bims-camemi 2020-11-08 papers

bims-camemi

Biomed News

on Mitochondrial metabolism in cancer

Issue of 2020‒11‒08
forty-two papers selected by
Christian Frezza,

Functional Genomics In Vivo Reveal Metabolic Dependencies of Pancreatic Cancer Cells.
BCAT1 affects mitochondrial metabolism independently of leucine transamination in activated human macrophages.
Mitochondria Define Intestinal Stem Cell Differentiation Downstream of a FOXO/Notch Axis.
The Roles of Mitochondrial Folate Metabolism in Supporting Mitochondrial DNA Synthesis, Oxidative Phosphorylation, and Cellular Function.
Functional Genomics Identifies Metabolic Vulnerabilities in Pancreatic Cancer.
Targeting Metabolic Plasticity and Flexibility Dynamics for Cancer Therapy.
Calcium influx through the mitochondrial calcium uniporter holocomplex, MCUcx.
OPA1 and MICOS Regulate mitochondrial crista dynamics and formation.
Metabolic shift underlies recovery in reversible infantile respiratory chain deficiency.
Roles of mitochondria in the hallmarks of metastasis.
Stem cell fate determination through protein O-GlcNAcylation.
Regulation of Mitochondrial Ca2+ Uptake.
Pyruvate Kinase Controls Signal Strength in the Insulin Secretory Pathway.
TCA cycle signalling and the evolution of eukaryotes.
Zmat3 Is a Key Splicing Regulator in the p53 Tumor Suppression Program.
Drp1 Tubulates the ER in a GTPase-Independent Manner.
Metabolic determinants of cellular fitness dependent on mitochondrial reactive oxygen species.
Isolation and Metabolic Assessment of Cancer Cell Mitochondria.
Succinate Dehydrogenase and Ribonucleic Acid Networks in Cancer and Other Diseases.
Cellular Control of Viscosity Counters Changes in Temperature and Energy Availability.
Loss of metabolic plasticity underlies metformin toxicity in aged Caenorhabditis elegans.
Molecular Subsets in Renal Cancer Determine Outcome to Checkpoint and Angiogenesis Blockade.
A Tug-of-War Over Methionine.
Amino Acids Enhance Polyubiquitination of Rheb and Its Binding to mTORC1 by Blocking Lysosomal ATXN3 Deubiquitinase Activity.
Mitochondrial dysfunction in inflammatory bowel disease alters intestinal epithelial metabolism of hepatic acylcarnitines.
Mitochondrial disorders of the oxphos system.
A Selective Sweep Conceals a MicroRNA with Broad Metabolic Effects.
Regulation of peroxisomal trafficking and distribution.
DNA Damage and Mitochondria in Cancer and Aging.
ER-Mitochondria Contact Sites Reporters: Strengths and Weaknesses of the Available Approaches.
Iron out, mitophagy in! A way to slow down hepatocellular carcinoma.
Biallelic mutations in NDUFA8 cause complex I deficiency in two siblings with favorable clinical evolution.
Ceramides in Metabolism: Key Lipotoxic Players.
Clear cell renal cell carcinoma ontogeny and mechanisms of lethality.
A trimeric Rab7 GEF controls NPC1-dependent lysosomal cholesterol export.
Multi-Tissue Acceleration of the Mitochondrial Phosphoenolpyruvate Cycle Improves Whole-Body Metabolic Health.
Protein phase separation and its role in tumorigenesis.
Mito Hacker: a set of tools to enable high-throughput analysis of mitochondrial network morphology.
TANK-Binding Kinase 1 Regulates the Localization of Acyl-CoA Synthetase ACSL1 to Control Hepatic Fatty Acid Oxidation.
Genomic control of metastasis.
Neurons Release Serine to Support mRNA Translation in Pancreatic Cancer.
3D Culture Models with CRISPR Screens Reveal Hyperactive NRF2 as a Prerequisite for Spheroid Formation via Regulation of Proliferation and Ferroptosis.

Cell Metab. 2020 Oct 28. pii: S1550-4131(20)30550-7. [Epub ahead of print]

Functional Genomics In Vivo Reveal Metabolic Dependencies of Pancreatic Cancer Cells.

Xiphias Ge Zhu, Aleksey Chudnovskiy, Lou Baudrier, Benjamin Prizer, Yuyang Liu, Benjamin N Ostendorf, Norihiro Yamaguchi, Abolfozl Arab, Bernardo Tavora, Rebecca Timson, Søren Heissel, Elisa de Stanchina, Henrik Molina, Gabriel D Victora, Hani Goodarzi, Kıvanç Birsoy.

  Pancreatic ductal adenocarcinoma (PDAC) cells require substantial metabolic rewiring to overcome nutrient limitations and immune surveillance. However, the metabolic pathways necessary for pancreatic tumor growth in vivo are poorly understood. To address this, we performed metabolism-focused CRISPR screens in PDAC cells grown in culture or engrafted in immunocompetent mice. While most metabolic gene essentialities are unexpectedly similar under these conditions, a small fraction of metabolic genes are differentially required for tumor progression. Among these, loss of heme synthesis reduces tumor growth due to a limiting role of heme in vivo, an effect independent of tissue origin or immune system. Our screens also identify autophagy as a metabolic requirement for pancreatic tumor immune evasion. Mechanistically, autophagy protects cancer cells from CD8+ T cell killing through TNFα-induced cell death in vitro. Altogether, this resource provides metabolic dependencies arising from microenvironmental limitations and the immune system, nominating potential anti-cancer targets.

Keywords:  cancer metabolism; in vivo CRISPR screen; pancreatic cancer; tumor immune evasion

DOI:  https://doi.org/10.1016/j.cmet.2020.10.017
J Cell Sci. 2020 Nov 04. pii: jcs.247957. [Epub ahead of print]

BCAT1 affects mitochondrial metabolism independently of leucine transamination in activated human macrophages.

Jeong-Hun Ko, Antoni Olona, Adonia E Papathanassiu, Norzawani Buang, Kwon-Sik Park, Ana S H Costa, Claudio Mauro, Christian Frezza, Jacques Behmoaras.

  In response to environmental stimuli, macrophages change their nutrient consumption and undergo an early metabolic adaptation that progressively shapes their polarization state. During the transient, early phase of pro-inflammatory macrophage activation, an increase in tricarboxylic acid (TCA) cycle activity has been reported but the relative contribution of branched chain amino acid (BCAA) leucine remain to be determined. Here we show that glucose but not glutamine is a major contributor of the increase in TCA cycle metabolites during early macrophage activation in humans. We then show that, although BCAA uptake is not altered, their transamination by BCAT1 is increased following 8h lipopolysaccharide (LPS) stimulation. Of note, leucine is not metabolized to integrate the TCA cycle in neither basal nor stimulated human macrophages. Surprisingly, the pharmacological inhibition of BCAT1 reduced glucose-derived itaconate, α-ketoglutarate, and 2-hydroxyglutarate levels, without affecting succinate and citrate levels, indicating a partial inhibition of TCA cycle. This indirect effect is associated with NRF2 activation and anti-oxidant responses. These results suggest a moonlighting role of BCAT1 through redox-mediated control of mitochondrial function during early macrophage activation.

Keywords:  BCAT1; Immunometabolism; Macrophages; Mitochondria; Redox biology; TCA cycle

DOI:  https://doi.org/10.1242/jcs.247957
Cell Metab. 2020 Nov 03. pii: S1550-4131(20)30538-6. [Epub ahead of print]32(5): 889-900.e7

Mitochondria Define Intestinal Stem Cell Differentiation Downstream of a FOXO/Notch Axis.

Marlies C Ludikhuize, Maaike Meerlo, Marc Pages Gallego, Despina Xanthakis, Mar Burgaya Julià, Nguyen T B Nguyen, Eline C Brombacher, Nalan Liv, Madelon M Maurice, Ji-Hye Paik, Boudewijn M T Burgering, Maria J Rodriguez Colman.

  Differential WNT and Notch signaling regulates differentiation of Lgr5+ crypt-based columnar cells (CBCs) into intestinal cell lineages. Recently we showed that mitochondrial activity supports CBCs, while adjacent Paneth cells (PCs) show reduced mitochondrial activity. This implies that CBC differentiation into PCs involves a metabolic transition toward downregulation of mitochondrial dependency. Here we show that Forkhead box O (FoxO) transcription factors and Notch signaling interact in determining CBC fate. In agreement with the organoid data, Foxo1/3/4 deletion in mouse intestine induces secretory cell differentiation. Importantly, we show that FOXO and Notch signaling converge on regulation of mitochondrial fission, which in turn provokes stem cell differentiation into goblet cells and PCs. Finally, scRNA-seq-based reconstruction of CBC differentiation trajectories supports the role of FOXO, Notch, and mitochondria in secretory differentiation. Together, this points at a new signaling-metabolic axis in CBC differentiation and highlights the importance of mitochondria in determining stem cell fate.

