bims-mibica 2021-11-21 papers

bims-mibica

Biomed News

on Mitochondrial bioenergetics in cancer

Issue of 2021–11–21
forty papers selected by
Kelsey Fisher-Wellman, East Carolina University

Papillary thyroid carcinoma tall cell variant shares accumulation of mitochondria, mitochondrial DNA mutations, and loss of oxidative phosphorylation complex I integrity with oncocytic tumors.
Interplay between Mitochondrial Metabolism and Cellular Redox State Dictates Cancer Cell Survival.
Metabolic resistance to the inhibition of mitochondrial transcription revealed by CRISPR-Cas9 screen.
Age-related changes in the energy of human mesenchymal stem cells.
Balancing of mitochondrial translation through METTL8-mediated m3C modification of mitochondrial tRNAs.
Beyond mitophagy: mitochondrial-derived vesicles can get the job done!
Intercellular nanotubes mediate mitochondrial trafficking between cancer and immune cells.
Methionine synthase is essential for cancer cell proliferation in physiological folate environments.
The role of mitochondrial reactive oxygen species in insulin resistance.
DLST-dependence dictates metabolic heterogeneity in TCA-cycle usage among triple-negative breast cancer.
Serine palmitoyltransferase assembles at ER-mitochondria contact sites.
Metformin treatment in old rats and effects on mitochondrial integrity.
Mitophagy Mediates Metabolic Reprogramming of Induced Pluripotent Stem Cells Undergoing Endothelial Differentiation.
NME6 is a phosphotransfer-inactive, monomeric NME/NDPK family member and functions in complexes at the interface of mitochondrial inner membrane and matrix.
The metabolic growth limitations of petite cells lacking the mitochondrial genome.
AKT1/HK2 Axis-mediated Glucose Metabolism: A Novel Therapeutic Target of Sulforaphane in Bladder Cancer.
The sulfiredoxin-peroxiredoxin redox system regulates the stemness and survival of colon cancer stem cells.
Histone N-terminal acetyltransferase NAA40 links one-carbon metabolism to chemoresistance.
AMBRA1 regulates mitophagy by interacting with ATAD3A and promoting PINK1 stability.
The role of the electron transport chain in immunity.
Optical/electrochemical methods for detecting mitochondrial energy metabolism.
Methionine synthase supports tumour tetrahydrofolate pools.
Cross-comparison of systemic and tissue-specific metabolomes in a mouse model of Leigh syndrome.
Hydrogen sulfide blocks HIV rebound by maintaining mitochondrial bioenergetics and redox homeostasis.
The autophagy protein ATG9A enables lipid mobilization from lipid droplets.
Comprehensive chemical proteomics analyses reveal that the new TRi-1 and TRi-2 compounds are more specific thioredoxin reductase 1 inhibitors than auranofin.
Folliculin impairs breast tumor growth by repressing TFE3-dependent induction of the Warburg effect and angiogenesis.
Cancer cells hijack T-cell mitochondria.
Contribution of branched chain amino acids to energy production and mevalonate synthesis in cancer cells.
Mapping protein carboxymethylation sites provides insights into their role in proteostasis and cell proliferation.
Widespread use of unconventional targeting signals in mitochondrial ribosome proteins.
High-Resolution Respirometry to assess Bioenergetics in Cells and Tissues using Chamber- and Plate-Based Respirometers.
Emergence of β1 integrin-deficient breast tumours from dormancy involves both inactivation of p53 and generation of a permissive tumour microenvironment.
Class I HDAC Modulates Angiotensin II-induced Fibroblast Migration and Mitochondrial Overactivity.
Impact of senescence on the transdifferentiation process of human hepatic progenitor-like cells.
Implementing a functional precision medicine tumor board for acute myeloid leukemia.
PP2A is a therapeutically targetable driver of cell fate decisions via a c-Myc/p21 axis in Acute Myeloid Leukemia.
Selectively down-regulated PD-L1 by albumin-phenformin nanoparticles mediated mitochondrial dysfunction to stimulate tumor-specific immunological response for enhanced mild-temperature photothermal efficacy.
Rational design of self-assembled mitochondria- targeting lytic peptide conjugates with enhanced tumor selectivity.
Fasting-mimicking diet is safe and reshapes metabolism and antitumor immunity in cancer patients.

J Pathol Clin Res. 2021 Nov 17.

Papillary thyroid carcinoma tall cell variant shares accumulation of mitochondria, mitochondrial DNA mutations, and loss of oxidative phosphorylation complex I integrity with oncocytic tumors.

Oleksiy Tsybrovskyy, Monica De Luise, Dario de Biase, Leonardo Caporali, Claudio Fiorini, Giuseppe Gasparre, Valerio Carelli, Dominik Hackl, Larisa Imamovic, Silke Haim, Manuel Sobrinho-Simões, Giovanni Tallini.

  Papillary thyroid carcinoma tall cell variant (PTC-TCV), a form of PTC regarded as an aggressive subtype, shares several morphologic features with oncocytic tumors. Pathogenic homoplasmic/highly heteroplasmic somatic mitochondrial DNA (mtDNA) mutations, usually affecting oxidative phosphorylation (OXPHOS) complex I subunits, are hallmarks of oncocytic cells. To clarify the relationship between PTC-TCV and oncocytic thyroid tumors, 17 PTC-TCV and 16 PTC non-TCV controls (cPTC) were subjected to: (1) transmission electron microscopy (TEM) to assess mitochondria accumulation, (2) next-generation sequencing to analyze mtDNA and nuclear genes frequently mutated in thyroid carcinoma, and (3) immunohistochemistry (IHC) for prohibitin and complex I subunit NDUFS4 to evaluate OXPHOS integrity. TEM showed replacement of cytoplasm by mitochondria in PTC-TCV but not in cPTC cells. All 17 PTC-TCV had at least one mtDNA mutation, totaling 21 mutations; 3/16 cPTC (19%) had mtDNA mutations (p < 0.001). PTC-TCV mtDNA mutations were homoplasmic/highly heteroplasmic, 16/21 (76%) mapping within mtDNA-encoded complex I subunits. MtDNA mutations in cPTC were homoplasmic in 2 cases and at low heteroplasmy in the third case, 2/3 mapping to mtDNA-encoded complex I subunits; 2/3 cPTC with mtDNA mutations had small tall cell subpopulations. PTC-TCV showed strong prohibitin expression and cPTC low-level expression, consistent with massive and limited mitochondrial content, respectively. All 17 PTC-TCV showed NDUFS4 loss (partial or complete) and 3 of 16 cPTC (19%) had (partial) NDUFS4 loss, consistent with lack of complex I integrity in PTC-TCV (p < 0.001). IHC loss of NDUFS4 was associated with mtDNA mutations (p < 0.001). Four BRAF V600E mutated PTCs had loss of NDUSF4 expression limited to neoplastic cell subpopulations with tall cell features, indicating that PTCs first acquire BRAF V600E and then mtDNA mutations. Similar to oncocytic thyroid tumors, PTC-TCV is characterized by mtDNA mutations, massive accumulation of mitochondria, and loss of OXPHOS integrity. IHC loss of NDUFS-4 can be used as a surrogate marker for OXPHOS disruption and to reliably diagnose PTC-TCV.

Keywords:  BRAF V600E; mitochondria; mitochondrial DNA mutations; oncocytic tumors; papillary thyroid carcinoma; tall cell variant papillary carcinoma; thyroid tumor diagnosis

DOI:  https://doi.org/10.1002/cjp2.247
Oxid Med Cell Longev. 2021 ;2021 1341604

Interplay between Mitochondrial Metabolism and Cellular Redox State Dictates Cancer Cell Survival.

Brittney Joy-Anne Foo, Jie Qing Eu, Jayshree L Hirpara, Shazib Pervaiz.

Mitochondria are the main powerhouse of the cell, generating ATP through the tricarboxylic acid cycle (TCA) and oxidative phosphorylation (OXPHOS), which drives myriad cellular processes. In addition to their role in maintaining bioenergetic homeostasis, changes in mitochondrial metabolism, permeability, and morphology are critical in cell fate decisions and determination. Notably, mitochondrial respiration coupled with the passage of electrons through the electron transport chain (ETC) set up a potential source of reactive oxygen species (ROS). While low to moderate increase in intracellular ROS serves as secondary messenger, an overwhelming increase as a result of either increased production and/or deficient antioxidant defenses is detrimental to biomolecules, cells, and tissues. Since ROS and mitochondria both regulate cell fate, attention has been drawn to their involvement in the various processes of carcinogenesis. To that end, the link between a prooxidant milieu and cell survival and proliferation as well as a switch to mitochondrial OXPHOS associated with recalcitrant cancers provide testimony for the remarkable metabolic plasticity as an important hallmark of cancers. In this review, the regulation of cell redox status by mitochondrial metabolism and its implications for cancer cell fate will be discussed followed by the significance of mitochondria-targeted therapies for cancer.

DOI: https://doi.org/10.1155/2021/1341604
EMBO Rep. 2021 Nov 15. e53054

Metabolic resistance to the inhibition of mitochondrial transcription revealed by CRISPR-Cas9 screen.

