bims-camemi 2022-12-25 papers

bims-camemi

Biomed News

on Mitochondrial metabolism in cancer

Issue of 2022–12–25
43 papers selected by
Christian Frezza, Universität zu Köln

mTORC1 regulates a lysosome-dependent adaptive shift in intracellular lipid species.
Dynamic partitioning of branched-chain amino acids-derived nitrogen supports renal cancer progression.
From passage to inhibition: Uncovering the structural and physiological inhibitory mechanisms of MCUb in mitochondrial calcium regulation.
Metabolic enzyme LDHA activates Rac1 GTPase as a noncanonical mechanism to promote cancer.
Chronic acidosis rewires cancer cell metabolism through PPARα signaling.
Reprogramming of Cellular Metabolism and Its Therapeutic Applications in Thyroid Cancer.
mTORC1 takes control of lysosomal lipid breakdown.
The structure of the human LACTB filament reveals the mechanisms of assembly and membrane binding.
Microenvironmental ammonia enhances T cell exhaustion in colorectal cancer.
Revisiting the Warburg Effect with Focus on Lactate.
Mitochondrial sodium/calcium exchanger NCLX regulates glycolysis in astrocytes, impacting on cognitive performance.
Beyond Warburg: LDHA activates RAC for tumour growth.
Ubiquitination Occurs in the Mitochondrial Matrix by Eclipsed Targeted Components of the Ubiquitination Machinery.
Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness.
Multi-color live-cell STED nanoscopy of mitochondria with a gentle inner membrane stain.
USP5-Beclin 1 axis overrides p53-dependent senescence and drives Kras-induced tumorigenicity.
Metabolomic and Mitochondrial Fingerprinting of the Epithelial-to-Mesenchymal Transition (EMT) in Non-Tumorigenic and Tumorigenic Human Breast Cells.
Succinate at the Crossroad of Metabolism and Angiogenesis: Roles of SDH, HIF1α and SUCNR1.
Mitochondria in Early Life.
The unbroken Krebs cycle. Hormonal-like regulation and mitochondrial signaling to control mitophagy and prevent cell death.
Acly Deficiency Enhances Myelopoiesis through Acetyl Coenzyme A and Metabolic-Epigenetic Cross-Talk.
Widespread, Reversible Cysteine Modification by Methylglyoxal Regulates Metabolic Enzyme Function.
Pharmacological targeting of the mitochondrial calcium-dependent potassium channel KCa3.1 triggers cell death and reduces tumor growth and metastasis in vivo.
Metabolic switch in cancer - Survival of the fittest.
Collagen VI expression is negatively mechanosensitive in pancreatic cancer cells and supports the metastatic niche.
scFASTCORMICS: A Contextualization Algorithm to Reconstruct Metabolic Multi-Cell Population Models from Single-Cell RNAseq Data.
The Role of Nuclear-Encoded Mitochondrial tRNA Charging Enzymes in Human Inherited Disease.
Glassfrogs conceal blood in their liver to maintain transparency.
T cell-independent abscopal responses to radiotherapy.
The Glacier Ice Worm, Mesenchytraeus solifugus, Elevates Mitochondrial Inorganic Polyphosphate (PolyP) Levels in Response to Stress.
Kir4.2 mediates proximal potassium effects on glutaminase activity and kidney injury.
Multiscale reorganization of the genome following DNA damage facilitates chromosome translocations via nuclear actin polymerization.
Ring domains are essential for GATOR2-dependent mTORC1 activation.
Metabolites of De Novo Purine Synthesis: Metabolic Regulators and Cytotoxic Compounds.
Epigenetic clocks, aging, and cancer.
Huntington disease oligodendrocyte maturation deficits revealed by single-nucleus RNAseq are rescued by thiamine-biotin supplementation.
The Aging Process: A Metabolomics Perspective.
Hypoxia drives CD39-dependent suppressor function in exhausted T cells to limit antitumor immunity.
R-loop-derived cytoplasmic RNA-DNA hybrids activate an immune response.
Extracellular arginine is required but the arginine transporter CAT3 (Slc7a3) is dispensable for mouse normal and malignant hematopoiesis.
A single-cell atlas of glioblastoma evolution under therapy reveals cell-intrinsic and cell-extrinsic therapeutic targets.
Diverse silent chromatin states modulate genome compartmentalization and loop extrusion barriers.
YAP/TAZ as master regulators in cancer: modulation, function and therapeutic approaches.

Nat Metab. 2022 Dec;4(12): 1792-1811

mTORC1 regulates a lysosome-dependent adaptive shift in intracellular lipid species.

Aaron M Hosios, Meghan E Wilkinson, Molly C McNamara, Krystle C Kalafut, Margaret E Torrence, John M Asara, Brendan D Manning.

The mechanistic target of rapamycin complex 1 (mTORC1) senses and relays environmental signals from growth factors and nutrients to metabolic networks and adaptive cellular systems to control the synthesis and breakdown of macromolecules; however, beyond inducing de novo lipid synthesis, the role of mTORC1 in controlling cellular lipid content remains poorly understood. Here we show that inhibition of mTORC1 via small molecule inhibitors or nutrient deprivation leads to the accumulation of intracellular triglycerides in both cultured cells and a mouse tumor model. The elevated triglyceride pool following mTORC1 inhibition stems from the lysosome-dependent, but autophagy-independent, hydrolysis of phospholipid fatty acids. The liberated fatty acids are available for either triglyceride synthesis or β-oxidation. Distinct from the established role of mTORC1 activation in promoting de novo lipid synthesis, our data indicate that mTORC1 inhibition triggers membrane phospholipid trafficking to the lysosome for catabolism and an adaptive shift in the use of constituent fatty acids for storage or energy production.

DOI: https://doi.org/10.1038/s42255-022-00706-6
Nat Commun. 2022 Dec 20. 13(1): 7830

Dynamic partitioning of branched-chain amino acids-derived nitrogen supports renal cancer progression.

Marco Sciacovelli, Aurelien Dugourd, Lorea Valcarcel Jimenez, Ming Yang, Efterpi Nikitopoulou, Ana S H Costa, Laura Tronci, Veronica Caraffini, Paulo Rodrigues, Christina Schmidt, Dylan Gerard Ryan, Timothy Young, Vincent R Zecchini, Sabrina H Rossi, Charlie Massie, Caroline Lohoff, Maria Masid, Vassily Hatzimanikatis, Christoph Kuppe, Alex Von Kriegsheim, Rafael Kramann, Vincent Gnanapragasam, Anne Y Warren, Grant D Stewart, Ayelet Erez, Sakari Vanharanta, Julio Saez-Rodriguez, Christian Frezza.

Metabolic reprogramming is critical for tumor initiation and progression. However, the exact impact of specific metabolic changes on cancer progression is poorly understood. Here, we integrate multimodal analyses of primary and metastatic clonally-related clear cell renal cancer cells (ccRCC) grown in physiological media to identify key stage-specific metabolic vulnerabilities. We show that a VHL loss-dependent reprogramming of branched-chain amino acid catabolism sustains the de novo biosynthesis of aspartate and arginine enabling tumor cells with the flexibility of partitioning the nitrogen of the amino acids depending on their needs. Importantly, we identify the epigenetic reactivation of argininosuccinate synthase (ASS1), a urea cycle enzyme suppressed in primary ccRCC, as a crucial event for metastatic renal cancer cells to acquire the capability to generate arginine, invade in vitro and metastasize in vivo. Overall, our study uncovers a mechanism of metabolic flexibility occurring during ccRCC progression, paving the way for the development of novel stage-specific therapies.

DOI: https://doi.org/10.1038/s41467-022-35036-4
FASEB J. 2023 Jan;37(1): e22678

From passage to inhibition: Uncovering the structural and physiological inhibitory mechanisms of MCUb in mitochondrial calcium regulation.

Danielle M Colussi, Peter B Stathopulos.

  Mitochondrial calcium (Ca2+ ) regulation is critically implicated in the regulation of bioenergetics and cell fate. Ca2+ , a universal signaling ion, passively diffuses into the mitochondrial intermembrane space (IMS) through voltage-dependent anion channels (VDAC), where uptake into the matrix is tightly regulated across the inner mitochondrial membrane (IMM) by the mitochondrial Ca2+ uniporter complex (mtCU). In recent years, immense progress has been made in identifying and characterizing distinct structural and physiological mechanisms of mtCU component function. One of the main regulatory components of the Ca2+ selective mtCU channel is the mitochondrial Ca2+ uniporter dominant-negative beta subunit (MCUb). The structural mechanisms underlying the inhibitory effect(s) exerted by MCUb are poorly understood, despite high homology to the main mitochondrial Ca2+ uniporter (MCU) channel-forming subunits. In this review, we provide an overview of the structural differences between MCUb and MCU, believed to contribute to the inhibition of mitochondrial Ca2+ uptake. We highlight the possible structural rationale for the absent interaction between MCUb and the mitochondrial Ca2+ uptake 1 (MICU1) gatekeeping subunit and a potential widening of the pore upon integration of MCUb into the channel. We discuss physiological and pathophysiological information known about MCUb, underscoring implications in cardiac function and arrhythmia as a basis for future therapeutic discovery. Finally, we discuss potential post-translational modifications on MCUb as another layer of important regulation.