Keywords:  FOXO; Notch; differentiation; intestine; metabolism; mitochondria; stem cells

DOI:  https://doi.org/10.1016/j.cmet.2020.10.005
Curr Dev Nutr. 2020 Oct;4(10): nzaa153

The Roles of Mitochondrial Folate Metabolism in Supporting Mitochondrial DNA Synthesis, Oxidative Phosphorylation, and Cellular Function.

Yuwen Xiu, Martha S Field.

  Folate-mediated one-carbon metabolism (FOCM) is compartmentalized within human cells to the cytosol, nucleus, and mitochondria. The recent identifications of mitochondria-specific, folate-dependent thymidylate [deoxythymidine monophosphate (dTMP)] synthesis together with discoveries indicating the critical role of mitochondrial FOCM in cancer progression have renewed interest in understanding this metabolic pathway. The goal of this narrative review is to summarize recent advances in the field of one-carbon metabolism, with an emphasis on the biological importance of mitochondrial FOCM in maintaining mitochondrial DNA integrity and mitochondrial function, as well as the reprogramming of mitochondrial FOCM in cancer. Elucidation of the roles and regulation of mitochondrial FOCM will contribute to a better understanding of the mechanisms underlying folate-associated pathologies.

Keywords:  cancer metabolism; folate; mitochondrial DNA; mitochondrial metabolism; thymidylate

DOI:  https://doi.org/10.1093/cdn/nzaa153
Cell Metab. 2020 Oct 28. pii: S1550-4131(20)30551-9. [Epub ahead of print]

Functional Genomics Identifies Metabolic Vulnerabilities in Pancreatic Cancer.

Douglas E Biancur, Kevin S Kapner, Keisuke Yamamoto, Robert S Banh, Jasper E Neggers, Albert S W Sohn, Warren Wu, Robert T Manguso, Adam Brown, David E Root, Andrew J Aguirre, Alec C Kimmelman.

  Pancreatic ductal adenocarcinoma (PDA) is a deadly cancer characterized by complex metabolic adaptations that promote survival in a severely hypoxic and nutrient-limited tumor microenvironment (TME). Modeling microenvironmental influences in cell culture has been challenging, and technical limitations have hampered the comprehensive study of tumor-specific metabolism in vivo. To systematically interrogate metabolic vulnerabilities in PDA, we employed parallel CRISPR-Cas9 screens using in vivo and in vitro systems. This work revealed striking overlap of in vivo metabolic dependencies with those in vitro. Moreover, we identified that intercellular nutrient sharing can mask dependencies in pooled screens, highlighting a limitation of this approach to study tumor metabolism. Furthermore, metabolic dependencies were similar between 2D and 3D culture, although 3D culture may better model vulnerabilities that influence certain oncogenic signaling pathways. Lastly, our work demonstrates the power of genetic screening approaches to define in vivo metabolic dependencies and pathways that may have therapeutic utility.

Keywords:  cancer cell signaling; metabolism; nutrient crosstalk; pancreatic cancer; tumor microenvironment

DOI:  https://doi.org/10.1016/j.cmet.2020.10.018
Cancer Discov. 2020 Nov 02.

Targeting Metabolic Plasticity and Flexibility Dynamics for Cancer Therapy.

Sarah-Maria Fendt, Christian Frezza, Ayelet Erez.

Cancer cells continuously rewire their metabolism to fulfill their need for rapid growth and survival while subject to changes in environmental cues. Thus, a vital component of a cancer cell lies in its metabolic adaptability. The constant demand for metabolic alterations requires flexibility, that is, the ability to utilize different metabolic substrates; as well as plasticity, that is, the ability to process metabolic substrates in different ways. In this review, we discuss how dynamic changes in cancer metabolism affect tumor progression and the consequential implications for cancer therapy. SIGNIFICANCE: Recognizing cancer dynamic metabolic adaptability as an entity can lead to targeted therapy that is expected to decrease drug resistance.

DOI: https://doi.org/10.1158/2159-8290.CD-20-0844
J Mol Cell Cardiol. 2020 Nov 01. pii: S0022-2828(20)30316-3. [Epub ahead of print]

Calcium influx through the mitochondrial calcium uniporter holocomplex, MCUcx.

Liron Boyman, Maura Greiser, W Jonathan Lederer.

  Ca2+ flux into the mitochondrial matrix through the MCU holocomplex (MCUcx) has recently been measured quantitatively and with milliseconds resolution for the first time under physiological conditions in both heart and skeletal muscle. Additionally, the dynamic levels of Ca2+ in the mitochondrial matrix ([Ca2+]m) of cardiomyocytes were measured as it was controlled by the balance between influx of Ca2+ into the mitochondrial matrix through MCUcx and efflux through the mitochondrial Na+ / Ca2+ exchanger (NCLX). Under these conditions [Ca2+]m was shown to regulate ATP production by the mitochondria at only a few critical sites. Additional functions attributed to [Ca2+]m continue to be reported in the literature. Here we review the new findings attributed to MCUcx function and provide a framework for understanding and investigating mitochondrial Ca2+ influx features, many of which remain controversial. The properties and functions of the MCUcx subunits that constitute the holocomplex are challenging to tease apart. Such distinct subunits include EMRE, MCUR1, MICUx (i.e. MICU1, MICU2, MICU3), and the pore-forming subunits (MCUpore). Currently, the specific set of functions of each subunit remains non-quantitative and controversial. The more contentious issues are discussed in the context of the newly measured native MCUcx Ca2+ flux from heart and skeletal muscle. These MCUcx Ca2+ flux measurements have been shown to be a highly-regulated, tissue-specific with femto-Siemens Ca2+ conductances and with distinct extramitochondrial Ca2+ ([Ca2+]i) dependencies. These data from cardiac and skeletal muscle mitochondria have been examined quantitatively for their threshold [Ca2+]i levels and for hypothesized gatekeeping function and are discussed in the context of model cell (e.g. HeLa, MEF, HEK293, COS7 cells) measurements. Our new findings on MCUcx dependent matrix [Ca2+]m signaling provide a quantitative basis for on-going and new investigations of the roles of MCUcx in cardiac function ranging from metabolic fuel selection, capillary blood-flow control and the pathological activation of the mitochondrial permeability transition pore (mPTP). Additionally, this review presents the use of advanced new methods that can be readily adapted by any investigator to enable them to carry out quantitative Ca2+ measurements in mitochondria while controlling the inner mitochondrial membrane potential, ΔΨm.

Keywords:  Heart; Mitochondrial Ca2+ signaling; Mitochondrial Na+/Ca2+ exchanger (NCLX); Mitochondrial calcium uniporter complex (MCUcx); Mitochondrial permeability transition pore (mPTP); Skeletal muscle

DOI:  https://doi.org/10.1016/j.yjmcc.2020.10.015
Cell Death Dis. 2020 Oct 31. 11(10): 940

OPA1 and MICOS Regulate mitochondrial crista dynamics and formation.

Chao Hu, Li Shu, Xiaoshuai Huang, Jianglong Yu, Liuju Li, Longlong Gong, Meigui Yang, Zhida Wu, Zhi Gao, Yungang Zhao, Liangyi Chen, Zhiyin Song.

Mitochondrial cristae are the main site for oxidative phosphorylation, which is critical for cellular energy production. Upon different physiological or pathological stresses, mitochondrial cristae undergo remodeling to reprogram mitochondrial function. However, how mitochondrial cristae are formed, maintained, and remolded is still largely unknown due to the technical challenges of tracking mitochondrial crista dynamics in living cells. Here, using live-cell Hessian structured illumination microscopy combined with transmission electron microscopy, focused ion beam/scanning electron microscopy, and three-dimensional tomographic reconstruction, we show, in living cells, that mitochondrial cristae are highly dynamic and undergo morphological changes, including elongation, shortening, fusion, division, and detachment from the mitochondrial inner boundary membrane (IBM). In addition, we find that OPA1, Yme1L, MICOS, and Sam50, along with the newly identified crista regulator ATAD3A, control mitochondrial crista dynamics. Furthermore, we discover two new types of mitochondrial crista in dysfunctional mitochondria, "cut-through crista" and "spherical crista", which are formed due to incomplete mitochondrial fusion and dysfunction of the MICOS complex. Interestingly, cut-through crista can convert to "lamellar crista". Overall, we provide a direct link between mitochondrial crista formation and mitochondrial crista dynamics.

