bims-camemi 2022-06-19 papers

bims-camemi

Biomed News

on Mitochondrial metabolism in cancer

Issue of 2022–06–19
39 papers selected by
Christian Frezza, Universität zu Köln

Fumarate suppresses B-cell activation and function through direct inactivation of LYN.
Metabolic-scale gene activation screens identify SLCO2B1 as a heme transporter that enhances cellular iron availability.
Inorganic Polyphosphate in Mitochondrial Energy Metabolism and Pathology.
An exercise-inducible metabolite that suppresses feeding and obesity.
The cation exchanger Letm1, circadian rhythms, and NAD(H) levels interconnect in diurnal zebrafish.
A mitochondrial contribution to anti-inflammatory shear stress signaling in vascular endothelial cells.
TMBIM5 loss of function alters mitochondrial matrix ion homeostasis and causes a skeletal myopathy.
CG7630 is the Drosophila melanogaster homolog of the cytochrome c oxidase subunit COX7B.
R-Loops and Mitochondrial DNA Metabolism.
Deletion of Lactate Dehydrogenase-A Impairs Oncogene-Induced Mouse Hepatocellular Carcinoma Development.
Ubiquitinating the way to T cell metabolism.
SLC25A47 is a novel determinant of hepatic mitochondrial function implicated in liver fibrosis.
OMA1 mediates local and global stress responses against protein misfolding in CHCHD10 mitochondrial myopathy.
Oncofusion-driven de novo enhancer assembly promotes malignancy in Ewing sarcoma via aberrant expression of the stereociliary protein LOXHD1.
CD38 reduces mitochondrial fitness and cytotoxic T cell response against viral infection in lupus patients by suppressing mitophagy.
A multi-omics analysis reveals that the lysine deacetylase ABHD14B influences glucose metabolism in mammals.
Vps33B controls Treg cell suppressive function through inhibiting lysosomal nutrient sensing complex-mediated mTORC1 activation.
Activation and execution of the hepatic integrated stress response by dietary essential amino acid deprivation is amino acid specific.
What puts the heat on thermogenic fat: metabolism of fuel substrates.
Are Multiple Mitochondrial Related Signalling Pathways Involved in Carotid Body Oxygen Sensing?
Targeting the methionine addiction of cancer.
Expanding the Therapeutic World of Tryptophan Metabolism.
Insights regarding mitochondrial DNA copy number alterations in human cancer (Review).
O-GlcNAc transferase maintains metabolic homeostasis in response to CDK9 inhibition.
Inorganic Polyphosphate and F0F1-ATP Synthase of Mammalian Mitochondria.
Remote solid cancers rewire hepatic nitrogen metabolism via host nicotinamide-N-methyltransferase.
A hexa-species transcriptome atlas of mammalian embryogenesis delineates metabolic regulation across three different implantation modes.
Regulation of the lysosome by sphingolipids: potential role in aging.
Interleukin-17 governs hypoxic adaptation of injured epithelium.
PPARα alleviates iron overload-induced ferroptosis in mouse liver.
Metabolic regulation in pluripotent stem cells.
Riboregulation of Enolase 1 activity controls glycolysis and embryonic stem cell differentiation.
Genome-scale modeling of the primary-specialized metabolism interface.
A protocol to measure lysosomal Zn2+ release through a genetically encoded Zn2+ indicator.
Indoleamine 2,3-dioxygenase 1 activation in mature cDC1 promotes tolerogenic education of inflammatory cDC2 via metabolic communication.
cGAS-STING drives the IL-6-dependent survival of chromosomally instable cancers.
A pan-cancer compendium of chromosomal instability.
Mechanisms that regulate the activities of TET proteins.
Mitochondrial H2S Regulates BCAA Catabolism in Heart Failure.

Nat Chem Biol. 2022 Jun 16.

Fumarate suppresses B-cell activation and function through direct inactivation of LYN.

Jie Cheng, Ying Liu, Jinxin Yan, Lina Zhao, Yinglin Zhou, Xuyang Shen, Yunan Chen, Yining Chen, Xianbin Meng, Xinxiang Zhang, Peng Jiang.

Activated B cells increase central carbon metabolism to fulfill their bioenergetic demands, yet the mechanistic basis for this, as well as metabolic regulation in B cells, remains largely unknown. Here, we demonstrate that B-cell activation reprograms the tricarboxylic acid cycle and boosts the expression of fumarate hydratase (FH), leading to decreased cellular fumarate abundance. Fumarate accumulation by FH inhibition or dimethyl-fumarate treatment suppresses B-cell activation, proliferation and antibody production. Mechanistically, fumarate is a covalent inhibitor of tyrosine kinase LYN, a key component of the BCR signaling pathway. Fumarate can directly succinate LYN at C381 and abrogate LYN activity, resulting in a block to B-cell activation and function in vitro and in vivo. Therefore, our findings uncover a previously unappreciated metabolic regulation of B cells, and reveal LYN is a natural sensor of fumarate, connecting cellular metabolism to B-cell antigen receptor signaling.

DOI: https://doi.org/10.1038/s41589-022-01052-0
Mol Cell. 2022 Jun 09. pii: S1097-2765(22)00491-9. [Epub ahead of print]

Metabolic-scale gene activation screens identify SLCO2B1 as a heme transporter that enhances cellular iron availability.

Gokhan Unlu, Benjamin Prizer, Ranya Erdal, Hsi-Wen Yeh, Erol C Bayraktar, Kıvanç Birsoy.

  Iron is the most abundant transition metal essential for numerous cellular processes. Although most mammalian cells acquire iron through transferrin receptors, molecular players of iron utilization under iron restriction are incompletely understood. To address this, we performed metabolism-focused CRISPRa gain-of-function screens, which revealed metabolic limitations under stress conditions. Iron restriction screens identified not only expected members of iron utilization pathways but also SLCO2B1, a poorly characterized membrane carrier. SLCO2B1 expression is sufficient to increase intracellular iron, bypass the essentiality of the transferrin receptor, and enable proliferation under iron restriction. Mechanistically, SLCO2B1 mediates heme analog import in cellular assays. Heme uptake by SLCO2B1 provides sufficient iron for proliferation through heme oxygenases. Notably, SLCO2B1 is predominantly expressed in microglia in the brain, and primary Slco2b1-/- mouse microglia exhibit strong defects in heme analog import. Altogether, our work identifies SLCO2B1 as a microglia-enriched plasma membrane heme importer and provides a genetic platform to identify metabolic limitations under stress conditions.

Keywords:  CRISPRa; SLCO2B1; heme; iron; metabolic limitation

DOI:  https://doi.org/10.1016/j.molcel.2022.05.024
Prog Mol Subcell Biol. 2022 ;61 15-26

Inorganic Polyphosphate in Mitochondrial Energy Metabolism and Pathology.

Maria A Neginskaya, Evgeny V Pavlov.

  In this chapter, the current understanding of the potential roles played by polyphosphate in mitochondrial function with a specific focus on energy metabolism and mitochondrial pathologies caused by stress is summarized. Here we will discuss details of the possible ion transporting mechanisms of mitochondria that might involve polyP and their role in mitochondrial physiology and pathology are discussed.

Keywords:  ATP; Calcium; Mitochondrial function; Oxidative phosphorylation; Permeability transition pore; PolyP hydrolyzing enzyme; Polyhydroxybutyrate; Polyphosphate kinase

DOI:  https://doi.org/10.1007/978-3-031-01237-2_2
Nature. 2022 Jun 15.

An exercise-inducible metabolite that suppresses feeding and obesity.

Veronica L Li, Yang He, Kévin Contrepois, Hailan Liu, Joon T Kim, Amanda L Wiggenhorn, Julia T Tanzo, Alan Sheng-Hwa Tung, Xuchao Lyu, Peter-James H Zushin, Robert S Jansen, Basil Michael, Kang Yong Loh, Andrew C Yang, Christian S Carl, Christian T Voldstedlund, Wei Wei, Stephanie M Terrell, Benjamin C Moeller, Rick M Arthur, Gareth A Wallis, Koen van de Wetering, Andreas Stahl, Bente Kiens, Erik A Richter, Steven M Banik, Michael P Snyder, Yong Xu, Jonathan Z Long.

