bims-camemi 2022-10-16 papers

bims-camemi

Biomed News

on Mitochondrial metabolism in cancer

Issue of 2022–10–16
forty-six papers selected by
Christian Frezza, Universität zu Köln

Rapid fractionation of mitochondria from mouse liver and heart reveals in vivo metabolite compartmentation.
Effect of TP53 deficiency and KRAS signaling on the bioenergetics of colon cancer cells in response to different substrates: A single cell study.
Cyclophilin D knockout mice do not accumulate succinate during cardiac ischemia.
Metabolite-derived protein modifications modulating oncogenic signaling.
Metabolic communication in the tumour-immune microenvironment.
Purification and biochemical characterization of the Rag GTPase heterodimer.
An ancestral interaction module promotes oligomerization in divergent mitochondrial ATP synthases.
Ultrahigh resolution MS1/MS2-based Reconstruction of Metabolic Networks in Mammalian Cells Reveals Changes for Selenite and Arsenite Action.
Dietary-derived vitamin B12 protects Caenorhabditis elegans from thiol-reducing agents.
Extra-cardiac BCAA catabolism lowers blood pressure and protects from heart failure.
Inhibition of Mitochondrial Redox Signaling with MitoQ Prevents Metastasis of Human Pancreatic Cancer in Mice.
Mitochondrial transporter expression patterns distinguish tumor from normal tissue and identify cancer subtypes with different survival and metabolism.
Mitochondrial Distress in Methylmalonic Acidemia: Novel Pathogenic Insights and Therapeutic Perspectives.
Mitochondrial fitness and cancer risk.
Metabolic Reprogramming in Tumor Endothelial Cells.
N-myc downstream regulated gene 1 (ndrg1) functions as a molecular switch for cellular adaptation to hypoxia.
Linking nutrient sensing, mitochondrial function, and PRR immune cell signaling in liver disease.
Mitochondrial network configuration influences sarcomere and myosin filament structure in striated muscles.
PGC-1β and ERRα Promote Glutamine Metabolism and Colorectal Cancer Survival via Transcriptional Upregulation of PCK2.
Congenital Hypermetabolism and Uncoupled Oxidative Phosphorylation.
Cell competition in carcinogenesis.
Spatial epitope barcoding reveals clonal tumor patch behaviors.
The "Sweet Spot" of Targeting Tumor Metabolism in Ovarian Cancers.
Metabolic and epigenetic orchestration of (CAR) T cell fate and function.
MYC and therapy resistance in cancer: risks and opportunities.
Parallel pathways for serotonin biosynthesis and metabolism in C. elegans.
Cold exposure as anti-cancer therapy.
Senescent cells in the brain and where to find them.
Rheumatoid arthritis and mitochondrial homeostasis: The crossroads of metabolism and immunity.
The metabolic plasticity of B cells.
Machine Learning and Hybrid Methods for Metabolic Pathway Modeling.
Lactate induces metabolic and epigenetic reprogramming of pro-inflammatory Th17 cells.
Epigenetic factor competition reshapes the EMT landscape.
An NRF2 Perspective on Stem Cells and Ageing.
Mono- and diunsaturated fatty acids sensitize cervical cancer to radiation therapy.
Dysregulation of hexosamine biosynthetic pathway wiring metabolic signaling circuits in cancer.
An unusual mode of baseline translation adjusts cellular protein synthesis capacity to metabolic needs.
The aldolase inhibitor aldometanib mimics glucose starvation to activate lysosomal AMPK.
Intracellular Ion Control of WNK Signaling.
Fluid shear stress enhances proliferation of breast cancer cells via downregulation of the c-subunit of the F1FO ATP synthase.
Experimental evolution reveals complex responses to environmental change.
Cellular barcoding to decipher clonal dynamics in disease.
Precision mitochondrial DNA editing with high-fidelity DddA-derived base editors.
Making liver cancer cells go ARGh!
Lysosomal solute and water transport.
Disabling Uncompetitive Inhibition of Oncogenic IDH Mutations Drives Acquired Resistance.

FEBS Lett. 2022 Oct 11.