DOI: https://doi.org/10.1038/s41419-020-03152-y
EMBO J. 2020 Oct 31. e105364

Metabolic shift underlies recovery in reversible infantile respiratory chain deficiency.

Denisa Hathazi, Helen Griffin, Matthew J Jennings, Michele Giunta, Christopher Powell, Sarah F Pearce, Benjamin Munro, Wei Wei, Veronika Boczonadi, Joanna Poulton, Angela Pyle, Claudia Calabrese, Aurora Gomez-Duran, Ulrike Schara, Robert Ds Pitceathly, Michael G Hanna, Kairit Joost, Ana Cotta, Julia Filardi Paim, Monica Machado Navarro, Jennifer Duff, Andre Mattmann, Kristine Chapman, Serenella Servidei, Adela Della Marina, Johanna Uusimaa, Andreas Roos, Vamsi Mootha, Michio Hirano, Mar Tulinius, Manta Giri, Eric P Hoffmann, Hanns Lochmüller, Salvatore DiMauro, Michal Minczuk, Patrick F Chinnery, Juliane S Müller, Rita Horvath.

  Reversible infantile respiratory chain deficiency (RIRCD) is a rare mitochondrial myopathy leading to severe metabolic disturbances in infants, which recover spontaneously after 6-months of age. RIRCD is associated with the homoplasmic m.14674T>C mitochondrial DNA mutation; however, only ~ 1/100 carriers develop the disease. We studied 27 affected and 15 unaffected individuals from 19 families and found additional heterozygous mutations in nuclear genes interacting with mt-tRNAGlu including EARS2 and TRMU in the majority of affected individuals, but not in healthy carriers of m.14674T>C, supporting a digenic inheritance. Our transcriptomic and proteomic analysis of patient muscle suggests a stepwise mechanism where first, the integrated stress response associated with increased FGF21 and GDF15 expression enhances the metabolism modulated by serine biosynthesis, one carbon metabolism, TCA lipid oxidation and amino acid availability, while in the second step mTOR activation leads to increased mitochondrial biogenesis. Our data suggest that the spontaneous recovery in infants with digenic mutations may be modulated by the above described changes. Similar mechanisms may explain the variable penetrance and tissue specificity of other mtDNA mutations and highlight the potential role of amino acids in improving mitochondrial disease.

Keywords:  digenic inheritance; homoplasmic tRNA mutation; mitochondrial myopathy; reversible infantile respiratory chain deficiency

DOI:  https://doi.org/10.15252/embj.2020105364
Br J Cancer. 2020 Nov 04.

Roles of mitochondria in the hallmarks of metastasis.

Adam D Scheid, Thomas C Beadnell, Danny R Welch.

Although mitochondrial contributions to cancer have been recognised for approximately a century, given that mitochondrial DNA (mtDNA) is dwarfed by the size of the nuclear genome (nDNA), nuclear genetics has represented a focal point in cancer biology, often at the expense of mtDNA and mitochondria. However, genomic sequencing and advances in in vivo models underscore the importance of mtDNA and mitochondria in cancer and metastasis. In this review, we explore the roles of mitochondria in the four defined 'hallmarks of metastasis': motility and invasion, microenvironment modulation, plasticity and colonisation. Biochemical processes within the mitochondria of both cancer cells and the stromal cells with which they interact are critical for each metastatic hallmark. We unravel complex dynamics in mitochondrial contributions to cancer, which are context-dependent and capable of either promoting metastasis or being leveraged to prevent it at various points of the metastatic cascade. Ultimately, mitochondrial contributions to cancer and metastasis are rooted in the capacity of these organelles to tune metabolic and genetic responses to dynamic microenvironmental cues.

DOI: https://doi.org/10.1038/s41416-020-01125-8
J Biol Chem. 2020 11 05. pii: jbc.REV120.014915. [Epub ahead of print]

Stem cell fate determination through protein O-GlcNAcylation.

Muhammad Abid Sheikh, Bright Starling Emerald, Suraiya Anjum Ansari.

  Embryonic and adult stem cells possess the capability of self-renewal and lineage specific differentiation. The intricate balance between self-renewal and differentiation is governed by developmental signals and cell type specific gene regulatory mechanisms. A perturbed intra/extracellular environment during lineage specification could affect stem cell fate decisions resulting in pathology. Growing evidence demonstrates that metabolic pathways govern epigenetic regulation of gene expression during stem cell fate commitment through the utilization of metabolic intermediates or end products of metabolic pathways as substrates for enzymatic histone/DNA modifications. UDP-GlcNAc is one such metabolite which acts as a substrate for enzymatic mono-glycosylation of various nuclear, cytosolic, and mitochondrial proteins on serine/threonine amino acid residues, a process termed protein O-GlcNAcylation. The levels of GlcNAc inside the cells depend on the nutrient availability, especially glucose. Thus, this metabolic sensor could modulate gene expression through O-GlcNAc modification of histones or other proteins in response to metabolic fluctuations. Herein, we review evidence demonstrating how stem cells couple metabolic inputs to gene regulatory pathways through O-GlcNAc-mediated epigenetic/transcriptional regulatory mechanisms to govern self-renewal and lineage specific differentiation programs. This review will serve as a primer for researchers seeking to better understand how O-GlcNAc influences stemness, and may catalyze the discovery of new stem cell-based therapeutic approaches.

Keywords:  Cell fate determination; Epigenetics; Gene expression; O-GlcNAcylation; Transcription; cell metabolism; epigenetics; gene expression; gene transcription; stem cells

DOI:  https://doi.org/10.1074/jbc.REV120.014915
Annu Rev Physiol. 2020 Nov 03.

Regulation of Mitochondrial Ca2+ Uptake.

Elizabeth Murphy, Charles Steenbergen.

Mitochondria are responsible for ATP production but are also known as regulators of cell death, and mitochondrial matrix Ca2+ is a key modulator of both ATP production and cell death. Although mitochondrial Ca2+ uptake and efflux have been studied for over 50 years, it is only in the past decade that the proteins responsible for mitochondrial Ca2+ uptake and efflux have been identified. The identification of the mitochondrial Ca2+ uniporter (MCU) led to an explosion of studies identifying regulators of the MCU. The levels of these regulators vary in a tissue- and disease-specific manner, providing new insight into how mitochondrial Ca2+ is regulated. This review focuses on the proteins responsible for mitochondrial transport and what we have learned from mouse studies with genetic alterations in these proteins. Expected final online publication date for the Annual Review of Physiology, Volume 83 is February 10, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

DOI: https://doi.org/10.1146/annurev-physiol-031920-092419
Cell Metab. 2020 Nov 03. pii: S1550-4131(20)30540-4. [Epub ahead of print]32(5): 736-750.e5

Pyruvate Kinase Controls Signal Strength in the Insulin Secretory Pathway.

Sophie L Lewandowski, Rebecca L Cardone, Hannah R Foster, Thuong Ho, Evgeniy Potapenko, Chetan Poudel, Halena R VanDeusen, Sophia M Sdao, Tiago C Alves, Xiaojian Zhao, Megan E Capozzi, Arnaldo H de Souza, Ishrat Jahan, Craig J Thomas, Craig S Nunemaker, Dawn Belt Davis, Jonathan E Campbell, Richard G Kibbey, Matthew J Merrins.

  Pancreatic β cells couple nutrient metabolism with appropriate insulin secretion. Here, we show that pyruvate kinase (PK), which converts ADP and phosphoenolpyruvate (PEP) into ATP and pyruvate, underlies β cell sensing of both glycolytic and mitochondrial fuels. Plasma membrane-localized PK is sufficient to close KATP channels and initiate calcium influx. Small-molecule PK activators increase the frequency of ATP/ADP and calcium oscillations and potently amplify insulin secretion. PK restricts respiration by cyclically depriving mitochondria of ADP, which accelerates PEP cycling until membrane depolarization restores ADP and oxidative phosphorylation. Our findings support a compartmentalized model of β cell metabolism in which PK locally generates the ATP/ADP required for insulin secretion. Oscillatory PK activity allows mitochondria to perform synthetic and oxidative functions without any net impact on glucose oxidation. These findings suggest a potential therapeutic route for diabetes based on PK activation that would not be predicted by the current consensus single-state model of β cell function.

Keywords:  K(ATP) channel; anaplerosis; biosensor imaging; insulin secretion; metabolic flux; metabolic oscillations; oxidative phosphorylation; phosphoenolpyruvate cycle; pyruvate kinase; β cell metabolism

DOI:  https://doi.org/10.1016/j.cmet.2020.10.007
Curr Opin Biotechnol. 2020 Oct 30. pii: S0958-1669(20)30144-0. [Epub ahead of print]68 72-88

TCA cycle signalling and the evolution of eukaryotes.

Dylan G Ryan, Christian Frezza, Luke Aj O'Neill.