Mara Mennuni, Roberta Filograna, Andrea Felser, Nina A Bonekamp, Patrick Giavalisco, Oleksandr Lytovchenko, Nils-Göran Larsson.

  Cancer cells depend on mitochondria to sustain their increased metabolic need and mitochondria therefore constitute possible targets for cancer treatment. We recently developed small-molecule inhibitors of mitochondrial transcription (IMTs) that selectively impair mitochondrial gene expression. IMTs have potent antitumor properties in vitro and in vivo, without affecting normal tissues. Because therapy-induced resistance is a major constraint to successful cancer therapy, we investigated mechanisms conferring resistance to IMTs. We employed a CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats)-(CRISP-associated protein 9) whole-genome screen to determine pathways conferring resistance to acute IMT1 treatment. Loss of genes belonging to von Hippel-Lindau (VHL) and mammalian target of rapamycin complex 1 (mTORC1) pathways caused resistance to acute IMT1 treatment and the relevance of these pathways was confirmed by chemical modulation. We also generated cells resistant to chronic IMT treatment to understand responses to persistent mitochondrial gene expression impairment. We report that IMT1-acquired resistance occurs through a compensatory increase of mitochondrial DNA (mtDNA) expression and cellular metabolites. We found that mitochondrial transcription factor A (TFAM) downregulation and inhibition of mitochondrial translation impaired survival of resistant cells. The identified susceptibility and resistance mechanisms to IMTs may be relevant for different types of mitochondria-targeted therapies.

Keywords:  CRISPR-Cas9 screen; cancer; chemoresistance; inhibitor of mitochondrial transcription; mtDNA

DOI:  https://doi.org/10.15252/embr.202153054
J Cell Physiol. 2021 Nov 17.

Age-related changes in the energy of human mesenchymal stem cells.

Mario Barilani, Christopher Lovejoy, Roberta Piras, Andrey Y Abramov, Lorenza Lazzari, Plamena R Angelova.

  Aging is a physiological process that leads to a higher risk for the most devastating diseases. There are a number of theories of human aging proposed, and many of them are directly or indirectly linked to mitochondria. Here, we used mesenchymal stem cells (MSCs) from young and older donors to study age-related changes in mitochondrial metabolism. We have found that aging in MSCs is associated with a decrease in mitochondrial membrane potential and lower NADH levels in mitochondria. Mitochondrial DNA content is higher in aged MSCs, but the overall mitochondrial mass is decreased due to increased rates of mitophagy. Despite the higher level of ATP in aged cells, a higher rate of ATP consumption renders them more vulnerable to energy deprivation compared to younger cells. Changes in mitochondrial metabolism in aged MSCs activate the overproduction of reactive oxygen species in mitochondria which is compensated by a higher level of the endogenous antioxidant glutathione. Thus, energy metabolism and redox state are the drivers for the aging of MSCs/mesenchymal stromal cells.

Keywords:  MSC; aging; bioenergetics; bone marrow; cellular senescence; mitochondria

DOI:  https://doi.org/10.1002/jcp.30638
Mol Cell. 2021 Nov 08. pii: S1097-2765(21)00910-2. [Epub ahead of print]

Balancing of mitochondrial translation through METTL8-mediated m3C modification of mitochondrial tRNAs.

Eva Schöller, James Marks, Virginie Marchand, Astrid Bruckmann, Christopher A Powell, Markus Reichold, Christian Daniel Mutti, Katja Dettmer, Regina Feederle, Stefan Hüttelmaier, Mark Helm, Peter Oefner, Michal Minczuk, Yuri Motorin, Markus Hafner, Gunter Meister.

  Mitochondria contain a specific translation machinery for the synthesis of mitochondria-encoded respiratory chain components. Mitochondrial tRNAs (mt-tRNAs) are also generated from the mitochondrial DNA and, similar to their cytoplasmic counterparts, are post-transcriptionally modified. Here, we find that the RNA methyltransferase METTL8 is a mitochondrial protein that facilitates 3-methyl-cytidine (m3C) methylation at position C32 of the mt-tRNASer(UCN) and mt-tRNAThr. METTL8 knockout cells show a reduction in respiratory chain activity, whereas overexpression increases activity. In pancreatic cancer, METTL8 levels are high, which correlates with lower patient survival and an enhanced respiratory chain activity. Mitochondrial ribosome profiling uncovered mitoribosome stalling on mt-tRNASer(UCN)- and mt-tRNAThr-dependent codons. Further analysis of the respiratory chain complexes using mass spectrometry revealed reduced incorporation of the mitochondrially encoded proteins ND6 and ND1 into complex I. The well-balanced translation of mt-tRNASer(UCN)- and mt-tRNAThr-dependent codons through METTL8-mediated m3C32 methylation might, therefore, facilitate the optimal composition and function of the mitochondrial respiratory chain.

Keywords:  METTL8; RNA modification; m(3)C; mt-tRNA; translation

DOI:  https://doi.org/10.1016/j.molcel.2021.10.018
Autophagy. 2021 Nov 15. 1-3

Beyond mitophagy: mitochondrial-derived vesicles can get the job done!

Payel Mondal, Christina Towers.

  Mitochondria are critical organelles that maintain cellular metabolism and overall function. The catabolic pathway of autophagy plays a central role in recycling damaged mitochondria. Although the autophagy pathway is indispensable for some cancer cell survival, our latest study shows that rare autophagy-dependent cancer cells can adapt to loss of this core pathway. In the process, the autophagy-deficient cells acquire unique dependencies on alternate forms of mitochondrial homeostasis. These rare autophagy-deficient clones circumvent the lack of canonical autophagy by increasing mitochondrial dynamics and by recycling damaged mitochondria via mitochondrial-derived vesicles (MDVs). These studies are the first to implicate MDVs in cancer cell metabolism although many unanswered questions remain about this non-canonical pathway.

Keywords:  Cancer; mitochondrial fusion; mitochondrial-derived vesicles; mitophagy; non-canonical autophagy

DOI:  https://doi.org/10.1080/15548627.2021.1999562
Nat Nanotechnol. 2021 Nov 18.

Intercellular nanotubes mediate mitochondrial trafficking between cancer and immune cells.

Tanmoy Saha, Chinmayee Dash, Ruparoshni Jayabalan, Sachin Khiste, Arpita Kulkarni, Kiran Kurmi, Jayanta Mondal, Pradip K Majumder, Aditya Bardia, Hae Lin Jang, Shiladitya Sengupta.

Cancer progresses by evading the immune system. Elucidating diverse immune evasion strategies is a critical step in the search for next-generation immunotherapies for cancer. Here we report that cancer cells can hijack the mitochondria from immune cells via physical nanotubes. Mitochondria are essential for metabolism and activation of immune cells. By using field-emission scanning electron microscopy, fluorophore-tagged mitochondrial transfer tracing and metabolic quantification, we demonstrate that the nanotube-mediated transfer of mitochondria from immune cells to cancer cells metabolically empowers the cancer cells and depletes the immune cells. Inhibiting the nanotube assembly machinery significantly reduced mitochondrial transfer and prevented the depletion of immune cells. Combining a farnesyltransferase and geranylgeranyltransferase 1 inhibitor, namely, L-778123, which partially inhibited nanotube formation and mitochondrial transfer, with a programmed cell death protein 1 immune checkpoint inhibitor improved the antitumour outcomes in an aggressive immunocompetent breast cancer model. Nanotube-mediated mitochondrial hijacking can emerge as a novel target for developing next-generation immunotherapy agents for cancer.

DOI: https://doi.org/10.1038/s41565-021-01000-4
Nat Metab. 2021 Nov;3(11): 1500-1511

Methionine synthase is essential for cancer cell proliferation in physiological folate environments.

Mark R Sullivan, Alicia M Darnell, Montana F Reilly, Tenzin Kunchok, Lena Joesch-Cohen, Daniel Rosenberg, Ahmed Ali, Matthew G Rees, Jennifer A Roth, Caroline A Lewis, Matthew G Vander Heiden.

Folate metabolism can be an effective target for cancer treatment. However, standard cell culture conditions utilize folic acid, a non-physiological folate source for most tissues. We find that the enzyme that couples folate and methionine metabolic cycles, methionine synthase, is required for cancer cell proliferation and tumour growth when 5-methyl tetrahydrofolate (THF), the major folate found in circulation, is the extracellular folate source. In such physiological conditions, methionine synthase incorporates 5-methyl THF into the folate cycle to maintain intracellular levels of the folates needed for nucleotide production. 5-methyl THF can sustain intracellular folate metabolism in the absence of folic acid. Therefore, cells exposed to 5-methyl THF are more resistant to methotrexate, an antifolate drug that specifically blocks folic acid incorporation into the folate cycle. Together, these data argue that the environmental folate source has a profound effect on folate metabolism, determining how both folate cycle enzymes and antifolate drugs impact proliferation.

DOI: https://doi.org/10.1038/s42255-021-00486-5
Free Radic Biol Med. 2021 Nov 11. pii: S0891-5849(21)00794-2. [Epub ahead of print]

The role of mitochondrial reactive oxygen species in insulin resistance.

