenario, the treatment with high doses of Rf might compensate for the secondary RFVT2 molecular defect, providing a molecular rationale for the Rf responsiveness in patients with loss of function variants in FLAD1 exon 2.HIGHLIGHTSFAD synthase deficiency alters mitochondrial morphology and bioenergetics;FAD synthase deficiency triggers a mitochondrial retrograde response;FAD synthase deficiency evokes nuclear signals that adapt the expression of RFVT2.

Keywords:  FLAD1; LSMFLAD; MADD; RFVT2; mitochondrial myopathy

DOI:  https://doi.org/10.1080/10715762.2022.2146501
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
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
Eur J Immunol. 2022 Nov 22.

Memory CD8+ T cells upregulate glycolysis and effector functions under limiting oxygen conditions.

Ammarina Beumer-Chuwonpad, Floris P J van Alphen, Natasja A M Kragten, Julian J Freen-van Heeren, Maria Rodriguez Gomez, Arthur J Verhoeven, Maartje van den Biggelaar, Klaas P J M van Gisbergen.

  Memory CD8+ T cells are indispensable for maintaining long-term immunity against intracellular pathogens and tumors. Despite their presence at oxygen-deprived infected tissue sites or in tumors, the impact of local oxygen pressure on memory CD8+ T cells remains largely unclear. We sought to elucidate how oxygen pressure impacts memory CD8+ T cells arising after infection with Listeria monocytogenes-OVA. Our data revealed that reduced oxygen pressure during in vitro culture switched CD8+ T cell metabolism from oxidative phosphorylation to a glycolytic phenotype. Quantitative proteomic analysis showed that limiting oxygen conditions increased the expression of glucose transporters and components of the glycolytic pathway, while decreasing TCA cycle and mitochondrial respiratory chain proteins. The altered CD8+ T cell metabolism did not affect the expansion potential, but enhanced the granzyme B and IFN-γ production capacity. In vivo, memory CD8+ T cells cultured under low oxygen pressure provided protection against bacterial rechallenge. Taken together, our study indicates that strategies of cellular immune therapy may benefit from reducing oxygen during culture to develop memory CD8+ T cells with superior effector functions.

Keywords:  CD8+ memory T cells; Cytotoxic T cells; Hypoxic T cell cultures; T cell metabolism; glycolysis

DOI:  https://doi.org/10.1002/eji.202249918
J Hepatol. 2022 Nov 30. pii: S0168-8278(22)03311-6. [Epub ahead of print]

Decreased propionyl-CoA metabolism facilitates metabolic reprogramming and promotes hepatocellular carcinoma.

Jiaqi Sun, Jun Ding, Qingsong Shen, Xiyang Wang, Min Wang, Yongping Huang, Xuechun Zhang, Huan Zhu, Feng Zhang, Dongde Wu, Min Peng, Zhonglin Zhang, Yufeng Yuan, Wenhua Li, Zhi-Gang She, Xiaojing Zhang, Hongliang Li, Peng Zhang, Zan Huang.

