bims-camemi 2021-06-27 papers

bims-camemi

Biomed News

on Mitochondrial metabolism in cancer

Issue of 2021–06–27
39 papers selected by
Christian Frezza, , University of Cambridge, MRC Cancer Unit

Hepcidin sequesters iron to sustain nucleotide metabolism and mitochondrial function in colorectal cancer epithelial cells.
Mitochondrial-derived vesicles compensate for loss of LC3-mediated mitophagy.
Mitochondrial metabolism regulates macrophage biology.
Mitochondrial function in development and disease.
Mitochondrial STAT5A promotes metabolic remodeling and the Warburg effect by inactivating the pyruvate dehydrogenase complex.
Identification and functional validation of FDA-approved positive and negative modulators of the mitochondrial calcium uniporter.
mTORC1 Activation is Not Sufficient to Suppress Hepatic PPARα Signaling or Ketogenesis.
The mitochondrial permeability transition pore: an evolving concept critical for cell life and death.
KEAP1 deficiency drives glucose dependency and sensitizes lung cancer cells and tumors to GLUT inhibition.
Protein tyrosine phosphatome metabolic screen identifies TC-PTP as a positive regulator of cancer cell bioenergetics and mitochondrial dynamics.
Monocarboxylate transporter antagonism reveals metabolic vulnerabilities of viral-driven lymphomas.
Prostate cancer cells survive anti-androgen and mitochondrial metabolic inhibitors by modulating glycolysis and mitochondrial metabolic activities.
Investigating Tumor Heterogeneity in Mouse Models.
Loss of neuronal Miro1 disrupts mitophagy and induces hyperactivation of the integrated stress response.
Myopathic mitochondrial DNA depletion syndrome associated with biallelic variants in LIG3.
Quantitative analysis of mitochondrial ATP synthesis.
Physiological extremes of the human blood metabolome: A metabolomics analysis of highly glycolytic, oxidative, and anabolic athletes.
Fever supports CD8+ effector T cell responses by promoting mitochondrial translation.
The HIF complex recruits the histone methyltransferase SET1B to activate specific hypoxia-inducible genes.
Histone acylations and chromatin dynamics: concepts, challenges, and links to metabolism.
Lactate Modulates Cellular Metabolism Through Histone Lactylation-Mediated Gene Expression in Non-Small Cell Lung Cancer.
Compensatory expression of NRF2-dependent antioxidant genes is required to overcome the lethal effects of Kv11.1 activation in breast cancer cells and PDOs.
Coordinated pyruvate kinase activity is crucial for metabolic adaptation and cell survival during mitochondrial dysfunction.
Systemic and cellular metabolism: the cause of and remedy for disease?
Impaired anaplerosis is a major contributor to glycolysis inhibitor toxicity in glioma.
Mitochondrial NAD(P)+ transhydrogenase: from molecular features to physiology and disease.
TGF-β-dependent reprogramming of amino acid metabolism induces epithelial-mesenchymal transition in non-small cell lung cancers.
Short- and Long-Term Adaptation to Altered Levels of Glucose: Fifty Years of Scientific Adventure.
A transcriptional switch governs fibroblast activation in heart disease.
LINC00842 inactivates transcription co-regulator PGC-1α to promote pancreatic cancer malignancy through metabolic remodelling.
MCT4 is induced by metastasis-enhancing pathogenic mitochondrial NADH dehydrogenase gene mutations and can be a therapeutic target.
Fascin1 empowers YAP mechanotransduction and promotes cholangiocarcinoma development.
Cellular and metabolic mechanisms of nutrient actions in immune function.
Arginine starvation elicits chromatin leakage and cGAS-STING activation via epigenetic silencing of metabolic and DNA-repair genes.
Serine hydroxymethyltransferase 2 expression promotes tumorigenesis in rhabdomyosarcoma with 12q13-14 amplification.
Systemic regulation of mitochondria by germline proteostasis prevents protein aggregation in the soma of C. elegans.
Developmental Consequences of Defective ATG7-Mediated Autophagy in Humans.
Lactate and IL6 define separable paths of inflammatory metabolic adaptation.
AMBRA1 has an impact on melanoma development beyond autophagy.

Nat Metab. 2021 Jun 21.

Hepcidin sequesters iron to sustain nucleotide metabolism and mitochondrial function in colorectal cancer epithelial cells.

Andrew J Schwartz, Joshua W Goyert, Sumeet Solanki, Samuel A Kerk, Brandon Chen, Cristina Castillo, Peggy P Hsu, Brian T Do, Rashi Singhal, Michael K Dame, Ho-Joon Lee, Jason R Spence, Samira Lakhal-Littleton, Matthew G Vander Heiden, Costas A Lyssiotis, Xiang Xue, Yatrik M Shah.

Colorectal cancer (CRC) requires massive iron stores, but the complete mechanisms by which CRC modulates local iron handling are poorly understood. Here, we demonstrate that hepcidin is activated ectopically in CRC. Mice deficient in hepcidin specifically in the colon tumour epithelium, compared with wild-type littermates, exhibit significantly diminished tumour number, burden and size in a sporadic model of CRC, whereas accumulation of intracellular iron by deletion of the iron exporter ferroportin exacerbates these tumour parameters. Metabolomic analysis of three-dimensional patient-derived CRC tumour enteroids indicates a prioritization of iron in CRC for the production of nucleotides, which is recapitulated in our hepcidin/ferroportin mouse CRC models. Mechanistically, our data suggest that iron chelation decreases mitochondrial function, thereby altering nucleotide synthesis, whereas exogenous supplementation of nucleosides or aspartate partially rescues tumour growth in patient-derived enteroids and CRC cell lines in the presence of an iron chelator. Collectively, these data suggest that ectopic hepcidin in the tumour epithelium establishes an axis to sequester iron in order to maintain the nucleotide pool and sustain proliferation in colorectal tumours.

DOI: https://doi.org/10.1038/s42255-021-00406-7
Dev Cell. 2021 Jun 24. pii: S1534-5807(21)00481-0. [Epub ahead of print]

Mitochondrial-derived vesicles compensate for loss of LC3-mediated mitophagy.

Christina G Towers, Darya K Wodetzki, Jacqueline Thorburn, Katharine R Smith, M Cecilia Caino, Andrew Thorburn.

  Mitochondria are critical metabolic and signaling hubs, and dysregulated mitochondrial homeostasis is implicated in many diseases. Degradation of damaged mitochondria by selective GABARAP/LC3-dependent macro-autophagy (mitophagy) is critical for maintaining mitochondrial homeostasis. To identify alternate forms of mitochondrial quality control that functionally compensate if mitophagy is inactive, we selected for autophagy-dependent cancer cells that survived loss of LC3-dependent autophagosome formation caused by inactivation of ATG7 or RB1CC1/FIP200. We discovered rare surviving autophagy-deficient clones that adapted to maintain mitochondrial homeostasis after gene inactivation and identified two enhanced mechanisms affecting mitochondria including mitochondrial dynamics and mitochondrial-derived vesicles (MDVs). To further understand these mechanisms, we quantified MDVs via flow cytometry and confirmed an SNX9-mediated mechanism necessary for flux of MDVs to lysosomes. We show that the autophagy-dependent cells acquire unique dependencies on these processes, indicating that these alternate forms of mitochondrial homeostasis compensate for loss of autophagy to maintain mitochondrial health.

Keywords:  ATG7; FIP200; SNX9; autophagy; cancer; late endosomes; mitochondria; mitochondrial dynamics; mitochondrial-derived vesicles; mitophagy

DOI:  https://doi.org/10.1016/j.devcel.2021.06.003
J Biol Chem. 2021 Jun 19. pii: S0021-9258(21)00704-3. [Epub ahead of print] 100904

Mitochondrial metabolism regulates macrophage biology.

Yafang Wang, Na Li, Xin Zhang, Tiffany Horng.

  Mitochondria are critical for regulation of the activation, differentiation, and survival of macrophages and other immune cells. In response to various extracellular signals, such as microbial or viral infection, changes to mitochondrial metabolism and physiology could underlie the corresponding state of macrophage activation. These changes include alterations of oxidative metabolism, mitochondrial membrane potential, and tricarboxylic acid (TCA) cycling, as well as the release of mitochondrial reactive oxygen species (mtROS) and mitochondrial DNA (mtDNA) and transformation of the mitochondrial ultrastructure. Here, we provide an updated review of how changes in mitochondrial metabolism and various metabolites such as fumarate, succinate, and itaconate coordinate to guide macrophage activation to distinct cellular states, thus clarifying the vital link between mitochondria metabolism and immunity. We also discuss how in disease settings, mitochondrial dysfunction and oxidative stress contribute to dysregulation of the inflammatory response. Therefore, mitochondria are a vital source of dynamic signals that regulate macrophage biology to fine-tune immune responses.