Anita Ayer, Daniel J Fazakerley, David E James, Roland Stocker.

  Insulin resistance is one of the earliest pathological features of a suite of diseases including type 2 diabetes collectively referred to as metabolic syndrome. There is a growing body of evidence from both pre-clinical studies and human cohorts indicating that reactive oxygen species, such as the superoxide radical anion and hydrogen peroxide are key players in the development of insulin resistance. Here we review the evidence linking mitochondrial reactive oxygen species generated within mitochondria with insulin resistance in adipose tissue and skeletal muscle, two major insulin sensitive tissues. We outline the relevant mitochondria-derived reactive species, how the mitochondrial redox state is regulated, and methodologies available to measure mitochondrial reactive oxygen species. Importantly, we highlight key experimental issues to be considered when studying the role of mitochondrial reactive oxygen species in insulin resistance. Evaluating the available literature on both mitochondrial reactive oxygen species/redox state and insulin resistance in a variety of biological systems, we conclude that the weight of evidence suggests a likely role for mitochondrial reactive oxygen species in the etiology of insulin resistance in adipose tissue and skeletal muscle. However, major limitations in the methods used to study reactive oxygen species in insulin resistance as well as the lack of data linking mitochondrial reactive oxygen species and cytosolic insulin signaling pathways are significant obstacles in proving the mechanistic link between these two processes. We provide a framework to guide future studies to provide stronger mechanistic information on the link between mitochondrial reactive oxygen species and insulin resistance as understanding the source, localization, nature, and quantity of mitochondrial reactive oxygen species, their targets and downstream signaling pathways may pave the way for important new therapeutic strategies.

Keywords:  Coenzyme Q; Hydrogen peroxide; Insulin resistance; Mitochondria; Redox signaling; Superoxide radical anion

DOI:  https://doi.org/10.1016/j.freeradbiomed.2021.11.007
Commun Biol. 2021 Nov 16. 4(1): 1289

DLST-dependence dictates metabolic heterogeneity in TCA-cycle usage among triple-negative breast cancer.

Ning Shen, Sovannarith Korm, Theodoros Karantanos, Dun Li, Xiaoyu Zhang, Eleni Ritou, Hanfei Xu, Andrew Lam, Justin English, Wei-Xing Zong, Ching-Ti Liu, Orian Shirihai, Hui Feng.

Triple-negative breast cancer (TNBC) is traditionally considered a glycolytic tumor with a poor prognosis while lacking targeted therapies. Here we show that high expression of dihydrolipoamide S-succinyltransferase (DLST), a tricarboxylic acid (TCA) cycle enzyme, predicts poor overall and recurrence-free survival among TNBC patients. DLST depletion suppresses growth and induces death in subsets of human TNBC cell lines, which are capable of utilizing glutamine anaplerosis. Metabolomics profiling reveals significant changes in the TCA cycle and reactive oxygen species (ROS) related pathways for sensitive but not resistant TNBC cells. Consequently, DLST depletion in sensitive TNBC cells increases ROS levels while N-acetyl-L-cysteine partially rescues cell growth. Importantly, suppression of the TCA cycle through DLST depletion or CPI-613, a drug currently in clinical trials for treating other cancers, decreases the burden and invasion of these TNBC. Together, our data demonstrate differential TCA-cycle usage in TNBC and provide therapeutic implications for the DLST-dependent subsets.

DOI: https://doi.org/10.1038/s42003-021-02805-8
Life Sci Alliance. 2022 Feb;pii: e202101278. [Epub ahead of print]5(2):

Serine palmitoyltransferase assembles at ER-mitochondria contact sites.

Mari J Aaltonen, Irina Alecu, Tim König, Steffany Al Bennett, Eric A Shoubridge.

The accumulation of sphingolipid species in the cell contributes to the development of obesity and neurological disease. However, the subcellular localization of sphingolipid-synthesizing enzymes is unclear, limiting the understanding of where and how these lipids accumulate inside the cell and why they are toxic. Here, we show that SPTLC2, a subunit of the serine palmitoyltransferase (SPT) complex, catalyzing the first step in de novo sphingolipid synthesis, localizes dually to the ER and the outer mitochondrial membrane. We demonstrate that mitochondrial SPTLC2 interacts and forms a complex in trans with the ER-localized SPT subunit SPTLC1. Loss of SPTLC2 prevents the synthesis of mitochondrial sphingolipids and protects from palmitate-induced mitochondrial toxicity, a process dependent on mitochondrial ceramides. Our results reveal the in trans assembly of an enzymatic complex at an organellar membrane contact site, providing novel insight into the localization of sphingolipid synthesis and the composition and function of ER-mitochondria contact sites.

DOI: https://doi.org/10.26508/lsa.202101278
Rejuvenation Res. 2021 Nov 13.

Metformin treatment in old rats and effects on mitochondrial integrity.

Allen Herbst, Austin Hoang, Chiye Kim, Judd Aiken, Debbie McKenzie, Deena Goldwater, Jonathan Wanagat.

Metformin, a commonly used, well-tolerated treatment for type 2 diabetes, is being deployed in clinical trials to ameliorate aging in older non-diabetic humans. Concerningly, some experiments in model organisms have suggested that metformin use at old ages shortens lifespan and is toxic to mitochondria. The demonstrated safety of metformin therapy in humans and the conflicting data from model organisms compelled us to test the hypothesis that metformin treatment would be toxic to older rats. To define an effective dose in 30-month-old hybrid rats, we evaluated two doses of metformin (0.1%, 0.75% of the diet) and treated the rats for four months. Body mass decreased at the 0.75% dose. Neither dose affected mortality between 30- and 34-months of age. We assessed mitochondrial integrity by measuring mitochondrial DNA copy number and deletion mutation frequency, and mitochondrial respiration in skeletal muscle and the heart. In skeletal muscle, we observed no effect of metformin on quadriceps mass, mtDNA copy number, or deletion frequency. In the heart, metformin-treated rats had higher mtDNA copy number, lower cardiac mass, with no change in mtDNA deletion frequency. Metformin treatment resulted in lower mitochondrial Complex I-dependent respiration in the heart. We found that, in old rats, metformin did not compromise mitochondrial DNA integrity, did not affect mortality, and may have cardiac benefits. These data provide some reassurance that a metformin intervention in aged mammals is not toxic at appropriate doses.

DOI: https://doi.org/10.1089/rej.2021.0052
J Biol Chem. 2021 Nov 13. pii: S0021-9258(21)01217-5. [Epub ahead of print] 101410

Mitophagy Mediates Metabolic Reprogramming of Induced Pluripotent Stem Cells Undergoing Endothelial Differentiation.

Sarah Krantz, Young-Mee Kim, Shubhi Srivastava, Joseph W Leasure, Peter T Toth, Glenn Marsboom, Jalees Rehman.

  Pluripotent stem cells are known to shift their mitochondrial metabolism upon differentiation, but the mechanisms underlying such metabolic rewiring are not fully understood. We hypothesized that during differentiation of human induced pluripotent stem cells (hiPSCs), mitochondria undergo mitophagy and are then replenished by the biogenesis of new mitochondria adapted to the metabolic needs of the differentiated cell. To evaluate mitophagy during iPSC differentiation, we performed live cell imaging of mitochondria and lysosomes in hiPSCs differentiating into vascular endothelial cells using confocal microscopy. We observed a burst of mitophagy during the initial phases of hiPSC differentiation into the endothelial lineage, followed by subsequent mitochondrial biogenesis as assessed by the mitochondrial biogenesis biosensor MitoTimer. Furthermore, hiPSCs undergoing differentiation showed greater mitochondrial oxidation of fatty acids and an increase in ATP levels as assessed by an ATP biosensor. We also found that during mitophagy, the mitochondrial phosphatase PGAM5 is cleaved in hiPSC-derived endothelial progenitor cells and in turn activates β-catenin-mediated transcription of the transcriptional co-activator PGC-1α, which upregulates mitochondrial biogenesis. These data suggest that mitophagy itself initiates the increase in mitochondrial biogenesis and oxidative metabolism through transcriptional changes during endothelial cell differentiation. In summary, these findings reveal a mitophagy-mediated mechanism for metabolic rewiring and maturation of differentiating cells via the β-catenin signaling pathway. We propose that such mitochondrial-nuclear crosstalk during hiPSC differentiation could be leveraged to enhance the metabolic maturation of differentiated cells.

Keywords:  cell differentiation; induced pluripotent stem cells; mitochondrial metabolism; mitophagy; β-catenin

DOI:  https://doi.org/10.1016/j.jbc.2021.101410
Cell Biosci. 2021 Nov 17. 11(1): 195

NME6 is a phosphotransfer-inactive, monomeric NME/NDPK family member and functions in complexes at the interface of mitochondrial inner membrane and matrix.

Bastien Proust, Martina Radić, Nikolina Škrobot Vidaček, Cécile Cottet, Stéphane Attia, Frédéric Lamarche, Lucija Ačkar, Vlatka Godinić Mikulčić, Malgorzata Tokarska-Schlattner, Helena Ćetković, Uwe Schlattner, Maja Herak Bosnar.