Exercise confers protection against obesity, type 2 diabetes and other cardiometabolic diseases1-5. However, the molecular and cellular mechanisms that mediate the metabolic benefits of physical activity remain unclear6. Here we show that exercise stimulates the production of N-lactoyl-phenylalanine (Lac-Phe), a blood-borne signalling metabolite that suppresses feeding and obesity. The biosynthesis of Lac-Phe from lactate and phenylalanine occurs in CNDP2+ cells, including macrophages, monocytes and other immune and epithelial cells localized to diverse organs. In diet-induced obese mice, pharmacological-mediated increases in Lac-Phe reduces food intake without affecting movement or energy expenditure. Chronic administration of Lac-Phe decreases adiposity and body weight and improves glucose homeostasis. Conversely, genetic ablation of Lac-Phe biosynthesis in mice increases food intake and obesity following exercise training. Last, large activity-inducible increases in circulating Lac-Phe are also observed in humans and racehorses, establishing this metabolite as a molecular effector associated with physical activity across multiple activity modalities and mammalian species. These data define a conserved exercise-inducible metabolite that controls food intake and influences systemic energy balance.

DOI: https://doi.org/10.1038/s41586-022-04828-5
Life Sci Alliance. 2022 Sep;pii: e202101194. [Epub ahead of print]5(9):

The cation exchanger Letm1, circadian rhythms, and NAD(H) levels interconnect in diurnal zebrafish.

Pauline Dao, Stefan Hajny, Ronald Mekis, Lukas Orel, Nora Dinhopl, Kristin Tessmar-Raible, Karin Nowikovsky.

Mitochondria are fundamental for life and require balanced ion exchange to maintain proper functioning. The mitochondrial cation exchanger LETM1 sparks interest because of its pathophysiological role in seizures in the Wolf Hirschhorn Syndrome (WHS). Despite observation of sleep disorganization in epileptic WHS patients, and growing studies linking mitochondria and epilepsy to circadian rhythms, LETM1 has not been studied from the chronobiological perspective. Here we established a viable letm1 knock-out, using the diurnal vertebrate Danio rerio to study the metabolic and chronobiological consequences of letm1 deficiency. We report diurnal rhythms of Letm1 protein levels in wild-type fish. We show that mitochondrial nucleotide metabolism is deregulated in letm1-/- mutant fish, the rate-limiting enzyme of NAD+ production is up-regulated, while NAD+ and NADH pools are reduced. These changes were associated with increased expression amplitude of circadian core clock genes in letm1-/- compared with wild-type under light/dark conditions, suggesting decreased NAD(H) levels as a possible mechanism for circadian system perturbation in Letm1 deficiency. Replenishing NAD pool may ameliorate WHS-associated sleep and neurological disorders.

DOI: https://doi.org/10.26508/lsa.202101194
J Cell Biol. 2022 Jul 04. pii: e202109144. [Epub ahead of print]221(7):

A mitochondrial contribution to anti-inflammatory shear stress signaling in vascular endothelial cells.

Brian G Coon, Sushma Timalsina, Matteo Astone, Zhen W Zhuang, Jennifer Fang, Jinah Han, Jurgen Themen, Minhwan Chung, Young Joo Yang-Klingler, Mukesh Jain, Karen K Hirschi, Ai Yamamato, Louis-Eric Trudeau, Massimo Santoro, Martin A Schwartz.

Atherosclerosis, the major cause of myocardial infarction and stroke, results from converging inflammatory, metabolic, and biomechanical factors. Arterial lesions form at sites of low and disturbed blood flow but are suppressed by high laminar shear stress (LSS) mainly via transcriptional induction of the anti-inflammatory transcription factor, Kruppel-like factor 2 (Klf2). We therefore performed a whole genome CRISPR-Cas9 screen to identify genes required for LSS induction of Klf2. Subsequent mechanistic investigation revealed that LSS induces Klf2 via activation of both a MEKK2/3-MEK5-ERK5 kinase module and mitochondrial metabolism. Mitochondrial calcium and ROS signaling regulate assembly of a mitophagy- and p62-dependent scaffolding complex that amplifies MEKK-MEK5-ERK5 signaling. Blocking the mitochondrial pathway in vivo reduces expression of KLF2-dependent genes such as eNOS and inhibits vascular remodeling. Failure to activate the mitochondrial pathway limits Klf2 expression in regions of disturbed flow. This work thus defines a connection between metabolism and vascular inflammation that provides a new framework for understanding and developing treatments for vascular disease.

DOI: https://doi.org/10.1083/jcb.202109144
Life Sci Alliance. 2022 Oct;pii: e202201478. [Epub ahead of print]5(10):

TMBIM5 loss of function alters mitochondrial matrix ion homeostasis and causes a skeletal myopathy.

Li Zhang, Felicia Dietsche, Bruno Seitaj, Liliana Rojas-Charry, Nadina Latchman, Dhanendra Tomar, Rob Ci Wüst, Alexander Nickel, Katrin Bm Frauenknecht, Benedikt Schoser, Sven Schumann, Michael J Schmeisser, Johannes Vom Berg, Thorsten Buch, Stefanie Finger, Philip Wenzel, Christoph Maack, John W Elrod, Jan B Parys, Geert Bultynck, Axel Methner.

Ion fluxes across the inner mitochondrial membrane control mitochondrial volume, energy production, and apoptosis. TMBIM5, a highly conserved protein with homology to putative pH-dependent ion channels, is involved in the maintenance of mitochondrial cristae architecture, ATP production, and apoptosis. Here, we demonstrate that overexpressed TMBIM5 can mediate mitochondrial calcium uptake. Under steady-state conditions, loss of TMBIM5 results in increased potassium and reduced proton levels in the mitochondrial matrix caused by attenuated exchange of these ions. To identify the in vivo consequences of TMBIM5 dysfunction, we generated mice carrying a mutation in the channel pore. These mutant mice display increased embryonic or perinatal lethality and a skeletal myopathy which strongly correlates with tissue-specific disruption of cristae architecture, early opening of the mitochondrial permeability transition pore, reduced calcium uptake capability, and mitochondrial swelling. Our results demonstrate that TMBIM5 is an essential and important part of the mitochondrial ion transport system machinery with particular importance for embryonic development and muscle function.

DOI: https://doi.org/10.26508/lsa.202201478
EMBO Rep. 2022 Jun 14. e54825

CG7630 is the Drosophila melanogaster homolog of the cytochrome c oxidase subunit COX7B.

Michele Brischigliaro, Alfredo Cabrera-Orefice, Mattia Sturlese, Dei M Elurbe, Elena Frigo, Erika Fernandez-Vizarra, Stefano Moro, Martijn A Huynen, Susanne Arnold, Carlo Viscomi, Massimo Zeviani.

  The mitochondrial respiratory chain (MRC) is composed of four multiheteromeric enzyme complexes. According to the endosymbiotic origin of mitochondria, eukaryotic MRC derives from ancestral proteobacterial respiratory structures consisting of a minimal set of complexes formed by a few subunits associated with redox prosthetic groups. These enzymes, which are the "core" redox centers of respiration, acquired additional subunits, and increased their complexity throughout evolution. Cytochrome c oxidase (COX), the terminal component of MRC, has a highly interspecific heterogeneous composition. Mammalian COX consists of 14 different polypeptides, of which COX7B is considered the evolutionarily youngest subunit. We applied proteomic, biochemical, and genetic approaches to investigate the COX composition in the invertebrate model Drosophila melanogaster. We identified and characterized a novel subunit which is widely different in amino acid sequence, but similar in secondary and tertiary structures to COX7B, and provided evidence that this object is in fact replacing the latter subunit in virtually all protostome invertebrates. These results demonstrate that although individual structures may differ the composition of COX is functionally conserved between vertebrate and invertebrate species.

Keywords:   D. melanogaster ; COX7B; cytochrome c oxidase; mitochondria; respiratory chain

DOI:  https://doi.org/10.15252/embr.202254825
Methods Mol Biol. 2022 ;2528 173-202

R-Loops and Mitochondrial DNA Metabolism.

Ian J Holt.