Keywords:  MCU; MCU dominant-negative beta subunit; MCUb; mitochondrial calcium uniporter; mitochondrial calcium uptake; post-translational modifications; structure-function

DOI:  https://doi.org/10.1096/fj.202201080R
Nat Metab. 2022 Dec;4(12): 1830-1846

Metabolic enzyme LDHA activates Rac1 GTPase as a noncanonical mechanism to promote cancer.

Juan Liu, Cen Zhang, Tianliang Zhang, Chun-Yuan Chang, Jianming Wang, Ludvinna Bazile, Lanjing Zhang, Bruce G Haffty, Wenwei Hu, Zhaohui Feng.

The glycolytic enzyme lactate dehydrogenase A (LDHA) is frequently overexpressed in cancer, which promotes glycolysis and cancer. The oncogenic effect of LDHA has been attributed to its glycolytic enzyme activity. Here we report an unexpected noncanonical oncogenic mechanism of LDHA; LDHA activates small GTPase Rac1 to promote cancer independently of its glycolytic enzyme activity. Mechanistically, LDHA interacts with the active form of Rac1, Rac1-GTP, to inhibit Rac1-GTP interaction with its negative regulator, GTPase-activating proteins, leading to Rac1 activation in cancer cells and mouse tissues. In clinical breast cancer specimens, LDHA overexpression is associated with higher Rac1 activity. Rac1 inhibition suppresses the oncogenic effect of LDHA. Combination inhibition of LDHA enzyme activity and Rac1 activity by small-molecule inhibitors displays a synergistic inhibitory effect on breast cancers with LDHA overexpression. These results reveal a critical oncogenic mechanism of LDHA and suggest a promising therapeutic strategy for breast cancers with LDHA overexpression.

DOI: https://doi.org/10.1038/s42255-022-00708-4
Int J Cancer. 2022 Dec 19.

Chronic acidosis rewires cancer cell metabolism through PPARα signaling.

Michala G Rolver, Lya K K Holland, Muthulakshmi Ponniah, Nanditha S Prasad, Jiayi Yao, Julie Schnipper, Signe Kramer, Line Elingaard-Larsen, Elena Pedraz-Cuesta, Bin Liu, Luis A Pardo, Kenji Maeda, Albin Sandelin, Stine F Pedersen.

  The mechanisms linking tumor microenvironment acidosis to disease progression are not understood. Here, we used mammary, pancreatic, and colon cancer cells to show that adaptation to growth at an extracellular pH (pHe ) mimicking acidic tumor niches is associated with upregulated net acid extrusion capacity and elevated intracellular pH at physiological pHe , but not at the acidic pHe . Using metabolic profiling, shotgun lipidomics, imaging, and biochemical analyses, we show that the acid adaptation-induced phenotype is characterized by a shift toward oxidative metabolism, increased lipid droplet-, triacylglycerol-, peroxisome content, and mitochondrial hyperfusion. Peroxisome proliferator-activated receptor-α (PPARA, PPARα) expression and activity are upregulated, at least in part by increased fatty acid uptake. PPARα upregulates genes driving increased mitochondrial and peroxisomal mass and β-oxidation capacity, including mitochondrial lipid import proteins CPT1A, CPT2, and SLC25A20, electron transport chain components, peroxisomal proteins PEX11A and ACOX1, and thioredoxin-interacting protein (TXNIP), a negative regulator of glycolysis. This endows acid-adapted cancer cells with increased capacity for utilizing fatty acids for metabolic needs, while limiting glycolysis. As a consequence, the acid-adapted cells exhibit increased sensitivity to PPARα inhibition. We conclude that PPARα is a key upstream regulator of metabolic changes favoring cancer cell survival in acidic tumor niches. This article is protected by copyright. All rights reserved.

Keywords:  PPARα; acidic microenvironment; cancer metabolism; fatty acid metabolism; β-oxidation

DOI:  https://doi.org/10.1002/ijc.34404
Metabolites. 2022 Dec 03. pii: 1214. [Epub ahead of print]12(12):

Reprogramming of Cellular Metabolism and Its Therapeutic Applications in Thyroid Cancer.

Yuji Nagayama, Koichiro Hamada.

  Metabolism is a series of life-sustaining chemical reactions in organisms, providing energy required for cellular processes and building blocks for cellular constituents of proteins, lipids, carbohydrates and nucleic acids. Cancer cells frequently reprogram their metabolic behaviors to adapt their rapid proliferation and altered tumor microenvironments. Not only aerobic glycolysis (also termed the Warburg effect) but also altered mitochondrial metabolism, amino acid metabolism and lipid metabolism play important roles for cancer growth and aggressiveness. Thus, the mechanistic elucidation of these metabolic changes is invaluable for understanding the pathogenesis of cancers and developing novel metabolism-targeted therapies. In this review article, we first provide an overview of essential metabolic mechanisms, and then summarize the recent findings of metabolic reprogramming and the recent reports of metabolism-targeted therapies for thyroid cancer.

Keywords:  TCA cycle; electron transport chain; glutaminolysis; glycolysis; lipid metabolism; metabolomics; the Warburg effect; thyroid cancer

DOI:  https://doi.org/10.3390/metabo12121214
Nat Metab. 2022 Dec;4(12): 1620-1622

mTORC1 takes control of lysosomal lipid breakdown.

Laura Tribouillard, Mathieu Laplante.

DOI: https://doi.org/10.1038/s42255-022-00702-w
PLoS Biol. 2022 Dec 19. 20(12): e3001899

The structure of the human LACTB filament reveals the mechanisms of assembly and membrane binding.

Jeremy A Bennett, Lottie R Steward, Johannes Rudolph, Adam P Voss, Halil Aydin.

Mitochondria are complex organelles that play a central role in metabolism. Dynamic membrane-associated processes regulate mitochondrial morphology and bioenergetics in response to cellular demand. In tumor cells, metabolic reprogramming requires active mitochondrial metabolism for providing key metabolites and building blocks for tumor growth and rapid proliferation. To counter this, the mitochondrial serine beta-lactamase-like protein (LACTB) alters mitochondrial lipid metabolism and potently inhibits the proliferation of a variety of tumor cells. Mammalian LACTB is localized in the mitochondrial intermembrane space (IMS), where it assembles into filaments to regulate the efficiency of essential metabolic processes. However, the structural basis of LACTB polymerization and regulation remains incompletely understood. Here, we describe how human LACTB self-assembles into micron-scale filaments that increase their catalytic activity. The electron cryo-microscopy (cryoEM) structure defines the mechanism of assembly and reveals how highly ordered filament bundles stabilize the active state of the enzyme. We identify and characterize residues that are located at the filament-forming interface and further show that mutations that disrupt filamentation reduce enzyme activity. Furthermore, our results provide evidence that LACTB filaments can bind lipid membranes. These data reveal the detailed molecular organization and polymerization-based regulation of human LACTB and provide new insights into the mechanism of mitochondrial membrane organization that modulates lipid metabolism.

DOI: https://doi.org/10.1371/journal.pbio.3001899
Cell Metab. 2022 Dec 12. pii: S1550-4131(22)00504-6. [Epub ahead of print]

Microenvironmental ammonia enhances T cell exhaustion in colorectal cancer.

Hannah N Bell, Amanda K Huber, Rashi Singhal, Navyateja Korimerla, Ryan J Rebernick, Roshan Kumar, Marwa O El-Derany, Peter Sajjakulnukit, Nupur K Das, Samuel A Kerk, Sumeet Solanki, Jadyn G James, Donghwan Kim, Li Zhang, Brandon Chen, Rohit Mehra, Timothy L Frankel, Balázs Győrffy, Eric R Fearon, Marina Pasca di Magliano, Frank J Gonzalez, Ruma Banerjee, Daniel R Wahl, Costas A Lyssiotis, Michael Green, Yatrik M Shah.

  Effective therapies are lacking for patients with advanced colorectal cancer (CRC). The CRC tumor microenvironment has elevated metabolic waste products due to altered metabolism and proximity to the microbiota. The role of metabolite waste in tumor development, progression, and treatment resistance is unclear. We generated an autochthonous metastatic mouse model of CRC and used unbiased multi-omic analyses to reveal a robust accumulation of tumoral ammonia. The high ammonia levels induce T cell metabolic reprogramming, increase exhaustion, and decrease proliferation. CRC patients have increased serum ammonia, and the ammonia-related gene signature correlates with altered T cell response, adverse patient outcomes, and lack of response to immune checkpoint blockade. We demonstrate that enhancing ammonia clearance reactivates T cells, decreases tumor growth, and extends survival. Moreover, decreasing tumor-associated ammonia enhances anti-PD-L1 efficacy. These findings indicate that enhancing ammonia detoxification can reactivate T cells, highlighting a new approach to enhance the efficacy of immunotherapies.