Keywords:  macrophage activation; macrophage biology; mitochondrial dysfunction; mitochondrial metabolism; oxidative stress

DOI:  https://doi.org/10.1016/j.jbc.2021.100904
Dis Model Mech. 2021 Jun 01. pii: dmm048912. [Epub ahead of print]14(6):

Mitochondrial function in development and disease.

Marlies P Rossmann, Sonia M Dubois, Suneet Agarwal, Leonard I Zon.

  Mitochondria are organelles with vital functions in almost all eukaryotic cells. Often described as the cellular 'powerhouses' due to their essential role in aerobic oxidative phosphorylation, mitochondria perform many other essential functions beyond energy production. As signaling organelles, mitochondria communicate with the nucleus and other organelles to help maintain cellular homeostasis, allow cellular adaptation to diverse stresses, and help steer cell fate decisions during development. Mitochondria have taken center stage in the research of normal and pathological processes, including normal tissue homeostasis and metabolism, neurodegeneration, immunity and infectious diseases. The central role that mitochondria assume within cells is evidenced by the broad impact of mitochondrial diseases, caused by defects in either mitochondrial or nuclear genes encoding for mitochondrial proteins, on different organ systems. In this Review, we will provide the reader with a foundation of the mitochondrial 'hardware', the mitochondrion itself, with its specific dynamics, quality control mechanisms and cross-organelle communication, including its roles as a driver of an innate immune response, all with a focus on development, disease and aging. We will further discuss how mitochondrial DNA is inherited, how its mutation affects cell and organismal fitness, and current therapeutic approaches for mitochondrial diseases in both model organisms and humans.

Keywords:  Mitochondrial diseases; Mitochondrial fusion and fission; Mitochondrial unfolded protein response; Mitophagy; mtDNA heteroplasmy and inheritance; mtDNA-mediated innate immune response

DOI:  https://doi.org/10.1242/dmm.048912
Cell Death Dis. 2021 Jun 19. 12(7): 634

Mitochondrial STAT5A promotes metabolic remodeling and the Warburg effect by inactivating the pyruvate dehydrogenase complex.

Liang Zhang, Jianong Zhang, Yan Liu, Pingzhao Zhang, Ji Nie, Rui Zhao, Qin Shi, Huiru Sun, Dongyue Jiao, Yingji Chen, Xiaying Zhao, Yan Huang, Yao Li, Jian-Yuan Zhao, Wei Xu, Shi-Min Zhao, Chenji Wang.

Signal transducer and activator 5a (STAT5A) is a classical transcription factor that plays pivotal roles in various biological processes, including tumor initiation and progression. A fraction of STAT5A is localized in the mitochondria, but the biological functions of mitochondrial STAT5A remain obscure. Here, we show that STAT5A interacts with pyruvate dehydrogenase complex (PDC), a mitochondrial gatekeeper enzyme connecting two key metabolic pathways, glycolysis and the tricarboxylic acid cycle. Mitochondrial STAT5A disrupts PDC integrity, thereby inhibiting PDC activity and remodeling cellular glycolysis and oxidative phosphorylation. Mitochondrial translocation of STAT5A is increased under hypoxic conditions. This strengthens the Warburg effect in cancer cells and promotes in vitro cell growth under hypoxia and in vivo tumor growth. Our findings indicate distinct pro-oncogenic roles of STAT5A in energy metabolism, which is different from its classical function as a transcription factor.

DOI: https://doi.org/10.1038/s41419-021-03908-0
Cell Rep. 2021 Jun 22. pii: S2211-1247(21)00642-2. [Epub ahead of print]35(12): 109275

Identification and functional validation of FDA-approved positive and negative modulators of the mitochondrial calcium uniporter.

Agnese De Mario, Anna Tosatto, Julia Marie Hill, Janos Kriston-Vizi, Robin Ketteler, Denis Vecellio Reane, Gino Cortopassi, Gyorgy Szabadkai, Rosario Rizzuto, Cristina Mammucari.

  The mitochondrial calcium uniporter (MCU), the highly selective channel responsible for mitochondrial Ca2+ entry, plays important roles in physiology and pathology. However, only few pharmacological compounds directly and selectively modulate its activity. Here, we perform high-throughput screening on a US Food and Drug Administration (FDA)-approved drug library comprising 1,600 compounds to identify molecules modulating mitochondrial Ca2+ uptake. We find amorolfine and benzethonium to be positive and negative MCU modulators, respectively. In agreement with the positive effect of MCU in muscle trophism, amorolfine increases muscle size, and MCU silencing is sufficient to blunt amorolfine-induced hypertrophy. Conversely, in the triple-negative breast cancer cell line MDA-MB-231, benzethonium delays cell growth and migration in an MCU-dependent manner and protects from ceramide-induced apoptosis, in line with the role of mitochondrial Ca2+ uptake in cancer progression. Overall, we identify amorolfine and benzethonium as effective MCU-targeting drugs applicable to a wide array of experimental and disease conditions.

Keywords:  FDA-approved drugs; MCU; amorolfine; benzethonium; high-throughput screening; mitochondrial Ca(2+) uptake; mitochondrial calcium uniporter; skeletal muscle hypertrophy; triple-negative breast cancer

DOI:  https://doi.org/10.1016/j.celrep.2021.109275
J Biol Chem. 2021 Jun 16. pii: S0021-9258(21)00684-0. [Epub ahead of print] 100884

mTORC1 Activation is Not Sufficient to Suppress Hepatic PPARα Signaling or Ketogenesis.

Ebru S Selen, Michael J Wolfgang.

  The mechanistic target of rapamycin (mTOR) is often referred to as a master regulator of cellular metabolism that can integrate growth factor and nutrient signaling. Fasting suppresses hepatic mTORC1 activity via the activity of the Tuberous Sclerosis Complex (TSC), a negative regulator of mTORC1, in order to suppress anabolic metabolism. The loss of TSC1 in the liver locks the liver in a constitutively anabolic state even during fasting, which was suggested to regulate PPARα signaling and ketogenesis, but the molecular determinants of this regulation are unknown. Here, we examined if the activation of the mTORC1 complex in mice by the liver-specific deletion of TSC1 (TSC1L-/-) is sufficient to suppress PPARα signaling and therefore ketogenesis in the fasted state. We found that the activation of mTORC1 in the fasted state is not sufficient to repress PPARα-responsive genes or ketogenesis. Further, we examined whether the activation of the anabolic program mediated by mTORC1 complex activation in the fasted state could suppress the robust catabolic programming and enhanced PPARα transcriptional response of mice with a liver-specific defect in mitochondrial long-chain fatty acid oxidation using Cpt2L-/- mice. We generated liver-specific Cpt2L-/-; Tsc1L-/- double knockout mice and showed that the activation of mTORC1 by deletion of TSC1 could not suppress the catabolic PPARα-mediated phenotype of Cpt2L-/- mice. These data demonstrate that the activation of mTORC1 by the deletion of TSC1 is not sufficient to suppress a PPARα transcriptional program or ketogenesis following fasting.

Keywords:  Ketogenesis; carnitine palmitoyltransferase 2 (Cpt2); fatty acid oxidation; mTOR; metabolism; peroxisome proliferator-activated receptor alpha (PPARα); β-hydroxybutyrate (βHB)

DOI:  https://doi.org/10.1016/j.jbc.2021.100884
Biol Rev Camb Philos Soc. 2021 Jun 21.

The mitochondrial permeability transition pore: an evolving concept critical for cell life and death.

Giampaolo Morciano, Natalia Naumova, Piotr Koprowski, Sara Valente, Vilma A Sardão, Yaiza Potes, Alessandro Rimessi, Mariusz R Wieckowski, Paulo J Oliveira.

  In this review, we summarize current knowledge of perhaps one of the most intriguing phenomena in cell biology: the mitochondrial permeability transition pore (mPTP). This phenomenon, which was initially observed as a sudden loss of inner mitochondrial membrane impermeability caused by excessive calcium, has been studied for almost 50 years, and still no definitive answer has been provided regarding its mechanisms. From its initial consideration as an in vitro artifact to the current notion that the mPTP is a phenomenon with physiological and pathological implications, a long road has been travelled. We here summarize the role of mitochondria in cytosolic calcium control and the evolving concepts regarding the mitochondrial permeability transition (mPT) and the mPTP. We show how the evolving mPTP models and mechanisms, which involve many proposed mitochondrial protein components, have arisen from methodological advances and more complex biological models. We describe how scientific progress and methodological advances have allowed milestone discoveries on mPTP regulation and composition and its recognition as a valid target for drug development and a critical component of mitochondrial biology.

Keywords:  calcium; cell death; mitochondria; mitochondrial permeability transition pore

DOI:  https://doi.org/10.1111/brv.12764
iScience. 2021 Jun 25. 24(6): 102649

KEAP1 deficiency drives glucose dependency and sensitizes lung cancer cells and tumors to GLUT inhibition.