  R-loops forming inadvertently during transcription can threaten genome stability, but R-loops are also formed intentionally, as a means of regulating transcription and other aspects of DNA metabolism. The study of R-loops in mitochondria is in its infancy, and yet there is already clear evidence that they are predominantly located in the major regulatory region of the mammalian mitochondrial genome. Here, we describe how mitochondrial R-loops have been characterized to date, with the emphasis on the problems of their being extremely labile, and how to minimize their loss during extraction. The oft-overlooked issues of RNA-DNA hybrids not being synonymous with R-loops, and adventitious RNA hybridization to DNA, are tackled head on; and possible new approaches are described and placed in the context of future research lines that could reveal the detailed roles of R-loops in the metabolism of mitochondrial DNA.

Keywords:  Mitochondrial DNA; Mitochondrial DNA replication; Mitochondrial transcription; R-loop; RNA–DNA hybrid

DOI:  https://doi.org/10.1007/978-1-0716-2477-7_12
Cell Mol Gastroenterol Hepatol. 2022 Jun 14. pii: S2352-345X(22)00102-3. [Epub ahead of print]

Deletion of Lactate Dehydrogenase-A Impairs Oncogene-Induced Mouse Hepatocellular Carcinoma Development.

Marina Serra, Mario Di Matteo, Jens Serneels, Rajesh Pal, Sarah Trusso Cafarello, Martina Lanza, Carlos Sanchez-Martin, Matthias Evert, Alessandra Castegna, Diego Francesco Calvisi, Massimiliano Mazzone, Amedeo Columbano.

   BACKGROUND AND AIMS: Hepatocellular carcinoma (HCC) is a multistep process whereby abnormally proliferating cancer cells undergo extensive metabolic reprogramming. Metabolic alterations in hepatocarcinogenesis depend on the activation of specific oncogenes, thus partially explaining HCC heterogeneity. C-Myc oncogene overexpression, frequently observed in human HCCs, leads to a metabolic rewiring toward a Warburg phenotype and production of lactate, resulting in the acidification of the extracellular space, favoring the emergence of an immune-permissive tumor microenvironment. Here, we investigated whether Lactate dehydrogenase alpha (Ldha) genetic ablation interferes with metabolic reprogramming and HCC development in the mouse.
METHODS: We characterized the metabolic reprogramming in tumors induced in C57BL/6J mice hydrodynamically co-transfected with c-Myc and h-Ras. Using the same experimental model, we investigated the effect of Ldha inhibition - gained through the inducible and hepatocyte-specific Ldha knockout - on cancer cell metabolic reprogramming, number and size of HCC lesions, and TME alterations.
RESULTS: C-Myc/h-Ras driven tumors display a striking glycolytic metabolism, suggesting a switch to a Warburg phenotype. The tumors also exhibited enhanced pentose phosphate pathway activity, the switch of glutamine to sustain glutathione synthesis instead of Tricarboxylic acid cycle, and the impairment of oxidative phosphorylation. In addition, Ldha abrogation significantly hampered tumor number and size together with an evident inhibition of the Warburg-like metabolic feature and a remarkable increase of CD4+ lymphocytes compared to Ldha wild-type livers.
CONCLUSIONS: These results demonstrate that Ldha deletion significantly impairs mouse HCC development and suggest LDH as a potential target to enhance the efficacy of the current therapeutic options.

Keywords:  C-Myc; HCC; Ldha; Metabolic Reprogramming; TME

DOI:  https://doi.org/10.1016/j.jcmgh.2022.06.003
J Cell Biol. 2022 Jul 04. pii: e202206006. [Epub ahead of print]221(7):

Ubiquitinating the way to T cell metabolism.

Sarah McPhedran, Julian J Lum.

In this issue, Harris et al. (2022. J. Cell Biol.https://doi.org/10.1083/jcb.202203095) show that phosphofructokinase is a substrate for ubiquitination by Fbxo7, a key protein in the ubiquitination pathway. Their findings point to a new interplay between metabolic enzyme degradation in the regulation of T cells.

DOI: https://doi.org/10.1083/jcb.202206006
J Hepatol. 2022 Jun 14. pii: S0168-8278(22)00364-6. [Epub ahead of print]

SLC25A47 is a novel determinant of hepatic mitochondrial function implicated in liver fibrosis.

Nadia Bresciani, Hadrien Demagny, Vera Lemos, Francesca Pontanari, Xiaoxu Li, Yu Sun, Hao Li, Alessia Perino, Johan Auwerx, Kristina Schoonjans.

   BACKGROUND & AIMS: Transporters of the SLC25 mitochondrial carrier superfamily bridge cytoplasmic and mitochondrial metabolism by channeling metabolites across mitochondrial membranes and are pivotal for metabolic homeostasis. Despite their physiological relevance as gatekeepers of cellular metabolism, most of the SLC25 family members remain uncharacterized. We undertook a comprehensive tissue distribution analysis of all Slc25 family members across metabolic organs and identified SLC25A47 as a liver-specific mitochondrial carrier.
METHOD: We used a murine loss-of-function model to unravel the role of this transporter in mitochondrial and hepatic homeostasis. We performed extensive metabolic phenotyping and molecular characterization of newly generated Slc25a47hep-/- and Slc25a47-Fgf21hep-/- mice.
RESULTS: Slc25a47hep-/- mice displayed a wide variety of metabolic abnormalities, as a result of sustained energy deficiency in the liver originating from impaired mitochondrial respiration in this organ. This mitochondrial phenotype was associated with an activation of the mitochondrial stress response (MSR) in the liver, and the development of fibrosis, which was exacerbated upon feeding a high-fat high-sucrose diet. The MSR induced the secretion of several mitokines, amongst which FGF21 played a preponderant role on systemic physiology. To dissect the FGF21-dependent and -independent physiological changes induced in Slc25a47hep-/- mice, we generated a double Slc25a47-Fgf21hep-/- mouse model and demonstrated that several aspects of the hypermetabolic state were driven by hepatic secretion of FGF21. On the other hand, the metabolic fuel inflexibility observed in Slc25a47hep-/- mice could not be rescued with the genetic removal of Fgf21.
CONCLUSION: Collectively, our data place SLC25A47 at the center of mitochondrial homeostasis, which upon dysfunction triggers robust liver-specific and systemic adaptive stress responses. The prominent role of SLC25A47 in hepatic fibrosis identifies this carrier, or its transported metabolite, as a potential target for therapeutic intervention.
LAY SUMMARY: SLC25A47 is a liver-specific mitochondrial carrier. Slc25a47hep-/- mice are unable to maintain mitochondrial homeostasis in hepatocytes and show impaired mitochondrial respiration resulting in chronic energy deficiency, mitochondrial stress, and fibrosis in hepatocytes. Hepatic mitochondrial stress is characterized by the secretion of the mitokine FGF21 which drives a strong and systemic hypermetabolic state impacting whole-body physiology.

Keywords:  FGF21; Fibrosis; Liver; Metabolism; Mitochondrial solute carriers; Mitochondrial stress response

DOI:  https://doi.org/10.1016/j.jhep.2022.05.040
J Clin Invest. 2022 Jun 14. pii: e157504. [Epub ahead of print]

OMA1 mediates local and global stress responses against protein misfolding in CHCHD10 mitochondrial myopathy.

Mario K Shammas, Xiaoping Huang, Beverly P Wu, Evelyn Fessler, Insung Song, Nicholas P Randolph, Yan Li, Christopher Ke Bleck, Danielle A Springer, Carl Fratter, Ines A Barbosa, Andrew F Powers, Pedro M Quirós, Carlos Lopez-Otin, Lucas T Jae, Joanna Poulton, Derek P Narendra.

  Mitochondrial stress triggers a response in the cell's mitochondria and nucleus, but how these stress responses are coordinated in vivo is poorly understood. Here, we characterize a family with myopathy caused by a dominant p.G58R mutation in the mitochondrial protein CHCHD10. To understand the disease etiology, we developed a knock-in mouse model and found that mutant CHCHD10 aggregates in affected tissues, applying a toxic protein stress to the inner mitochondrial membrane. Unexpectedly, survival of CHCHD10 knock-in mice depended on a protective stress response mediated by OMA1. The OMA1 stress response acted both locally within mitochondria, causing mitochondrial fragmentation, and signaled outside the mitochondria, activating the integrated stress response through cleavage of DELE1. We additionally identified an isoform switch in the terminal complex of the electron transport chain as a component of this response. Our results demonstrate that OMA1 is critical for neonatal survival conditionally in the setting of inner mitochondrial membrane stress, coordinating local and global stress responses to reshape the mitochondrial network and proteome.