Rapid fractionation of mitochondria from mouse liver and heart reveals in vivo metabolite compartmentation.

Fay M Allen, Ana S H Costa, Anja V Gruszczyk, Georgina R Bates, Hiran A Prag, Efterpi Nikitopoulou, Carlo Viscomi, Christian Frezza, Andrew M James, Michael P Murphy.

  The compartmentation and distribution of metabolites between mitochondria and the rest of the cell is a key parameter of cell signalling and pathology. Here, we have developed a rapid fractionation procedure that enables us to take mouse heart and liver from in vivo and within ~ 30 seconds stabilise the distribution of metabolites between mitochondria and the cytosol by rapid cooling, homogenisation and dilution. This is followed by centrifugation of mitochondria through an oil layer to separate mitochondrial and cytosolic fractions for subsequent metabolic analysis. Using this procedure revealed the in vivo compartmentation of mitochondrial metabolites and will enable assessment of the distribution of metabolites between the cytosol and mitochondria during a range of situations in vivo.

Keywords:  compartmentation; in vivo; ischemia; metabolites; mitochondria; rapid fractionation

DOI:  https://doi.org/10.1002/1873-3468.14511
Front Cell Dev Biol. 2022 ;10 893677

Effect of TP53 deficiency and KRAS signaling on the bioenergetics of colon cancer cells in response to different substrates: A single cell study.

James Kealey, Heiko Düssmann, Irene Llorente-Folch, Natalia Niewidok, Manuela Salvucci, Jochen H M Prehn, Beatrice D'Orsi.

  Metabolic reprogramming is a hallmark of cancer. Somatic mutations in genes involved in oncogenic signaling pathways, including KRAS and TP53, rewire the metabolic machinery in cancer cells. We here set out to determine, at the single cell level, metabolic signatures in human colon cancer cells engineered to express combinations of activating KRAS gene mutations and TP53 gene deletions. Specifically, we explored how somatic mutations in these genes and substrate availability (lactate, glucose, substrate deprivation) from the extracellular microenvironment affect bioenergetic parameters, including cellular ATP, NADH and mitochondrial membrane potential dynamics. Employing cytosolic and mitochondrial FRET-based ATP probes, fluorescent NADH sensors, and the membrane-permeant cationic fluorescent probe TMRM in HCT-116 cells as a model system, we observed that TP53 deletion and KRAS mutations drive a shift in metabolic signatures enabling lactate to become an efficient metabolite to replenish both ATP and NADH following nutrient deprivation. Intriguingly, cytosolic, mitochondrial and overall cellular ATP measurements revealed that, in WT KRAS cells, TP53 deficiency leads to an enhanced ATP production in the presence of extracellular lactate and glucose, and to the greatest increase in ATP following a starvation period. On the other hand, oncogenic KRAS in TP53-deficient cells reversed the alterations in cellular ATP levels. Moreover, cell population measurements of mitochondrial and glycolytic metabolism using a Seahorse analyzer demonstrated that WT KRAS TP53-silenced cells display an increase of the basal respiration and tightly-coupled mitochondria, in the presence of glucose as substrate, compared to TP53 competent cells. Furthermore, cells possessing oncogenic KRAS, independently of TP53 status, showed less pronounced mitochondrial membrane potential changes in response to metabolic nutrients. Furthermore, analysis of cytosolic and mitochondrial NADH levels revealed that the simultaneous presence of TP53 deletion and oncogenic KRAS showed the most pronounced alteration in cytosolic and mitochondrial NADH during metabolic stress. In conclusion, our findings demonstrate how activating KRAS mutation and loss of TP53 remodel cancer metabolism and lead to alterations in bioenergetics under metabolic stress conditions by modulating cellular ATP production, NADH oxidation, mitochondrial respiration and function.

Keywords:  Cancer Metabolism; OxPhos; bioenergetics; colorectal cancer; metabolic stress

DOI:  https://doi.org/10.3389/fcell.2022.893677
J Mol Cell Cardiol. 2022 Oct 06. pii: S0022-2828(22)00531-4. [Epub ahead of print]173 73-74

Cyclophilin D knockout mice do not accumulate succinate during cardiac ischemia.