Pranavi Koppula, Kellen Olszewski, Yilei Zhang, Lavanya Kondiparthi, Xiaoguang Liu, Guang Lei, Molina Das, Bingliang Fang, Masha V Poyurovsky, Boyi Gan.

  Metabolic reprogramming in cancer cells can create metabolic liabilities. KEAP1-mutant lung cancer is refractory to most current therapies. Here we show that KEAP1 deficiency promotes glucose dependency in lung cancer cells, and KEAP1-mutant/deficient lung cancer cells are more vulnerable to glucose deprivation than their WT counterparts. Mechanistically, KEAP1 inactivation in lung cancer cells induces constitutive activation of NRF2 transcription factor and aberrant expression of NRF2 target cystine transporter SLC7A11; under glucose limitation, high cystine uptake in KEAP1-inactivated lung cancer cells stimulates toxic intracellular disulfide buildup, NADPH depletion, and cell death, which can be rescued by genetic ablation of NRF2-SLC7A11 axis or treatments inhibiting disulfide accumulation. Finally, we show that KEAP1-inactivated lung cancer cells or xenograft tumors are sensitive to glucose transporter inhibitor. Together, our results reveal that KEAP1 deficiency induces glucose dependency in lung cancer cells and uncover a therapeutically relevant metabolic liability.

Keywords:  cancer; cell biology; physiology

DOI:  https://doi.org/10.1016/j.isci.2021.102649
FASEB J. 2021 Jul;35(7): e21708

Protein tyrosine phosphatome metabolic screen identifies TC-PTP as a positive regulator of cancer cell bioenergetics and mitochondrial dynamics.

Valerie Vinette, Isabelle Aubry, Hayley Insull, Noriko Uetani, Serge Hardy, Michel L Tremblay.

  Metabolic reprogramming occurs in cancer cells and is regulated partly by the opposing actions of tyrosine kinases and tyrosine phosphatases. Several members of the protein tyrosine phosphatase (PTP) superfamily have been linked to cancer as either pro-oncogenic or tumor-suppressive enzymes. In order to investigate which PTPs can modulate the metabolic state of cancer cells, we performed an shRNA screen of PTPs in HCT116 human colorectal cancer cells. Among the 72 PTPs efficiently targeted, 24 were found to regulate mitochondrial respiration, 8 as negative and 16 as positive regulators. Of the latter, we selected TC-PTP (PTPN2) for further characterization since inhibition of this PTP resulted in major functional defects in oxidative metabolism without affecting glycolytic flux. Transmission electron microscopy revealed an increase in the number of damaged mitochondria in TC-PTP-null cells, demonstrating the potential role of this PTP in regulating mitochondrial homeostasis. Downregulation of STAT3 by siRNA-mediated silencing partially rescued the mitochondrial respiration defect observed in TC-PTP-deficient cells, supporting the role of this signaling axis in regulating mitochondrial activity. In addition, mitochondrial stress prevented an increased expression of electron transport chain-related genes in cells with TC-PTP silencing, correlating with decreased ATP production, cellular proliferation, and migration. Our shRNA-based metabolic screen revealed that PTPs can serve as either positive or negative regulators of cancer cell metabolism. Taken together, our findings uncover a new role for TC-PTP as an activator of mitochondrial metabolism, validating this PTP as a key target for cancer therapeutics.

Keywords:  PTPN2; TC-PTP; cancer; metabolism; mitochondria; protein tyrosine phosphatases

DOI:  https://doi.org/10.1096/fj.202100207R
Proc Natl Acad Sci U S A. 2021 Jun 22. pii: e2022495118. [Epub ahead of print]118(25):

Monocarboxylate transporter antagonism reveals metabolic vulnerabilities of viral-driven lymphomas.

Emmanuela N Bonglack, Joshua E Messinger, Jana M Cable, James Ch'ng, K Mark Parnell, Nicolás M Reinoso-Vizcaíno, Ashley P Barry, Veronica S Russell, Sandeep S Dave, Heather R Christofk, Micah A Luftig.

  Epstein-Barr virus (EBV) is a ubiquitous herpesvirus that typically causes asymptomatic infection but can promote B lymphoid tumors in the immune suppressed. In vitro, EBV infection of primary B cells stimulates glycolysis during immortalization into lymphoblastoid cell lines (LCLs). Lactate export during glycolysis is crucial for continued proliferation of many cancer cells-part of a phenomenon known as the "Warburg effect"- and is mediated by monocarboxylate transporters (MCTs). However, the role of MCTs has yet to be studied in EBV-associated malignancies, which display Warburg-like metabolism in vitro. Here, we show that EBV infection of B lymphocytes directly promotes temporal induction of MCT1 and MCT4 through the viral proteins EBNA2 and LMP1, respectively. Functionally, MCT1 was required for early B cell proliferation, and MCT4 up-regulation promoted acquired resistance to MCT1 antagonism in LCLs. However, dual MCT1/4 inhibition led to LCL growth arrest and lactate buildup. Metabolic profiling in LCLs revealed significantly reduced oxygen consumption rates (OCRs) and NAD+/NADH ratios, contrary to previous observations of increased OCR and unaltered NAD+/NADH ratios in MCT1/4-inhibited cancer cells. Furthermore, U-13C6-glucose labeling of MCT1/4-inhibited LCLs revealed depleted glutathione pools that correlated with elevated reactive oxygen species. Finally, we found that dual MCT1/4 inhibition also sensitized LCLs to killing by the electron transport chain complex I inhibitors phenformin and metformin. These findings were extended to viral lymphomas associated with EBV and the related gammaherpesvirus KSHV, pointing at a therapeutic approach for targeting both viral lymphomas.

Keywords:  Epstein–Barr virus; cancer metabolism; lactate export; monocarboxylate transporter; viral lymphoma

DOI:  https://doi.org/10.1073/pnas.2022495118
Prostate. 2021 Jun 25.

Prostate cancer cells survive anti-androgen and mitochondrial metabolic inhibitors by modulating glycolysis and mitochondrial metabolic activities.

Hirak S Basu, Nathaniel Wilganowski, Samantha Robertson, James M Reuben, Evan N Cohen, Amado Zurita, Sumankalai Ramachandran, Lian-Chun Xiao, Mark Titus, George Wilding.

BACKGROUND: Most cancer cells are more glycolytic even under aerobic conditions compared with their normal counterparts. Recent evidence of tumor cell metabolism, however, shows that some tumors also increase mitochondrial oxidative phosphorylation (ox-phos) at some disease states during progression and/or development of drug resistance. Our data show that anti-androgen enzalutamide (ENZA) resistant prostate cancer (PCa) cells use more mitochondrial metabolism leading to higher ox-phos as compared to the ENZA-sensitive cells and can become vulnerable to mitochondrial metabolism targeted therapies.
METHODS: Seahorse assay, mass spectrometry and high resolution fluorescence confocal microscopy coupled with image analysis has been used to compare mitochondrial metabolism in ENZA-treated and -untreated anti-androgen-sensitive LNCaP and -resistant C4-2, CWR22ν1, and PCa2b cells. Ex vivo fluorescence microscopy and image analysis has been standardized to monitor mitochondrial electron transport (ETS) activity that likely increases ox-phos in circulating tumor cells (CTCs) isolated fom patients undergoing AR-targeted therapies.
RESULTS: Our data show that PCa cells that are resistant to anti-androgen ENZA switch from glycolysis to ox-phos leading to an increased ETS activity. ENZA pretreated cells are more vulnerable to ETS component complex I inhibitor IACS-010759 (IACS) and mitochondrial glutaminase inhibitor CB-839 that reduces glutamate supply to tricarboxylic acid cycle. CTCs isolated from 6 of 20 patient blood samples showed relatively higher ETS activity than the rest of the patients. All six patients have developed ENZA resistance within less than 6 months of the sample collection.
CONCLUSION: The enhanced growth inhibitory effects of mitochondrial metabolic inhibitors IACS and CB-839 in ENZA pretreated PCa cells provides a rationale for designing a drug combination trial. Patients can be selected for such trials by monitoring the mitochondrial ETS activities in their CTCs to maximize success.

DOI: https://doi.org/10.1002/pros.24146
Annu Rev Cancer Biol. 2020 Mar;4(1): 99-119

Investigating Tumor Heterogeneity in Mouse Models.

Tuomas Tammela, Julien Sage.

  Cancer arises from a single cell through a series of acquired mutations and epigenetic alterations. Tumors gradually develop into a complex tissue comprised of phenotypically heterogeneous cancer cell populations, as well as noncancer cells that make up the tumor microenvironment. The phenotype, or state, of each cancer and stromal cell is influenced by a plethora of cell-intrinsic and cell-extrinsic factors. The diversity of these cellular states promotes tumor progression, enables metastasis, and poses a challenge for effective cancer treatments. Thus, the identification of strategies for the therapeutic manipulation of tumor heterogeneity would have significant clinical implications. A major barrier in the field is the difficulty in functionally investigating heterogeneity in tumors in cancer patients. Here we review how mouse models of human cancer can be leveraged to interrogate tumor heterogeneity and to help design better therapeutic strategies.