Keywords:  ammonia; cancer metabolism; immunotherapy; tumor microenvironment

DOI:  https://doi.org/10.1016/j.cmet.2022.11.013
Cancers (Basel). 2022 Dec 07. pii: 6028. [Epub ahead of print]14(24):

Revisiting the Warburg Effect with Focus on Lactate.

Eva Kocianova, Viktoria Piatrikova, Tereza Golias.

  Rewired metabolism is acknowledged as one of the drivers of tumor growth. As a result, aerobic glycolysis, or the Warburg effect, is a feature of many cancers. Increased glucose uptake and glycolysis provide intermediates for anabolic reactions necessary for cancer cell proliferation while contributing sufficient energy. However, the accompanying increased lactate production, seemingly wasting glucose carbon, was originally explained only by the need to regenerate NAD+ for successive rounds of glycolysis by the lactate dehydrogenase (LDH) reaction in the cytosol. After the discovery of a mitochondrial LDH isoform, lactate oxidation entered the picture, and lactate was recognized as an important oxidative fuel. It has also been revealed that lactate serves a variety of signaling functions and helps cells adapt to the new environment. Here, we discuss recent findings on lactate metabolism and signaling in cancer while attempting to explain why the Warburg effect is adopted by cancer cells.

Keywords:  Warburg effect; glucose metabolism; lactate; lactate dehydrogenase; lactate oxidation; lactate shuttle; lactate signaling; lactylation

DOI:  https://doi.org/10.3390/cancers14246028
J Neurochem. 2022 Dec 23.

Mitochondrial sodium/calcium exchanger NCLX regulates glycolysis in astrocytes, impacting on cognitive performance.

João Victor Cabral-Costa, Carlos Vicente-Gutiérrez, Jesús Agulla, Rebeca Lapresa, John W Elrod, Ángeles Almeida, Juan P Bolaños, Alicia J Kowaltowski.

  Intracellular Ca2+ concentrations are strictly controlled by plasma membrane transporters, the endoplasmic reticulum, and mitochondria, in which Ca2+ uptake is mediated by the mitochondrial calcium uniporter complex (MCUc), while efflux occurs mainly through the mitochondrial Na+ /Ca2+ exchanger (NCLX). RNAseq database repository searches led us to identify the Nclx transcript as highly enriched in astrocytes when compared to neurons. To assess the role of NCLX in mouse primary culture astrocytes, we inhibited its function both pharmacologically or genetically. This resulted in re-shaping of cytosolic Ca2+ signaling and a metabolic shift that increased glycolytic flux and lactate secretion in a Ca2+ -dependent manner. Interestingly, in vivo genetic deletion of NCLX in hippocampal astrocytes improved cognitive performance in behavioral tasks, whereas hippocampal neuron-specific deletion of NCLX impaired cognitive performance. These results unveil a role for NCLX as a novel modulator of astrocytic glucose metabolism, impacting on cognition.

Keywords:  NCLX; astrocyte; brain metabolism; calcium transport; energy metabolism; glycolysis; lactate; metabolic regulation; mitochondrial metabolism; sodium transport; sodium-calcium exchange

DOI:  https://doi.org/10.1111/jnc.15745
Nat Metab. 2022 Dec;4(12): 1623-1625

Beyond Warburg: LDHA activates RAC for tumour growth.

Natsuski Osaka, Atsuo T Sasaki.

DOI: https://doi.org/10.1038/s42255-022-00709-3
Cells. 2022 Dec 17. pii: 4109. [Epub ahead of print]11(24):

Ubiquitination Occurs in the Mitochondrial Matrix by Eclipsed Targeted Components of the Ubiquitination Machinery.

Yu Zhang, Ofri Karmon, Koyeli Das, Reuven Wiener, Norbert Lehming, Ophry Pines.

  Ubiquitination is a critical type of post-translational modification in eukaryotic cells. It is involved in regulating nearly all cellular processes in the cytosol and nucleus. Mitochondria, known as the metabolism heart of the cell, are organelles that evolved from bacteria. Using the subcellular compartment-dependent α-complementation, we detect multiple components of ubiquitination machinery as being eclipsed distributed to yeast mitochondria. Ubiquitin conjugates and mono-ubiquitin can be detected in lysates of isolated mitochondria from cells expressing HA-Ub and treated with trypsin. By expressing MTS (mitochondrial targeting sequence) targeted HA-tagged ubiquitin, we demonstrate that certain ubiquitination events specifically occur in yeast mitochondria and are independent of proteasome activity. Importantly, we show that the E2 Rad6 affects the pattern of protein ubiquitination in mitochondria and provides an in vivo assay for its activity in the matrix of the organelle. This study shows that ubiquitination occurs in the mitochondrial matrix by eclipsed targeted components of the ubiquitin machinery, providing a new perspective on mitochondrial and ubiquitination research.

Keywords:  E2; Rad6; dual targeting; eclipsed distribution; mitochondrial matrix; ubiquitination

DOI:  https://doi.org/10.3390/cells11244109
Cancer Cell. 2022 Dec 20. pii: S1535-6108(22)00565-7. [Epub ahead of print]

Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness.

Clinical Proteomic Tumor Analysis Consortium

  Clear cell renal cell carcinomas (ccRCCs) represent ∼75% of RCC cases and account for most RCC-associated deaths. Inter- and intratumoral heterogeneity (ITH) results in varying prognosis and treatment outcomes. To obtain the most comprehensive profile of ccRCC, we perform integrative histopathologic, proteogenomic, and metabolomic analyses on 305 ccRCC tumor segments and 166 paired adjacent normal tissues from 213 cases. Combining histologic and molecular profiles reveals ITH in 90% of ccRCCs, with 50% demonstrating immune signature heterogeneity. High tumor grade, along with BAP1 mutation, genome instability, increased hypermethylation, and a specific protein glycosylation signature define a high-risk disease subset, where UCHL1 expression displays prognostic value. Single-nuclei RNA sequencing of the adverse sarcomatoid and rhabdoid phenotypes uncover gene signatures and potential insights into tumor evolution. In vitro cell line studies confirm the potential of inhibiting identified phosphoproteome targets. This study molecularly stratifies aggressive histopathologic subtypes that may inform more effective treatment strategies.

Keywords:  CPTAC; UCHL1; clear cell renal cell carcinoma; glycoproteomics; histology; metabolome; phosphoproteomics; proteogenomics; single-nuclei RNA-seq; tumor heterogeneity

DOI:  https://doi.org/10.1016/j.ccell.2022.12.001
Proc Natl Acad Sci U S A. 2022 Dec 27. 119(52): e2215799119

Multi-color live-cell STED nanoscopy of mitochondria with a gentle inner membrane stain.

Tianyan Liu, Till Stephan, Peng Chen, Jan Keller-Findeisen, Jingting Chen, Dietmar Riedel, Zhongtian Yang, Stefan Jakobs, Zhixing Chen.

  Capturing mitochondria's intricate and dynamic structure poses a daunting challenge for optical nanoscopy. Different labeling strategies have been demonstrated for live-cell stimulated emission depletion (STED) microscopy of mitochondria, but orthogonal strategies are yet to be established, and image acquisition has suffered either from photodamage to the organelles or from rapid photobleaching. Therefore, live-cell nanoscopy of mitochondria has been largely restricted to two-dimensional (2D) single-color recordings of cancer cells. Here, by conjugation of cyclooctatetraene (COT) to a benzo-fused cyanine dye, we report a mitochondrial inner membrane (IM) fluorescent marker, PK Mito Orange (PKMO), featuring efficient STED at 775 nm, strong photostability, and markedly reduced phototoxicity. PKMO enables super-resolution (SR) recordings of IM dynamics for extended periods in immortalized mammalian cell lines, primary cells, and organoids. Photostability and reduced phototoxicity of PKMO open the door to live-cell three-dimensional (3D) STED nanoscopy of mitochondria for 3D analysis of the convoluted IM. PKMO is optically orthogonal with green and far-red markers, allowing multiplexed recordings of mitochondria using commercial STED microscopes. Using multi-color STED microscopy, we demonstrate that imaging with PKMO can capture interactions of mitochondria with different cellular components such as the endoplasmic reticulum (ER) or the cytoskeleton, Bcl-2-associated X protein (BAX)-induced apoptotic process, or crista phenotypes in genetically modified cells, all at sub-100 nm resolution. Thereby, this work offers a versatile tool for studying mitochondrial IM architecture and dynamics in a multiplexed manner.