   BACKGROUND: NME6 is a member of the nucleoside diphosphate kinase (NDPK/NME/Nm23) family which has key roles in nucleotide homeostasis, signal transduction, membrane remodeling and metastasis suppression. The well-studied NME1-NME4 proteins are hexameric and catalyze, via a phospho-histidine intermediate, the transfer of the terminal phosphate from (d)NTPs to (d)NDPs (NDP kinase) or proteins (protein histidine kinase). For the NME6, a gene/protein that emerged early in eukaryotic evolution, only scarce and partially inconsistent data are available. Here we aim to clarify and extend our knowledge on the human NME6.
RESULTS: We show that NME6 is mostly expressed as a 186 amino acid protein, but that a second albeit much less abundant isoform exists. The recombinant NME6 remains monomeric, and does not assemble into homo-oligomers or hetero-oligomers with NME1-NME4. Consequently, NME6 is unable to catalyze phosphotransfer: it does not generate the phospho-histidine intermediate, and no NDPK activity can be detected. In cells, we could resolve and extend existing contradictory reports by localizing NME6 within mitochondria, largely associated with the mitochondrial inner membrane and matrix space. Overexpressing NME6 reduces ADP-stimulated mitochondrial respiration and complex III abundance, thus linking NME6 to dysfunctional oxidative phosphorylation. However, it did not alter mitochondrial membrane potential, mass, or network characteristics. Our screen for NME6 protein partners revealed its association with NME4 and OPA1, but a direct interaction was observed only with RCC1L, a protein involved in mitochondrial ribosome assembly and mitochondrial translation, and identified as essential for oxidative phosphorylation.
CONCLUSIONS: NME6, RCC1L and mitoribosomes localize together at the inner membrane/matrix space where NME6, in concert with RCC1L, may be involved in regulation of the mitochondrial translation of essential oxidative phosphorylation subunits. Our findings suggest new functions for NME6, independent of the classical phosphotransfer activity associated with NME proteins.

Keywords:  Mitochondria; NDP kinase; NME; RCC1L; WBSCR16; nm23

DOI:  https://doi.org/10.1186/s13578-021-00707-0
Nat Metab. 2021 Nov;3(11): 1521-1535

The metabolic growth limitations of petite cells lacking the mitochondrial genome.

Jakob Vowinckel, Johannes Hartl, Hans Marx, Martin Kerick, Kathrin Runggatscher, Markus A Keller, Michael Mülleder, Jason Day, Manuela Weber, Mark Rinnerthaler, Jason S L Yu, Simran Kaur Aulakh, Andrea Lehmann, Diethard Mattanovich, Bernd Timmermann, Nianshu Zhang, Cory D Dunn, James I MacRae, Michael Breitenbach, Markus Ralser.

Eukaryotic cells can survive the loss of their mitochondrial genome, but consequently suffer from severe growth defects. 'Petite yeasts', characterized by mitochondrial genome loss, are instrumental for studying mitochondrial function and physiology. However, the molecular cause of their reduced growth rate remains an open question. Here we show that petite cells suffer from an insufficient capacity to synthesize glutamate, glutamine, leucine and arginine, negatively impacting their growth. Using a combination of molecular genetics and omics approaches, we demonstrate the evolution of fast growth overcomes these amino acid deficiencies, by alleviating a perturbation in mitochondrial iron metabolism and by restoring a defect in the mitochondrial tricarboxylic acid cycle, caused by aconitase inhibition. Our results hence explain the slow growth of mitochondrial genome-deficient cells with a partial auxotrophy in four amino acids that results from distorted iron metabolism and an inhibited tricarboxylic acid cycle.

DOI: https://doi.org/10.1038/s42255-021-00477-6
Mol Nutr Food Res. 2021 Nov 17. e2100738

AKT1/HK2 Axis-mediated Glucose Metabolism: A Novel Therapeutic Target of Sulforaphane in Bladder Cancer.

Lei Huang, Canxia He, Sicong Zheng, Chao Wu, Minghua Ren, Yujuan Shan.

   SCOPE: Metabolic disorder is a pivotal hallmark of cancer cells. Sulforaphane (SFN) is reported to improve lipid metabolism. However, the effect of SFN on glucose metabolism in bladder cancer remains unclear. Hence, we investigated the effect and underling mechanism.
METHODS AND RESULTS: We collected biological samples from bladder cancer patients, and also investigated using N-butyl-N-(4-hydroxybutyl) nitrosamine-induced bladder cancer mice and bladder cancer cell lines. A novel glucose transport aberrant-independent aerobic glycolysis was found in bladder cancer patients, and the lower malignancy tissues have the more obvious abnormality. SFN strongly down-regulated ATP production by inhibiting glycolysis and mitochondrial oxidative phosphorylation (OXPHOS). Both in vitro cell culture and in bladder tumor mice, SFN weakened the glycolytic flux by suppressing multiple metabolic enzymes, including hexokinase 2 (HK2) and pyruvate dehydrogenase (PDH). Moreover, SFN decreased the level of AKT1 and p-AKT ser473 , especially in low-invasive UMUC3 cells. The down-regulation of ATP and HK2 by SFN were both reversed by AKT1 overexpression.
CONCLUSIONS: SFN down-regulated the unique glucose transport aberrant-independent aerobic glycolysis existed in bladder cancer via blocking the AKT1/HK2 axis and PDH expression. This article is protected by copyright. All rights reserved.

Keywords:  aerobic glycolysis; bladder cancer; glucose metabolism; glycolysis; sulforaphane

DOI:  https://doi.org/10.1002/mnfr.202100738
Redox Biol. 2021 Nov 15. pii: S2213-2317(21)00350-5. [Epub ahead of print]48 102190

The sulfiredoxin-peroxiredoxin redox system regulates the stemness and survival of colon cancer stem cells.

In-Sung Song, Yu Jeong Jeong, Yena Jung, Young-Ho Park, Sungbo Shim, Sung Joo Kim, Dae-Woon Eom, Seung-Mo Hong, Peter C W Lee, Sun-Uk Kim, Sung-Wuk Jang.

  Cancer stem cells (CSCs) initiate tumor formation and are known to be resistant to chemotherapy. A metabolic alteration in CSCs plays a critical role in stemness and survival. However, the association between mitochondrial energy metabolism and the redox system remains undefined in colon CSCs. In this study, we assessed the role of the Sulfiredoxin-Peroxiredoxin (Srx-Prx) redox system and mitochondrial oxidative phosphorylation (OXPHOS) in maintaining the stemness and survival of colon CSCs. Notably, Srx contributed to the stability of PrxI, PrxII, and PrxIII proteins in colon CSCs. Increased Srx expression promoted the stemness and survival of CSCs and was important for the maintenance of the mitochondrial OXPHOS system. Furthermore, Nrf2 and FoxM1 led to OXPHOS activation and upregulated expression of Srx-Prx redox system-related genes. Therefore, the Nrf2/FoxM1-induced Srx-Prx redox system is a potential therapeutic target for eliminating CSCs in colon cancer.

Keywords:  Cancer stem cell; Colon; OXPHOS; Peroxiredoxin; ROS; Stemness; Sulfiredoxin

DOI:  https://doi.org/10.1016/j.redox.2021.102190
Oncogene. 2021 Nov 16.

Histone N-terminal acetyltransferase NAA40 links one-carbon metabolism to chemoresistance.

Christina Demetriadou, Anastasia Raoukka, Evelina Charidemou, Constantine Mylonas, Christina Michael, Swati Parekh, Costas Koufaris, Paris Skourides, Panagiotis Papageorgis, Peter Tessarz, Antonis Kirmizis.

Aberrant function of epigenetic modifiers plays an important role not only in the progression of cancer but also the development of drug resistance. N-alpha-acetyltransferase 40 (NAA40) is a highly specific epigenetic enzyme catalyzing the transfer of an acetyl moiety at the N-terminal end of histones H4 and H2A. Recent studies have illustrated the essential oncogenic role of NAA40 in various cancer types but its role in chemoresistance remains unclear. Here, using transcriptomic followed by metabolomic analysis in colorectal cancer (CRC) cells, we demonstrate that NAA40 controls key one-carbon metabolic genes and corresponding metabolites. In particular, through its acetyltransferase activity NAA40 regulates the methionine cycle thereby affecting global histone methylation and CRC cell survival. Importantly, NAA40-mediated metabolic rewiring promotes resistance of CRC cells to antimetabolite chemotherapy in vitro and in xenograft models. Specifically, NAA40 stimulates transcription of the one-carbon metabolic gene thymidylate synthase (TYMS), whose product is targeted by 5-fluorouracil (5-FU) and accordingly in primary CRC tumours NAA40 expression associates with TYMS levels and poorer 5-FU response. Mechanistically, NAA40 activates TYMS by preventing enrichment of repressive H2A/H4S1ph at the nuclear periphery. Overall, these findings define a novel regulatory link between epigenetics and cellular metabolism mediated by NAA40, which is harnessed by cancer cells to evade chemotherapy.