Keywords:  cancer stem cells; epigenetics; genetics; mouse models; tumor heterogeneity; tumor microenvironment

DOI:  https://doi.org/10.1146/annurev-cancerbio-030419-033413
EMBO J. 2021 Jun 21. e100715

Loss of neuronal Miro1 disrupts mitophagy and induces hyperactivation of the integrated stress response.

Guillermo López-Doménech, Jack H Howden, Christian Covill-Cooke, Corinne Morfill, Jigna V Patel, Roland Bürli, Damian Crowther, Nicol Birsa, Nicholas J Brandon, Josef T Kittler.

  Clearance of mitochondria following damage is critical for neuronal homeostasis. Here, we investigate the role of Miro proteins in mitochondrial turnover by the PINK1/Parkin mitochondrial quality control system in vitro and in vivo. We find that upon mitochondrial damage, Miro is promiscuously ubiquitinated on multiple lysine residues. Genetic deletion of Miro or block of Miro1 ubiquitination and subsequent degradation lead to delayed translocation of the E3 ubiquitin ligase Parkin onto damaged mitochondria and reduced mitochondrial clearance in both fibroblasts and cultured neurons. Disrupted mitophagy in vivo, upon post-natal knockout of Miro1 in hippocampus and cortex, leads to a dramatic increase in mitofusin levels, the appearance of enlarged and hyperfused mitochondria and hyperactivation of the integrated stress response (ISR). Altogether, our results provide new insights into the central role of Miro1 in the regulation of mitochondrial homeostasis and further implicate Miro1 dysfunction in the pathogenesis of human neurodegenerative disease.

Keywords:  Parkinson’s disease; Rhot1; Rhot2; eIF2α; megamitochondria

DOI:  https://doi.org/10.15252/embj.2018100715
Brain. 2021 Jun 24. pii: awab238. [Epub ahead of print]

Myopathic mitochondrial DNA depletion syndrome associated with biallelic variants in LIG3.

Federica Invernizzi, Andrea Legati, Alessia Nasca, Eleonora Lamantea, Barbara Garavaglia, Mjriana Gusic, Robert Kopajtich, Holger Prokisch, Massimo Zeviani, Costanza Lamperti, Daniele Ghezzi.

DOI: https://doi.org/10.1093/brain/awab238
Math Biosci. 2021 Jun 16. pii: S0025-5564(21)00083-3. [Epub ahead of print] 108646

Quantitative analysis of mitochondrial ATP synthesis.

E Benjamin Randall, Marcus Hock, Rachel Lopez, Bahador Marzban, Collin Marshall, Daniel A Beard.

  We present a computational framework for analyzing and simulating mitochondrial ATP synthesis using basic thermodynamic and kinetic principles. The framework invokes detailed descriptions of the thermodynamic driving forces associated with the processes of the electron transport chain, mitochondrial ATP synthetase, and phosphate and adenine nucleotide transporters. Assembling models of these discrete processes into an integrated model of mitochondrial ATP synthesis, we illustrate how to analyze and simulate in vitro respirometry experiments and how models identified from in vitro experimental data effectively explain cardiac respiratory control in vivo. Computer codes for these analyses are embedded as Python scripts in a Jupyter Book to facilitate easy adoption and modification of the concepts developed here. This accessible framework may also prove useful in supporting educational applications. All source codes are available on at https://beards-lab.github.io/QAMAS_book/.

Keywords:  Biochemical thermodynamics; Bioenergetics; Computational modeling; Metabolic pathways; Respiratory

DOI:  https://doi.org/10.1016/j.mbs.2021.108646
Physiol Rep. 2021 Jun;9(12): e14885

Physiological extremes of the human blood metabolome: A metabolomics analysis of highly glycolytic, oxidative, and anabolic athletes.

Daniela Schranner, Martin Schönfelder, Werner Römisch-Margl, Johannes Scherr, Jürgen Schlegel, Otto Zelger, Annett Riermeier, Stephanie Kaps, Cornelia Prehn, Jerzy Adamski, Quirin Söhnlein, Fabian Stöcker, Florian Kreuzpointner, Martin Halle, Gabi Kastenmüller, Henning Wackerhage.

  Human metabolism is highly variable. At one end of the spectrum, defects of enzymes, transporters, and metabolic regulation result in metabolic diseases such as diabetes mellitus or inborn errors of metabolism. At the other end of the spectrum, favorable genetics and years of training combine to result in physiologically extreme forms of metabolism in athletes. Here, we investigated how the highly glycolytic metabolism of sprinters, highly oxidative metabolism of endurance athletes, and highly anabolic metabolism of natural bodybuilders affect their serum metabolome at rest and after a bout of exercise to exhaustion. We used targeted mass spectrometry-based metabolomics to measure the serum concentrations of 151 metabolites and 43 metabolite ratios or sums in 15 competitive male athletes (6 endurance athletes, 5 sprinters, and 4 natural bodybuilders) and 4 untrained control subjects at fasted rest and 5 minutes after a maximum graded bicycle test to exhaustion. The analysis of all 194 metabolite concentrations, ratios and sums revealed that natural bodybuilders and endurance athletes had overall different metabolite profiles, whereas sprinters and untrained controls were more similar. Specifically, natural bodybuilders had 1.5 to 1.8-fold higher concentrations of specific phosphatidylcholines and lower levels of branched chain amino acids than all other subjects. Endurance athletes had 1.4-fold higher levels of a metabolite ratio showing the activity of carnitine-palmitoyl-transferase I and 1.4-fold lower levels of various alkyl-acyl-phosphatidylcholines. When we compared the effect of exercise between groups, endurance athletes showed 1.3-fold higher increases of hexose and of tetradecenoylcarnitine (C14:1). In summary, physiologically extreme metabolic capacities of endurance athletes and natural bodybuilders are associated with unique blood metabolite concentrations, ratios, and sums at rest and after exercise. Our results suggest that long-term specific training, along with genetics and other athlete-specific factors systematically change metabolite concentrations at rest and after exercise.

Keywords:  athlete; energy metabolism; exercise biomarker; exercise phenotype

DOI:  https://doi.org/10.14814/phy2.14885
Proc Natl Acad Sci U S A. 2021 Jun 22. pii: e2023752118. [Epub ahead of print]118(25):

Fever supports CD8+ effector T cell responses by promoting mitochondrial translation.

David O'Sullivan, Michal A Stanczak, Matteo Villa, Franziska M Uhl, Mauro Corrado, Ramon I Klein Geltink, David E Sanin, Petya Apostolova, Nisha Rana, Joy Edwards-Hicks, Katarzyna M Grzes, Agnieszka M Kabat, Ryan L Kyle, Mario Fabri, Jonathan D Curtis, Michael D Buck, Annette E Patterson, Annamaria Regina, Cameron S Field, Francesc Baixauli, Daniel J Puleston, Edward J Pearce, Robert Zeiser, Erika L Pearce.

  Fever can provide a survival advantage during infection. Metabolic processes are sensitive to environmental conditions, but the effect of fever on T cell metabolism is not well characterized. We show that in activated CD8+ T cells, exposure to febrile temperature (39 °C) augmented metabolic activity and T cell effector functions, despite having a limited effect on proliferation or activation marker expression. Transcriptional profiling revealed an up-regulation of mitochondrial pathways, which was consistent with increased mass and metabolism observed in T cells exposed to 39 °C. Through in vitro and in vivo models, we determined that mitochondrial translation is integral to the enhanced metabolic activity and function of CD8+ T cells exposed to febrile temperature. Transiently exposing donor lymphocytes to 39 °C prior to infusion in a myeloid leukemia mouse model conferred enhanced therapeutic efficacy, raising the possibility that exposure of T cells to febrile temperatures could have clinical potential.

Keywords:  T cell; fever; immunology; metabolism; mitochondria

DOI:  https://doi.org/10.1073/pnas.2023752118
Nat Genet. 2021 Jun 21.

The HIF complex recruits the histone methyltransferase SET1B to activate specific hypoxia-inducible genes.

Brian M Ortmann, Natalie Burrows, Ian T Lobb, Esther Arnaiz, Niek Wit, Peter S J Bailey, Louise H Jordon, Olivia Lombardi, Ana Peñalver, James McCaffrey, Rachel Seear, David R Mole, Peter J Ratcliffe, Patrick H Maxwell, James A Nathan.