A major question remaining in the field of evolutionary biology is how prokaryotic organisms made the leap to complex eukaryotic life. The prevailing theory depicts the origin of eukaryotic cell complexity as emerging from the symbiosis between an α-proteobacterium, the ancestor of present-day mitochondria, and an archaeal host (endosymbiont theory). A primary contribution of mitochondria to eukaryogenesis has been attributed to the mitochondrial genome, which enabled the successful internalisation of bioenergetic membranes and facilitated remarkable genome expansion. It has also been postulated that a key contribution of the archaeal host during eukaryogenesis was in providing 'archaeal histones' that would enable compaction and regulation of an expanded genome. Yet, how the communication between the host and the symbiont evolved is unclear. Here, we propose an evolutionary concept in which mitochondrial TCA cycle signalling was also a crucial player during eukaryogenesis enabling the dynamic control of an expanded genome via regulation of DNA and histone modifications. Furthermore, we discuss how TCA cycle remodelling is a common evolutionary strategy invoked by eukaryotic organisms to coordinate stress responses and gene expression programmes, with a particular focus on the TCA cycle-derived metabolite itaconate.

DOI: https://doi.org/10.1016/j.copbio.2020.09.014
Mol Cell. 2020 Nov 05. pii: S1097-2765(20)30729-2. [Epub ahead of print]80(3): 452-469.e9

Zmat3 Is a Key Splicing Regulator in the p53 Tumor Suppression Program.

Kathryn T Bieging-Rolett, Alyssa M Kaiser, David W Morgens, Anthony M Boutelle, Jose A Seoane, Eric L Van Nostrand, Changyu Zhu, Shauna L Houlihan, Stephano S Mello, Brian A Yee, Jacob McClendon, Sarah E Pierce, Ian P Winters, Mengxiong Wang, Andrew J Connolly, Scott W Lowe, Christina Curtis, Gene W Yeo, Monte M Winslow, Michael C Bassik, Laura D Attardi.

  Although TP53 is the most commonly mutated gene in human cancers, the p53-dependent transcriptional programs mediating tumor suppression remain incompletely understood. Here, to uncover critical components downstream of p53 in tumor suppression, we perform unbiased RNAi and CRISPR-Cas9-based genetic screens in vivo. These screens converge upon the p53-inducible gene Zmat3, encoding an RNA-binding protein, and we demonstrate that ZMAT3 is an important tumor suppressor downstream of p53 in mouse KrasG12D-driven lung and liver cancers and human carcinomas. Integrative analysis of the ZMAT3 RNA-binding landscape and transcriptomic profiling reveals that ZMAT3 directly modulates exon inclusion in transcripts encoding proteins of diverse functions, including the p53 inhibitors MDM4 and MDM2, splicing regulators, and components of varied cellular processes. Interestingly, these exons are enriched in NMD signals, and, accordingly, ZMAT3 broadly affects target transcript stability. Collectively, these studies reveal ZMAT3 as a novel RNA-splicing and homeostasis regulator and a key component of p53-mediated tumor suppression.

Keywords:  CRISPR screen; Mdm4; RBP; RNAi screen; Zmat3; alternative splicing; hepatocellular carcinoma; lung adenocarcinoma; p53; tumor suppression

DOI:  https://doi.org/10.1016/j.molcel.2020.10.022
Mol Cell. 2020 Oct 26. pii: S1097-2765(20)30720-6. [Epub ahead of print]

Drp1 Tubulates the ER in a GTPase-Independent Manner.

Yoshihiro Adachi, Takashi Kato, Tatsuya Yamada, Daisuke Murata, Kenta Arai, Robert V Stahelin, David C Chan, Miho Iijima, Hiromi Sesaki.

  Mitochondria are highly dynamic organelles that continuously grow, divide, and fuse. The division of mitochondria is crucial for human health. During mitochondrial division, the mechano-guanosine triphosphatase (GTPase) dynamin-related protein (Drp1) severs mitochondria at endoplasmic reticulum (ER)-mitochondria contact sites, where peripheral ER tubules interact with mitochondria. Here, we report that Drp1 directly shapes peripheral ER tubules in human and mouse cells. This ER-shaping activity is independent of GTP hydrolysis and located in a highly conserved peptide of 18 amino acids (termed D-octadecapeptide), which is predicted to form an amphipathic α helix. Synthetic D-octadecapeptide tubulates liposomes in vitro and the ER in cells. ER tubules formed by Drp1 promote mitochondrial division by facilitating ER-mitochondria interactions. Thus, Drp1 functions as a two-in-one protein during mitochondrial division, with ER tubulation and mechano-GTPase activities.

Keywords:  Drp1; mitochondria; mitochondrial division; organelle contact sites; phosphaditic acid; the endoplasmic reticulum

DOI:  https://doi.org/10.1016/j.molcel.2020.10.013
Sci Adv. 2020 Nov;pii: eabb7272. [Epub ahead of print]6(45):

Metabolic determinants of cellular fitness dependent on mitochondrial reactive oxygen species.

Hyewon Kong, Colleen R Reczek, Gregory S McElroy, Elizabeth M Steinert, Tim Wang, David M Sabatini, Navdeep S Chandel.

Mitochondria-derived reactive oxygen species (mROS) are required for the survival, proliferation, and metastasis of cancer cells. The mechanism by which mitochondrial metabolism regulates mROS levels to support cancer cells is not fully understood. To address this, we conducted a metabolism-focused CRISPR-Cas9 genetic screen and uncovered that loss of genes encoding subunits of mitochondrial complex I was deleterious in the presence of the mitochondria-targeted antioxidant mito-vitamin E (MVE). Genetic or pharmacologic inhibition of mitochondrial complex I in combination with the mitochondria-targeted antioxidants, MVE or MitoTEMPO, induced a robust integrated stress response (ISR) and markedly diminished cell survival and proliferation in vitro. This was not observed following inhibition of mitochondrial complex III. Administration of MitoTEMPO in combination with the mitochondrial complex I inhibitor phenformin decreased the leukemic burden in a mouse model of T cell acute lymphoblastic leukemia. Thus, mitochondrial complex I is a dominant metabolic determinant of mROS-dependent cellular fitness.

DOI: https://doi.org/10.1126/sciadv.abb7272
ACS Omega. 2020 Oct 27. 5(42): 27304-27313

Isolation and Metabolic Assessment of Cancer Cell Mitochondria.

Nguyen Phuoc Long, Jung Eun Min, Nguyen Hoang Anh, Sun Jo Kim, Seongoh Park, Hyung Min Kim, Sang Jun Yoon, Johan Lim, Seul Ji Lee, Sung Won Kwon.

Mitochondrial metabolism plays an essential role in various biological processes of cancer cells. Herein, we established an experimental procedure for the metabolic assessment of mitochondria in cancer cells. We examined procedures for mitochondrial isolation coupled with various mitochondrial extraction buffers in three major cancer cell lines (PANC1, A549, and MDA-MB-231) and identified a potentially optimal and generalized approach. The purity of the mitochondrial fraction isolated by the selected protocol was verified using specific protein markers of cellular components, and the ultrastructure of the isolated mitochondria was also analyzed by transmission electron microscopy. The isolation procedure, involving a bead beater for cell lysis, a modified sucrose buffer, and differential centrifugation, appeared to be a suitable method for the extraction of mitochondria from cancer cells. Electron micrographs indicated an intact two-layer membrane and inner structures of mitochondria isolated by this procedure. Metabolomic and lipidomic analyses were conducted to examine the metabolic phenotypes of the mitochondria-enriched fractions and associated bulk cancer cells. A total of 44 metabolites, including malate and succinate, occurred at significantly higher levels in the mitochondrial fractions, whereas 51 metabolites, including citrate, oxaloacetate, and fumarate of the Krebs cycle and the oncometabolites glutamine and glutamate, were reduced in mitochondria compared to that in the corresponding bulk cells of PANC1. Similar patterns were observed in mitochondria and bulk cells of MDA-MB-231 and A549 cell lines. A clear difference between the lipid profiles of bulk PANC1, MDA-MB-231, and A549 and corresponding mitochondrial fractions of these cell lines was detected by principal component analysis. In conclusion, we developed an experimental procedure for a large-scale metabolic assessment for suborganelle metabolic profiling and multiple omics data integration in cancer cells with broad applications.

DOI: https://doi.org/10.1021/acsomega.0c03612
Cancers (Basel). 2020 Nov 03. pii: E3237. [Epub ahead of print]12(11):

Succinate Dehydrogenase and Ribonucleic Acid Networks in Cancer and Other Diseases.

Cerena Moreno, Ruben Mercado Santos, Robert Burns, Wen Cai Zhang.