DOI: https://doi.org/10.1038/s41388-021-02113-9
Autophagy. 2021 Nov 19. 1-11

AMBRA1 regulates mitophagy by interacting with ATAD3A and promoting PINK1 stability.

Martina Di Rienzo, Alessandra Romagnoli, Fabiola Ciccosanti, Giulia Refolo, Veronica Consalvi, Giuseppe Arena, Enza Maria Valente, Mauro Piacentini, Gian Maria Fimia.

  PINK1 accumulation at the outer mitochondrial membrane (OMM) is a key event required to signal depolarized mitochondria to the autophagy machinery. How this early step is, in turn, modulated by autophagy proteins remains less characterized. Here, we show that, upon mitochondrial depolarization, the proautophagic protein AMBRA1 is recruited to the OMM and interacts with PINK1 and ATAD3A, a transmembrane protein that mediates mitochondrial import and degradation of PINK1. Downregulation of AMBRA1 expression results in reduced levels of PINK1 due to its enhanced degradation by the mitochondrial protease LONP1, which leads to a decrease in PINK1-mediated ubiquitin phosphorylation and mitochondrial PRKN/PARKIN recruitment. Notably, ATAD3A silencing rescues defective PINK1 accumulation in AMBRA1-deficient cells upon mitochondrial damage. Overall, our findings underline an upstream contribution of AMBRA1 in the control of PINK1-PRKN mitophagy by interacting with ATAD3A and promoting PINK1 stability. This novel regulatory element may account for changes of PINK1 levels in neuropathological conditions.

Keywords:  Autophagy; LONP1; PRKN/PARKIN; TOMM complex; ubiquitin phosphorylation

DOI:  https://doi.org/10.1080/15548627.2021.1997052
FASEB J. 2021 Dec;35(12): e21974

The role of the electron transport chain in immunity.

Maureen Yin, Luke A J O'Neill.

  The electron transport chain (ETC) couples oxidative phosphorylation (OXPHOS) with ATP synthase to drive the generation of ATP. In immune cells, research surrounding the ETC has drifted away from bioenergetics since the discovery of cytochrome c (Cyt c) release as a signal for programmed cell death. Complex I has been shown to generate reactive oxygen species (ROS), with key roles identified in inflammatory macrophages and T helper 17 cells (TH 17) cells. Complex II is the site of reverse electron transport (RET) in inflammatory macrophages and is also responsible for regulating fumarate levels linking to epigenetic changes. Complex III also produces ROS which activate hypoxia-inducible factor 1-alpha (HIF-1α) and can participate in regulatory T cell (Treg ) function. Complex IV is required for T cell activation and differentiation and the proper development of Treg subsets. Complex V is required for TH 17 differentiation and can be expressed on the surface of tumor cells where it is recognized by anti-tumor T and NK cells. In this review, we summarize these findings and speculate on the therapeutic potential of targeting the ETC as an anti-inflammatory strategy.

Keywords:  T-lymphocytes; electron transport chain (ETC); immunometabolism; macrophage; mitochondria; oxidative phosphorylation

DOI:  https://doi.org/10.1096/fj.202101161R
Chem Soc Rev. 2021 Nov 18.

Optical/electrochemical methods for detecting mitochondrial energy metabolism.

Wenhui Ji, Xiao Tang, Wei Du, Yao Lu, Nanxiang Wang, Qiong Wu, Wei Wei, Jie Liu, Haidong Yu, Bo Ma, Lin Li, Wei Huang.

This review highlights the biological importance of mitochondrial energy metabolism and the applications of multiple optical/electrochemical approaches to determine energy metabolites. Mitochondria, the main sites of oxidative phosphorylation and adenosine triphosphate (ATP) biosynthesis, provide the majority of energy required by aerobic cells for maintaining their physiological activity. They also participate in cell growth, differentiation, information transmission, and apoptosis. Multiple mitochondrial diseases, caused by internal or external factors, including oxidative stress, intense fluctuations of the ionic concentration, abnormal oxidative phosphorylation, changes in electron transport chain complex enzymes and mutations in mitochondrial DNA, can occur during mitochondrial energy metabolism. Therefore, developing accurate, sensitive, and specific methods for the in vivo and in vitro detection of mitochondrial energy metabolites is of great importance. In this review, we summarise the mitochondrial structure, functions, and crucial energy metabolic signalling pathways. The mechanism and applications of different optical/electrochemical methods are thoroughly reviewed. Finally, future research directions and challenges are proposed.

DOI: https://doi.org/10.1039/d0cs01610a
Nat Metab. 2021 Nov;3(11): 1512-1520

Methionine synthase supports tumour tetrahydrofolate pools.

Jonathan M Ghergurovich, Xincheng Xu, Joshua Z Wang, Lifeng Yang, Rolf-Peter Ryseck, Lin Wang, Joshua D Rabinowitz.

Mammalian cells require activated folates to generate nucleotides for growth and division. The most abundant circulating folate species is 5-methyl tetrahydrofolate (5-methyl-THF), which is used to synthesize methionine from homocysteine via the cobalamin-dependent enzyme methionine synthase (MTR). Cobalamin deficiency traps folates as 5-methyl-THF. Here, we show using isotope tracing that MTR is only a minor source of methionine in cell culture, tissues or xenografted tumours. Instead, MTR is required for cells to avoid folate trapping and assimilate 5-methyl-THF into other folate species. Under conditions of physiological extracellular folates, genetic MTR knockout in tumour cells leads to folate trapping, purine synthesis stalling, nucleotide depletion and impaired growth in cell culture and as xenografts. These defects are rescued by free folate but not one-carbon unit supplementation. Thus, MTR plays a crucial role in liberating THF for use in one-carbon metabolism.

DOI: https://doi.org/10.1038/s42255-021-00465-w
Metabolomics. 2021 Nov 18. 17(12): 101

Cross-comparison of systemic and tissue-specific metabolomes in a mouse model of Leigh syndrome.

Karin Terburgh, Jeremie Z Lindeque, Francois H van der Westhuizen, Roan Louw.

   INTRODUCTION: The value of metabolomics in multi-systemic mitochondrial disease research has been increasingly recognized, with the ability to investigate a variety of biofluids and tissues considered a particular advantage. Although minimally invasive biofluids are the generally favored sample type, it remains unknown whether systemic metabolomes provide a clear reflection of tissue-specific metabolic alterations.
OBJECTIVES: Here we cross-compare urine and tissue-specific metabolomes in the Ndufs4 knockout mouse model of Leigh syndrome-a complex neurometabolic MD defined by progressive focal lesions in specific brain regions-to identify and evaluate the extent of common and unique metabolic alterations on a systemic and brain regional level.
METHODS: Untargeted and semi-targeted multi-platform metabolomics were performed on urine, four brain regions, and two muscle types of Ndufs4 KO (n≥19) vs wildtype (n≥20) mice.
RESULTS: Widespread alterations were evident in alanine, aspartate, glutamate, and arginine metabolism in Ndufs4 KO mice; while brain-region specific metabolic signatures include the accumulation of branched-chain amino acids, proline, and glycolytic intermediates. Furthermore, we describe a systemic dysregulation in one-carbon metabolism and the tricarboxylic acid cycle, which was not clearly reflected in the Ndufs4 KO brain.
CONCLUSION: Our results confirm the value of urinary metabolomics when evaluating MD-associated metabolites, while cautioning against mechanistic studies relying solely on systemic biofluids.

Keywords:  Brain regions; Complex I deficiency; Leigh syndrome; Metabolomics; Mitochondrial disease; Ndufs4 knockout mice

DOI:  https://doi.org/10.1007/s11306-021-01854-8
Elife. 2021 Nov 18. pii: e68487. [Epub ahead of print]10

Hydrogen sulfide blocks HIV rebound by maintaining mitochondrial bioenergetics and redox homeostasis.

Virender Kumar Pal, Ragini Agrawal, Srabanti Rakshit, Pooja Shekar, Diwakar Tumkur Narasimha Murthy, Annapurna Vyakarnam, Amit Singh.

  A fundamental challenge in HIV eradication is to understand how the virus establishes latency, maintains stable cellular reservoirs, and promotes rebound upon interruption of antiretroviral treatment (ART). Here, we discovered an unexpected role of the ubiquitous gasotransmitter hydrogen sulfide (H2S) in HIV latency and reactivation. We show that reactivation of HIV-1 is associated with down-regulation of the key H2S producing enzyme cystathionine-g-lyase (CTH) and reduction in endogenous H2S. Genetic silencing of CTH disrupts redox homeostasis, impairs mitochondrial function, and remodels the transcriptome of latent cells to trigger HIV reactivation. Chemical complementation of CTH activity using a slow-releasing H2S donor, GYY4137, suppressed HIV reactivation and diminished virus replication. Mechanistically, GYY4137 blocked HIV reactivation by inducing the Keap1-Nrf2 pathway, inhibiting NF-kB, and recruiting the epigenetic silencer, YY1, to the HIV promoter. In latently infected CD4+ T cells from ART-suppressed human subjects, GYY4137 in combination with ART prevented viral rebound and improved mitochondrial bioenergetics. Moreover, prolonged exposure to GYY4137 exhibited no adverse influence on proviral content or CD4+ T cell subsets, indicating that diminished viral rebound is due to a loss of transcription rather than a selective loss of infected cells. In summary, this work provides mechanistic insight into H2S-mediated suppression of viral rebound and suggests exploration of H2S donors to maintain HIV in a latent form.