Keywords:  STED nanoscopy; cristae; mitochondria

DOI:  https://doi.org/10.1073/pnas.2215799119
Nat Commun. 2022 Dec 17. 13(1): 7799

USP5-Beclin 1 axis overrides p53-dependent senescence and drives Kras-induced tumorigenicity.

Juan Li, Yang Wang, Yue Luo, Yang Liu, Yong Yi, Jinsong Li, Yang Pan, Weiyuxin Li, Wanbang You, Qingyong Hu, Zhiqiang Zhao, Yujun Zhang, Yang Cao, Lingqiang Zhang, Junying Yuan, Zhi-Xiong Jim Xiao.

Non-small cell lung cancers (NSCLC) frequently contain KRAS mutation but retain wild-type TP53. Abundant senescent cells are observed in premalignant but not in malignant tumors derived from the Kras-driven mouse model, suggesting that KRAS oncogenic signaling would have to overcome the intrinsic senescence burden for cancer progression. Here, we show that the nuclear Beclin 1-mediated inhibition of p53-dependent senescence drives Kras-mediated tumorigenesis. KRAS activates USP5 to stabilize nuclear Beclin 1, leading to MDM2-mediated p53 protein instability. KrasG12D mice lacking Beclin 1 display retarded lung tumor growth. Knockdown of USP5 or knockout of Becn1 leads to increased senescence and reduced autophagy. Mechanistically, KRAS elevates ROS to induce USP5 homodimer formation by forming the C195 disulfide bond, resulting in stabilization and activation of USP5. Together, these results demonstrate that activation of the USP5-Beclin 1 axis is pivotal in overriding intrinsic p53-dependent senescence in Kras-driven lung cancer development.

DOI: https://doi.org/10.1038/s41467-022-35557-y
Cancers (Basel). 2022 Dec 16. pii: 6214. [Epub ahead of print]14(24):

Metabolomic and Mitochondrial Fingerprinting of the Epithelial-to-Mesenchymal Transition (EMT) in Non-Tumorigenic and Tumorigenic Human Breast Cells.

Elisabet Cuyàs, Salvador Fernández-Arroyo, Sara Verdura, Ruth Lupu, Jorge Joven, Javier A Menendez.

  Epithelial-to-mesenchymal transition (EMT) is key to tumor aggressiveness, therapy resistance, and immune escape in breast cancer. Because metabolic traits might be involved along the EMT continuum, we investigated whether human breast epithelial cells engineered to stably acquire a mesenchymal phenotype in non-tumorigenic and H-RasV12-driven tumorigenic backgrounds possess unique metabolic fingerprints. We profiled mitochondrial-cytosolic bioenergetic and one-carbon (1C) metabolites by metabolomic analysis, and then questioned the utilization of different mitochondrial substrates by EMT mitochondria and their sensitivity to mitochondria-centered inhibitors. "Upper" and "lower" glycolysis were the preferred glucose fluxes activated by EMT in non-tumorigenic and tumorigenic backgrounds, respectively. EMT in non-tumorigenic and tumorigenic backgrounds could be distinguished by the differential contribution of the homocysteine-methionine 1C cycle to the transsulfuration pathway. Both non-tumorigenic and tumorigenic EMT-activated cells showed elevated mitochondrial utilization of glycolysis end-products such as lactic acid, β-oxidation substrates including palmitoyl-carnitine, and tricarboxylic acid pathway substrates such as succinic acid. Notably, mitochondria in tumorigenic EMT cells distinctively exhibited a significant alteration in the electron flow intensity from succinate to mitochondrial complex III as they were highly refractory to the inhibitory effects of antimycin A and myxothiazol. Our results show that the bioenergetic/1C metabolic signature, the utilization rates of preferred mitochondrial substrates, and sensitivity to mitochondrial drugs significantly differs upon execution of EMT in non-tumorigenic and tumorigenic backgrounds, which could help to resolve the relationship between EMT, malignancy, and therapeutic resistance in breast cancer.

Keywords:  breast cancer; complex III; metabolism; mitochondria; phenotypic screening; therapy resistance

DOI:  https://doi.org/10.3390/cancers14246214
Biomedicines. 2022 Dec 01. pii: 3089. [Epub ahead of print]10(12):

Succinate at the Crossroad of Metabolism and Angiogenesis: Roles of SDH, HIF1α and SUCNR1.

Reham Atallah, Andrea Olschewski, Akos Heinemann.

  Angiogenesis is an essential process by which new blood vessels develop from existing ones. While adequate angiogenesis is a physiological process during, for example, tissue repair, insufficient and excessive angiogenesis stands on the pathological side. Fine balance between pro- and anti-angiogenic factors in the tissue environment regulates angiogenesis. Identification of these factors and how they function is a pressing topic to develop angiogenesis-targeted therapeutics. During the last decade, exciting data highlighted non-metabolic functions of intermediates of the mitochondrial Krebs cycle including succinate. Among these functions is the contribution of succinate to angiogenesis in various contexts and through different mechanisms. As the concept of targeting metabolism to treat a wide range of diseases is rising, in this review we summarize the mechanisms by which succinate regulates angiogenesis in normal and pathological settings. Gaining a comprehensive insight into how this metabolite functions as an angiogenic signal will provide a useful approach to understand diseases with aberrant or excessive angiogenic background, and may provide strategies to tackle them.

Keywords:  angiogenesis; hypoxia-inducible factor 1-alpha (HIF1α); succinate; succinate dehydrogenase (SDH); succinate receptor-1 (SUCNR1)

DOI:  https://doi.org/10.3390/biomedicines10123089
Curr Pediatr Rev. 2022 Dec 21.

Mitochondria in Early Life.

Ling He, Akhil Maheshwari.

  Mitochondria are highly-dynamic, membrane-bound organelles that generate most of the chemical energy needed to power the biochemical reactions in eukaryotic cells. These organelles also communicate with the nucleus and other cellular structures to help maintain somatic homeostasis, allow cellular adaptation to stress, and help maintain the developmental trajectory. Mitochondria also perform numerous other functions to support metabolic, energetic, and epigenetic regulation in our cells. There is increasing information on various disorders caused by defects in intrinsic mitochondrial or supporting nuclear genes in different organ systems. In this review, we have summarized the ultrastructural morphology, structural components, our current understanding of the evolution, biogenesis, dynamics, function, clinical manifestations of mitochondrial dysfunction, and future possibilities. The implications of deficits in mitochondrial dynamics and signaling for embryo viability and offspring health are also explored. We present information from our own clinical and laboratory research in conjunction with information collected from an extensive search in the databases PubMed, EMBASE, and Scopus.

Keywords:  Archezoan; Biogenesis; Epigenetic; Inner membrane; Intermembrane space; Matrix; Mitochondrial DNA; Mitochondrial function; Mitochondrion-related organelles; Neonate; Outer membrane

DOI:  https://doi.org/10.2174/1573396319666221221110728
Bioessays. 2022 Dec 22. e2200194

The unbroken Krebs cycle. Hormonal-like regulation and mitochondrial signaling to control mitophagy and prevent cell death.

Rafael Franco, Joan Serrano-Marín.

  The tricarboxylic acid (TCA) or Krebs cycle, which takes place in prokaryotic cells and in the mitochondria of eukaryotic cells, is central to life on Earth and participates in key events such as energy production and anabolic processes. Despite its relevance, it is not perceived as tightly regulated compared to other key metabolisms such as glycolysis/gluconeogenesis. A better understanding of the functioning of the TCA cycle is crucial due to mitochondrial function impairment in several diseases, especially those that occur with neurodegeneration. This article revisits what is known about the regulation of the Krebs cycle and hypothesizes the need for large-scale, rapid regulation of TCA cycle enzyme activity. Evidence of mitochondrial enzyme activity regulation by activation/deactivation of protein kinases and phosphatases exists in the literature. Apart from indirect regulation via G protein-coupled receptors (GPCRs) at the cell surface, signaling upon activation of GPCRs in mitochondrial membranes may lead to a direct regulation of the enzymes of the Krebs cycle. Hormonal-like regulation by posttranscriptional events mediated by activable kinases and phosphatases deserve proper assessment using isolated mitochondria.

Keywords:  G protein-coupled receptor; Mitochondrial alterations; anaplerotic; glutamate; glutamine; mitophagy; neurodegeneration; signal transduction; signaling in mitochondria; α-ketoglutarate

DOI:  https://doi.org/10.1002/bies.202200194
Immunohorizons. 2022 Dec 01. 6(12): 837-850

Acly Deficiency Enhances Myelopoiesis through Acetyl Coenzyme A and Metabolic-Epigenetic Cross-Talk.