Hypoxia-inducible transcription factors (HIFs) are fundamental to cellular adaptation to low oxygen levels, but it is unclear how they interact with chromatin and activate their target genes. Here, we use genome-wide mutagenesis to identify genes involved in HIF transcriptional activity, and define a requirement for the histone H3 lysine 4 (H3K4) methyltransferase SET1B. SET1B loss leads to a selective reduction in transcriptional activation of HIF target genes, resulting in impaired cell growth, angiogenesis and tumor establishment in SET1B-deficient xenografts. Mechanistically, we show that SET1B accumulates on chromatin in hypoxia, and is recruited to HIF target genes by the HIF complex. The selective induction of H3K4 trimethylation at HIF target loci is both HIF- and SET1B-dependent and, when impaired, correlates with decreased promoter acetylation and gene expression. Together, these findings show SET1B as a determinant of site-specific histone methylation and provide insight into how HIF target genes are differentially regulated.

DOI: https://doi.org/10.1038/s41588-021-00887-y
EMBO Rep. 2021 Jun 23. e52774

Histone acylations and chromatin dynamics: concepts, challenges, and links to metabolism.

Sandra Nitsch, Lara Zorro Shahidian, Robert Schneider.

  In eukaryotic cells, DNA is tightly packed with the help of histone proteins into chromatin. Chromatin architecture can be modified by various post-translational modifications of histone proteins. For almost 60 years now, studies on histone lysine acetylation have unraveled the contribution of this acylation to an open chromatin state with increased DNA accessibility, permissive for gene expression. Additional complexity emerged from the discovery of other types of histone lysine acylations. The acyl group donors are products of cellular metabolism, and distinct histone acylations can link the metabolic state of a cell with chromatin architecture and contribute to cellular adaptation through changes in gene expression. Currently, various technical challenges limit our full understanding of the actual impact of most histone acylations on chromatin dynamics and of their biological relevance. In this review, we summarize the state of the art and provide an overview of approaches to overcome these challenges. We further discuss the concept of subnuclear metabolic niches that could regulate local CoA availability and thus couple cellular metabolisms with the epigenome.

Keywords:  acylation; chromatin; histones; metabolism; microdomains

DOI:  https://doi.org/10.15252/embr.202152774
Front Oncol. 2021 ;11 647559

Lactate Modulates Cellular Metabolism Through Histone Lactylation-Mediated Gene Expression in Non-Small Cell Lung Cancer.

Jun Jiang, DengLiang Huang, Yuan Jiang, Jing Hou, MeiYuan Tian, JianHua Li, Li Sun, YaoGang Zhang, Tao Zhang, ZhiQin Li, ZhongCheng Li, SiXian Tong, YanYan Ma.

  Lactate has been observed to fuel TCA cycle and is associated with cancer progression in human lung cancer, the leading cause of cancer deaths worldwide, but the effect of lactate on lung cancer metabolism is rarely reported. In this study, disordered metabolism in non-small cell lung cancer was demonstrated by increased G6PD and SDHA protein levels via immunofluorescence, and up-regulated lactate dehydrogenase was found to be associated with poor prognosis. Then flow cytometry and Seahorse XFe analyzer were utilized to detect the effect of lactate on glycolysis and mitochondrial function in non-small cell lung cancer cells. The results show that in non-small cell lung cancer cells lactate attenuates glucose uptake and glycolysis while maintaining mitochondrial homeostasis as indicated by improved mitochondrial membrane potential. Further exploration found that mRNA levels of glycolytic enzymes (HK-1, PKM) and TCA cycle enzymes (SDHA, IDH3G) are respectively down-regulated and up-regulated by lactate, and increased histone lactylation was observed in promoters of HK-1 and IDH3G via chromatin immunoprecipitation assay. Taken together, the above results indicate that lactate modulates cellular metabolism at least in part through histone lactylation-mediated gene expression in non-small cell lung cancer.

Keywords:  gene expression; lactate; lactylation; metabolism; non-small cell lung cancer

DOI:  https://doi.org/10.3389/fonc.2021.647559
Redox Biol. 2021 Jun 12. pii: S2213-2317(21)00188-9. [Epub ahead of print]45 102030

Compensatory expression of NRF2-dependent antioxidant genes is required to overcome the lethal effects of Kv11.1 activation in breast cancer cells and PDOs.

Vitalyi Senyuk, Najmeh Eskandari, Ying Jiang, Rebeca Garcia-Varela, Rachel Sundstrom, Luigi Leanza, Roberta Peruzzo, Mark Burkard, Richard D Minshall, Saverio Gentile.

  Potassium channels are important regulators of cellular homeostasis and targeting these proteins pharmacologically is unveiling important mechanisms in cancer cell biology. Here we demonstrate that pharmacological stimulation of the Kv11.1 potassium channel activity results in mitochondrial reactive oxygen species (ROS) production and fragmentation in breast cancer cell lines and patient-derived organoids independent of breast cancer subtype. mRNA expression profiling revealed that Kv11.1 activity significantly altered expression of genes controlling the production of ROS and endoplasmic-reticulum (ER) stress. Characterization of the transcriptional signature of breast cancer cells treated with Kv11.1 potassium channel activators strikingly revealed an adaptive response to the potentially lethal augmentation of ROS by increasing Nrf2-dependent transcription of antioxidant genes. Nrf2 in this context was shown to promote survival in breast cancer, whereas knockdown of Nrf2 lead to Kv11.1-induced cell death. In conclusion, we found that the Kv11.1 channel activity promotes oxidative stress in breast cancer cells and that suppression of the Nrf2-mediated anti-oxidant survival mechanism strongly sensitized breast cancer cells to a lethal effect of pharmacological activation of Kv11.1.

Keywords:  Cancer cell survival; Mitochondria; NRF2; Potassium channels

DOI:  https://doi.org/10.1016/j.redox.2021.102030
Hum Mol Genet. 2021 Jun 24. pii: ddab168. [Epub ahead of print]

Coordinated pyruvate kinase activity is crucial for metabolic adaptation and cell survival during mitochondrial dysfunction.

Xiaoshan Zhou, Flora Mikaeloff, Sophie Curbo, Qian Zhao, Raoul V Kuiper, Ákos Végvári, Ujjwal Neogi, Anna Karlsson.

Deoxyguanosine kinase (DGUOK) deficiency causes mtDNA depletion and mitochondrial dysfunction. We reported long survival of DGUOK knockout (Dguok-/-) mice despite low (<5%) mtDNA content in liver tissue. However, the molecular mechanisms enabling the extended survival remain unknown. Using transcriptomics, proteomics and metabolomics followed by in vitro assays, we aimed to identify the molecular pathways involved in the extended survival of the Dguok-/- mice. At the early stage, the serine synthesis and folate cycle were activated but declined later. Increased activity of the mitochondrial citric acid cycle (TCA cycle) and the urea cycle and degradation of branched chain amino acids were hallmarks of the extended lifespan in DGUOK deficiency. Furthermore, the increased synthesis of TCA cycle intermediates was supported by coordination of two pyruvate kinase genes, PKLR and PKM, indicating a central coordinating role of pyruvate kinases to support the long-term survival in mitochondrial dysfunction.

DOI: https://doi.org/10.1093/hmg/ddab168
FEBS J. 2021 Jun;288(12): 3624-3627

Systemic and cellular metabolism: the cause of and remedy for disease?

Colin Adrain.

  The word 'metabolism' is derived from the Greek word μεταβολή (metabolē), denoting 'change'. True to this definition, it is now appreciated that a cell or tissue cannot change its behaviour without altering its metabolism. Hence, most key cell decision-making processes are tightly coupled to metabolic change. Conversely, perturbations in metabolite abundance or flux can alter cellular (and whole-body) function profoundly, giving rise to disease. This Special Issue on Systemic and Cellular Metabolism and Disease provides an integrative perspective on the importance of metabolism for health and disease alike. Spanning several orders of scale (from metabolites, proteins, organelles, organs/tissues and whole-body physiology), these review articles cover a breadth of topics, including the importance of metabolites as signalling regulators, metabolic disease, immunity, organelle function/dysfunction, ageing and neurodegenerative disease. One of the emergent themes is that just as metabolism is the fulcrum of biology, metabolic perturbances underpin most forms of acute, chronic, infectious and non-infectious human disease; ageing and senescence could be similarly viewed. Arguably most diseases are metabolic diseases; hence, modulating metabolism may help to 'change' disease outcomes.

Keywords:  adipose tissue; disease; energy homeostasis; immunity; metabolism; metabolites; organelles

DOI:  https://doi.org/10.1111/febs.16033
Cancer Metab. 2021 Jun 25. 9(1): 27

Impaired anaplerosis is a major contributor to glycolysis inhibitor toxicity in glioma.

Sunada Khadka, Kenisha Arthur, Yasaman Barekatain, Eliot Behr, Mykia Washington, Jeffrey Ackroyd, Kaitlyn Crowley, Pornpa Suriyamongkol, Yu-Hsi Lin, Cong-Dat Pham, Rafal Zielinski, Marissa Trujillo, James Galligan, Dimitra K Georgiou, John Asara, Florian Muller.