   BACKGROUND & AIMS: Alterations of multiple metabolites characterize distinct features of metabolic reprograming in hepatocellular carcinoma (HCC). However, most metabolites including propionyl-CoA (Pro-CoA) are illusive for their functions in metabolic reprograming and hepatocarcinogenesis. This study aims to dissect how Pro-CoA metabolism affects these processes.
METHODS: TCGA data and HCC samples were used to analyze the ALDH6A1-mediated Pro-CoA metabolism and its correlation with HCC. Multiple metabolites were assayed by targeted mass spectrometry. The function of ALDH6A1-generated Pro-CoA was evaluated by HCC proliferation, migration, xenograft nude mouse model and primary liver cancer mouse models. Nontargeted metabolomic and targeted energy metabolomic analyses followed by multiple biochemical assays were performed to dissect the underlying mechanisms.
RESULTS: Decreases in Pro-CoA and its derivative propionyl-L-carnitine (PLC) due to ALDH6A1 downregulation were tightly associated with HCC. Functionally, ALDH6A1-mediated Pro-CoA metabolism suppressed HCC proliferation and impaired hepatocarcinogenesis in mice. The aldehyde dehydrogenase activity was indispensable for the ALDH6A1 function while Pro-CoA carboxylases antagonized ALDH6A1 function by eliminating Pro-CoA. Mechanistically, ALDH6A1 caused a signature enrichment of central carbon metabolism in cancer and impaired energy metabolism: ALDH6A1-generated Pro-CoA suppressed citrate synthase (CS) activity that subsequently reduced TCA cycle flux, impaired mitochondrial respiration and membrane potential, and decreased ATP production. Moreover, Pro-CoA metabolism generated 2-methylcitric acid (MCA), which mimicked the inhibitory effect of Pro-CoA on CS and dampened mitochondrial respiration and HCC proliferation.
CONCLUSIONS: Our study unveils novel features that the decline of ALDH6A1-mediated Pro-CoA metabolism contributes to metabolic remodeling and facilitates hepatocarcinogenesis. Pro-CoA, PLC and MCA may serve as novel metabolic biomarkers for diagnosis and therapy of HCC. Pro-CoA metabolism may provide potential targets for development of novel strategies against HCC.
IMPACT AND IMPLICATIONS: Our study presents new insights on metabolic reprogramming and hepatocarcinogenesis attribute to the decline of ALDH6A1-mediated propionyl-CoA. These findings may enrich molecular and metabolic indicators for physicians to improve clinical practice. These biomarkers may potentially be used for diagnosis and serve as targets for the development of therapeutic strategies against HCC.

Keywords:  2-Methylcitric acid; ALDH6A1; Metabolic reprogramming; Propionyl-CoA; Propionyl-L-carnitine

DOI:  https://doi.org/10.1016/j.jhep.2022.11.017
Cancer Metab. 2022 Dec 06. 10(1): 23

PDK1- and PDK2-mediated metabolic reprogramming contributes to the TGFβ1-promoted stem-like properties in head and neck cancer.

Wan-Hsuan Sun, Yun-Hsuan Chen, Hou-Hsuan Lee, Yu-Wen Tang, Kuang-Hui Sun.

   BACKGROUND: Resistance to chemotherapeutic drugs is a key factor for cancer recurrence and metastases in head and neck cancer (HNC). Cancer stem cells (CSCs) in tumors have self-renewal, differentiation, and higher drug resistance capabilities, resulting in a poor prognosis for patients. In glucose metabolism, pyruvate dehydrogenase kinase (PDK) inhibits pyruvate dehydrogenase and impedes pyruvate from being metabolized into acetyl-CoA and entering the tricarboxylic acid cycle to generate energy. Studies have reported that PDK1 and PDK2 inhibition suppresses the growth, motility, and drug resistance of cancer cells. Furthermore, while TGFβ1 levels are persistently elevated in HNC patients with poor prognosis, the role of PDK isoforms in the TGFβ1-promoted progression and stem-like properties of HNC is unclear.
METHODS: Levels of PDK1 and PDK2 were evaluated in HNC tissue microarrays by immunohistochemistry to explore potential clinical relevance. PDK1 and PDK2 were knocked down by the lentivirus shRNA system to investigate their role in TGFβ1-promoted tumor progression in vitro.
RESULTS: We found that PDK2 levels were increased in the later stage of HNC tissues compared to constant PDK1 expression. After PDK1 and PDK2 knockdown, we discovered increased ATP production and decreased lactate production in TGFβ1-treated and untreated HNC cells. However, only PDK2 silencing significantly inhibited the clonogenic ability of HNC cells. We subsequently found that TGFβ1-promoted migration and invasion capabilities were decreased in PDK1 and PDK2 knockdown cells. The tumor spheroid-forming capability, motility, CSC genes, and multidrug-resistant genes were downregulated in PDK1 and PDK2 silencing CSCs. PDK1 and PDK2 inhibition reversed cisplatin and gemcitabine resistance of CSCs, but not paclitaxel resistance.
CONCLUSION: The results demonstrated that the PDK1- and PDK2-mediated Warburg effect contributes to the TGFβ1-enhanced stemness properties of HNC. Therefore, PDK1 and PDK2 may serve as molecular targets for the combination therapy of HNC.