Dalton L Greenwood, Haley E Ramsey, Phuong T T Nguyen, Andrew R Patterson, Kelsey Voss, Jackie E Bader, Ayaka Sugiura, Zachary A Bacigalupa, Samuel Schaefer, Xiang Ye, Debolanle O Dahunsi, Matthew Z Madden, Kathryn E Wellen, Michael R Savona, P Brent Ferrell, Jeffrey C Rathmell.

Hematopoiesis integrates cytokine signaling, metabolism, and epigenetic modifications to regulate blood cell generation. These processes are linked, as metabolites provide essential substrates for epigenetic marks. In this study, we demonstrate that ATP citrate lyase (Acly), which metabolizes citrate to generate cytosolic acetyl-CoA and is of clinical interest, can regulate chromatin accessibility to limit myeloid differentiation. Acly was tested for a role in murine hematopoiesis by small-molecule inhibition or genetic deletion in lineage-depleted, c-Kit-enriched hematopoietic stem and progenitor cells from Mus musculus. Treatments increased the abundance of cell populations that expressed the myeloid integrin CD11b and other markers of myeloid differentiation. When single-cell RNA sequencing was performed, we found that Acly inhibitor-treated hematopoietic stem and progenitor cells exhibited greater gene expression signatures for macrophages and enrichment of these populations. Similarly, the single-cell assay for transposase-accessible chromatin sequencing showed increased chromatin accessibility at genes associated with myeloid differentiation, including CD11b, CD11c, and IRF8. Mechanistically, Acly deficiency altered chromatin accessibility and expression of multiple C/EBP family transcription factors known to regulate myeloid differentiation and cell metabolism, with increased Cebpe and decreased Cebpa and Cebpb. This effect of Acly deficiency was accompanied by altered mitochondrial metabolism with decreased mitochondrial polarization but increased mitochondrial content and production of reactive oxygen species. The bias to myeloid differentiation appeared due to insufficient generation of acetyl-CoA, as exogenous acetate to support alternate compensatory pathways to produce acetyl-CoA reversed this phenotype. Acly inhibition thus can promote myelopoiesis through deprivation of acetyl-CoA and altered histone acetylome to regulate C/EBP transcription factor family activity for myeloid differentiation.

DOI: https://doi.org/10.4049/immunohorizons.2200086
ACS Chem Biol. 2022 Dec 23.

Widespread, Reversible Cysteine Modification by Methylglyoxal Regulates Metabolic Enzyme Function.

John S Coukos, Chris W Lee, Kavya S Pillai, Kimberly J Liu, Raymond E Moellering.

Methylglyoxal (MGO), a reactive metabolite byproduct of glucose metabolism, is known to form a variety of posttranslational modifications (PTMs) on nucleophilic amino acids. For example, cysteine, the most nucleophilic proteinogenic amino acid, forms reversible hemithioacetal and stable mercaptomethylimidazole adducts with MGO. The high reactivity of cysteine toward MGO and the rate of formation of such modifications provide the opportunity for mechanisms by which proteins and pathways might rapidly sense and respond to alterations in levels of MGO. This indirect measure of alterations in glycolytic flux would thereby allow disparate cellular processes to dynamically respond to changes in nutrient availability and utilization. Here we report the use of quantitative LC-MS/MS-based chemoproteomic profiling approaches with a cysteine-reactive probe to map the proteome-wide landscape of MGO modification of cysteine residues. This approach led to the identification of many sites of potential functional regulation by MGO. We further characterized the role that such modifications have in a catalytic cysteine residue in a key metabolic enzyme and the resulting effects on cellular metabolism.

DOI: https://doi.org/10.1021/acschembio.2c00727
Cell Death Dis. 2022 Dec 20. 13(12): 1055

Pharmacological targeting of the mitochondrial calcium-dependent potassium channel KCa3.1 triggers cell death and reduces tumor growth and metastasis in vivo.

Magdalena Bachmann, Andrea Rossa, Tatiana Varanita, Bernard Fioretti, Lucia Biasutto, Stefan Milenkovic, Vanessa Checchetto, Roberta Peruzzo, Syed A Ahmad, Sameer H Patel, Robert Lukowski, Michael J Edwards, Matteo Ceccarelli, Erich Gulbins, Mario Zoratti, Andrea Mattarei, Ildiko Szabo.

Ion channels are non-conventional, druggable oncological targets. The intermediate-conductance calcium-dependent potassium channel (KCa3.1) is highly expressed in the plasma membrane and in the inner mitochondrial membrane (mitoKCa3.1) of various cancer cell lines. The role mitoKCa3.1 plays in cancer cells is still undefined. Here we report the synthesis and characterization of two mitochondria-targeted novel derivatives of a high-affinity KCa3.1 antagonist, TRAM-34, which retain the ability to block channel activity. The effects of these drugs were tested in melanoma, pancreatic ductal adenocarcinoma and breast cancer lines, as well as in vivo in two orthotopic models. We show that the mitochondria-targeted TRAM-34 derivatives induce release of mitochondrial reactive oxygen species, rapid depolarization of the mitochondrial membrane, fragmentation of the mitochondrial network. They trigger cancer cell death with an EC50 in the µM range, depending on channel expression. In contrast, inhibition of the plasma membrane KCa3.1 by membrane-impermeant Maurotoxin is without effect, indicating a specific role of mitoKCa3.1 in determining cell fate. At sub-lethal concentrations, pharmacological targeting of mitoKCa3.1 significantly reduced cancer cell migration by enhancing production of mitochondrial reactive oxygen species and nuclear factor-κB (NF-κB) activation, and by downregulating expression of Bcl-2 Nineteen kD-Interacting Protein (BNIP-3) and of Rho GTPase CDC-42. This signaling cascade finally leads to cytoskeletal reorganization and impaired migration. Overexpression of BNIP-3 or pharmacological modulation of NF-κB and CDC-42 prevented the migration-reducing effect of mitoTRAM-34. In orthotopic models of melanoma and pancreatic ductal adenocarcinoma, the tumors at sacrifice were 60% smaller in treated versus untreated animals. Metastasis of melanoma cells to lymph nodes was also drastically reduced. No signs of toxicity were observed. In summary, our results identify mitochondrial KCa3.1 as an unexpected player in cancer cell migration and show that its pharmacological targeting is efficient against both tumor growth and metastatic spread in vivo.

DOI: https://doi.org/10.1038/s41419-022-05463-8
Eur J Cancer. 2022 Nov 26. pii: S0959-8049(22)01770-1. [Epub ahead of print]180 30-51

Metabolic switch in cancer - Survival of the fittest.

Hans Raskov, Shruti Gaggar, Asma Tajik, Adile Orhan, Ismail Gögenur.

  Cell metabolism is characterised by the highly coordinated conversion of nutrients into energy and biomass. In solid cancers, hypoxia, nutrient deficiencies, and tumour vasculature are incompatible with accelerated anabolic growth and require a rewiring of cancer cell metabolism. Driver gene mutations direct malignant cells away from oxidation to maximise energy production and biosynthesis while tumour-secreted factors degrade peripheral tissues to fuel disease progression and initiate metastasis. As it is vital to understand cancer cell metabolism and survival mechanisms, this review discusses the metabolic switch and current drug targets and clinical trials. In the future, metabolic markers may be included when phenotyping individual tumours to improve the therapeutic opportunities for personalised therapy.

Keywords:  Biosynthesis; Energy production; Hypoxia; Metabolic reprogramming; Nutrient exploitation; Wasting syndrome

DOI:  https://doi.org/10.1016/j.ejca.2022.11.025
J Cell Sci. 2022 Dec 15. pii: jcs259978. [Epub ahead of print]135(24):

Collagen VI expression is negatively mechanosensitive in pancreatic cancer cells and supports the metastatic niche.

Vasileios Papalazarou, James Drew, Amelie Juin, Heather J Spence, Jamie Whitelaw, Colin Nixon, Manuel Salmeron-Sanchez, Laura M Machesky.

  Pancreatic cancer is a deadly and highly metastatic disease, although how metastatic lesions establish is not fully understood. A key feature of pancreatic tumours is extensive fibrosis and deposition of extracellular matrix (ECM). While pancreatic cancer cells are programmed by stimuli derived from a stiff ECM, metastasis requires loss of attachment and adaptation to a softer microenvironment at distant sites. Growing evidence suggests that stiff ECM influences pancreatic cancer cell behaviour. Here, we argue that this influence is reversible and that pancreatic cancer cells can be reprogrammed upon sensing soft substrates. Using engineered polyacrylamide hydrogels with tuneable mechanical properties, we show that collagen VI is specifically upregulated in pancreatic cancer cells on soft substrates, due to a lack of integrin engagement. Furthermore, the expression of collagen VI is inversely correlated with mechanosensing and activity of YAP (also known as YAP1), which might be due to a direct or indirect effect on transcription of genes encoding collagen VI. Collagen VI supports migration in vitro and metastasis formation in vivo. Metastatic nodules formed by pancreatic cancer cells lacking Col6a1 display stromal cell-derived collagen VI deposition, suggesting that collagen VI derived from either cancer cells or the stroma is an essential component of the metastatic niche. This article has an associated First Person interview with Vasileios Papalazarou, joint first author of the paper.