   BACKGROUND: Reprogramming of metabolic pathways is crucial to satisfy the bioenergetic and biosynthetic demands and maintain the redox status of rapidly proliferating cancer cells. In tumors, the tricarboxylic acid (TCA) cycle generates biosynthetic intermediates and must be replenished (anaplerosis), mainly from pyruvate and glutamine. We recently described a novel enolase inhibitor, HEX, and its pro-drug POMHEX. Since glycolysis inhibition would deprive the cell of a key source of pyruvate, we hypothesized that enolase inhibitors might inhibit anaplerosis and synergize with other inhibitors of anaplerosis, such as the glutaminase inhibitor, CB-839.
METHODS: We analyzed polar metabolites in sensitive (ENO1-deleted) and resistant (ENO1-WT) glioma cells treated with enolase and glutaminase inhibitors. We investigated whether sensitivity to enolase inhibitors could be attenuated by exogenous anaplerotic metabolites. We also determined the synergy between enolase inhibitors and the glutaminase inhibitor CB-839 in glioma cells in vitro and in vivo in both intracranial and subcutaneous tumor models.
RESULTS: Metabolomic profiling of ENO1-deleted glioma cells treated with the enolase inhibitor revealed a profound decrease in the TCA cycle metabolites with the toxicity reversible upon exogenous supplementation of supraphysiological levels of anaplerotic substrates, including pyruvate. ENO1-deleted cells also exhibited selective sensitivity to the glutaminase inhibitor CB-839, in a manner rescuable by supplementation of anaplerotic substrates or plasma-like media PlasmaxTM. In vitro, the interaction of these two drugs yielded a strong synergistic interaction but the antineoplastic effects of CB-839 as a single agent in ENO1-deleted xenograft tumors in vivo were modest in both intracranial orthotopic tumors, where the limited efficacy could be attributed to the blood-brain barrier (BBB), and subcutaneous xenografts, where BBB penetration is not an issue. This contrasts with the enolase inhibitor HEX, which, despite its negative charge, achieved antineoplastic effects in both intracranial and subcutaneous tumors.
CONCLUSION: Together, these data suggest that at least for ENO1-deleted gliomas, tumors in vivo-unlike cells in culture-show limited dependence on glutaminolysis and instead primarily depend on glycolysis for anaplerosis. Our findings reinforce the previously reported metabolic idiosyncrasies of in vitro culture and suggest that cell culture media nutrient composition more faithful to the in vivo environment will more accurately predict in vivo efficacy of metabolism targeting drugs.

Keywords:  Anaplerosis; CB-839; Cancer metabolism; Collateral lethality; Enolase inhibitor; Glutaminolysis; Glycolysis; POMHEX

DOI:  https://doi.org/10.1186/s40170-021-00259-4
Antioxid Redox Signal. 2021 Jun 22.

Mitochondrial NAD(P)+ transhydrogenase: from molecular features to physiology and disease.

Annelise Francisco, Tiago Rezende Figueira, Roger Frigerio Castilho.

SIGNIFICANCE: Proton-translocating NAD(P)+ transhydrogenase, also known as nicotinamide nucleotide transhydrogenase (NNT), catalyzes a reversible reaction coupling the protonmotive force across the inner mitochondrial membrane and hydride (H-, a proton plus two electrons) transfer between the mitochondrial pools of NAD(H) and NADP(H). The forward NNT reaction is a source of NADPH in the mitochondrial matrix, fueling antioxidant and biosynthetic pathways with reductive potential. Despite the greater emphasis given to the net forward reaction, the reverse NNT reaction that oxidizes NADPH also occurs in physiological and pathological conditions. Recent Advances: NNT (dys)function has been linked to various metabolic pathways and disease phenotypes. Most of these findings have been based on spontaneous loss-of-function Nnt mutations found in the C57BL/6J mouse strain (NntC57BL/6J mutation) and disease-causing Nnt mutations in humans. The present review focuses on recent advances based on the mouse NntC57BL/6J mutation.
CRITICAL ISSUES: Most studies associating NNT function with disease phenotypes have been based on comparisons of inbred mouse strains (with or without the NntC57BL/6J mutation), which creates uncertainties over the actual contribution of NNT in the context of other potential genetic modifiers.
FUTURE DIRECTIONS: Future research might contribute to understanding the role of NNT in pathological conditions and elucidate how NNT regulates physiological signaling through its forward and reverse reactions. The importance of NNT in redox balance and tumor cell proliferation makes it a potential target of new therapeutic strategies for oxidative-stress-mediated diseases and cancer.

DOI: https://doi.org/10.1089/ars.2021.0111
Commun Biol. 2021 Jun 24. 4(1): 782

TGF-β-dependent reprogramming of amino acid metabolism induces epithelial-mesenchymal transition in non-small cell lung cancers.

Fumie Nakasuka, Sho Tabata, Takeharu Sakamoto, Akiyoshi Hirayama, Hiromichi Ebi, Tadaaki Yamada, Ko Umetsu, Maki Ohishi, Ayano Ueno, Hisatsugu Goto, Masahiro Sugimoto, Yasuhiko Nishioka, Yasuhiro Yamada, Masaru Tomita, Atsuo T Sasaki, Seiji Yano, Tomoyoshi Soga.

Epithelial-mesenchymal transition (EMT)-a fundamental process in embryogenesis and wound healing-promotes tumor metastasis and resistance to chemotherapy. While studies have identified signaling components and transcriptional factors responsible in the TGF-β-dependent EMT, whether and how intracellular metabolism is integrated with EMT remains to be fully elucidated. Here, we showed that TGF-β induces reprogramming of intracellular amino acid metabolism, which is necessary to promote EMT in non-small cell lung cancer cells. Combined metabolome and transcriptome analysis identified prolyl 4-hydroxylase α3 (P4HA3), an enzyme implicated in cancer metabolism, to be upregulated during TGF-β stimulation. Further, knockdown of P4HA3 diminished TGF-β-dependent changes in amino acids, EMT, and tumor metastasis. Conversely, manipulation of extracellular amino acids induced EMT-like responses without TGF-β stimulation. These results suggest a previously unappreciated requirement for the reprogramming of amino acid metabolism via P4HA3 for TGF-β-dependent EMT and implicate a P4HA3 inhibitor as a potential therapeutic agent for cancer.

DOI: https://doi.org/10.1038/s42003-021-02323-7
Annu Rev Biochem. 2021 Jun 20. 90 31-55

Short- and Long-Term Adaptation to Altered Levels of Glucose: Fifty Years of Scientific Adventure.

Kosaku Uyeda.

  My graduate and postdoctoral training in metabolism and enzymology eventually led me to study the short- and long-term regulation of glucose and lipid metabolism. In the early phase of my career, my trainees and I identified, purified, and characterized a variety of phosphofructokinase enzymes from mammalian tissues. These studies led us to discover fructose 2,6-P2, the most potent activator of phosphofructokinase and glycolysis. The discovery of fructose 2,6-P2 led to the identification and characterization of the tissue-specific bifunctional enzyme 6-phosphofructo-2-kinase:fructose 2,6-bisphosphatase. We discovered a glucose signaling mechanism by which the liver maintains glucose homeostasis by regulating the activities of this bifunctional enzyme. With a rise in glucose, a signaling metabolite, xylulose 5-phosphate, triggers rapid activation of a specific protein phosphatase (PP2ABδC), which dephosphorylates the bifunctional enzyme, thereby increasing fructose 2,6-P2 levels and upregulating glycolysis. These endeavors paved the way for us to initiate the later phase of my career in which we discovered a new transcription factor termed the carbohydrate response element binding protein (ChREBP). Now ChREBP is recognized as the masterregulator controlling conversion of excess carbohydrates to storage of fat in the liver. ChREBP functions as a central metabolic coordinator that responds to nutrients independently of insulin. The ChREBP transcription factor facilitates metabolic adaptation to excess glucose, leading to obesity and its associated diseases.

Keywords:  6-phosphofructo-2-kinase:fructose 2,6-bisphosphatase; ChREBP; autobiography; bifunctional enzyme; carbohydrate response element binding protein; fructose 2,6-P2; glucose signaling; glycolysis; lipogenesis; phosphofructokinase

DOI:  https://doi.org/10.1146/annurev-biochem-070820-125228
Nature. 2021 Jun 23.

A transcriptional switch governs fibroblast activation in heart disease.

Michael Alexanian, Pawel F Przytycki, Rudi Micheletti, Arun Padmanabhan, Lin Ye, Joshua G Travers, Barbara Gonzalez-Teran, Ana Catarina Silva, Qiming Duan, Sanjeev S Ranade, Franco Felix, Ricardo Linares-Saldana, Li Li, Clara Youngna Lee, Nandhini Sadagopan, Angelo Pelonero, Yu Huang, Gaia Andreoletti, Rajan Jain, Timothy A McKinsey, Michael G Rosenfeld, Casey A Gifford, Katherine S Pollard, Saptarsi M Haldar, Deepak Srivastava.