Keywords:  Cell Biology; Cell stress; Genetics; Mitochondria; Proteases

DOI:  https://doi.org/10.1172/JCI157504
Cell Rep. 2022 Jun 14. pii: S2211-1247(22)00757-4. [Epub ahead of print]39(11): 110971

Oncofusion-driven de novo enhancer assembly promotes malignancy in Ewing sarcoma via aberrant expression of the stereociliary protein LOXHD1.

Qu Deng, Ramakrishnan Natesan, Florencia Cidre-Aranaz, Shehbeel Arif, Ying Liu, Reyaz Ur Rasool, Pei Wang, Erick Mitchell-Velasquez, Chandan Kanta Das, Endrit Vinca, Zvi Cramer, Patrick J Grohar, Margaret Chou, Chandan Kumar-Sinha, Kristy Weber, T S Karin Eisinger-Mathason, Nicolas Grillet, Thomas Grünewald, Irfan A Asangani.

  Ewing sarcoma (EwS) is a highly aggressive tumor of bone and soft tissues that mostly affects children and adolescents. The pathognomonic oncofusion EWSR1::FLI1 transcription factor drives EwS by orchestrating an oncogenic transcription program through de novo enhancers. By integrative analysis of thousands of transcriptomes representing pan-cancer cell lines, primary cancers, metastasis, and normal tissues, we identify a 32-gene signature (ESS32 [Ewing Sarcoma Specific 32]) that stratifies EwS from pan-cancer. Among the ESS32, LOXHD1, encoding a stereociliary protein, is the most highly expressed gene through an alternative transcription start site. Deletion or silencing of EWSR1::FLI1 bound upstream de novo enhancer results in loss of the LOXHD1 short isoform, altering EWSR1::FLI1 and HIF1α pathway genes and resulting in decreased proliferation/invasion of EwS cells. These observations implicate LOXHD1 as a biomarker and a determinant of EwS metastasis and suggest new avenues for developing LOXHD1-targeted drugs or cellular therapies for this deadly disease.

Keywords:  CP: Cancer; CP: Molecular biology; EWSR1::FLI1; Ewing sarcoma; LOXHD1; biomarker; enhancer; hypoxia; integrative genomics; metastasis; transcription

DOI:  https://doi.org/10.1016/j.celrep.2022.110971
Sci Adv. 2022 Jun 17. 8(24): eabo4271

CD38 reduces mitochondrial fitness and cytotoxic T cell response against viral infection in lupus patients by suppressing mitophagy.

Ping-Min Chen, Eri Katsuyama, Abhigyan Satyam, Hao Li, Jose Rubio, Sungwook Jung, Sylvia Andrzejewski, J David Becherer, Maria G Tsokos, Reza Abdi, George C Tsokos.

Infection is one of the major causes of mortality in patients with systemic lupus erythematosus (SLE). We previously found that CD38, an ectoenzyme that regulates the production of NAD+, is up-regulated in CD8+ T cells of SLE patients and correlates with the risk of infection. Here, we report that CD38 reduces CD8+ T cell function by negatively affecting mitochondrial fitness through the inhibition of multiple steps of mitophagy, a process that is critical for mitochondria quality control. Using a murine lupus model, we found that administration of a CD38 inhibitor in a CD8+ T cell-targeted manner reinvigorated their effector function, reversed the defects in autophagy and mitochondria, and improved viral clearance. We conclude that CD38 represents a target to mitigate infection rates in people with SLE.

DOI: https://doi.org/10.1126/sciadv.abo4271
J Biol Chem. 2022 Jun 11. pii: S0021-9258(22)00569-5. [Epub ahead of print] 102128

A multi-omics analysis reveals that the lysine deacetylase ABHD14B influences glucose metabolism in mammals.

Abinaya Rajendran, Amarendranath Soory, Neha Khandelwal, Girish Ratnaparkhi, Siddhesh S Kamat.

  The sirtuins and histone deacetylases are the best characterized members of the lysine deacetylase (KDAC) enzyme family. Recently, we annotated the "orphan" enzyme ABHD14B (α/β-hydrolase domain containing protein # 14B) as a novel KDAC, showed this enzyme's ability to transfer an acetyl-group from protein lysine residue(s) to coenzyme-A (CoA) to yield acetyl-CoA, expanding the repertoire of this enzyme family. However, the role of ABHD14B in metabolic processes is not fully elucidated. Here, we investigated the role of this enzyme using mammalian cell knockdowns in a combined transcriptomics, and metabolomics analysis. We found from these complementary experiments in vivo, that the loss of ABHD14B results in significantly altered glucose metabolism, specifically the decreased flux of glucose through glycolysis and the citric acid cycle. Further, we show that depleting hepatic ABHD14B in mice, also results in defective systemic glucose metabolism, particularly during fasting. Taken together, our findings illuminate the important metabolic functions that the KDAC ABHD14B plays in mammalian physiology, and poses new questions regarding the role of this hitherto cryptic metabolism-regulating enzyme.

Keywords:  ABHD14B; Glucose Metabolism; Lysine deacetylase; Metabolomics; Transcriptomics

DOI:  https://doi.org/10.1016/j.jbc.2022.102128
Cell Rep. 2022 Jun 14. pii: S2211-1247(22)00725-2. [Epub ahead of print]39(11): 110943

Vps33B controls Treg cell suppressive function through inhibiting lysosomal nutrient sensing complex-mediated mTORC1 activation.

Hongrui Xiang, Yuexiao Tao, Zhenyan Jiang, Xian Huang, Huizi Wang, Wei Cao, Jia Li, Rui Ding, Mingyi Shen, Ru Feng, Linsen Li, Chenyang Guan, Jiamin Liu, Jun Ni, Lei Chen, Zhengting Wang, Youqiong Ye, Qing Zhong, Junling Liu, Qiang Zou, Xuefeng Wu.

  The suppressive function of regulatory T (Treg) cells is tightly controlled by nutrient-fueled mechanistic target of rapamycin complex 1 (mTORC1) activation, yet its dynamics and negative regulation remain unclear. Here we show that Treg-specific depletion of vacuolar protein sorting 33B (Vps33B) in mice results in defective Treg cell suppressive function and acquisition of effector phenotype, which in turn leads to disturbed T cell homeostasis and boosted antitumor immunity. Mechanistically, Vps33B binds with lysosomal nutrient-sensing complex (LYNUS) and promotes late endosome and lysosome fusion and clearance of the LYNUS-containing late endosome/lysosome, and therefore suppresses mTORC1 activation. Vps33B deficiency in Treg cells results in disordered endosome lysosome fusion, which leads to accumulation of LYNUS that causes elevated mTORC1 activation and hyper-glycolytic metabolism. Taken together, our study reveals that Vps33B maintains Treg cell suppressive function through sustaining endolysosomal homeostasis and therefore restricting amino acid-licensed mTORC1 activation and metabolism.

Keywords:  CP: Immunology; CP: Metabolism; Foxp3; Treg; Vps33B; endolysosomal system; mTORC1

DOI:  https://doi.org/10.1016/j.celrep.2022.110943
FASEB J. 2022 07;36(7): e22396

Activation and execution of the hepatic integrated stress response by dietary essential amino acid deprivation is amino acid specific.

William O Jonsson, Emily T Mirek, Ronald C Wek, Tracy G Anthony.