Keywords:  Cancer stem cells; Head and neck cancer; PDK1; PDK2; TGFβ1

DOI:  https://doi.org/10.1186/s40170-022-00300-0
Metabolism. 2022 Dec 02. pii: S0026-0495(22)00250-5. [Epub ahead of print] 155372

FAM3A maintains metabolic homeostasis by interacting with F1-ATP synthase to regulate the activity and assembly of ATP synthase.

Han Yan, Yuhong Meng, Xin Li, Rui Xiang, Song Hou, Junpei Wang, Lin Wang, Xiaoxing Yu, Ming Xu, Yujing Chi, Jichun Yang.

  Reduced mitochondrial ATP synthase (ATPS) capacity plays crucial roles in the pathogenesis of metabolic disorders. However, there is currently no effective strategy for synchronously stimulating the expressions of ATPS key subunits to restore its assembly. This study determined the roles of mitochondrial protein FAM3A in regulating the activity and assembly of ATPS's in hepatocytes. FAM3A is localized in mitochondrial matrix, where it interacts with F1-ATPS to initially activate ATP synthesis and release, and released ATP further activates P2 receptor-Akt-CREB pathway to induce FOXD3 expression. FOXD3 synchronously stimulates the transcriptions of ATPS key subunits and assembly genes to increase its assembly and capacity, augmenting ATP synthesis and inhibiting ROS production. FAM3A, FOXD3 and ATPS expressions were reduced in livers of diabetic mice and NAFLD patients. FOXD3 expression, ATPS capacity and ATP content were reduced in various tissues of FAM3A-deficient mice with dysregulated glucose and lipid metabolism. Hepatic FOXD3 activation increased ATPS assembly to ameliorate dysregulated glucose and lipid metabolism in obese mice. Hepatic FOXD3 inhibition or knockout reduced ATPS capacity to aggravate HFD-induced hyperglycemia and steatosis. In conclusion, FAM3A is an active ATPS component, and regulates its activity and assembly by activating FOXD3. Activating FAM3A-FOXD3 axis represents a viable strategy for restoring ATPS assembly to treat metabolic disorders.

Keywords:  ATP production; ATPS; FAM3A; Glucose and lipid metabolism

DOI:  https://doi.org/10.1016/j.metabol.2022.155372
Elife. 2022 Dec 08. pii: e84702. [Epub ahead of print]11

Teaching old drugs new tricks.

Alexandre Faille, Alan J Warren.

  Understanding the mechanism by which streptomycin binds to the small subunit of the mitoribosome may help researchers design less toxic derivatives of this antibiotic.

Keywords:  Fe-S cluster; antibiotics; bacteria; human; mitochondria; mitoribosome; molecular biophysics; ototoxicity; structural biology

DOI:  https://doi.org/10.7554/eLife.84702
Toxicol Appl Pharmacol. 2022 Nov 14. pii: S0041-008X(22)00461-6. [Epub ahead of print] 116316

Preliminary study to classify mechanisms of mitochondrial toxicity by in vitro metabolomics and bioinformatics.

Yui Hibino, Akira Iguchi, Kei Zaitsu.