In diseased organs, stress-activated signalling cascades alter chromatin, thereby triggering maladaptive cell state transitions. Fibroblast activation is a common stress response in tissues that worsens lung, liver, kidney and heart disease, yet its mechanistic basis remains unclear1,2. Pharmacological inhibition of bromodomain and extra-terminal domain (BET) proteins alleviates cardiac dysfunction3-7, providing a tool to interrogate and modulate cardiac cell states as a potential therapeutic approach. Here we use single-cell epigenomic analyses of hearts dynamically exposed to BET inhibitors to reveal a reversible transcriptional switch that underlies the activation of fibroblasts. Resident cardiac fibroblasts demonstrated robust toggling between the quiescent and activated state in a manner directly correlating with BET inhibitor exposure and cardiac function. Single-cell chromatin accessibility revealed previously undescribed DNA elements, the accessibility of which dynamically correlated with cardiac performance. Among the most dynamic elements was an enhancer that regulated the transcription factor MEOX1, which was specifically expressed in activated fibroblasts, occupied putative regulatory elements of a broad fibrotic gene program and was required for TGFβ-induced fibroblast activation. Selective CRISPR inhibition of the single most dynamic cis-element within the enhancer blocked TGFβ-induced Meox1 activation. We identify MEOX1 as a central regulator of fibroblast activation associated with cardiac dysfunction and demonstrate its upregulation after activation of human lung, liver and kidney fibroblasts. The plasticity and specificity of BET-dependent regulation of MEOX1 in tissue fibroblasts provide previously unknown trans- and cis-targets for treating fibrotic disease.

DOI: https://doi.org/10.1038/s41586-021-03674-1
Nat Commun. 2021 06 22. 12(1): 3830

LINC00842 inactivates transcription co-regulator PGC-1α to promote pancreatic cancer malignancy through metabolic remodelling.

Xudong Huang, Ling Pan, Zhixiang Zuo, Mei Li, Lingxing Zeng, Rui Li, Ying Ye, Jialiang Zhang, Guandi Wu, Ruihong Bai, Lisha Zhuang, Lusheng Wei, Yanfen Zheng, Jiachun Su, Junge Deng, Shuang Deng, Shaoping Zhang, Shihao Zhu, Xu Che, Chengfeng Wang, Chen Wu, Rufu Chen, Dongxin Lin, Jian Zheng.

The molecular mechanism underlying pancreatic ductal adenocarcinoma (PDAC) malignancy remains unclear. Here, we characterize a long intergenic non-coding RNA LINC00842 that plays a role in PDAC progression. LINC00842 expression is upregulated in PDAC and induced by high concentration of glucose via transcription factor YY1. LINC00842 binds to and prevents acetylated PGC-1α from deacetylation by deacetylase SIRT1 to form PGC-1α, an important transcription co-factor in regulating cellular metabolism. LINC00842 overexpression causes metabolic switch from mitochondrial oxidative catabolic process to fatty acid synthesis, enhancing the malignant phenotypes of PDAC cells. High LINC00842 levels are correlated with elevated acetylated- PGC-1α levels in PDAC and poor patient survival. Decreasing LINC00842 level and inhibiting fatty acid synthase activity significantly repress PDAC growth and invasiveness in mouse pancreatic xenograft or patient-derived xenograft models. These results demonstrate that LINC00842 plays a role in promoting PDAC malignancy and thus might serve as a druggable target.

DOI: https://doi.org/10.1038/s41467-021-23904-4
Sci Rep. 2021 Jun 25. 11(1): 13302

MCT4 is induced by metastasis-enhancing pathogenic mitochondrial NADH dehydrogenase gene mutations and can be a therapeutic target.

Keizo Takenaga, Nobuko Koshikawa, Miho Akimoto, Yasutoshi Tatsumi, Jason Lin, Makiko Itami, Hiroki Nagase.

Pathogenic mitochondrial NADH dehydrogenase (ND) gene mutations enhance the invasion and metastasis of various cancer cells, and they are associated with metastasis in human non-small cell lung cancer (NSCLC). Moreover, monocarboxylate transporter 4 (MCT4) is overexpressed in solid cancers and plays a role in cancer cell proliferation and survival. Here, we report that MCT4 is exclusively expressed in mouse transmitochondrial cybrids with metastasis-enhancing pathogenic ND6 mutations. A high level of MCT4 is also detected in human NSCLC cell lines and tissues predicted to carry pathogenic ND mutations and is associated with poor prognosis in NSCLC patients. MCT4 expression in the cell lines is suppressed by N-acetyl-L-cysteine. Phosphatidylinositol-3 kinase (PI3K), AMP-activated protein kinase (AMPK) and mechanistic target of rapamycin (mTOR) are involved in the regulation of MCT4 expression in the transmitochondrial cybrid cells. An MCT1/4 inhibitor effectively kills NSCLC cells with predicted pathogenic ND mutations, but an MCT1/2 inhibitor does not have the same effect. Thus, MCT4 expression is augmented by pathogenic ND mutations and could be a biomarker and a therapeutic target in pathogenic ND mutation-harbouring metastatic tumours.

DOI: https://doi.org/10.1038/s41598-021-92772-1
Commun Biol. 2021 Jun 21. 4(1): 763

Fascin1 empowers YAP mechanotransduction and promotes cholangiocarcinoma development.

Arianna Pocaterra, Gloria Scattolin, Patrizia Romani, Cindy Ament, Silvia Ribback, Xin Chen, Matthias Evert, Diego F Calvisi, Sirio Dupont.

Mechanical forces control cell behavior, including cancer progression. Cells sense forces through actomyosin to activate YAP. However, the regulators of F-actin dynamics playing relevant roles during mechanostransduction in vitro and in vivo remain poorly characterized. Here we identify the Fascin1 F-actin bundling protein as a factor that sustains YAP activation in response to ECM mechanical cues. This is conserved in the mouse liver, where Fascin1 regulates YAP-dependent phenotypes, and in human cholangiocarcinoma cell lines. Moreover, this is relevant for liver tumorigenesis, because Fascin1 is required in the AKT/NICD cholangiocarcinogenesis model and it is sufficient, together with AKT, to induce cholangiocellular lesions in mice, recapitulating genetic YAP requirements. In support of these findings, Fascin1 expression in human intrahepatic cholangiocarcinomas strongly correlates with poor patient prognosis. We propose that Fascin1 represents a pro-oncogenic mechanism that can be exploited during intrahepatic cholangiocarcinoma development to overcome a mechanical tumor-suppressive environment.

DOI: https://doi.org/10.1038/s42003-021-02286-9
Eur J Clin Nutr. 2021 Jun 23.

Cellular and metabolic mechanisms of nutrient actions in immune function.

Philip Newsholme.

Various nutrients can change cell structure, cellular metabolism, and cell function which is particularly important for cells of the immune system as nutrient availability is associated with the activation and function of diverse immune subsets. The most important nutrients for immune cell function and fate appear to be glucose, amino acids, fatty acids, and vitamin D. This perspective will describe recently published information describing the mechanism of action of prominent nutritional intervention agents where evidence exists as to their action and potency.

DOI: https://doi.org/10.1038/s41430-021-00960-z
Theranostics. 2021 ;11(15): 7527-7545

Arginine starvation elicits chromatin leakage and cGAS-STING activation via epigenetic silencing of metabolic and DNA-repair genes.

Sheng-Chieh Hsu, Chia-Lin Chen, Mei-Ling Cheng, Cheng-Ying Chu, Chun A Changou, Yen-Ling Yu, Shauh-Der Yeh, Tse-Chun Kuo, Cheng-Chin Kuo, Chih-Pin Chuu, Chien-Feng Li, Lu-Hai Wang, Hong-Wu Chen, Yun Yen, David K Ann, Hung-Jung Wang, Hsing-Jien Kung.

  Rationale: One of the most common metabolic defects in cancers is the deficiency in arginine synthesis, which has been exploited therapeutically. Yet, challenges remain, and the mechanisms of arginine-starvation induced killing are largely unclear. Here, we sought to demonstrate the underlying mechanisms by which arginine starvation-induced cell death and to develop a dietary arginine-restriction xenograft model to study the in vivo effects. Methods: Multiple castration-resistant prostate cancer cell lines were treated with arginine starvation followed by comprehensive analysis of microarray, RNA-seq and ChIP-seq were to identify the molecular and epigenetic pathways affected by arginine starvation. Metabolomics and Seahorse Flux analyses were used to determine the metabolic profiles. A dietary arginine-restriction xenograft mouse model was developed to assess the effects of arginine starvation on tumor growth and inflammatory responses. Results: We showed that arginine starvation coordinately and epigenetically suppressed gene expressions, including those involved in oxidative phosphorylation and DNA repair, resulting in DNA damage, chromatin-leakage and cGAS-STING activation, accompanied by the upregulation of type I interferon response. We further demonstrated that arginine starvation-caused depletion of α-ketoglutarate and inactivation of histone demethylases are the underlying causes of epigenetic silencing. Significantly, our dietary arginine-restriction model showed that arginine starvation suppressed prostate cancer growth in vivo, with evidence of enhanced interferon responses and recruitment of immune cells. Conclusions: Arginine-starvation induces tumor cell killing by metabolite depletion and epigenetic silencing of metabolic genes, leading to DNA damage and chromatin leakage. The resulting cGAS-STING activation may further enhance these killing effects.