Keywords:  Cancer metastasis; Collagen VI; Extracellular matrix; Integrin adhesion; Mechanosensing; Pancreatic cancer

DOI:  https://doi.org/10.1242/jcs.259978
Metabolites. 2022 Dec 02. pii: 1211. [Epub ahead of print]12(12):

scFASTCORMICS: A Contextualization Algorithm to Reconstruct Metabolic Multi-Cell Population Models from Single-Cell RNAseq Data.

Maria Pires Pacheco, Jimmy Ji, Tessy Prohaska, María Moscardó García, Thomas Sauter.

  Tumours are composed of various cancer cell populations with different mutation profiles, phenotypes and metabolism that cause them to react to drugs in diverse manners. Increasing the resolution of metabolic models based on single-cell expression data will provide deeper insight into such metabolic differences and improve the predictive power of the models. scFASTCORMICS is a network contextualization algorithm that builds multi-cell population genome-scale models from single-cell RNAseq data. The models contain a subnetwork for each cell population in a tumour, allowing to capture metabolic variations between these clusters. The subnetworks are connected by a union compartment that permits to simulate metabolite exchanges between cell populations in the microenvironment. scFASTCORMICS uses Pareto optimization to simultaneously maximise the compactness, completeness and specificity of the reconstructed metabolic models. scFASTCORMICS is implemented in MATLAB and requires the installation of the COBRA toolbox, rFASTCORMICS and the IBM CPLEX solver.

Keywords:  algorithm; metabolic modelling; metabolism; single-cell RNAseq

DOI:  https://doi.org/10.3390/metabo12121211
Genes (Basel). 2022 Dec 09. pii: 2319. [Epub ahead of print]13(12):

The Role of Nuclear-Encoded Mitochondrial tRNA Charging Enzymes in Human Inherited Disease.

Christina Del Greco, Anthony Antonellis.

  Aminoacyl-tRNA synthetases (ARSs) are highly conserved essential enzymes that charge tRNA with cognate amino acids-the first step of protein synthesis. Of the 37 nuclear-encoded human ARS genes, 17 encode enzymes are exclusively targeted to the mitochondria (mt-ARSs). Mutations in nuclear mt-ARS genes are associated with rare, recessive human diseases with a broad range of clinical phenotypes. While the hypothesized disease mechanism is a loss-of-function effect, there is significant clinical heterogeneity among patients that have mutations in different mt-ARS genes and also among patients that have mutations in the same mt-ARS gene. This observation suggests that additional factors are involved in disease etiology. In this review, we present our current understanding of diseases caused by mutations in the genes encoding mt-ARSs and propose explanations for the observed clinical heterogeneity.

Keywords:  aminoacyl-tRNA synthetases; mitochondrial biology; neurological disease; protein synthesis; tRNA biology

DOI:  https://doi.org/10.3390/genes13122319
Science. 2022 Dec 23. 378(6626): 1315-1320

Glassfrogs conceal blood in their liver to maintain transparency.

Carlos Taboada, Jesse Delia, Maomao Chen, Chenshuo Ma, Xiaorui Peng, Xiaoyi Zhu, Laiming Jiang, Tri Vu, Qifa Zhou, Junjie Yao, Lauren O'Connell, Sönke Johnsen.

Transparency in animals is a complex form of camouflage involving mechanisms that reduce light scattering and absorption throughout the organism. In vertebrates, attaining transparency is difficult because their circulatory system is full of red blood cells (RBCs) that strongly attenuate light. Here, we document how glassfrogs overcome this challenge by concealing these cells from view. Using photoacoustic imaging to track RBCs in vivo, we show that resting glassfrogs increase transparency two- to threefold by removing ~89% of their RBCs from circulation and packing them within their liver. Vertebrate transparency thus requires both see-through tissues and active mechanisms that "clear" respiratory pigments from these tissues. Furthermore, glassfrogs' ability to regulate the location, density, and packing of RBCs without clotting offers insight in metabolic, hemodynamic, and blood-clot research.

DOI: https://doi.org/10.1126/science.abl6620
Trends Cancer. 2022 Dec 20. pii: S2405-8033(22)00266-7. [Epub ahead of print]

T cell-independent abscopal responses to radiotherapy.

Emma Guilbaud, Takahiro Yamazaki, Lorenzo Galluzzi.

  When used according to specific dose/fractionation schedules, focal radiotherapy can elicit a systemic anticancer immune response that limits the growth of distant, non-irradiated tumors. Recent data suggest that, at least in some settings, intratumoral macrophages can be educated by CD47 blockage to promote such an 'abscopal' response independent of CD8+ T cells.

Keywords:  CALR; CGAS; immunogenic cell death; mitochondrial DNA; phagocytosis; type I interferon

DOI:  https://doi.org/10.1016/j.trecan.2022.12.005
Biology (Basel). 2022 Dec 06. pii: 1771. [Epub ahead of print]11(12):

The Glacier Ice Worm, Mesenchytraeus solifugus, Elevates Mitochondrial Inorganic Polyphosphate (PolyP) Levels in Response to Stress.

Teresa Osorio, Ernest R Scoma, Daniel H Shain, Diana S Melissaratos, Lindsey M Riggs, Vedangi Hambardikar, Maria E Solesio.

  The inorganic polymer, polyphosphate (polyP), is present in all organisms examined to date with putative functions ranging from the maintenance of bioenergetics to stress resilience and protein homeostasis. Bioenergetics in the glacier-obligate, segmented worm, Mesenchytraeus solifugus, is characterized by a paradoxical increase in intracellular ATP levels as temperatures decline. We show here that steady-state, mitochondrial polyP levels vary among species of Annelida, but were elevated only in M. solifugus in response to thermal stress. In contrast, polyP levels decreased with temperature in the mesophilic worm, Enchytraeus crypticus. These results identify fundamentally different bioenergetic strategies between closely related annelid worms, and suggest that I worm mitochondria maintain ATP and polyP in a dynamic equilibrium.

Keywords:  ATP; M. solifugus; annelids; bioenergetics; ice worms; inorganic polyphosphate; polyP; stress

DOI:  https://doi.org/10.3390/biology11121771
Cell Rep. 2022 Dec 20. pii: S2211-1247(22)01732-6. [Epub ahead of print]41(12): 111840

Kir4.2 mediates proximal potassium effects on glutaminase activity and kidney injury.

Andrew S Terker, Yahua Zhang, Juan Pablo Arroyo, Shirong Cao, Suwan Wang, Xiaofeng Fan, Jerod S Denton, Ming-Zhi Zhang, Raymond C Harris.

  Inadequate potassium (K+) consumption correlates with increased mortality and poor cardiovascular outcomes. Potassium effects on blood pressure have been described previously; however, whether or not low K+ independently affects kidney disease progression remains unclear. Here, we demonstrate that dietary K+ deficiency causes direct kidney injury. Effects depend on reduced blood K+ and are kidney specific. In response to reduced K+, the channel Kir4.2 mediates altered proximal tubule (PT) basolateral K+ flux, causing intracellular acidosis and activation of the enzyme glutaminase and the ammoniagenesis pathway. Deletion of either Kir4.2 or glutaminase protects from low-K+ injury. Reduced K+ also mediates injury and fibrosis in a model of aldosteronism. These results demonstrate that the PT epithelium, like the distal nephron, is K+ sensitive, with reduced blood K+ causing direct PT injury. Kir4.2 and glutaminase are essential mediators of this injury process, and we identify their potential for future targeting in the treatment of chronic kidney disease.

Keywords:  CP: Metabolism; Kir4.2; aldosterone; ammoniagenesis; glutaminase; kidney injury; potassium; proximal tubule

DOI:  https://doi.org/10.1016/j.celrep.2022.111840
Nat Struct Mol Biol. 2022 Dec 23.

Multiscale reorganization of the genome following DNA damage facilitates chromosome translocations via nuclear actin polymerization.

Jennifer Zagelbaum, Allana Schooley, Junfei Zhao, Benjamin R Schrank, Elsa Callen, Shan Zha, Max E Gottesman, André Nussenzweig, Raul Rabadan, Job Dekker, Jean Gautier.