  Dietary removal of an essential amino acid (EAA) triggers the integrated stress response (ISR) in liver. Herein, we explored the mechanisms that activate the ISR and execute changes in transcription and translation according to the missing EAA. Wild-type mice and mice lacking general control nonderepressible 2 (Gcn2) were fed an amino acid complete diet or a diet devoid of either leucine or sulfur amino acids (methionine and cysteine). Serum and liver leucine concentrations were significantly reduced within the first 6 h of feeding a diet lacking leucine, corresponding with modest, GCN2-dependent increases in Atf4 mRNA translation and induction of selected ISR target genes (Fgf21, Slc7a5, Slc7a11). In contrast, dietary removal of the sulfur amino acids lowered serum methionine, but not intracellular methionine, and yet hepatic mRNA abundance of Atf4, Fgf21, Slc7a5, Slc7a11 substantially increased regardless of GCN2 status. Liver tRNA charging levels did not correlate with intracellular EAA concentrations or GCN2 status and remained similar to mice fed a complete diet. Furthermore, loss of Gcn2 increased the occurrence of ribosome collisions in liver and derepressed mechanistic target of rapamycin complex 1 signal transduction, but these changes did not influence execution of the ISR. We conclude that ISR activation is directed by intracellular EAA concentrations, but ISR execution is not. Furthermore, a diet devoid of sulfur amino acids does not require GCN2 for the ISR to execute changes to the transcriptome.

Keywords:  dietary restriction; feeding; mammalian; polysomes; postprandial period; protein synthesis

DOI:  https://doi.org/10.1096/fj.202200204RR
Trends Endocrinol Metab. 2022 Jun 10. pii: S1043-2760(22)00100-X. [Epub ahead of print]

What puts the heat on thermogenic fat: metabolism of fuel substrates.

Carlos H Sponton, Jose Carlos de Lima-Junior, Luiz O Leiria.

  Owing to its unique capacity to clear macronutrients from circulation and use them to produce heat, thermogenic fat is capable of regulating glucose, lipids, and branched-chain amino acids (BCAA) circulatory levels. At the same time, its activity yields a higher energy expenditure, thereby conferring protection against cardiometabolic diseases. Our knowledge on the mechanisms of uptake and intracellular metabolism of such energy substrates into thermogenic fat has meaningfully evolved in recent years. This has allowed us to better understand how the thermogenic machinery processes those molecules to utilize them as substrates for heating up the body. Here, we discuss recent advances in the molecular and cellular regulatory process that governs the uptake and metabolism of such substrates within thermogenic fat.

Keywords:  UCP1; brown adipose tissue; metabolism; thermogenesis

DOI:  https://doi.org/10.1016/j.tem.2022.05.003
Front Physiol. 2022 ;13 908617

Are Multiple Mitochondrial Related Signalling Pathways Involved in Carotid Body Oxygen Sensing?

Andrew P Holmes, Agnieszka Swiderska, Demitris Nathanael, Hayyaf S Aldossary, Clare J Ray, Andrew M Coney, Prem Kumar.

  It is generally acknowledged that the carotid body (CB) type I cell mitochondria are unique, being inhibited by relatively small falls in PaO2 well above those known to inhibit electron transport in other cell types. This feature is suggested to allow for the CB to function as an acute O2 sensor, being stimulated and activating systemic protective reflexes before the metabolism of other cells becomes compromised. What is less clear is precisely how a fall in mitochondrial activity links to type I cell depolarisation, a process that is required for initiation of the chemotransduction cascade and post-synaptic action potential generation. Multiple mitochondrial/metabolic signalling mechanisms have been proposed including local generation of mitochondrial reactive oxygen species (mitoROS), a change in mitochondrial/cellular redox status, a fall in MgATP and an increase in lactate. Although each mechanism is based on compelling experimental evidence, they are all not without question. The current review aims to explore the importance of each of these signalling pathways in mediating the overall CB response to hypoxia. We suggest that there is unlikely to be a single mechanism, but instead multiple mitochondrial related signalling pathways are recruited at different PaO2s during hypoxia. Furthermore, it still remains to be determined if mitochondrial signalling acts independently or in partnership with extra-mitochondrial O2-sensors.

Keywords:  O2 sensor; arterial chemoreceptor; carotid body; hypoxia; metabolism; mitochondria; mitochondrial inhibitors; succinate

DOI:  https://doi.org/10.3389/fphys.2022.908617
Am J Cancer Res. 2022 ;12(5): 2249-2276

Targeting the methionine addiction of cancer.

Joni C Sedillo, Vincent L Cryns.

Methionine is the initiator amino acid for protein synthesis, the methyl source for most nucleotide, chromatin, and protein methylation, and the carbon backbone for various aspects of the cellular antioxidant response and nucleotide biosynthesis. Methionine is provided in the diet and serum methionine levels fluctuate based on dietary methionine content. Within the cell, methionine is recycled from homocysteine via the methionine cycle, which is linked to nutrient status via one-carbon metabolism. Unlike normal cells, many cancer cells, both in vitro and in vivo, show high methionine cycle activity and are dependent on exogenous methionine for continued growth. However, the molecular mechanisms underlying the methionine dependence of diverse malignancies are poorly understood. Methionine deprivation initiates widespread metabolic alterations in cancer cells that enable them to survive despite limited methionine availability, and these adaptive alterations can be specifically targeted to enhance the activity of methionine deprivation, a strategy we have termed "metabolic priming". Chemotherapy-resistant cell populations such as cancer stem cells, which drive treatment-resistance, are also sensitive to methionine deprivation, suggesting dietary methionine restriction may inhibit metastasis and recurrence. Several clinical trials in cancer are investigating methionine restriction in combination with other agents. This review will explore new insights into the mechanisms of methionine dependence in cancer and therapeutic efforts to translate these insights into enhanced clinical activity of methionine restriction in cancer.

Keywords: Methionine; cancer therapy; epigenetics; metabolism; nutrition; one-carbon; oxidative stress
Circulation. 2022 Jun 14. 145(24): 1799-1802

Expanding the Therapeutic World of Tryptophan Metabolism.

Gregory A Wyant, Javid Moslehi.



Keywords:  Editorials; amino acids; kynurenine; metabolism; tryptophan; vascular diseases

DOI:  https://doi.org/10.1161/CIRCULATIONAHA.122.059812
Int J Mol Med. 2022 Aug;pii: 104. [Epub ahead of print]50(2):

Insights regarding mitochondrial DNA copy number alterations in human cancer (Review).

Siti Muslihah Abd Radzak, Siti Zulaikha Nashwa Mohd Khair, Farizan Ahmad, Azim Patar, Zamzuri Idris, Abdul Aziz Mohamed Yusoff.

  Mitochondria are the critical organelles involved in various cellular functions. Mitochondrial biogenesis is activated by multiple cellular mechanisms which require a synchronous regulation between mitochondrial DNA (mtDNA) and nuclear DNA (nDNA). The mitochondrial DNA copy number (mtDNA‑CN) is a proxy indicator for mitochondrial activity, and its alteration reflects mitochondrial biogenesis and function. Despite the precise mechanisms that modulate the amount and composition of mtDNA, which have not been fully elucidated, mtDNA‑CN is known to influence numerous cellular pathways that are associated with cancer and as well as multiple other diseases. In addition, the utility of current technology in measuring mtDNA‑CN contributes to its extensive assessment of diverse traits and tumorigenesis. The present review provides an overview of mtDNA‑CN variations across human cancers and an extensive summary of the existing knowledge on the regulation and machinery of mtDNA‑CN. The current information on the advanced methods used for mtDNA‑CN assessment is also presented.

Keywords:  biomarker; cancer; mitochondrial DNA; mtDNA copy number alterations; mtDNA replication

DOI:  https://doi.org/10.3892/ijmm.2022.5160
Glycobiology. 2022 Jun 16. pii: cwac038. [Epub ahead of print]

O-GlcNAc transferase maintains metabolic homeostasis in response to CDK9 inhibition.

Aishwarya Gondane, Ninu Poulose, Suzanne Walker, Ian G Mills, Harri M Itkonen.

  Co-targeting of O-GlcNAc transferase (OGT) and the transcriptional kinase CDK9 is toxic to prostate cancer cells. As OGT is an essential glycosyltransferase, identifying an alternative target showing similar effects is of great interest. Here, we used a multiomics approach (transcriptomics, metabolomics and proteomics) to better understand the mechanistic basis of the combinatorial lethality between OGT and CDK9 inhibition. CDK9 inhibition preferentially affected transcription. In contrast, depletion of OGT activity predominantly remodeled the metabolome. Using an unbiased systems biology approach (weighted gene correlation network analysis), we discovered that CDK9 inhibition alters mitochondrial activity / flux, and high OGT activity is essential to maintain mitochondrial respiration when CDK9 activity is depleted. Our metabolite profiling data revealed that pantothenic acid (vitamin B5) is the metabolite that is most robustly induced by both OGT and OGT+CDK9 inhibitor treatments, but not by CDK9 inhibition alone. Finally, supplementing prostate cancer cell lines with vitamin B5 in the presence of CDK9 inhibitor mimics the effects of co-targeting OGT and CDK9.