  Succinate dehydrogenase (SDH) complex connects both the tricarboxylic acid (TCA) cycle and the electron transport chain (ETC) in the mitochondria. However, SDH mutation or dysfunction-induced succinate accumulation results in multiple cancers and non-cancer diseases. The mechanistic studies show that succinate activates hypoxia response and other signal pathways via binding to 2-oxoglutarate-dependent oxygenases and succinate receptors. Recently, the increasing knowledge of ribonucleic acid (RNA) networks, including non-coding RNAs, RNA editors, and RNA modifiers has expanded our understanding of the interplay between SDH and RNA networks in cancer and other diseases. Here, we summarize recent discoveries in the RNA networks and their connections to SDH. Additionally, we discuss current therapeutics targeting SDH in both pre-clinical and clinical trials. Thus, we propose a new model of SDH-RNA network interaction and bring promising RNA therapeutics against SDH-relevant cancer and other diseases.

Keywords:  RNA-editing; RNA-modification; cancer; disease; electron transport chain; metabolism; non-coding RNA; reactive oxygen species; succinate dehydrogenase; tricarboxylic acid cycle

DOI:  https://doi.org/10.3390/cancers12113237
Cell. 2020 Nov 03. pii: S0092-8674(20)31380-5. [Epub ahead of print]

Cellular Control of Viscosity Counters Changes in Temperature and Energy Availability.

Laura B Persson, Vardhaan S Ambati, Onn Brandman.

  Cellular functioning requires the orchestration of thousands of molecular interactions in time and space. Yet most molecules in a cell move by diffusion, which is sensitive to external factors like temperature. How cells sustain complex, diffusion-based systems across wide temperature ranges is unknown. Here, we uncover a mechanism by which budding yeast modulate viscosity in response to temperature and energy availability. This "viscoadaptation" uses regulated synthesis of glycogen and trehalose to vary the viscosity of the cytosol. Viscoadaptation functions as a stress response and a homeostatic mechanism, allowing cells to maintain invariant diffusion across a 20°C temperature range. Perturbations to viscoadaptation affect solubility and phase separation, suggesting that viscoadaptation may have implications for multiple biophysical processes in the cell. Conditions that lower ATP trigger viscoadaptation, linking energy availability to rate regulation of diffusion-controlled processes. Viscoadaptation reveals viscosity to be a tunable property for regulating diffusion-controlled processes in a changing environment.

Keywords:  ATP; diffusion; glycogen; heat shock; homeostasis; phase separation; starvation; stress response; trehalose; viscosity

DOI:  https://doi.org/10.1016/j.cell.2020.10.017
Nat Metab. 2020 Nov 02.

Loss of metabolic plasticity underlies metformin toxicity in aged Caenorhabditis elegans.

Lilia Espada, Alexander Dakhovnik, Prerana Chaudhari, Asya Martirosyan, Laura Miek, Tetiana Poliezhaieva, Yvonne Schaub, Ashish Nair, Nadia Döring, Norman Rahnis, Oliver Werz, Andreas Koeberle, Joanna Kirkpatrick, Alessandro Ori, Maria A Ermolaeva.

Current clinical trials are testing the life-extending benefits of the diabetes drug metformin in healthy individuals without diabetes. However, the metabolic response of a non-diabetic cohort to metformin treatment has not been studied. Here, we show in C. elegans and human primary cells that metformin shortens lifespan when provided in late life, contrary to its positive effects in young organisms. We find that metformin exacerbates ageing-associated mitochondrial dysfunction, causing respiratory failure. Age-related failure to induce glycolysis and activate the dietary-restriction-like mobilization of lipid reserves in response to metformin result in lethal ATP exhaustion in metformin-treated aged worms and late-passage human cells, which can be rescued by ectopic stabilization of cellular ATP content. Metformin toxicity is alleviated in worms harbouring disruptions in insulin-receptor signalling, which show enhanced resilience to mitochondrial distortions at old age. Together, our data show that metformin induces deleterious changes of conserved metabolic pathways in late life, which could bring into question its benefits for older individuals without diabetes.

DOI: https://doi.org/10.1038/s42255-020-00307-1
Cancer Cell. 2020 Oct 28. pii: S1535-6108(20)30542-0. [Epub ahead of print]

Molecular Subsets in Renal Cancer Determine Outcome to Checkpoint and Angiogenesis Blockade.

Robert J Motzer, Romain Banchereau, Habib Hamidi, Thomas Powles, David McDermott, Michael B Atkins, Bernard Escudier, Li-Fen Liu, Ning Leng, Alexander R Abbas, Jinzhen Fan, Hartmut Koeppen, Jennifer Lin, Susheela Carroll, Kenji Hashimoto, Sanjeev Mariathasan, Marjorie Green, Darren Tayama, Priti S Hegde, Christina Schiff, Mahrukh A Huseni, Brian Rini.

  Integrated multi-omics evaluation of 823 tumors from advanced renal cell carcinoma (RCC) patients identifies molecular subsets associated with differential clinical outcomes to angiogenesis blockade alone or with a checkpoint inhibitor. Unsupervised transcriptomic analysis reveals seven molecular subsets with distinct angiogenesis, immune, cell-cycle, metabolism, and stromal programs. While sunitinib and atezolizumab + bevacizumab are effective in subsets with high angiogenesis, atezolizumab + bevacizumab improves clinical benefit in tumors with high T-effector and/or cell-cycle transcription. Somatic mutations in PBRM1 and KDM5C associate with high angiogenesis and AMPK/fatty acid oxidation gene expression, while CDKN2A/B and TP53 alterations associate with increased cell-cycle and anabolic metabolism. Sarcomatoid tumors exhibit lower prevalence of PBRM1 mutations and angiogenesis markers, frequent CDKN2A/B alterations, and increased PD-L1 expression. These findings can be applied to molecularly stratify patients, explain improved outcomes of sarcomatoid tumors to checkpoint blockade versus antiangiogenics alone, and develop personalized therapies in RCC and other indications.

Keywords:  CDKN2A/B; PBRM1; PD-L1; VHL; atezolizumab; bevacizumab; checkpoint blockade; integrated genomics; renal cell carcinoma; sarcomatoid; sunitinib

DOI:  https://doi.org/10.1016/j.ccell.2020.10.011
Cell Metab. 2020 Nov 03. pii: S1550-4131(20)30549-0. [Epub ahead of print]32(5): 699-701

A Tug-of-War Over Methionine.

Ke Xu, Amy Shyu, Ming O Li.

Nutrient acquisition and metabolism are integral components of cell growth, proliferation, and differentiation programs. In a recent study in Nature, Bian et al. (2020) revealed that cancer cells outcompete T cells for methionine uptake, resulting in diminished SAM production, attenuated H3K79 dimethylation, decreased STAT5 expression, and impaired T cell immunity to cancer.

DOI: https://doi.org/10.1016/j.cmet.2020.10.016
Mol Cell. 2020 Nov 05. pii: S1097-2765(20)30687-0. [Epub ahead of print]80(3): 437-451.e6

Amino Acids Enhance Polyubiquitination of Rheb and Its Binding to mTORC1 by Blocking Lysosomal ATXN3 Deubiquitinase Activity.

Yao Yao, Sungki Hong, Takayuki Ikeda, Hiroyuki Mori, Ormond A MacDougald, Shigeyuki Nada, Masato Okada, Ken Inoki.

  Amino-acid-induced lysosomal mechanistic target of rapamycin complex 1 (mTORC1) localization through the Rag GTPases is a critical step for its activation by Rheb GTPase. However, how the mTORC1 interacts with Rheb on the lysosome remains elusive. We report that amino acids enhance the polyubiquitination of Rheb (Ub-Rheb), which shows a strong binding preference for mTORC1 and supports its activation, while the Ub-Rheb is subjected to subsequent degradation. Mechanistically, we identified ATXN3 as a Ub-Rheb deubiquitinase whose lysosomal localization is blocked by active Rag heterodimer in response to amino acid stimulation. Consistently, cells lacking functional Rag heterodimer on the lysosome accumulate Ub-Rheb, and blockade of its degradation instigates robust lysosomal mTORC1 localization and its activation without the Ragulator-Rag system. Thus, polyubiquitination of Rheb is an important post-translational modification, which facilitates the binding of mTORC1 to Rheb on the lysosome and is another crosstalk between the amino acid and growth factor signaling for mTORC1 activation.

Keywords:  ATXN3; Rag; Ragulator; Rheb; amino acids; deubiquitination; lysosome; mTORC1; ubiquitin

DOI:  https://doi.org/10.1016/j.molcel.2020.10.004
J Clin Invest. 2020 Nov 03. pii: 133371. [Epub ahead of print]

Mitochondrial dysfunction in inflammatory bowel disease alters intestinal epithelial metabolism of hepatic acylcarnitines.