Hiran A Prag, Duvaraka Kula-Alwar, Paolo Bernardi, Fabio Di Lisa, Michael P Murphy, Thomas Krieg.



Keywords:  Cyclophilin D; Cyclosporin A; Ischemia/reperfusion injury; Mitochondrial permeability transition pore; Reactive oxygen species; Succinate

DOI:  https://doi.org/10.1016/j.yjmcc.2022.09.006
Front Oncol. 2022 ;12 988626

Metabolite-derived protein modifications modulating oncogenic signaling.

Yawen Liu, Anke Vandekeere, Min Xu, Sarah-Maria Fendt, Patricia Altea-Manzano.

  Malignant growth is defined by multiple aberrant cellular features, including metabolic rewiring, inactivation of tumor suppressors and the activation of oncogenes. Even though these features have been described as separate hallmarks, many studies have shown an extensive mutual regulatory relationship amongst them. On one hand, the change in expression or activity of tumor suppressors and oncogenes has extensive direct and indirect effects on cellular metabolism, activating metabolic pathways required for malignant growth. On the other hand, the tumor microenvironment and tumor intrinsic metabolic alterations result in changes in intracellular metabolite levels, which directly modulate the protein modification of oncogenes and tumor suppressors at both epigenetic and post-translational levels. In this mini-review, we summarize the crosstalk between tumor suppressors/oncogenes and metabolism-induced protein modifications at both levels and explore the impact of metabolic (micro)environments in shaping these.

Keywords:  metabolites; oncogenic signaling; post-translational modification; tumor microenvironment; tumor suppressor gene

DOI:  https://doi.org/10.3389/fonc.2022.988626
Nat Cell Biol. 2022 Oct 13.

Metabolic communication in the tumour-immune microenvironment.

Kung-Chi Kao, Stefania Vilbois, Chin-Hsien Tsai, Ping-Chih Ho.

The metabolically hostile tumour microenvironment imposes barriers to tumour-infiltrating immune cells and impedes durable clinical remission following immunotherapy. Metabolic communication between cancer cells and their neighbouring immune cells could determine the amplitude and type of immune responses, highlighting a potential involvement of metabolic crosstalk in immune surveillance and escape. In this Review, we explore tumour-immune metabolic crosstalk and discuss potential nutrient-limiting strategies that favour anti-tumour immune responses.

DOI: https://doi.org/10.1038/s41556-022-01002-x
Methods Enzymol. 2022 ;pii: S0076-6879(22)00245-2. [Epub ahead of print]675 131-158

Purification and biochemical characterization of the Rag GTPase heterodimer.

Dylan D Doxsey, Kuang Shen.

  The mechanistic target of rapamycin complex 1 (mTORC1) senses nutrient levels in the cell and based on the availability, regulates cellular growth and proliferation. Its activity is tightly modulated by two GTPase units, the Rag GTPases and the Rheb GTPase. The Rag GTPases are the central hub of amino acid sensing as they summarize the amino acid signals from upstream regulators and control the subcellular localization of mTORC1. Unique from canonical signaling GTPases, the Rag GTPases are obligatory heterodimers, and the two subunits coordinate their nucleotide loading states to regulate their functional states. Robust biochemical analysis is indispensable to understanding the molecular mechanism governing the GTPase cycle. This chapter discusses protocols for purifying and biochemically characterizing the Rag GTPase heterodimer. We described two purification protocols to recombinantly produce the Rag GTPase heterodimer in large quantities. We then described assays to quantitatively measure the nucleotide binding and hydrolysis by the Rag GTPases. These assays allow for a thorough investigation of this unique heterodimeric GTPase, and they could be applicable to investigations of other noncanonical GTPases.

Keywords:  Cooperativity; Enzymatic mechanism; GTP hydrolysis; Kinetics; Rag GTPase; mTORC1

DOI:  https://doi.org/10.1016/bs.mie.2022.07.007
Nat Commun. 2022 Oct 11. 13(1): 5989

An ancestral interaction module promotes oligomerization in divergent mitochondrial ATP synthases.