Keywords:  Arginine starvation; DNA leakage; Epigenetic gene silencing; cGAS-STING activation

DOI:  https://doi.org/10.7150/thno.54695
J Clin Invest. 2021 Jun 24. pii: 138022. [Epub ahead of print]

Serine hydroxymethyltransferase 2 expression promotes tumorigenesis in rhabdomyosarcoma with 12q13-14 amplification.

Thanh H Nguyen, Prasantha L Vemu, Gregory E Hoy, Salah Boudjadi, Bishwanath Chatterjee, Jack F Shern, Javed Khan, Wenyue Sun, Frederic G Barr.

  The 12q13-q14 chromosomal region is recurrently amplified in 25% of fusion-positive (FP) rhabdomyosarcoma (RMS) cases and is associated with a poor prognosis. To identify amplified oncogenes in FP RMS, we compared the size, gene composition and expression of 12q13-q14 amplicons in FP RMS with other cancer categories (glioblastoma multiforme, lung adenocarcinoma and liposarcoma) in which 12q13-q14 amplification frequently occurs. We uncovered a 0.2 Mb region that is commonly amplified across these cancers and includes CDK4 and six other genes that are overexpressed in amplicon-positive samples. Additionally, we identified a 0.5 Mb segment that is only recurrently amplified in FP RMS and includes four genes that are overexpressed in amplicon-positive RMS. Among these genes, only SHMT2 was overexpressed at the protein level in an amplicon-positive RMS cell line. SHMT2 knockdown in amplicon- positive RMS cells suppressed growth, transformation and tumorigenesis, whereas overexpression in amplicon-negative RMS cells promoted these phenotypes. High SHMT2 expression reduced sensitivity of FP RMS cells to SHIN1, a direct SHMT2 inhibitor, but sensitized cells to pemetrexed, an inhibitor of the folate cycle. In conclusion, our study demonstrated that SHMT2 contributes to tumorigenesis in FP RMS and that SHMT2 amplification predicts differential response to drugs targeting this metabolic pathway.

Keywords:  Cancer; Cell Biology; Oncogenes; Oncology

DOI:  https://doi.org/10.1172/JCI138022
Sci Adv. 2021 Jun;pii: eabg3012. [Epub ahead of print]7(26):

Systemic regulation of mitochondria by germline proteostasis prevents protein aggregation in the soma of C. elegans.

Giuseppe Calculli, Hyun Ju Lee, Koning Shen, Uyen Pham, Marija Herholz, Aleksandra Trifunovic, Andrew Dillin, David Vilchez.

Protein aggregation causes intracellular changes in neurons, which elicit signals to modulate proteostasis in the periphery. Beyond the nervous system, a fundamental question is whether other organs also communicate their proteostasis status to distal tissues. Here, we examine whether proteostasis of the germ line influences somatic tissues. To this end, we induce aggregation of germline-specific PGL-1 protein in germline stem cells of Caenorhabditis elegans Besides altering the intracellular mitochondrial network of germline cells, PGL-1 aggregation also reduces the mitochondrial content of somatic tissues through long-range Wnt signaling pathway. This process induces the unfolded protein response of the mitochondria in the soma, promoting somatic mitochondrial fragmentation and aggregation of proteins linked with neurodegenerative diseases such as Huntington's and amyotrophic lateral sclerosis. Thus, the proteostasis status of germline stem cells coordinates mitochondrial networks and protein aggregation through the organism.

DOI: https://doi.org/10.1126/sciadv.abg3012
N Engl J Med. 2021 Jun 24. 384(25): 2406-2417

Developmental Consequences of Defective ATG7-Mediated Autophagy in Humans.

Jack J Collier, Claire Guissart, Monika Oláhová, Souphatta Sasorith, Florence Piron-Prunier, Fumi Suomi, David Zhang, Nuria Martinez-Lopez, Nicolas Leboucq, Angela Bahr, Silvia Azzarello-Burri, Selina Reich, Ludger Schöls, Tuomo M Polvikoski, Pierre Meyer, Lise Larrieu, Andrew M Schaefer, Hessa S Alsaif, Suad Alyamani, Stephan Zuchner, Inês A Barbosa, Charu Deshpande, Angela Pyle, Anita Rauch, Matthis Synofzik, Fowzan S Alkuraya, François Rivier, Mina Ryten, Robert McFarland, Agnès Delahodde, Thomas G McWilliams, Michel Koenig, Robert W Taylor.

BACKGROUND: Autophagy is the major intracellular degradation route in mammalian cells. Systemic ablation of core autophagy-related (ATG) genes in mice leads to embryonic or perinatal lethality, and conditional models show neurodegeneration. Impaired autophagy has been associated with a range of complex human diseases, yet congenital autophagy disorders are rare.
METHODS: We performed a genetic, clinical, and neuroimaging analysis involving five families. Mechanistic investigations were conducted with the use of patient-derived fibroblasts, skeletal muscle-biopsy specimens, mouse embryonic fibroblasts, and yeast.
RESULTS: We found deleterious, recessive variants in human ATG7, a core autophagy-related gene encoding a protein that is indispensable to classical degradative autophagy. Twelve patients from five families with distinct ATG7 variants had complex neurodevelopmental disorders with brain, muscle, and endocrine involvement. Patients had abnormalities of the cerebellum and corpus callosum and various degrees of facial dysmorphism. These patients have survived with impaired autophagic flux arising from a diminishment or absence of ATG7 protein. Although autophagic sequestration was markedly reduced, evidence of basal autophagy was readily identified in fibroblasts and skeletal muscle with loss of ATG7. Complementation of different model systems by deleterious ATG7 variants resulted in poor or absent autophagic function as compared with the reintroduction of wild-type ATG7.
CONCLUSIONS: We identified several patients with a neurodevelopmental disorder who have survived with a severe loss or complete absence of ATG7, an essential effector enzyme for autophagy without a known functional paralogue. (Funded by the Wellcome Centre for Mitochondrial Research and others.).

DOI: https://doi.org/10.1056/NEJMoa1915722
Sci Adv. 2021 Jun;pii: eabg3505. [Epub ahead of print]7(26):

Lactate and IL6 define separable paths of inflammatory metabolic adaptation.

Stefanie Dichtl, Laura Lindenthal, Leonie Zeitler, Kristina Behnke, Daniela Schlösser, Birgit Strobl, Jürgen Scheller, Karim C El Kasmi, Peter J Murray.

Lactate is an end point of Warburg-type metabolism found in inflammatory macrophages. Recently, lactate was shown to modify histones of lipopolysaccharide (LPS)-activated macrophages in a time-dependent way and promote the expression of genes linked to tissue repair, including arginase-1 (Arg1). We tested the interrelationships between histone lactylation (Kla) and tissue reparative gene expression and found that Kla was uncoupled from changes in gene expression linked to resolving M2 macrophage activation but correlated with Arg1 expression. LPS-induced Arg1 was instead dependent on autocrine-paracrine interleukin-6 (IL6) production, the IL6 receptor, and Stat3 signal transduction. We found that Kla increases as macrophages prepare to die under inflammatory stress, and Kla was absent in macrophages that cannot generate reactive nitrogen or have defects in diverse macrophage death pathways. Thus, Kla is a consequence rather than a cause of macrophage activation but occurs coincidently with an IL6- and Arg1-dependent metabolic rewiring under inflammatory duress.

DOI: https://doi.org/10.1126/sciadv.abg3505
Autophagy. 2021 Jun 22. 1-2

AMBRA1 has an impact on melanoma development beyond autophagy.

Luca Di Leo, Daniela De Zio.

  AMBRA1 (autophagy/beclin 1 regulator 1) is a multifunctional scaffold protein involved in several cellular processes spanning from cell proliferation to apoptosis and to regulation of macroautophagy/autophagy. Our recent publication revealed that Ambra1 has an antitumorigenic role in melanoma, the most aggressive and deadly skin cancer. We have indeed collected data indicating that the increased proliferative and invasive/metastatic features that we observed in ambra1-ablated melanomas are related to a remarkable regulation by Ambra1 on cellular processes which are beyond autophagy. Our study therefore sheds light on intriguing processes affected by Ambra1 which can be exploited as therapeutic targets in AMBRA1 low-expressing melanoma.

Keywords:  AMBRA1; FAK1; GEMMs; cyclin D1; melanoma; metastasis; proliferation

DOI:  https://doi.org/10.1080/15548627.2021.1940608