Sarah A Smith, Sayaka A Ogawa, Lillian Chau, Kelly A Whelan, Kathryn E Hamilton, Jie Chen, Lu Tan, Eric Z Chen, Sue Keilbaugh, Franz Fogt, Meenakshi Bewtra, Jonathan Braun, Ramnik J Xavier, Clary B Clish, Barry Slaff, Aalim M Weljie, Frederic D Bushman, James D Lewis, Hongzhe Li, Stephen R Master, Michael J Bennett, Hiroshi Nakagawa, Gary D Wu.

  As the interface between the gut microbiota and the mucosal immune system, there has been great interest in the maintenance of colonic epithelial integrity through mitochondrial oxidation of butyrate, a short-chain fatty acid produced by the gut microbiota. Herein, we showed that the intestinal epithelium can also oxidize long-chain fatty acids, and that luminally-delivered acylcarnitines in bile can be consumed via apical absorption by the intestinal epithelium resulting in mitochondrial oxidation. Finally, intestinal inflammation led to mitochondrial dysfunction in the apical domain of the surface epithelium that may reduce the consumption of fatty acids, contributing to higher concentrations of fecal acylcarnitines in murine Citrobacter rodentium-induced colitis and human inflammatory bowel disease. These results emphasized the importance of both the gut microbiota and the liver in the delivery of energy substrates for mitochondrial metabolism by the intestinal epithelium.

Keywords:  Fatty acid oxidation; Gastroenterology; Inflammation; Inflammatory bowel disease; Mitochondria

DOI:  https://doi.org/10.1172/JCI133371
FEBS Lett. 2020 Nov 07.

Mitochondrial disorders of the oxphos system.

Erika Fernandez-Vizarra, Massimo Zeviani.

  Mitochondrial disorders are amongst the most frequent inborn errors of metabolism, their primary cause being the dysfunction of the oxidative phosphorylation system (OXPHOS). OXPHOS is composed of the electron transport chain (ETC), formed by four multimeric enzymes and two mobile electron carriers, plus an ATP synthase (also called complex V). The ETC performs the redox reactions involved in cellular respiration while generating the proton motive force used by complex V to synthesize ATP. OXPHOS biogenesis involves multiple steps, starting from the expression of genes encoded in physically separated genomes, namely the mitochondrial and nuclear DNA, to the coordinated assembly of components and cofactors building each individual complex and eventually the supercomplexes. The genetic cause underlying around half of the diagnosed mitochondrial disease cases is currently known. Many of these cases result from pathogenic variants in genes encoding structural subunits or additional factors directly involved in the assembly of the ETC complexes. Here we review the historical and most recent findings concerning the clinical phenotypes and the molecular pathological mechanisms underlying this particular group of disorders.

Keywords:  ATP production; Mitochondrial respiratory chain; biogenesis of the respiratory chain; mitochondrial disease; mitochondrial electrochemical gradient; mitochondrial potential; mitochondrial proton pumping; oxidative phosphorylation; respiratory complex; respiratory supercomplex

DOI:  https://doi.org/10.1002/1873-3468.13995
Cell Metab. 2020 Nov 03. pii: S1550-4131(20)30547-7. [Epub ahead of print]32(5): 697-698

A Selective Sweep Conceals a MicroRNA with Broad Metabolic Effects.

Iain Mathieson, Struan F A Grant.

The need for discovering new genes driving metabolic disease susceptibility is clear; even clearer is the need for their subsequent functional characterization. A new paper reports a role for miR-128-1 in metabolic control through a series of elegant mouse studies, and an intriguing hypothesis about its "thrifty" role in metabolism.

DOI: https://doi.org/10.1016/j.cmet.2020.10.014
Cell Mol Life Sci. 2020 Nov 03.

Regulation of peroxisomal trafficking and distribution.

Christian Covill-Cooke, Viktoriya S Toncheva, Josef T Kittler.

  Peroxisomes are organelles that perform a wide range of essential metabolic processes. To ensure that peroxisomes are optimally positioned in the cell, they must be transported by both long- and short-range trafficking events in response to cellular needs. Here, we review our current understanding of the mechanisms by which the cytoskeleton and organelle contact sites alter peroxisomal distribution. Though the focus of the review is peroxisomal transport in mammalian cells, findings from flies and fungi are used for comparison and to inform the gaps in our understanding. Attention is given to the apparent overlap in regulatory mechanisms for mitochondrial and peroxisomal trafficking, along with the recently discovered role of the mitochondrial Rho-GTPases, Miro, in peroxisomal dynamics. Moreover, we outline and discuss the known pathological and pharmacological conditions that perturb peroxisomal positioning. We conclude by highlighting several gaps in our current knowledge and suggest future directions that require attention.

Keywords:  Actin; Disease; Dynein; Kinesin; Microtubule

DOI:  https://doi.org/10.1007/s00018-020-03687-5
Carcinogenesis. 2020 Nov 04. pii: bgaa114. [Epub ahead of print]

DNA Damage and Mitochondria in Cancer and Aging.

Jaimin Patel, Beverly A Baptiste, Edward Kim, Mansoor Hussain, Deborah L Croteau, Vilhelm A Bohr.

Age and DNA repair deficiencies are strong risk factors for developing cancer. This is reflected in the comorbidity of cancer with premature aging diseases associated with DNA damage repair deficiencies. Recent research has suggested that DNA damage accumulation, telomere dysfunction, and the accompanying mitochondrial dysfunction exacerbate the aging process and may increase the risk of cancer development. Thus, an area of interest in both cancer and aging research is the elucidation of the dynamic crosstalk between the nucleus and the mitochondria. In this review, we discuss current research on aging and cancer with specific focus on the role of mitochondrial dysfunction in cancer and aging as well as how nuclear to mitochondrial DNA damage signaling may be a driving factor in the increased cancer incidence with aging. We suggest that therapeutic interventions aimed at induction of autophagy and mediation of nuclear to mitochondrial signaling may provide a mechanism for healthier aging and reduced tumorigenesis.

DOI: https://doi.org/10.1093/carcin/bgaa114
Int J Mol Sci. 2020 Oct 31. pii: E8157. [Epub ahead of print]21(21):

ER-Mitochondria Contact Sites Reporters: Strengths and Weaknesses of the Available Approaches.

Flavia Giamogante, Lucia Barazzuol, Marisa Brini, Tito Calì.

  Organelle intercommunication represents a wide area of interest. Over the last few decades, increasing evidence has highlighted the importance of organelle contact sites in many biological processes including Ca2+ signaling, lipid biosynthesis, apoptosis, and autophagy but also their involvement in pathological conditions. ER-mitochondria tethering is one of the most investigated inter-organelle communications and it is differently modulated in response to several cellular conditions including, but not limited to, starvation, Endoplasmic Reticulum (ER) stress, and mitochondrial shape modifications. Despite many studies aiming to understand their functions and how they are perturbed under different conditions, approaches to assess organelle proximity are still limited. Indeed, better visualization and characterization of contact sites remain a fascinating challenge. The aim of this review is to summarize strengths and weaknesses of the available methods to detect and quantify contact sites, with a main focus on ER-mitochondria tethering.

Keywords:  ER–mitochondria tethering; SPLICS; organelle contact sites; split-GFP

DOI:  https://doi.org/10.3390/ijms21218157
EMBO Rep. 2020 Nov 05. 21(11): e51652

Iron out, mitophagy in! A way to slow down hepatocellular carcinoma.

Yahyah Aman, Shuqin Cao, Evandro F Fang.

Mitochondrial homeostasis is necessary for the maintenance of cellular function and neuronal survival. Mitochondrial quality is tightly regulated by mitophagy, in which defective/superfluous mitochondria are degraded and recycled. Here, Hara et al demonstrate that induction of mitophagy via iron depletion suppresses the development of hepatocellular carcinoma (HCC). This work suggests turning up mitophagy as a potential therapeutic strategy against liver cancer.

DOI: https://doi.org/10.15252/embr.202051652
Mol Genet Metab. 2020 Oct 13. pii: S1096-7192(20)30205-5. [Epub ahead of print]

Biallelic mutations in NDUFA8 cause complex I deficiency in two siblings with favorable clinical evolution.

Frederic Tort, Estibaliz Barredo, Ranjani Parthasarathy, Olatz Ugarteburu, Xenia Ferrer-Cortès, Judit García-Villoria, Laura Gort, Adrián González-Quintana, Miguel A Martín, Erika Fernández-Vizarra, Massimo Zeviani, Antonia Ribes.