Nuclear actin-based movements have been shown to orchestrate clustering of DNA double-strand breaks (DSBs) into homology-directed repair domains. Here we describe multiscale three-dimensional genome reorganization following DNA damage and analyze the contribution of the nuclear WASP-ARP2/3-actin pathway toward chromatin topology alterations and pathologic repair. Hi-C analysis reveals genome-wide, DNA damage-induced chromatin compartment flips facilitated by ARP2/3 that enrich for open, A compartments. Damage promotes interactions between DSBs, which in turn facilitate aberrant, actin-dependent intra- and inter-chromosomal rearrangements. Our work establishes that clustering of resected DSBs into repair domains by nuclear actin assembly is coordinated with multiscale alterations in genome architecture that enable homology-directed repair while also increasing nonhomologous end-joining-dependent translocation frequency.

DOI: https://doi.org/10.1038/s41594-022-00893-6
Mol Cell. 2022 Dec 08. pii: S1097-2765(22)01134-0. [Epub ahead of print]

Ring domains are essential for GATOR2-dependent mTORC1 activation.

Cong Jiang, Xiaoming Dai, Shaohui He, Hongfei Zhou, Lan Fang, Jianping Guo, Songlei Liu, Tao Zhang, Weijuan Pan, Haihong Yu, Tianmin Fu, Dali Li, Hiroyuki Inuzuka, Ping Wang, Jianru Xiao, Wenyi Wei.

  The GATOR2-GATOR1 signaling axis is essential for amino-acid-dependent mTORC1 activation. However, the molecular function of the GATOR2 complex remains unknown. Here, we report that disruption of the Ring domains of Mios, WDR24, or WDR59 completely impedes amino-acid-mediated mTORC1 activation. Mechanistically, via interacting with Ring domains of WDR59 and WDR24, the Ring domain of Mios acts as a hub to maintain GATOR2 integrity, disruption of which leads to self-ubiquitination of WDR24. Physiologically, leucine stimulation dissociates Sestrin2 from the Ring domain of WDR24 and confers its availability to UBE2D3 and subsequent ubiquitination of NPRL2, contributing to GATOR2-mediated GATOR1 inactivation. As such, WDR24 ablation or Ring deletion prevents mTORC1 activation, leading to severe growth defects and embryonic lethality at E10.5 in mice. Hence, our findings demonstrate that Ring domains are essential for GATOR2 to transmit amino acid availability to mTORC1 and further reveal the essentiality of nutrient sensing during embryonic development.

Keywords:  Gator1; Gator2; NPRL2; Sestrin; WDR24; amino acid sensing; mTOR; ubiquitination

DOI:  https://doi.org/10.1016/j.molcel.2022.11.021
Metabolites. 2022 Dec 02. pii: 1210. [Epub ahead of print]12(12):

Metabolites of De Novo Purine Synthesis: Metabolic Regulators and Cytotoxic Compounds.

Olga Souckova, Vaclava Skopova, Veronika Baresova, David Sedlak, Anthony J Bleyer, Stanislav Kmoch, Marie Zikanova.

  Cytotoxicity of de novo purine synthesis (DNPS) metabolites is critical to the pathogenesis of three known and one putative autosomal recessive disorder affecting DNPS. These rare disorders are caused by biallelic mutations in the DNPS genes phosphoribosylformylglycineamidine synthase (PFAS), phosphoribosylaminoimidazolecarboxylase/phosphoribosylaminoimidazolesuccinocarboxamide synthase (PAICS), adenylosuccinate lyase (ADSL), and aminoimidazole carboxamide ribonucleotide transformylase/inosine monophosphate cyclohydrolase (ATIC) and are clinically characterized by developmental abnormalities, psychomotor retardation, and nonspecific neurological impairment. At a biochemical level, loss of function of specific mutated enzymes results in elevated levels of DNPS ribosides in body fluids. The main pathogenic effect is attributed to the accumulation of DNPS ribosides, which are postulated to be toxic to the organism. Therefore, we decided to characterize the uptake and flux of several DNPS metabolites in HeLa cells and the impact of DNPS metabolites to viability of cancer cell lines and primary skin fibroblasts. We treated cells with DNPS metabolites and followed their flux in purine synthesis and degradation. In this study, we show for the first time the transport of formylglycinamide ribotide (FGAR), aminoimidazole ribotide (AIR), succinylaminoimidazolecarboxamide ribotide (SAICAR), and aminoimidazolecarboxamide ribotide (AICAR) into cells and their flux in DNPS and the degradation pathway. We found diminished cell viability mostly in the presence of FGAR and AIR. Our results suggest that direct cellular toxicity of DNPS metabolites may not be the primary pathogenetic mechanism in these disorders.

Keywords:  ADSL; AICAR; AIR; ATIC; FGAR; PAICS; PFAS; SAICAR; cytotoxicity; purine synthesis

DOI:  https://doi.org/10.3390/metabo12121210
Science. 2022 Dec 23. 378(6626): 1276-1277

Epigenetic clocks, aging, and cancer.

Sarah E Johnstone, Vadim N Gladyshev, Martin J Aryee, Bradley E Bernstein.

Global methylation changes in aging cells affect cancer risk and tissue homeostasis.

DOI: https://doi.org/10.1126/science.abn4009
Nat Commun. 2022 Dec 21. 13(1): 7791

Huntington disease oligodendrocyte maturation deficits revealed by single-nucleus RNAseq are rescued by thiamine-biotin supplementation.

Ryan G Lim, Osama Al-Dalahmah, Jie Wu, Maxwell P Gold, Jack C Reidling, Guomei Tang, Miriam Adam, David K Dansu, Hye-Jin Park, Patrizia Casaccia, Ricardo Miramontes, Andrea M Reyes-Ortiz, Alice Lau, Richard A Hickman, Fatima Khan, Fahad Paryani, Alice Tang, Kenneth Ofori, Emily Miyoshi, Neethu Michael, Nicolette McClure, Xena E Flowers, Jean Paul Vonsattel, Shawn Davidson, Vilas Menon, Vivek Swarup, Ernest Fraenkel, James E Goldman, Leslie M Thompson.

The complexity of affected brain regions and cell types is a challenge for Huntington's disease (HD) treatment. Here we use single nucleus RNA sequencing to investigate molecular pathology in the cortex and striatum from R6/2 mice and human HD post-mortem tissue. We identify cell type-specific and -agnostic signatures suggesting oligodendrocytes (OLs) and oligodendrocyte precursors (OPCs) are arrested in intermediate maturation states. OL-lineage regulators OLIG1 and OLIG2 are negatively correlated with CAG length in human OPCs, and ATACseq analysis of HD mouse NeuN-negative cells shows decreased accessibility regulated by OL maturation genes. The data implicates glucose and lipid metabolism in abnormal cell maturation and identify PRKCE and Thiamine Pyrophosphokinase 1 (TPK1) as central genes. Thiamine/biotin treatment of R6/1 HD mice to compensate for TPK1 dysregulation restores OL maturation and rescues neuronal pathology. Our insights into HD OL pathology spans multiple brain regions and link OL maturation deficits to abnormal thiamine metabolism.

DOI: https://doi.org/10.1038/s41467-022-35388-x
Molecules. 2022 Dec 07. pii: 8656. [Epub ahead of print]27(24):

The Aging Process: A Metabolomics Perspective.

Alex Castro, Étore F Signini, Juliana Magalhães De Oliveira, Maria Carolina Bezerra Di Medeiros Leal, Patrícia Rehder-Santos, Juliana C Millan-Mattos, Vinicius Minatel, Camila B F Pantoni, Regina V Oliveira, Aparecida M Catai, Antônio G Ferreira.

  Aging process is characterized by a progressive decline of several organic, physiological, and metabolic functions whose precise mechanism remains unclear. Metabolomics allows the identification of several metabolites and may contribute to clarifying the aging-regulated metabolic pathways. We aimed to investigate aging-related serum metabolic changes using a metabolomics approach. Fasting blood serum samples from 138 apparently healthy individuals (20-70 years old, 56% men) were analyzed by Proton Nuclear Magnetic Resonance spectroscopy (1H NMR) and Liquid Chromatography-High-Resolution Mass Spectrometry (LC-HRMS), and for clinical markers. Associations of the metabolic profile with age were explored via Correlations (r); Metabolite Set Enrichment Analysis; Multiple Linear Regression; and Aging Metabolism Breakpoint. The age increase was positively correlated (0.212 ≤ r ≤ 0.370, p < 0.05) with the clinical markers (total cholesterol, HDL, LDL, VLDL, triacylglyceride, and glucose levels); negatively correlated (-0.285 ≤ r ≤ -0.214, p < 0.05) with tryptophan, 3-hydroxyisobutyrate, asparagine, isoleucine, leucine, and valine levels, but positively (0.237 ≤ r ≤ 0.269, p < 0.05) with aspartate and ornithine levels. These metabolites resulted in three enriched pathways: valine, leucine, and isoleucine degradation, urea cycle, and ammonia recycling. Additionally, serum metabolic levels of 3-hydroxyisobutyrate, isoleucine, aspartate, and ornithine explained 27.3% of the age variation, with the aging metabolism breakpoint occurring after the third decade of life. These results indicate that the aging process is potentially associated with reduced serum branched-chain amino acid levels (especially after the third decade of life) and progressively increased levels of serum metabolites indicative of the urea cycle.