Ondřej Gahura, Alexander Mühleip, Carolina Hierro-Yap, Brian Panicucci, Minal Jain, David Hollaus, Martina Slapničková, Alena Zíková, Alexey Amunts.

Mitochondrial ATP synthase forms stable dimers arranged into oligomeric assemblies that generate the inner-membrane curvature essential for efficient energy conversion. Here, we report cryo-EM structures of the intact ATP synthase dimer from Trypanosoma brucei in ten different rotational states. The model consists of 25 subunits, including nine lineage-specific, as well as 36 lipids. The rotary mechanism is influenced by the divergent peripheral stalk, conferring a greater conformational flexibility. Proton transfer in the lumenal half-channel occurs via a chain of five ordered water molecules. The dimerization interface is formed by subunit-g that is critical for interactions but not for the catalytic activity. Although overall dimer architecture varies among eukaryotes, we find that subunit-g together with subunit-e form an ancestral oligomerization motif, which is shared between the trypanosomal and mammalian lineages. Therefore, our data defines the subunit-g/e module as a structural component determining ATP synthase oligomeric assemblies.

DOI: https://doi.org/10.1038/s41467-022-33588-z
J Biol Chem. 2022 Oct 09. pii: S0021-9258(22)01029-8. [Epub ahead of print] 102586

Ultrahigh resolution MS1/MS2-based Reconstruction of Metabolic Networks in Mammalian Cells Reveals Changes for Selenite and Arsenite Action.

Teresa W-M Fan, Qiushi Sun, Richard M Higashi.

  Metabolic networks are complex, intersecting, and composed of numerous enzyme-catalyzed biochemical reactions that transfer various molecular moieties among metabolites. Thus, robust reconstruction of metabolic networks requires metabolite moieties to be tracked, which cannot be readily achieved with mass spectrometry (MS) alone. We previously developed an Ion Chromatography (IC)-ultrahigh resolution (UHR)-MS1/data independent (DI)-MS2 method to track the simultaneous incorporation of the heavy isotopes 13C and 15N into the moieties of purine/pyrimidine nucleotides in mammalian cells. UHR-MS1 resolves and counts multiple tracer atoms in intact metabolites while DI-tandem MS (MS2) determines isotopic enrichment in their moieties without concern for the numerous mass isotopologue source ions to be fragmented. Together, they enabled rigorous MS-based reconstruction of metabolic networks at specific enzyme levels. We have expanded this approach to trace the labeled atom fate of [13C6]-glucose in 3D A549 spheroids in response to the anti-cancer agent selenite and that of [13C5,15N2]-glutamine in 2D BEAS-2B cells in response to arsenite transformation. We deduced altered activities of specific enzymes in the Krebs cycle, pentose phosphate pathway, gluconeogenesis, and UDP N-acetylglucosamine synthesis pathways elicited by the stressors. These metabolic details help elucidate the resistance mechanism of 3D versus 2D A549 cultures to selenite and metabolic reprogramming that can mediate the transformation of BEAS2B cells by arsenite.

Keywords:  Selenite; [(13)C(5),(15)N(2)]-glutamine; [(13)C(6)]-glucose; arsenite; metabolic pathway reconstruction; positional isotopologues; stable isotope resolved metabolomics (SIRM)

DOI:  https://doi.org/10.1016/j.jbc.2022.102586
BMC Biol. 2022 Oct 08. 20(1): 228

Dietary-derived vitamin B12 protects Caenorhabditis elegans from thiol-reducing agents.

Alan D Winter, Elissa Tjahjono, Leonardo J Beltrán, Iain L Johnstone, Neil J Bulleid, Antony P Page.