Keywords:  biochemistry; chemical biology; infectious disease; microbiology; viruses

DOI:  https://doi.org/10.7554/eLife.68487
Nat Commun. 2021 Nov 19. 12(1): 6750

The autophagy protein ATG9A enables lipid mobilization from lipid droplets.

Elodie Mailler, Carlos M Guardia, Xiaofei Bai, Michal Jarnik, Chad D Williamson, Yan Li, Nunziata Maio, Andy Golden, Juan S Bonifacino.

The multispanning membrane protein ATG9A is a scramblase that flips phospholipids between the two membrane leaflets, thus contributing to the expansion of the phagophore membrane in the early stages of autophagy. Herein, we show that depletion of ATG9A does not only inhibit autophagy but also increases the size and/or number of lipid droplets in human cell lines and C. elegans. Moreover, ATG9A depletion blocks transfer of fatty acids from lipid droplets to mitochondria and, consequently, utilization of fatty acids in mitochondrial respiration. ATG9A localizes to vesicular-tubular clusters (VTCs) that are tightly associated with an ER subdomain enriched in another multispanning membrane scramblase, TMEM41B, and also in close proximity to phagophores, lipid droplets and mitochondria. These findings indicate that ATG9A plays a critical role in lipid mobilization from lipid droplets to autophagosomes and mitochondria, highlighting the importance of ATG9A in both autophagic and non-autophagic processes.

DOI: https://doi.org/10.1038/s41467-021-26999-x
Redox Biol. 2021 Nov 11. pii: S2213-2317(21)00344-X. [Epub ahead of print]48 102184

Comprehensive chemical proteomics analyses reveal that the new TRi-1 and TRi-2 compounds are more specific thioredoxin reductase 1 inhibitors than auranofin.

Pierre Sabatier, Christian M Beusch, Radosveta Gencheva, Qing Cheng, Roman Zubarev, Elias S J Arnér.

  Anticancer drugs that target cellular antioxidant systems have recently attracted much attention. Auranofin (AF) is currently evaluated in several clinical trials as an anticancer agent that targets the cytosolic and mitochondrial forms of the selenoprotein thioredoxin reductase, TXNRD1 and TXNRD2. Recently, two novel TXNRD1 inhibitors (TRi-1 and TRi-2) have been developed that showed anticancer efficacy comparable to AF, but with lower mitochondrial toxicity. However, the cellular action mechanisms of these drugs have not yet been thoroughly studied. Here we used several proteomics approaches to determine the effects of AF, TRi-1 and TRi-2 when used at IC50 concentrations with the mouse B16 melanoma and LLC lung adenocarcinoma cells, as these are often used for preclinical mouse models in evaluation of anticancer drugs. The results demonstrate that TRi-1 and TRi-2 are more specific TXNRD1 inhibitors than AF and reveal additional AF-specific effects on the cellular proteome. Interestingly, AF triggered stronger Nrf2-driven antioxidant responses than the other two compounds. Furthermore, AF affected several additional proteins, including GSK3A, GSK3B, MCMBP and EEFSEC, implicating additional effects on glycogen metabolism, cellular differentiation, inflammatory pathways, DNA replication and selenoprotein synthesis processes. Our proteomics data provide a resource for researchers interested in the multidimensional analysis of proteome changes associated with oxidative stress in general, and the effects of TXNRD1 inhibitors and AF protein targets in particular.

Keywords:  Cancer; Inhibition; Mouse; Proteomics; Thioredoxin reductase

DOI:  https://doi.org/10.1016/j.redox.2021.102184
J Clin Invest. 2021 Nov 15. pii: e144871. [Epub ahead of print]131(22):

Folliculin impairs breast tumor growth by repressing TFE3-dependent induction of the Warburg effect and angiogenesis.

Leeanna El-Houjeiri, Marco Biondini, Mathieu Paquette, Helen Kuasne, Alain Pacis, Morag Park, Peter M Siegel, Arnim Pause.

  Growing tumors exist in metabolically compromised environments that require activation of multiple pathways to scavenge nutrients to support accelerated rates of growth. The folliculin (FLCN) tumor suppressor complex (FLCN, FNIP1, FNIP2) is implicated in the regulation of energy homeostasis via 2 metabolic master kinases: AMPK and mTORC1. Loss-of-function mutations of the FLCN tumor suppressor complex have only been reported in renal tumors in patients with the rare Birt-Hogg-Dube syndrome. Here, we revealed that FLCN, FNIP1, and FNIP2 are downregulated in many human cancers, including poor-prognosis invasive basal-like breast carcinomas where AMPK and TFE3 targets are activated compared with the luminal, less aggressive subtypes. FLCN loss in luminal breast cancer promoted tumor growth through TFE3 activation and subsequent induction of several pathways, including autophagy, lysosomal biogenesis, aerobic glycolysis, and angiogenesis. Strikingly, induction of aerobic glycolysis and angiogenesis in FLCN-deficient cells was dictated by the activation of the PGC-1α/HIF-1α pathway, which we showed to be TFE3 dependent, directly linking TFE3 to Warburg metabolic reprogramming and angiogenesis. Conversely, FLCN overexpression in invasive basal-like breast cancer models attenuated TFE3 nuclear localization, TFE3-dependent transcriptional activity, and tumor growth. These findings support a general role of a deregulated FLCN/TFE3 tumor suppressor pathway in human cancers.

Keywords:  Angiogenesis; Breast cancer; Cancer; Metabolism

DOI:  https://doi.org/10.1172/JCI144871
Nat Nanotechnol. 2021 Nov 18.

Cancer cells hijack T-cell mitochondria.

Jeremy G Baldwin, Luca Gattinoni.

DOI: https://doi.org/10.1038/s41565-021-01006-y
Biochem Biophys Res Commun. 2021 Nov 12. pii: S0006-291X(21)01545-X. [Epub ahead of print]585 61-67

Contribution of branched chain amino acids to energy production and mevalonate synthesis in cancer cells.

Valeryia Mikalayeva, Monika Pankevičiūtė, Vaidotas Žvikas, V Arvydas Skeberdis, Sergio Bordel.

  Leucine, isoleucine and valine, known as branched chain amino acids (BCAAs), have been reported to be degraded by different cancer cells, and their biodegradation pathways have been suggested as anticancer targets. However, the mechanisms by which the degradation of BCAAs could support the growth of cancer cells remains unclear. In this work, 13C experiments have been carried out in order to elucidate the metabolic role of BCAA degradation in two breast cancer cell lines (MCF-7 and BCC). The results revealed that up to 36% of the energy production via respiration by MCF-7 cells was supported by the degradation of BCAAs. Also, 67% of the mevalonate (the precursor of cholesterol) synthesized by the cells was coming from the degradation of leucine. The results were lower for BCC cells (14 and 30%, respectively). The non-tumorigenic epythelial cell line MCF-10A was used as a control, showing that 10% of the mitochondrial acetyl-CoA comes from the degradation of BCAAs and no mevalonate production. Metabolic flux analysis around the mevalonate node, also revealed that significant amounts of acetoacetate are being produced from BCAA derived carbon, which could be at the source of lipid synthesis. From these results we can conclude that the degradation of BCAAs is an important energy and carbon source for the proliferation of some cancer cells and its therapeutic targeting could be an interesting option.

Keywords:  Branched chain amino-acids; Cancer metabolism; Metabolic flux analysis

DOI:  https://doi.org/10.1016/j.bbrc.2021.11.034
Nat Commun. 2021 Nov 18. 12(1): 6743

Mapping protein carboxymethylation sites provides insights into their role in proteostasis and cell proliferation.

Simone Di Sanzo, Katrin Spengler, Anja Leheis, Joanna M Kirkpatrick, Theresa L Rändler, Tim Baldensperger, Therese Dau, Christian Henning, Luca Parca, Christian Marx, Zhao-Qi Wang, Marcus A Glomb, Alessandro Ori, Regine Heller.

Posttranslational mechanisms play a key role in modifying the abundance and function of cellular proteins. Among these, modification by advanced glycation end products has been shown to accumulate during aging and age-associated diseases but specific protein targets and functional consequences remain largely unexplored. Here, we devise a proteomic strategy to identify sites of carboxymethyllysine modification, one of the most abundant advanced glycation end products. We identify over 1000 sites of protein carboxymethylation in mouse and primary human cells treated with the glycating agent glyoxal. By using quantitative proteomics, we find that protein glycation triggers a proteotoxic response and indirectly affects the protein degradation machinery. In primary endothelial cells, we show that glyoxal induces cell cycle perturbation and that carboxymethyllysine modification reduces acetylation of tubulins and impairs microtubule dynamics. Our data demonstrate the relevance of carboxymethyllysine modification for cellular function and pinpoint specific protein networks that might become compromised during aging.