Keywords:  liquid chromatography-high-resolution mass spectrometry; metabolism; metabolome; nuclear magnetic resonance

DOI:  https://doi.org/10.3390/molecules27248656
Nat Immunol. 2022 Dec 21.

Hypoxia drives CD39-dependent suppressor function in exhausted T cells to limit antitumor immunity.

Paolo D A Vignali, Kristin DePeaux, McLane J Watson, Chenxian Ye, B Rhodes Ford, Konstantinos Lontos, Nicole K McGaa, Nicole E Scharping, Ashley V Menk, Simon C Robson, Amanda C Poholek, Dayana B Rivadeneira, Greg M Delgoffe.

CD8+ T cells are critical for elimination of cancer cells. Factors within the tumor microenvironment (TME) can drive these cells to a hypofunctional state known as exhaustion. The most terminally exhausted T (tTex) cells are resistant to checkpoint blockade immunotherapy and might instead limit immunotherapeutic efficacy. Here we show that intratumoral CD8+ tTex cells possess transcriptional features of CD4+Foxp3+ regulatory T cells and are similarly capable of directly suppressing T cell proliferation ex vivo. tTex cell suppression requires CD39, which generates immunosuppressive adenosine. Restricted deletion of CD39 in endogenous CD8+ T cells resulted in slowed tumor progression, improved immunotherapy responsiveness and enhanced infiltration of transferred tumor-specific T cells. CD39 is induced on tTex cells by tumor hypoxia, thus mitigation of hypoxia limits tTex suppression. Together, these data suggest tTex cells are an important regulatory population in cancer and strategies to limit their generation, reprogram their immunosuppressive state or remove them from the TME might potentiate immunotherapy.

DOI: https://doi.org/10.1038/s41590-022-01379-9
Nature. 2022 Dec 21.

R-loop-derived cytoplasmic RNA-DNA hybrids activate an immune response.

Magdalena P Crossley, Chenlin Song, Michael J Bocek, Jun-Hyuk Choi, Joseph Kousorous, Ataya Sathirachinda, Cindy Lin, Joshua R Brickner, Gongshi Bai, Hannes Lans, Wim Vermeulen, Monther Abu-Remaileh, Karlene A Cimprich.

R-loops are RNA-DNA-hybrid-containing nucleic acids with important cellular roles. Deregulation of R-loop dynamics can lead to DNA damage and genome instability1, which has been linked to the action of endonucleases such as XPG2-4. However, the mechanisms and cellular consequences of such processing have remained unclear. Here we identify a new population of RNA-DNA hybrids in the cytoplasm that are R-loop-processing products. When nuclear R-loops were perturbed by depleting the RNA-DNA helicase senataxin (SETX) or the breast cancer gene BRCA1 (refs. 5-7), we observed XPG- and XPF-dependent cytoplasmic hybrid formation. We identify their source as a subset of stable, overlapping nuclear hybrids with a specific nucleotide signature. Cytoplasmic hybrids bind to the pattern recognition receptors cGAS and TLR3 (ref. 8), activating IRF3 and inducing apoptosis. Excised hybrids and an R-loop-induced innate immune response were also observed in SETX-mutated cells from patients with ataxia oculomotor apraxia type 2 (ref. 9) and in BRCA1-mutated cancer cells10. These findings establish RNA-DNA hybrids as immunogenic species that aberrantly accumulate in the cytoplasm after R-loop processing, linking R-loop accumulation to cell death through the innate immune response. Aberrant R-loop processing and subsequent innate immune activation may contribute to many diseases, such as neurodegeneration and cancer.

DOI: https://doi.org/10.1038/s41586-022-05545-9
Sci Rep. 2022 Dec 17. 12(1): 21832

Extracellular arginine is required but the arginine transporter CAT3 (Slc7a3) is dispensable for mouse normal and malignant hematopoiesis.

Yuhan Yan, Chao Chen, Zhiguo Li, Jing Zhang, Narin Park, Cheng-Kui Qu.

Amino acid-mediated metabolism is one of the key catabolic and anabolic processes involved in diverse cellular functions. However, the role of the semi-essential amino acid arginine in normal and malignant hematopoietic cell development is poorly understood. Here we report that a continuous supply of exogenous arginine is required for the maintenance/function of normal hematopoietic stem cells (HSCs). Surprisingly, knockout of Slc7a3 (CAT3), a major L-arginine transporter, does not affect HSCs in steady-state or under stress. Although Slc7a3 is highly expressed in naïve and activated CD8 T cells, neither T cell development nor activation/proliferation is impacted by Slc7a3 depletion. Furthermore, the Slc7a3 deletion does not attenuate leukemia development driven by Pten loss or the oncogenic Ptpn11E76K mutation. Arginine uptake assays reveal that L-arginine uptake is not disrupted in Slc7a3 knockout cells. These data suggest that extracellular arginine is critically important for HSCs, but CAT3 is dispensable for normal hematopoiesis and leukemogenesis.

DOI: https://doi.org/10.1038/s41598-022-24554-2
Nat Cancer. 2022 Dec;3(12): 1534-1552

A single-cell atlas of glioblastoma evolution under therapy reveals cell-intrinsic and cell-extrinsic therapeutic targets.

Lin Wang, Jangham Jung, Husam Babikir, Karin Shamardani, Saket Jain, Xi Feng, Nalin Gupta, Susanna Rosi, Susan Chang, David Raleigh, David Solomon, Joanna J Phillips, Aaron A Diaz.

Recent longitudinal studies of glioblastoma (GBM) have demonstrated a lack of apparent selection pressure for specific DNA mutations in recurrent disease. Single-cell lineage tracing has shown that GBM cells possess a high degree of plasticity. Together this suggests that phenotype switching, as opposed to genetic evolution, may be the escape mechanism that explains the failure of precision therapies to date. We profiled 86 primary-recurrent patient-matched paired GBM specimens with single-nucleus RNA, single-cell open-chromatin, DNA and spatial transcriptomic/proteomic assays. We found that recurrent GBMs are characterized by a shift to a mesenchymal phenotype. We show that the mesenchymal state is mediated by activator protein 1. Increased T-cell abundance at recurrence was prognostic and correlated with hypermutation status. We identified tumor-supportive networks of paracrine and autocrine signals between GBM cells, nonmalignant neuroglia and immune cells. We present cell-intrinsic and cell-extrinsic targets and a single-cell multiomics atlas of GBM under therapy.

DOI: https://doi.org/10.1038/s43018-022-00475-x
Nat Struct Mol Biol. 2022 Dec 22.

Diverse silent chromatin states modulate genome compartmentalization and loop extrusion barriers.

George Spracklin, Nezar Abdennur, Maxim Imakaev, Neil Chowdhury, Sriharsa Pradhan, Leonid A Mirny, Job Dekker.

The relationships between chromosomal compartmentalization, chromatin state and function are poorly understood. Here by profiling long-range contact frequencies in HCT116 colon cancer cells, we distinguish three silent chromatin states, comprising two types of heterochromatin and a state enriched for H3K9me2 and H2A.Z that exhibits neutral three-dimensional interaction preferences and which, to our knowledge, has not previously been characterized. We find that heterochromatin marked by H3K9me3, HP1α and HP1β correlates with strong compartmentalization. We demonstrate that disruption of DNA methyltransferase activity greatly remodels genome compartmentalization whereby domains lose H3K9me3-HP1α/β binding and acquire the neutrally interacting state while retaining late replication timing. Furthermore, we show that H3K9me3-HP1α/β heterochromatin is permissive to loop extrusion by cohesin but refractory to CTCF binding. Together, our work reveals a dynamic structural and organizational diversity of the silent portion of the genome and establishes connections between the regulation of chromatin state and chromosome organization, including an interplay between DNA methylation, compartmentalization and loop extrusion.

DOI: https://doi.org/10.1038/s41594-022-00892-7
Nat Cancer. 2022 Dec 23.

YAP/TAZ as master regulators in cancer: modulation, function and therapeutic approaches.

Stefano Piccolo, Tito Panciera, Paolo Contessotto, Michelangelo Cordenonsi.

Our understanding of the function of the transcriptional regulators YAP and TAZ (YAP/TAZ) in cancer is advancing. In this Review, we provide an update on recent progress in YAP/TAZ biology, their regulation by Hippo signaling and mechanotransduction and highlight open questions. YAP/TAZ signaling is an addiction shared by multiple tumor types and their microenvironments, providing many malignant attributes. As such, it represents an important vulnerability that may offer a broad window of therapeutic efficacy, and here we give an overview of the current treatment strategies and pioneering clinical trials.

DOI: https://doi.org/10.1038/s43018-022-00473-z