  Isolated complex I (CI) deficiency is the most common cause of oxidative phosphorylation (OXPHOS) dysfunction. Whole-exome sequencing identified biallelic mutations in NDUFA8 (c.[293G > T]; [293G > T], encoding for an accessory subunit of CI, in two siblings with a favorable clinical evolution. The individuals reported here are practically asymptomatic, with the exception of slight failure to thrive and some language difficulties at the age of 6 and 9 years, respectively. These observations are remarkable since the vast majority of patients with CI deficiency, including the only NDUFA8 patient reported so far, showed an extremely poor clinical outcome. Western blot studies demonstrated that NDUFA8 protein was strongly reduced in the patients' fibroblasts and muscle extracts. In addition, there was a marked and specific decrease in the steady-state levels of CI subunits. BN-PAGE demonstrated an isolated defect in the assembly and the activity of CI with impaired supercomplexes formation and abnormal accumulation of CI subassemblies. Confocal microscopy analysis in fibroblasts showed rounder mitochondria and diminished branching degree of the mitochondrial network. Functional complementation studies demonstrated disease-causality for the identified mutation as lentiviral transduction with wild-type NDUFA8 cDNA restored the steady-state levels of CI subunits and completely recovered the deficient enzymatic activity in immortalized mutant fibroblasts. In summary, we provide additional evidence of the involvement of NDUFA8 as a mitochondrial disease-causing gene associated with altered mitochondrial morphology, CI deficiency, impaired supercomplexes formation, and very mild progression of the disease.

Keywords:  Complex I; Exome; Mitochondrial morphology; NDUFA8; OXPHOS; Supercomplexes

DOI:  https://doi.org/10.1016/j.ymgme.2020.10.005
Annu Rev Physiol. 2020 Nov 06.

Ceramides in Metabolism: Key Lipotoxic Players.

Bhagirath Chaurasia, Scott A Summers.

The global prevalence of metabolic diseases such as type 2 diabetes mellitus, steatohepatitis, myocardial infarction, and stroke has increased dramatically over the past two decades. These obesity-fueled disorders result, in part, from the aberrant accumulation of harmful lipid metabolites in tissues not suited for lipid storage (e.g., the liver, vasculature, heart, and pancreatic beta-cells). Among the numerous lipid subtypes that accumulate, sphingolipids such as ceramides are particularly impactful, as they elicit the selective insulin resistance, dyslipidemia, and ultimately cell death that underlie nearly all metabolic disorders. This review summarizes recent findings on the regulatory pathways controlling ceramide production, the molecular mechanisms linking the lipids to these discrete pathogenic events, and exciting attempts to develop therapeutics to reduce ceramide levels to combat metabolic disease. Expected final online publication date for the Annual Review of Physiology, Volume 83 is February 10, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

DOI: https://doi.org/10.1146/annurev-physiol-031620-093815
Nat Rev Nephrol. 2020 Nov 03.

Clear cell renal cell carcinoma ontogeny and mechanisms of lethality.

Eric Jonasch, Cheryl Lyn Walker, W Kimryn Rathmell.

The molecular features that define clear cell renal cell carcinoma (ccRCC) initiation and progression are being increasingly defined. The TRACERx Renal studies and others that have described the interaction between tumour genomics and remodelling of the tumour microenvironment provide important new insights into the molecular drivers underlying ccRCC ontogeny and progression. Our understanding of common genomic and chromosomal copy number abnormalities in ccRCC, including chromosome 3p loss, provides a mechanistic framework with which to organize these abnormalities into those that drive tumour initiation events, those that drive tumour progression and those that confer lethality. Truncal mutations in ccRCC, including those in VHL, SET2, PBRM1 and BAP1, may engender genomic instability and promote defects in DNA repair pathways. The molecular features that arise from these defects enable categorization of ccRCC into clinically and therapeutically relevant subtypes. Consideration of the interaction of these subtypes with the tumour microenvironment reveals that specific mutations seem to modulate immune cell populations in ccRCC tumours. These findings present opportunities for disease prevention, early detection, prognostication and treatment.

DOI: https://doi.org/10.1038/s41581-020-00359-2
Nat Commun. 2020 11 03. 11(1): 5559

A trimeric Rab7 GEF controls NPC1-dependent lysosomal cholesterol export.

Dick J H van den Boomen, Agata Sienkiewicz, Ilana Berlin, Marlieke L M Jongsma, Daphne M van Elsland, J Paul Luzio, Jacques J C Neefjes, Paul J Lehner.

Cholesterol import in mammalian cells is mediated by the LDL receptor pathway. Here, we perform a genome-wide CRISPR screen using an endogenous cholesterol reporter and identify >100 genes involved in LDL-cholesterol import. We characterise C18orf8 as a core subunit of the mammalian Mon1-Ccz1 guanidine exchange factor (GEF) for Rab7, required for complex stability and function. C18orf8-deficient cells lack Rab7 activation and show severe defects in late endosome morphology and endosomal LDL trafficking, resulting in cellular cholesterol deficiency. Unexpectedly, free cholesterol accumulates within swollen lysosomes, suggesting a critical defect in lysosomal cholesterol export. We find that active Rab7 interacts with the NPC1 cholesterol transporter and licenses lysosomal cholesterol export. This process is abolished in C18orf8-, Ccz1- and Mon1A/B-deficient cells and restored by a constitutively active Rab7. The trimeric Mon1-Ccz1-C18orf8 (MCC) GEF therefore plays a central role in cellular cholesterol homeostasis coordinating Rab7 activation, endosomal LDL trafficking and NPC1-dependent lysosomal cholesterol export.

DOI: https://doi.org/10.1038/s41467-020-19032-0
Cell Metab. 2020 Nov 03. pii: S1550-4131(20)30539-8. [Epub ahead of print]32(5): 751-766.e11

Multi-Tissue Acceleration of the Mitochondrial Phosphoenolpyruvate Cycle Improves Whole-Body Metabolic Health.

Abudukadier Abulizi, Rebecca L Cardone, Romana Stark, Sophie L Lewandowski, Xiaojian Zhao, Joelle Hillion, Lingjun Ma, Raghav Sehgal, Tiago C Alves, Craig Thomas, Charles Kung, Bei Wang, Stephan Siebel, Zane B Andrews, Graeme F Mason, Jesse Rinehart, Matthew J Merrins, Richard G Kibbey.

  The mitochondrial GTP (mtGTP)-dependent phosphoenolpyruvate (PEP) cycle couples mitochondrial PEPCK (PCK2) to pyruvate kinase (PK) in the liver and pancreatic islets to regulate glucose homeostasis. Here, small molecule PK activators accelerated the PEP cycle to improve islet function, as well as metabolic homeostasis, in preclinical rodent models of diabetes. In contrast, treatment with a PK activator did not improve insulin secretion in pck2-/- mice. Unlike other clinical secretagogues, PK activation enhanced insulin secretion but also had higher insulin content and markers of differentiation. In addition to improving insulin secretion, acute PK activation short-circuited gluconeogenesis to reduce endogenous glucose production while accelerating red blood cell glucose turnover. Four-week delivery of a PK activator in vivo remodeled PK phosphorylation, reduced liver fat, and improved hepatic and peripheral insulin sensitivity in HFD-fed rats. These data provide a preclinical rationale for PK activation to accelerate the PEP cycle to improve metabolic homeostasis and insulin sensitivity.

Keywords:  anaplerosis; cataplerosis; fatty liver; human islets; insulin resistance; insulin secretion; mitochondrial GTP; mitochondrial PEPCK; phosphoenolpyruvate cycle; pyruvate kinase

DOI:  https://doi.org/10.1016/j.cmet.2020.10.006
Elife. 2020 Nov 03. pii: e60264. [Epub ahead of print]9

Protein phase separation and its role in tumorigenesis.

Shan Jiang, Johan Bourghardt Fagman, Changyan Chen, Simon Alberti, Beidong Liu.

  Cancer is a disease characterized by uncontrolled cell proliferation, but the precise pathological mechanisms underlying tumorigenesis often remain to be elucidated. In recent years, condensates formed by phase separation have emerged as a new principle governing the organization and functional regulation of cells. Increasing evidence links cancer-related mutations to aberrantly altered condensate assembly, suggesting that condensates play a key role in tumorigenesis. In this review, we summarize and discuss the latest progress on the formation, regulation, and function of condensates. Special emphasis is given to emerging evidence regarding the link between condensates and the initiation and progression of cancers.

Keywords:  C. elegans; E. coli; S. cerevisiae; biomolecular condensate; cancer; cancer biology; human; membraneless organelle; mouse; phase separation

DOI:  https://doi.org/10.7554/eLife.60264
Sci Rep. 2020 Nov 03. 10(1): 18941

Mito Hacker: a set of tools to enable high-throughput analysis of mitochondrial network morphology.