DOI: https://doi.org/10.1038/s41467-021-26982-6
EMBO J. 2021 Nov 17. e109519

Widespread use of unconventional targeting signals in mitochondrial ribosome proteins.

Yury S Bykov, Tamara Flohr, Felix Boos, Naama Zung, Johannes M Herrmann, Maya Schuldiner.

  Mitochondrial ribosomes are complex molecular machines indispensable for respiration. Their assembly involves the import of several dozens of mitochondrial ribosomal proteins (MRPs), encoded in the nuclear genome, into the mitochondrial matrix. Proteomic and structural data as well as computational predictions indicate that up to 25% of yeast MRPs do not have a conventional N-terminal mitochondrial targeting signal (MTS). We experimentally characterized a set of 15 yeast MRPs in vivo and found that five use internal MTSs. Further analysis of a conserved model MRP, Mrp17/bS6m, revealed the identity of the internal targeting signal. Similar to conventional MTS-containing proteins, the internal sequence mediates binding to TOM complexes. The entire sequence of Mrp17 contains positive charges mediating translocation. The fact that these sequence properties could not be reliably predicted by standard methods shows that mitochondrial protein targeting is more versatile than expected. We hypothesize that structural constraints imposed by ribosome assembly interfaces may have disfavored N-terminal presequences and driven the evolution of internal targeting signals in MRPs.

Keywords:  mitochondria; mitochondrial ribosome; mitochondrial targeting signal; targeting; translocation

DOI:  https://doi.org/10.15252/embj.2021109519
J Vis Exp. 2021 Oct 26.

High-Resolution Respirometry to assess Bioenergetics in Cells and Tissues using Chamber- and Plate-Based Respirometers.

Ryan Awadhpersad, Christopher B Jackson.

High-resolution respirometry (HRR) allows monitoring oxidative phosphorylation in real-time for analysis of individual cellular energy states and assessment of respiratory complexes using diversified substrate-uncoupler-inhibitor titration (SUIT) protocols. Here, the usage of two high-resolution respirometry devices is demonstrated, and a basic collection of protocols applicable for the analysis of cultured cells, skeletal and heart muscle fibers, and soft tissues such as the brain and liver are presented. Protocols for cultured cells and tissues are provided for a chamber-based respirometer and cultured cells for a microplate-based respirometer, both encompassing standard respiration protocols. For comparative purposes, CRISPR-engineered HEK293 cells deficient in mitochondrial translation causing multiple respiratory system deficiency are used with both devices to demonstrate cellular defects in respiration. Both respirometers allow for comprehensive measurement of cellular respiration with their respective technical merits and suitability dependent on the research question and model under study.

DOI: https://doi.org/10.3791/63000
Oncogene. 2021 Nov 15.

Emergence of β1 integrin-deficient breast tumours from dormancy involves both inactivation of p53 and generation of a permissive tumour microenvironment.

Tung Bui, Yu Gu, Frédéric Ancot, Virginie Sanguin-Gendreau, Dongmei Zuo, William J Muller.

The molecular and cellular mechanisms underlying mammary tumour dormancy and cancer recurrence are unclear and remain to be elucidated. Here, we report that mammary epithelial-specific disruption of β1 integrin in a murine model of Luminal B human breast cancer drastically impairs tumour growth with proliferation block, apoptosis induction and cellular senescence. β1 integrin-deficient dormant lesions show activation of the tumour suppressor p53, and tumours that circumvent dormancy possess p53 mutation analogous to those in human disease. We further demonstrate that mammary epithelial deletion of p53 in β1 integrin-deficient mice fully rescues tumour dormancy and bypasses cellular senescence. Additionally, recurrent β1 integrin-deficient tumours exhibit fibrosis with increased cancer-associated fibroblast infiltration and extracellular matrix deposition, absent in fast-growing β1 integrin/p53-deficient lesions. Taken together, these observations argue that β1 integrin modulates p53-dependent cellular senescence resulting in tumour dormancy and that pro-tumourigenic stromal cues and intrinsic genetic mutation are required for dormancy exit.

DOI: https://doi.org/10.1038/s41388-021-02107-7
Eur J Clin Invest. 2021 Nov 16. e13712

Class I HDAC Modulates Angiotensin II-induced Fibroblast Migration and Mitochondrial Overactivity.

Huynh Van Tin, R Lekha, Cheng-Chih Chung, Yung-Hsin Yeh, Yu-Hsun Kao, Yi-Jen Chen.

   BACKGROUND: Inhibition of histone deacetylases (HDACs) attenuates cardiac fibrosis. In this study, we evaluated whether the inhibition of class I HDACs can attenuate angiotensin II (ANG II)-induced fibrogenesis and mitochondrial malfunction through its effects on reactive oxygen species (ROS) and calcium dysregulation in human cardiac fibroblasts (CFs).
METHODS: Seahorse XF24 extracellular flux analyzer, fluorescence staining, Western blotting, HDAC activity assays, and Transwell migration assay were used to study mitochondrial respiration, adenosine triphosphate (ATP) production, mitochondrial calcium uptake and ROS, HDAC expression and activity, and fibroblast activity in CFs without (control) or with ANG II (100 nM) and/or MS-275 (HDAC class 1 inhibitor, 10 μM) for 24 h.
RESULTS: ANG II increased HDAC activity without changing protein expression in CFs. Compared with controls, ANG II-treated CFs had greater migration activity, higher ATP production, maximal respiration, and spare capacity with higher mitochondrial Ca2+ uptake and ROS generation, which was attenuated by the administration of MS-275. ANG II activated CFs by increasing mitochondrial calcium content and ATP production, which may be caused by increased HDAC activity. Inhibition of HDAC1 attenuated the effects of ANG II by reducing mitochondrial ROS generation and calcium overload.
CONCLUSIONS: Modulating mitochondrial function by regulation of HDAC may be a novel strategy for controlling CFs activity.

Keywords:  Angiotensin II; Cardiac fibrosis; Class I histone deacetylases; Mitochondria; Reactive oxygen species

DOI:  https://doi.org/10.1111/eci.13712
World J Stem Cells. 2021 Oct 26. 13(10): 1595-1609

Impact of senescence on the transdifferentiation process of human hepatic progenitor-like cells.

Francesco Bellanti, Giorgia di Bello, Rosanna Tamborra, Marco Amatruda, Aurelio Lo Buglio, Michał Dobrakowski, Aleksandra Kasperczyk, Sławomir Kasperczyk, Gaetano Serviddio, Gianluigi Vendemiale.

   BACKGROUND: Senescence is characterized by a decline in hepatocyte function, with impairment of metabolism and regenerative capacity. Several models that duplicate liver functions in vitro are essential tools for studying drug metabolism, liver diseases, and organ regeneration. The human HepaRG cell line represents an effective model for the study of liver metabolism and hepatic progenitors. However, the impact of senescence on HepaRG cells is not yet known.
AIM: To characterize the effects of senescence on the transdifferentiation capacity and mitochondrial metabolism of human HepaRG cells.
METHODS: We compared the transdifferentiation capacity of cells over 10 (passage 10 [P10]) vs P20. Aging was evaluated by senescence-associated (SA) beta-galactosidase activity and the comet assay. HepaRG transdifferentiation was analyzed by confocal microscopy and flow cytometry (expression of cluster of differentiation 49a [CD49a], CD49f, CD184, epithelial cell adhesion molecule [EpCAM], and cytokeratin 19 [CK19]), quantitative PCR analysis (expression of albumin, cytochrome P450 3A4 [CYP3A4], γ-glutamyl transpeptidase [γ-GT], and carcinoembryonic antigen [CEA]), and functional analyses (albumin secretion, CYP3A4, and γ-GT). Mitochondrial respiration and the ATP and nicotinamide adenine dinucleotide (NAD+)/NAD with hydrogen (NADH) content were also measured.
RESULTS: SA β-galactosidase staining was higher in P20 than P10 HepaRG cells; in parallel, the comet assay showed consistent DNA damage in P20 HepaRG cells. With respect to P10, P20 HepaRG cells exhibited a reduction of CD49a, CD49f, CD184, EpCAM, and CK19 after the induction of transdifferentiation. Furthermore, lower gene expression of albumin, CYP3A4, and γ-GT, as well as reduced albumin secretion capacity, CYP3A4, and γ-GT activity were reported in transdifferentiated P20 compared to P10 cells. By contrast, the gene expression level of CEA was not reduced by transdifferentiation in P20 cells. Of note, both cellular and mitochondrial oxygen consumption was lower in P20 than in P10 transdifferentiated cells. Finally, both ATP and NAD+/NADH were depleted in P20 cells with respect to P10 cells.
CONCLUSION: SA mitochondrial dysfunction may limit the transdifferentiation potential of HepaRG cells, with consequent impairment of metabolic and regenerative properties, which may alter applications in basic studies.

Keywords:  HepaRG cells; Mitochondria; Nicotinamide adenine dinucleotide; Regeneration; Senescence; Transdifferentiation

DOI:  https://doi.org/10.4252/wjsc.v13.i10.1595
Cancer Discov. 2021 Nov 17. pii: candisc.0410.2021. [Epub ahead of print]

Implementing a functional precision medicine tumor board for acute myeloid leukemia.