Keywords:  Cyclin-dependent kinase 9; O-GlcNAc transferase; metabolism; prostate cancer; systems biology

DOI:  https://doi.org/10.1093/glycob/cwac038
Prog Mol Subcell Biol. 2022 ;61 1-13

Inorganic Polyphosphate and F0F1-ATP Synthase of Mammalian Mitochondria.

Artyom Y Baev, Andrey Y Abramov.

  Inorganic polyphosphate is a polymer which plays multiple important roles in yeast and bacteria. In higher organisms the role of polyP has been intensively studied in last decades and involvements of this polymer in signal transduction, cell death mechanisms, energy production, and many other processes were demonstrated. In contrast to yeast and bacteria, where enzymes responsible for synthesis and hydrolysis of polyP were identified, in mammalian cells polyP clearly plays important role in physiology and pathology but enzymes responsible for synthesis of polyP or consumption of this polymer are still not identified. Here, we discuss the role of mitochondrial F0F1-ATP synthase in polyP synthesis with results, which confirm this proposal. We also discuss the role of other enzymes which may play important roles in polyP metabolism.

Keywords:  ADP/O ratio; Alkaline phosphatase; Endopolyphosphatase; F0F1-ATP synthase; H-prune; Membrane potential; Mitochondria; NAD kinase; Plasma membrane calcium pump; Tartrate-resistant acid phosphatase

DOI:  https://doi.org/10.1007/978-3-031-01237-2_1
Nat Commun. 2022 Jun 15. 13(1): 3346

Remote solid cancers rewire hepatic nitrogen metabolism via host nicotinamide-N-methyltransferase.

Rin Mizuno, Hiroaki Hojo, Masatomo Takahashi, Soshiro Kashio, Sora Enya, Motonao Nakao, Riyo Konishi, Mayuko Yoda, Ayano Harata, Junzo Hamanishi, Hiroshi Kawamoto, Masaki Mandai, Yutaka Suzuki, Masayuki Miura, Takeshi Bamba, Yoshihiro Izumi, Shinpei Kawaoka.

Cancers disrupt host homeostasis in various manners but the identity of host factors underlying such disruption remains largely unknown. Here we show that nicotinamide-N-methyltransferase (NNMT) is a host factor that mediates metabolic dysfunction in the livers of cancer-bearing mice. Multiple solid cancers distantly increase expression of Nnmt and its product 1-methylnicotinamide (MNAM) in the liver. Multi-omics analyses reveal suppression of the urea cycle accompanied by accumulation of amino acids, and enhancement of uracil biogenesis in the livers of cancer-bearing mice. Importantly, genetic deletion of Nnmt leads to alleviation of these metabolic abnormalities, and buffers cancer-dependent weight loss and reduction of the voluntary wheel-running activity. Our data also demonstrate that MNAM is capable of affecting urea cycle metabolites in the liver. These results suggest that cancers up-regulate the hepatic NNMT pathway to rewire liver metabolism towards uracil biogenesis rather than nitrogen disposal via the urea cycle, thereby disrupting host homeostasis.

DOI: https://doi.org/10.1038/s41467-022-30926-z
Nat Commun. 2022 Jun 16. 13(1): 3407

A hexa-species transcriptome atlas of mammalian embryogenesis delineates metabolic regulation across three different implantation modes.

Anna Malkowska, Christopher Penfold, Sophie Bergmann, Thorsten E Boroviak.

Mammalian embryogenesis relies on glycolysis and oxidative phosphorylation to balance the generation of biomass with energy production. However, the dynamics of metabolic regulation in the postimplantation embryo in vivo have remained elusive due to the inaccessibility of the implanted conceptus for biochemical studies. To address this issue, we compiled single-cell embryo profiling data in six mammalian species and determined their metabolic dynamics through glycolysis and oxidative phosphorylation associated gene expression. Strikingly, we identify a conserved switch from bivalent respiration in the late blastocyst towards a glycolytic metabolism in early gastrulation stages across species, which is independent of embryo implantation. Extraembryonic lineages followed the dynamics of the embryonic lineage, except visceral endoderm. Finally, we demonstrate that in vitro primate embryo culture substantially impacts metabolic gene regulation by comparison to in vivo samples. Our work reveals a conserved metabolic programme despite different implantation modes and highlights the need to optimise postimplantation embryo culture protocols.

DOI: https://doi.org/10.1038/s41467-022-30194-x
J Biol Chem. 2022 Jun 09. pii: S0021-9258(22)00559-2. [Epub ahead of print] 102118

Regulation of the lysosome by sphingolipids: potential role in aging.

Haiqing Tang, Xiaokun Huang, Shanshan Pang.

  Sphingolipids are a class of bioactive complex lipids that have been closely associated with aging and aging-related diseases. However, the mechanism through which sphingolipids control aging has long been a mystery. Emerging studies reveal that sphingolipids exert tight control over lysosomal homeostasis and function, as evidenced by sphingolipid-related diseases, including but not limited to lysosomal storage disorders. These diseases are defined by primary lysosomal defects and a few secondary defects such as mitochondrial dysfunction. Intriguingly, recent research indicates that the majority of these defects are also associated with aging, implying that sphingolipid-related diseases and aging may share common mechanisms. We propose that the lysosome is a pivotal hub for sphingolipid-mediated aging regulation. This review discusses the critical roles of sphingolipid metabolism in regulating various lysosomal functions, with an emphasis on how such regulation may contribute to aging and aging-related diseases.

Keywords:  aging; lifespan; lysosomal calcium; lysosomal cell death; lysosome; lysosome-mitochondria communication; mTOR; sphingolipid

DOI:  https://doi.org/10.1016/j.jbc.2022.102118
Science. 2022 Jun 16. eabg9302

Interleukin-17 governs hypoxic adaptation of injured epithelium.

Piotr Konieczny, Yue Xing, Ikjot Sidhu, Ipsita Subudhi, Kody P Mansfield, Brandon Hsieh, Douglas E Biancur, Samantha B Larsen, Michael Cammer, Dongqing Li, Ning Xu Landén, Cynthia Loomis, Adriana Heguy, Anastasia N Tikhonova, Aristotelis Tsirigos, Shruti Naik.

Mammalian cells autonomously activate hypoxia-inducible transcription factors to ensure survival in low-oxygen environments. We report that injury-induced hypoxia is insufficient to trigger hypoxia-inducible factor 1 alpha (HIF1α) in damaged epithelium. Instead, multimodal single-cell and spatial transcriptomics analyses and functional studies reveal that RORγt+ γδ T cell-derived interleukin (IL)-17A, is necessary and sufficient to activate HIF1α. Protein kinase B (AKT) and ERK1/2 signaling proximal of IL-17RC activates mammalian target of rapamycin (mTOR) and consequently HIF1α. The IL-17A-HIF1α drives glycolysis in wound front epithelia. Epithelial-specific loss of IL-17RC, HIF1α, or blockade of glycolysis derails repair. Our findings underscore the coupling of inflammatory, metabolic, and migratory programs to expedite epithelial healing and illuminate the immune cell-derived inputs in cellular adaptation to hypoxic stress during repair.

DOI: https://doi.org/10.1126/science.abg9302
EMBO Rep. 2022 Jun 15. e52280

PPARα alleviates iron overload-induced ferroptosis in mouse liver.

Guowei Xing, Lihua Meng, Shiyao Cao, Shenghui Liu, Jiayan Wu, Qian Li, Wendong Huang, Lisheng Zhang.