   AIM: Mitochondrial toxicity is one of the causes for drug-induced liver injury, and the classification of phenotypes or mitochondrial toxicity are highly required though there are no molecular-profiling approaches for classifying mitochondrial toxicity. Therefore, the aim of this study was to classify the mechanisms of mitochondrial toxicity by metabolic profiling in vitro and bioinformatics.
MAIN METHODS: We applied an established gas chromatography tandem mass spectrometry-based metabolomics to human hepatoma grade 2 (HepG2) cells that were exposed to mitochondrial toxicants, whose mechanisms are different, such as rotenone (0.1 μM), carbonyl cyanide-3-chlorophenylhydrazone (CCCP, 0.5 μM), nefazodone (20 μM), perhexiline (6.25 μM), or digitonin (positive cytotoxic substance, 4 μM). These concentrations were determined by the Mitochondrial ToxGlo Assay. Galactose medium was used for suppressing the Warburg effect in HepG2 cells, and the metabolome analysis successfully identified 125 metabolites in HepG2 cells. Multivariate, metabolic pathway and network analyses were performed by the R software.
KEY FINDINGS: Metabolic profiling enabled the classifying the mitochondrial toxicity mechanisms of RCC inhibition and uncoupling. The metabolic profiles of respiratory chain complex (RCC) inhibitors (rotenone and nefazodone) and an uncoupler (CCCP) were fully differentiated from those of other compounds. The metabolic pathway analysis revealed that the RCC inhibitors and the uncoupler mainly disrupted TCA-cycle and related metabolic pathways. In addition, the correlation-based network analysis revealed that succinic acid, β-alanine, and glutamic acid were potential metabolic indicators for RCC inhibition and uncoupling.
SIGNIFICANCE: Our results provided new insights into classifying mechanisms of mitochondrial toxicity by in vitro metabolomics.

Keywords:  Bioinformatics; Gas chromatography-mass spectrometry; HepG2 cells; Hepatocyte; Metabolomics; Mitochondrial toxicants

DOI:  https://doi.org/10.1016/j.taap.2022.116316
J Clin Endocrinol Metab. 2022 Dec 07. pii: dgac705. [Epub ahead of print]

Nicotinamide Nucleotide Transhydrogenase (NNT) is essential for adrenal steroidogenesis: clinical and in vitro lessons.

Aline Faccioli Bodoni, Fernanda Borchers Coeli-Lacchini, Juliana Lourenço Gebenlian, Lays Martin Sobral, Cristiana Bernadelli Garcia, Wilson Araújo Silva, Kamila Chagas Peronni, Leandra Náira Zambelli Ramalho, Fernando Silva Ramalho, Ayrton C Moreira, Margaret de Castro, Andreia Machado Leopoldino, Sonir Roberto Rauber Antonini.

   BACKGROUND: Nicotinamide nucleotide transhydrogenase (NNT) acts as an antioxidant defense mechanism. NNT mutations cause familial glucocorticoid deficiency (FGD). How impaired oxidative stress disrupts adrenal steroidogenesis remains poorly understood.
OBJECTIVE: To ascertain the role played by NNT in adrenal steroidogenesis.
METHODS: The genotype-phenotype association of a novel pathogenic NNT variant was evaluated in a boy with FGD. Under basal and oxidative stress (OS) induced conditions, transient cell cultures of the patient's and controls wild type (WT) mononuclear blood cells were used to evaluate antioxidant mechanisms and mitochondrial parameters [reactive oxygen species (ROS) production, reduced glutathione (GSH), and mitochondrial mass]. Using CRISPR/Cas9, a stable NNT gene knockdown model was built in H295R adrenocortical carcinoma cells to determine the role played by NNT in mitochondrial parameters and steroidogenesis. NNT immunohistochemistry was assessed in fetal and post-natal human adrenals.
RESULTS: The homozygous NNT p.G866D variant segregated with the FGD phenotype. Under basal and OS conditions, p.G866D homozygous mononuclear blood cells exhibited increased ROS production, and decreased GSH levels and mitochondrial mass when compared to WT NNT cells. In line, H295R NNT knocked-down cells presented impaired NNT protein expression, increased ROS production, decreased the mitochondrial mass, as well as the size and the density of cholesterol lipid droplets. NNT knockdown affected steroidogenic enzyme expression, impairing cortisol and aldosterone secretion. In human adrenals, NNT is abundantly expressed in the transition fetal zone and in zona fasciculata.
CONCLUSION: Together, these studies demonstrate the essential role of NNT in adrenal redox homeostasis and steroidogenesis.

Keywords:  Adrenal insufficiency; CRISPR/Cas9; FGD; NNT; mutations

DOI:  https://doi.org/10.1210/clinem/dgac705