Disha Malani, Ashwini Kumar, Oscar Bruck, Mika Kontro, Bhagwan Yadav, Monica Hellesoy, Heikki Kuusanmaki, Olli Dufva, Matti Kankainen, Samuli Eldfors, Swapnil Potdar, Jani Saarela, Laura Turunen, Alun Parsons, Imre Vastrik, Katja Kivinen, Janna Saarela, Riikka Raty, Minna Lehto, Maija Wolf, Bjorn Tore Gjertsen, Satu Mustjoki, Tero Aittokallio, Krister Wennerberg, Caroline A Heckman, Olli Kallioniemi, Kimmo Porkka.

We generated ex vivo drug response and multi-omics profiling data for a prospective series of 252 samples from 186 acute myeloid leukemia (AML) patients. Functional precision medicine tumor board (FPMTB) integrated clinical, molecular and functional data for application in clinical treatment decisions. Actionable drugs were found for 97% of AML patients and the recommendations were clinically implemented in 37 relapsed or refractory patients. We report a 59% objective response rate for the individually tailored therapies, including 13 complete responses, as well as bridging five AML patients to allogeneic hematopoietic stem cell transplantation. Data integration across all cases enabled identification of drug response biomarkers, such as the association of IL15 overexpression with resistance to FLT3-inhibitors. Integration of molecular profiling and large-scale drug response data across many patients will enable continuous improvement of the FPMTB recommendations, providing a paradigm for individualized implementation of functional precision cancer medicine.

DOI: https://doi.org/10.1158/2159-8290.CD-21-0410
Blood. 2021 Nov 17. pii: blood.2020010344. [Epub ahead of print]

PP2A is a therapeutically targetable driver of cell fate decisions via a c-Myc/p21 axis in Acute Myeloid Leukemia.

Swagata Goswami, Rajeswaran Mani, Jessica Nunes, Chi-Ling Chiang, Kevan Zapolnik, Eileen Y Hu, Frank W Frissora, Xiaokui M Mo, Logan A Walker, Pearlly S Yan, Ralf Bundschuh, Larry Beaver, Raymond David Devine, Yo-Ting Tsai, Ann Marie Ventura, Zhiliang Xie, Min Chen, Rosa Lapalombella, Alison R Walker, Alice S Mims, Karilyn Larkin, Nicole Renee Grieselhuber, Chad Bennett, Mitch A Phelps, Erin Hertlein, Gregory K Behbehani, Sumithira Vasu, John C Byrd, Natarajan Muthusamy.

Dysregulated cellular differentiation is a hallmark of acute leukemogenesis. Phosphatases are widely suppressed in cancers but have not been traditionally associated with differentiation. Herein, we identified that the silencing of Protein Phosphatase 2A (PP2A) directly contributes to differentiation block in acute myeloid leukemia (AML). Gene expression and mass cytometric profiling reveal that PP2A activation modulates cell cycle and transcriptional regulators that program terminal myeloid differentiation. Using a novel pharmacological agent OSU-2S in parallel with genetic approaches, we discovered that PP2A enforces c-Myc and p21 dependent terminal differentiation, proliferation arrest and apoptosis in AML. Finally, we demonstrate that PP2A activation decreases leukemia initiating stem cells, increases leukemic blast maturation, and improves overall survival in murine Tet2-/-Flt3ITD/WT and human AML models in-vivo. Our findings identify the PP2A/c-Myc/p21 axis as a critical regulator of the differentiation/proliferation switch in AML that can be therapeutically targeted in malignancies with dysregulated maturation fate.

DOI: https://doi.org/10.1182/blood.2020010344
J Nanobiotechnology. 2021 Nov 18. 19(1): 375

Selectively down-regulated PD-L1 by albumin-phenformin nanoparticles mediated mitochondrial dysfunction to stimulate tumor-specific immunological response for enhanced mild-temperature photothermal efficacy.

Zaigang Zhou, Ning Jiang, Jiashe Chen, Chunjuan Zheng, Yuanyuan Guo, Ruirong Ye, Ruogu Qi, Jianliang Shen.

   BACKGROUND: Mild-temperature photothermal therapy (mild-PTT) has emerged as a highly promising antitumor strategy by triggering immunogenic cell death (ICD) to elicit both innate and adaptive immune responses for tumor control. However, mild-PTT still leads to the risk of tumor recurrence or metastasis because it could hardly completely eradicate tumors due to its impaired immunological efficacy owing to the enhanced PD-L1 expression in tumor cells after treatment.
RESULTS: In this study, we described a hydrogen peroxide (H2O2) responsive manganese dioxide mineralized albumin nanocomposite loading with mitochondria function inhibitor phenformin (PM) and near-infrared photothermal dye indocyanine green (ICG) by modified two-step biomineralization method. In combination with ICG induced mild-PTT and PM mediated mitochondria dysfunction, PD-L1 expression was obviously down-regulated and the generated immunological responses was able to effectively attack the remaining tumor cells. Meanwhile, the risk of tumor metastasis was effectively inhibited by reducing the expression of tumor invasion-related signal molecules (TGF-β and vimentin) after combining treatment.
CONCLUSION: Such a strategy offers novel insight into the development of nanomedicine for mild-PTT as well as cancer immunotherapy, which can provide protection against tumor relapse post elimination of their initial and metastatic tumors.

Keywords:  Biomineralization; Mild-temperature photothermal therapy; Mitochondrial inhibition; Programmed cell death-ligand 1; Tumor metastasis

DOI:  https://doi.org/10.1186/s12951-021-01124-8
Chemistry. 2021 Nov 17.

Rational design of self-assembled mitochondria- targeting lytic peptide conjugates with enhanced tumor selectivity.

Sijin Liu, Biao Wang, Yina Sheng, Suwei Dong, Guoquan Liu.

  Membrane lytic peptides (MLP) are widely explored as cellular delivery vehicles or antitumor/antibacterial agents. However, the poor selectivity between cancer and normal cells slims their prospects as potential anti-tumor drugs. Herein, we have developed a rationally designed self-assembly strategy to enhance tumor selectivity of MLP-based conjugates, incorporating a hydrophobic triphenylphosphonium (TPP) group for mitochondria targeting, and a hydrophilic Arginine-Glycine-Aspartic acid (RGD) sequence targeting integrin. The self-assembly nanoparticles can enhance the stability of the peptides in vitro plasma and be endocytosed selectively into the cancer cells. The histidine-rich lytic peptide component assists the disruption of endosomal/lysosomal membranes and subsequent the mitochondria membrane, which leads to apoptosis. This rational design of MLP-based conjugates provides a practical strategy to increase the application prospects of lytic peptides in cancer treatment.

Keywords:  Membrane lytic peptides; lysosomal escape; mitochondria-targeting; self-assembly; tumor selectivity

DOI:  https://doi.org/10.1002/chem.202103517
Cancer Discov. 2021 Nov 17. pii: candisc.0030.2021. [Epub ahead of print]

Fasting-mimicking diet is safe and reshapes metabolism and antitumor immunity in cancer patients.

Claudio Vernieri, Giovanni Fuca, Francesca Ligorio, Veronica Huber, Andrea Vingiani, Fabio Iannelli, Alessandra Raimondi, Darawan Rinchai, Gianmaria Frige, Antonino Belfiore, Luca Lalli, Claudia Chiodoni, Valeria Cancila, Federica Zanardi, Arta Ajazi, Salvatore Cortellino, Viviana Vallacchi, Paola Squarcina, Agata Cova, Samantha Pesce, Paola Frati, Raghvendra Mall, Paola Antonia Corsetto, Angela Maria Rizzo, Cristina Ferraris, Secondo Folli, Marina Chiara Garassino, Giuseppe Capri, Giulia Bianchi, Mario Paolo Colombo, Saverio Minucci, Marco Foiani, Valter Daniel Longo, Giovanni Apolone, Valter Torri, Giancarlo Pruneri, Davide Bedognetti, Licia Rivoltini, Filippo de Braud.

In tumor-bearing mice, cyclic fasting or fasting-mimicking diets (FMDs) enhance the activity of antineoplastic treatments by modulating systemic metabolism and boosting antitumor immunity. Here we conducted a clinical trial to investigate the safety and biological effects of cyclic, five-day FMD in combination with standard antitumor therapies. In 101 patients, the FMD was safe, feasible, and resulted in a consistent decrease of blood glucose and growth factor concentration, thus recapitulating metabolic changes that mediate fasting/FMD anticancer effects in preclinical experiments. Integrated transcriptomic and deep-phenotyping analyses revealed that FMD profoundly reshapes anticancer immunity by inducing the contraction of peripheral blood immunosuppressive myeloid and regulatory T-cell compartments, paralleled by enhanced intratumor T-helper 1/cytotoxic responses and an enrichment of interferon-gamma and other immune signatures associated with better clinical outcomes in cancer patients. Our findings lay the foundations for phase II/III clinical trials aimed at investigating FMD antitumor efficacy in combination with standard antineoplastic treatments.

DOI: https://doi.org/10.1158/2159-8290.CD-21-0030