  Ferroptosis is an iron-dependent form of non-apoptotic cell death implicated in liver, brain, kidney, and heart pathology. How ferroptosis is regulated remains poorly understood. Here, we show that PPARα suppresses ferroptosis by promoting the expression of glutathione peroxidase 4 (Gpx4) and by inhibiting the expression of the plasma iron carrier TRF. PPARα directly induces Gpx4 expression by binding to a PPRE element within intron 3. PPARα knockout mice develop more severe iron accumulation and ferroptosis in the liver when fed a high-iron diet than wild-type mice. Ferrous iron (Fe2+ ) triggers ferroptosis via Fenton reactions and ROS accumulation. We further find that a rhodamine-based "turn-on" fluorescent probe(probe1) is suitable for the in vivo detection of Fe2+ . Probe1 displays high selectivity towards Fe2+ , and exhibits a stable response for Fe2+ with a concentration of 20 μM in tissue. Our data thus show that PPARα activation alleviates iron overload-induced ferroptosis in mouse livers through Gpx4 and TRF, suggesting that PPARα may be a promising therapeutic target for drug discovery in ferroptosis-related tissue injuries. Moreover, we identified a fluorescent probe that specifically labels ferrous ions and can be used to monitor Fe2+ in vivo.

Keywords:  Ferroptosis; Gpx4; Liver; PPARα; TRF

DOI:  https://doi.org/10.15252/embr.202052280
Curr Opin Genet Dev. 2022 Jun 08. pii: S0959-437X(22)00032-6. [Epub ahead of print]75 101923

Metabolic regulation in pluripotent stem cells.

Linda Diamante, Graziano Martello.

Pluripotent stem cells (PSCs) have the capacity to give rise to all cell types of the adult body and to expand rapidly while retaining genome integrity, representing a perfect tool for regenerative medicine. PSCs are obtained from preimplantation embryos as embryonic stem cells (ESCs), or by reprogramming of somatic cells as induced pluripotent stem cells (iPSCs). Understanding the metabolic requirements of PSCs is instrumental for their efficient generation, expansion and differentiation. PSCs reshape their metabolic profile during developmental progression. Fatty acid oxidation is strictly required for energy production in naive PSCs, but becomes dispensable in more advanced, or primed, PSCs. Other metabolites directly affect proliferation, differentiation or the epigenetic profile of PSCs, showing how metabolism plays an instructive role on PSC behaviour. Developmental progression of pluripotent cells can be paused, both in vitro and in vivo, in response to hormonal and metabolic alterations. Such reversible pausing has been recently linked to mammalian target of rapamycin activity, lipid metabolism and mitochondrial activity. Finally, metabolism is not simply regulated by exogenous stimuli or nutrient availability in PSCs, as key pluripotency regulators, such as Oct4, Stat3 and Tfcp2l1, actively shape the metabolic profile of PSCs.

DOI: https://doi.org/10.1016/j.gde.2022.101923
Mol Cell. 2022 Jun 10. pii: S1097-2765(22)00486-5. [Epub ahead of print]

Riboregulation of Enolase 1 activity controls glycolysis and embryonic stem cell differentiation.

Ina Huppertz, Joel I Perez-Perri, Panagiotis Mantas, Thileepan Sekaran, Thomas Schwarzl, Francesco Russo, Dunja Ferring-Appel, Zuzana Koskova, Lyudmila Dimitrova-Paternoga, Eleni Kafkia, Janosch Hennig, Pierre A Neveu, Kiran Patil, Matthias W Hentze.

  Differentiating stem cells must coordinate their metabolism and fate trajectories. Here, we report that the catalytic activity of the glycolytic enzyme Enolase 1 (ENO1) is directly regulated by RNAs leading to metabolic rewiring in mouse embryonic stem cells (mESCs). We identify RNA ligands that specifically inhibit ENO1's enzymatic activity in vitro and diminish glycolysis in cultured human cells and mESCs. Pharmacological inhibition or RNAi-mediated depletion of the protein deacetylase SIRT2 increases ENO1's acetylation and enhances its RNA binding. Similarly, induction of mESC differentiation leads to increased ENO1 acetylation, enhanced RNA binding, and inhibition of glycolysis. Stem cells expressing mutant forms of ENO1 that escape or hyper-activate this regulation display impaired germ layer differentiation. Our findings uncover acetylation-driven riboregulation of ENO1 as a physiological mechanism of glycolytic control and of the regulation of stem cell differentiation. Riboregulation may represent a more widespread principle of biological control.

Keywords:  Enolase 1; RNA-binding proteins; RNA-protein interactions; acetylation; cancer; embryonic stem cell differentiation; glycolysis; metabolism

DOI:  https://doi.org/10.1016/j.molcel.2022.05.019
Curr Opin Plant Biol. 2022 Jun 14. pii: S1369-5266(22)00073-5. [Epub ahead of print]68 102244

Genome-scale modeling of the primary-specialized metabolism interface.

Kathleen Beilsmith, Christopher S Henry, Samuel M D Seaver.

  Environmental challenges and development require plants to reallocate resources between primary and specialized metabolites to survive. Genome-scale metabolic models, which map carbon flux through metabolic pathways, are a valuable tool in the study of tradeoffs that arise at this interface. Due to annotation gaps, models that characterize all the enzymatic steps in individual specialized pathways and their linkages to each other and to central carbon metabolism are difficult to construct. Recent studies have successfully curated subsystems of specialized metabolism and characterized the interfaces where flux is diverted to the precursors of glucosinolates, terpenes, and anthocyanins. Although advances in metabolite profiling can help to constrain models at this interface, quantitative analysis remains challenging because of the different timescales on which specialized metabolites from constitutive and reactive pathways accumulate.

Keywords:  Flux balance analysis; Genome-scale metabolic models; Mass spectrometry; Metabolism; Primary-specialized metabolism tradeoff

DOI:  https://doi.org/10.1016/j.pbi.2022.102244
STAR Protoc. 2022 Jun 17. 3(2): 101453

A protocol to measure lysosomal Zn2+ release through a genetically encoded Zn2+ indicator.

Mingxue Gu, Meiqin Hu, Taylor Minckley, Prateeksunder Pinchi, Haoxing Xu, Yan Qin, Wanlu Du.

  Intracellular vesicles such as lysosomes contain micromolar to millimolar concentrations of Zn2+, and disturbing lysosomal Zn2+ homeostasis via lysosomal Zn2+ release leads to mitochondria damage and consequent lytic cell death. Methods have been developed to image cellular Zn2+ dynamics. Here, we present a protocol using GZnP3, a genetically encoded fluorescent Zn2+ indicator, to assess lysosomal Zn2+ release in cultured cells by fluorescence microscopy imaging. For complete details on the use and execution of this protocol, please refer to Du et al. (2021) or Minckley et al. (2019).

Keywords:  Cell culture; Microscopy; Molecular/Chemical Probes

DOI:  https://doi.org/10.1016/j.xpro.2022.101453
Immunity. 2022 Jun 14. pii: S1074-7613(22)00233-3. [Epub ahead of print]55(6): 1032-1050.e14

Indoleamine 2,3-dioxygenase 1 activation in mature cDC1 promotes tolerogenic education of inflammatory cDC2 via metabolic communication.

Marco Gargaro, Giulia Scalisi, Giorgia Manni, Carlos G Briseño, Prachi Bagadia, Vivek Durai, Derek J Theisen, Sunkyung Kim, Marilena Castelli, Chenling A Xu, Gerd Meyer Zu Hörste, Giuseppe Servillo, Maria A Della Fazia, Giulia Mencarelli, Doriana Ricciuti, Eleonora Padiglioni, Nicola Giacchè, Carolina Colliva, Roberto Pellicciari, Mario Calvitti, Teresa Zelante, Dietmar Fuchs, Ciriana Orabona, Louis Boon, Alban Bessede, Marco Colonna, Paolo Puccetti, Theresa L Murphy, Kenneth M Murphy, Francesca Fallarino.