Ali Rohani, Jennifer A Kashatus, Dane T Sessions, Salma Sharmin, David F Kashatus.

Mitochondria are highly dynamic organelles that can exhibit a wide range of morphologies. Mitochondrial morphology can differ significantly across cell types, reflecting different physiological needs, but can also change rapidly in response to stress or the activation of signaling pathways. Understanding both the cause and consequences of these morphological changes is critical to fully understanding how mitochondrial function contributes to both normal and pathological physiology. However, while robust and quantitative analysis of mitochondrial morphology has become increasingly accessible, there is a need for new tools to generate and analyze large data sets of mitochondrial images in high throughput. The generation of such datasets is critical to fully benefit from rapidly evolving methods in data science, such as neural networks, that have shown tremendous value in extracting novel biological insights and generating new hypotheses. Here we describe a set of three computational tools, Cell Catcher, Mito Catcher and MiA, that we have developed to extract extensive mitochondrial network data on a single-cell level from multi-cell fluorescence images. Cell Catcher automatically separates and isolates individual cells from multi-cell images; Mito Catcher uses the statistical distribution of pixel intensities across the mitochondrial network to detect and remove background noise from the cell and segment the mitochondrial network; MiA uses the binarized mitochondrial network to perform more than 100 mitochondria-level and cell-level morphometric measurements. To validate the utility of this set of tools, we generated a database of morphological features for 630 individual cells that encode 0, 1 or 2 alleles of the mitochondrial fission GTPase Drp1 and demonstrate that these mitochondrial data could be used to predict Drp1 genotype with 87% accuracy. Together, this suite of tools enables the high-throughput and automated collection of detailed and quantitative mitochondrial structural information at a single-cell level. Furthermore, the data generated with these tools, when combined with advanced data science approaches, can be used to generate novel biological insights.

DOI: https://doi.org/10.1038/s41598-020-75899-5
Cell Metab. 2020 Oct 26. pii: S1550-4131(20)30543-X. [Epub ahead of print]

TANK-Binding Kinase 1 Regulates the Localization of Acyl-CoA Synthetase ACSL1 to Control Hepatic Fatty Acid Oxidation.

Jin Young Huh, Shannon M Reilly, Mohammad Abu-Odeh, Anne N Murphy, Sushil K Mahata, Jinyu Zhang, Yoori Cho, Jong Bae Seo, Chao-Wei Hung, Courtney R Green, Christian M Metallo, Alan R Saltiel.

  Hepatic TANK (TRAF family member associated NFκB activator)-binding kinase 1 (TBK1) activity is increased during obesity, and administration of a TBK1 inhibitor reduces fatty liver. Surprisingly, liver-specific TBK1 knockout in mice produces fatty liver by reducing fatty acid oxidation. TBK1 functions as a scaffolding protein to localize acyl-CoA synthetase long-chain family member 1 (ACSL1) to mitochondria, which generates acyl-CoAs that are channeled for β-oxidation. TBK1 is induced during fasting and maintained in the unphosphorylated, inactive state, enabling its high affinity binding to ACSL1 in mitochondria. In TBK1-deficient liver, ACSL1 is shifted to the endoplasmic reticulum to promote fatty acid re-esterification in lieu of oxidation in response to fasting, which accelerates hepatic lipid accumulation. The impaired fatty acid oxidation in TBK1-deficient hepatocytes is rescued by the expression of kinase-dead TBK1. Thus, TBK1 operates as a rheostat to direct the fate of fatty acids in hepatocytes, supporting oxidation when inactive during fasting and promoting re-esterification when activated during obesity.

Keywords:  acyl-CoA synthetase long-chain family member 1 (ACSL1); fasting; hepatic lipid metabolism; mitochondria; nonalcoholic fatty liver disease (NAFLD); re-esterification; tank-binding kinase 1 (TBK1); β-oxidation

DOI:  https://doi.org/10.1016/j.cmet.2020.10.010
Br J Cancer. 2020 Nov 04.

Genomic control of metastasis.

Saroor A Patel, Paulo Rodrigues, Ludovic Wesolowski, Sakari Vanharanta.

Metastasis remains the leading cause of cancer-associated mortality, and a detailed understanding of the metastatic process could suggest new therapeutic avenues. However, how metastatic phenotypes arise at the genomic level has remained a major open question in cancer biology. Comparative genetic studies of primary and metastatic cancers have revealed a complex picture of metastatic evolution with diverse temporal patterns and trajectories to dissemination. Whole-genome amplification is associated with metastatic cancer clones, but no metastasis-exclusive driver mutations have emerged. Instead, genetically activated oncogenic pathways that drive tumour initiation and early progression acquire metastatic traits by co-opting physiological programmes from stem cell, developmental and regenerative pathways. The functional consequences of oncogenic driver mutations therefore change via epigenetic mechanisms to promote metastasis. Increasing evidence is starting to uncover the molecular mechanisms that determine how specific oncogenic drivers interact with various physiological programmes, and what triggers their activation in support of metastasis. Detailed insight into the mechanisms that control metastasis is likely to reveal novel opportunities for intervention at different stages of metastatic progression.

DOI: https://doi.org/10.1038/s41416-020-01127-6
Cell. 2020 Oct 28. pii: S0092-8674(20)31322-2. [Epub ahead of print]

Neurons Release Serine to Support mRNA Translation in Pancreatic Cancer.

Robert S Banh, Douglas E Biancur, Keisuke Yamamoto, Albert S W Sohn, Beth Walters, Miljan Kuljanin, Ajami Gikandi, Huamin Wang, Joseph D Mancias, Robert J Schneider, Michael E Pacold, Alec C Kimmelman.

  Pancreatic ductal adenocarcinoma (PDAC) tumors have a nutrient-poor, desmoplastic, and highly innervated tumor microenvironment. Although neurons can release stimulatory factors to accelerate PDAC tumorigenesis, the metabolic contribution of peripheral axons has not been explored. We found that peripheral axons release serine (Ser) to support the growth of exogenous Ser (exSer)-dependent PDAC cells during Ser/Gly (glycine) deprivation. Ser deprivation resulted in ribosomal stalling on two of the six Ser codons, TCC and TCT, and allowed the selective translation and secretion of nerve growth factor (NGF) by PDAC cells to promote tumor innervation. Consistent with this, exSer-dependent PDAC tumors grew slower and displayed enhanced innervation in mice on a Ser/Gly-free diet. Blockade of compensatory neuronal innervation using LOXO-101, a Trk-NGF inhibitor, further decreased PDAC tumor growth. Our data indicate that axonal-cancer metabolic crosstalk is a critical adaptation to support PDAC growth in nutrient poor environments.

Keywords:  mRNA translation; metabolic crosstalk; neurons; pancreatic cancer; serine

DOI:  https://doi.org/10.1016/j.cell.2020.10.016
Mol Cell. 2020 Oct 26. pii: S1097-2765(20)30693-6. [Epub ahead of print]

3D Culture Models with CRISPR Screens Reveal Hyperactive NRF2 as a Prerequisite for Spheroid Formation via Regulation of Proliferation and Ferroptosis.

Nobuaki Takahashi, Patricia Cho, Laura M Selfors, Hendrik J Kuiken, Roma Kaul, Takuro Fujiwara, Isaac S Harris, Tian Zhang, Steven P Gygi, Joan S Brugge.

  Cancer-associated mutations that stabilize NRF2, an oxidant defense transcription factor, are predicted to promote tumor development. Here, utilizing 3D cancer spheroid models coupled with CRISPR-Cas9 screens, we investigate the molecular pathogenesis mediated by NRF2 hyperactivation. NRF2 hyperactivation was necessary for proliferation and survival in lung tumor spheroids. Antioxidant treatment rescued survival but not proliferation, suggesting the presence of distinct mechanisms. CRISPR screens revealed that spheroids are differentially dependent on the mammalian target of rapamycin (mTOR) for proliferation and the lipid peroxidase GPX4 for protection from ferroptosis of inner, matrix-deprived cells. Ferroptosis inhibitors blocked death from NRF2 downregulation, demonstrating a critical role of NRF2 in protecting matrix-deprived cells from ferroptosis. Interestingly, proteomics analyses show global enrichment of selenoproteins, including GPX4, by NRF2 downregulation, and targeting NRF2 and GPX4 killed spheroids overall. These results illustrate the value of spheroid culture in revealing environmental or spatial differential dependencies on NRF2 and reveal exploitable vulnerabilities of NRF2-hyperactivated tumors.

Keywords:  oxidative stress, cancer, cell death, ferroptosis, 3D culture, NRF2, CRISPR screening, selenoprotein, GPX4

DOI:  https://doi.org/10.1016/j.molcel.2020.10.010