  Conventional dendritic cells (cDCs), cDC1 and cDC2, act both to initiate immunity and maintain self-tolerance. The tryptophan metabolic enzyme indoleamine 2,3-dioxygenase 1 (IDO1) is used by cDCs in maintaining tolerance, but its role in different subsets remains unclear. At homeostasis, only mature CCR7+ cDC1 expressed IDO1 that was dependent on IRF8. Lipopolysaccharide treatment induced maturation and IDO1-dependent tolerogenic activity in isolated immature cDC1, but not isolated cDC2. However, both human and mouse cDC2 could induce IDO1 and acquire tolerogenic function when co-cultured with mature cDC1 through the action of cDC1-derived l-kynurenine. Accordingly, cDC1-specific inactivation of IDO1 in vivo exacerbated disease in experimental autoimmune encephalomyelitis. This study identifies a previously unrecognized metabolic communication in which IDO1-expressing cDC1 cells extend their immunoregulatory capacity to the cDC2 subset through their production of tryptophan metabolite l-kynurenine. This metabolic axis represents a potential therapeutic target in treating autoimmune demyelinating diseases.

Keywords:  AhR; IDO1; IL-6; RelB; dendritic cells; immunotolerance; kynurenine; metabolites; neuroinflammation; tryptophan metabolism

DOI:  https://doi.org/10.1016/j.immuni.2022.05.013
Nature. 2022 Jun 15.

cGAS-STING drives the IL-6-dependent survival of chromosomally instable cancers.

Christy Hong, Michael Schubert, Andréa E Tijhuis, Marta Requesens, Maurits Roorda, Anouk van den Brink, Lorena Andrade Ruiz, Petra L Bakker, Tineke van der Sluis, Wietske Pieters, Mengting Chen, René Wardenaar, Bert van der Vegt, Diana C J Spierings, Marco de Bruyn, Marcel A T M van Vugt, Floris Foijer.

Chromosomal instability (CIN) drives cancer cell evolution, metastasis and therapy resistance, and is associated with poor prognosis1. CIN leads to micronuclei that release DNA into the cytoplasm after rupture, which triggers activation of inflammatory signalling mediated by cGAS and STING2,3. These two proteins are considered to be tumour suppressors as they promote apoptosis and immunosurveillance. However, cGAS and STING are rarely inactivated in cancer4, and, although they have been implicated in metastasis5, it is not known why loss-of-function mutations do not arise in primary tumours4. Here we show that inactivation of cGAS-STING signalling selectively impairs the survival of triple-negative breast cancer cells that display CIN. CIN triggers IL-6-STAT3-mediated signalling, which depends on the cGAS-STING pathway and the non-canonical NF-κB pathway. Blockade of IL-6 signalling by tocilizumab, a clinically used drug that targets the IL-6 receptor (IL-6R), selectively impairs the growth of cultured triple-negative breast cancer cells that exhibit CIN. Moreover, outgrowth of chromosomally instable tumours is significantly delayed compared with tumours that do not display CIN. Notably, this targetable vulnerability is conserved across cancer types that express high levels of IL-6 and/or IL-6R in vitro and in vivo. Together, our work demonstrates pro-tumorigenic traits of cGAS-STING signalling and explains why the cGAS-STING pathway is rarely inactivated in primary tumours. Repurposing tocilizumab could be a strategy to treat cancers with CIN that overexpress IL-6R.

DOI: https://doi.org/10.1038/s41586-022-04847-2
Nature. 2022 Jun 15.

A pan-cancer compendium of chromosomal instability.

Ruben M Drews, Barbara Hernando, Maxime Tarabichi, Kerstin Haase, Tom Lesluyes, Philip S Smith, Lena Morrill Gavarró, Dominique-Laurent Couturier, Lydia Liu, Michael Schneider, James D Brenton, Peter Van Loo, Geoff Macintyre, Florian Markowetz.

Chromosomal instability (CIN) results in the accumulation of large-scale losses, gains and rearrangements of DNA1. The broad genomic complexity caused by CIN is a hallmark of cancer2; however, there is no systematic framework to measure different types of CIN and their effect on clinical phenotypes pan-cancer. Here we evaluate the extent, diversity and origin of CIN across 7,880 tumours representing 33 cancer types. We present a compendium of 17 copy number signatures that characterize specific types of CIN, with putative aetiologies supported by multiple independent data sources. The signatures predict drug response and identify new drug targets. Our framework refines the understanding of impaired homologous recombination, which is one of the most therapeutically targetable types of CIN. Our results illuminate a fundamental structure underlying genomic complexity in human cancers and provide a resource to guide future CIN research.

DOI: https://doi.org/10.1038/s41586-022-04789-9
Cell Mol Life Sci. 2022 Jun 15. 79(7): 363

Mechanisms that regulate the activities of TET proteins.

Kanak Joshi, Shanhui Liu, Peter Breslin S J, Jiwang Zhang.

  The ten-eleven translocation (TET) family of dioxygenases consists of three members, TET1, TET2, and TET3. All three TET enzymes have Fe+2 and α-ketoglutarate (α-KG)-dependent dioxygenase activities, catalyzing the 1st step of DNA demethylation by converting 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), and further oxidize 5hmC to 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). Gene knockout studies demonstrated that all three TET proteins are involved in the regulation of fetal organ generation during embryonic development and normal tissue generation postnatally. TET proteins play such roles by regulating the expression of key differentiation and fate-determining genes via (1) enzymatic activity-dependent DNA methylation of the promoters and enhancers of target genes; and (2) enzymatic activity-independent regulation of histone modification. Interacting partner proteins and post-translational regulatory mechanisms regulate the activities of TET proteins. Mutations and dysregulation of TET proteins are involved in the pathogenesis of human diseases, specifically cancers. Here, we summarize the research on the interaction partners and post-translational modifications of TET proteins. We also discuss the molecular mechanisms by which these partner proteins and modifications regulate TET functioning and target gene expression. Such information will help in the design of medications useful for targeted therapy of TET-mutant-related diseases.

Keywords:  Gene expression; Interaction partners; Mutations; Post-translational modifications; TETs

DOI:  https://doi.org/10.1007/s00018-022-04396-x
Circ Res. 2022 Jun 14. 101161CIRCRESAHA121319817

Mitochondrial H2S Regulates BCAA Catabolism in Heart Failure.

Zhen Li, Huijing Xia, Thomas E Sharp, Kyle B LaPenna, John W Elrod, Kevin M Casin, Ken Liu, John W Calvert, Vinh Q Chau, Fadi N Salloum, Shi Xu, Ming Xian, Noriyuki Nagahara, Traci T Goodchild, David J Lefer.

   BACKGROUND: Hydrogen sulfide (H2S) exerts mitochondria-specific actions that include the preservation of oxidative phosphorylation, biogenesis, and ATP synthesis, while inhibiting cell death. 3-MST (3-mercaptopyruvate sulfurtransferase) is a mitochondrial H2S-producing enzyme whose functions in the cardiovascular disease are not fully understood. In the current study, we investigated the effects of global 3-MST deficiency in the setting of pressure overload-induced heart failure.
METHODS: Human myocardial samples obtained from patients with heart failure undergoing cardiac surgeries were probed for 3-MST protein expression. 3-MST knockout mice and C57BL/6J wild-type mice were subjected to transverse aortic constriction to induce pressure overload heart failure with reduced ejection fraction. Cardiac structure and function, vascular reactivity, exercise performance, mitochondrial respiration, and ATP synthesis efficiency were assessed. In addition, untargeted metabolomics were utilized to identify key pathways altered by 3-MST deficiency.
RESULTS: Myocardial 3-MST was significantly reduced in patients with heart failure compared with nonfailing controls. 3-MST KO mice exhibited increased accumulation of branched-chain amino acids in the myocardium, which was associated with reduced mitochondrial respiration and ATP synthesis, exacerbated cardiac and vascular dysfunction, and worsened exercise performance following transverse aortic constriction. Restoring myocardial branched-chain amino acid catabolism with 3,6-dichlorobenzo1[b]thiophene-2-carboxylic acid (BT2) and administration of a potent H2S donor JK-1 ameliorates the detrimental effects of 3-MST deficiency in heart failure with reduced ejection fraction.
CONCLUSIONS: Our data suggest that 3-MST derived mitochondrial H2S may play a regulatory role in branched-chain amino acid catabolism and mediate critical cardiovascular protection in heart failure.

Keywords:  branched chain amino acid; cell death; heart failure; hydrogen sulfide; mitochondrial respiration

DOI:  https://doi.org/10.1161/CIRCRESAHA.121.319817