   BACKGROUND: One-carbon metabolism, which includes the folate and methionine cycles, involves the transfer of methyl groups which are then utilised as a part of multiple physiological processes including redox defence. During the methionine cycle, the vitamin B12-dependent enzyme methionine synthetase converts homocysteine to methionine. The enzyme S-adenosylmethionine (SAM) synthetase then uses methionine in the production of the reactive methyl carrier SAM. SAM-binding methyltransferases then utilise SAM as a cofactor to methylate proteins, small molecules, lipids, and nucleic acids.
RESULTS: We describe a novel SAM methyltransferase, RIPS-1, which was the single gene identified from forward genetic screens in Caenorhabditis elegans looking for resistance to lethal concentrations of the thiol-reducing agent dithiothreitol (DTT). As well as RIPS-1 mutation, we show that in wild-type worms, DTT toxicity can be overcome by modulating vitamin B12 levels, either by using growth media and/or bacterial food that provide higher levels of vitamin B12 or by vitamin B12 supplementation. We show that active methionine synthetase is required for vitamin B12-mediated DTT resistance in wild types but is not required for resistance resulting from RIPS-1 mutation and that susceptibility to DTT is partially suppressed by methionine supplementation. A targeted RNAi modifier screen identified the mitochondrial enzyme methylmalonyl-CoA epimerase as a strong genetic enhancer of DTT resistance in a RIPS-1 mutant. We show that RIPS-1 is expressed in the intestinal and hypodermal tissues of the nematode and that treating with DTT, β-mercaptoethanol, or hydrogen sulfide induces RIPS-1 expression. We demonstrate that RIPS-1 expression is controlled by the hypoxia-inducible factor pathway and that homologues of RIPS-1 are found in a small subset of eukaryotes and bacteria, many of which can adapt to fluctuations in environmental oxygen levels.
CONCLUSIONS: This work highlights the central importance of dietary vitamin B12 in normal metabolic processes in C. elegans, defines a new role for this vitamin in countering reductive stress, and identifies RIPS-1 as a novel methyltransferase in the methionine cycle.

Keywords:  DTT; Methionine; Methyltransferase; Reductive stress; Vitamin B12

DOI:  https://doi.org/10.1186/s12915-022-01415-y
Cell Metab. 2022 Oct 04. pii: S1550-4131(22)00398-9. [Epub ahead of print]

Extra-cardiac BCAA catabolism lowers blood pressure and protects from heart failure.

Danielle Murashige, Jae Woo Jung, Michael D Neinast, Michael G Levin, Qingwei Chu, Jonathan P Lambert, Joanne F Garbincius, Boa Kim, Atsushi Hoshino, Ingrid Marti-Pamies, Kendra S McDaid, Swapnil V Shewale, Emily Flam, Steven Yang, Emilia Roberts, Li Li, Michael P Morley, Kenneth C Bedi, Matthew C Hyman, David S Frankel, Kenneth B Margulies, Richard K Assoian, John W Elrod, Cholsoon Jang, Joshua D Rabinowitz, Zoltan Arany.

  Pharmacologic activation of branched-chain amino acid (BCAA) catabolism is protective in models of heart failure (HF). How protection occurs remains unclear, although a causative block in cardiac BCAA oxidation is widely assumed. Here, we use in vivo isotope infusions to show that cardiac BCAA oxidation in fact increases, rather than decreases, in HF. Moreover, cardiac-specific activation of BCAA oxidation does not protect from HF even though systemic activation does. Lowering plasma and cardiac BCAAs also fails to confer significant protection, suggesting alternative mechanisms of protection. Surprisingly, activation of BCAA catabolism lowers blood pressure (BP), a known cardioprotective mechanism. BP lowering occurred independently of nitric oxide and reflected vascular resistance to adrenergic constriction. Mendelian randomization studies revealed that elevated plasma BCAAs portend higher BP in humans. Together, these data indicate that BCAA oxidation lowers vascular resistance, perhaps in part explaining cardioprotection in HF that is not mediated directly in cardiomyocytes.

Keywords:  BCAA; Mendelian randomization; blood pressure; branched-chain amino acid; cardiac metabolism; cardiovascular metabolism; heart failure; hypertension; metabolomics

DOI:  https://doi.org/10.1016/j.cmet.2022.09.008
Cancers (Basel). 2022 Oct 07. pii: 4918. [Epub ahead of print]14(19):

Inhibition of Mitochondrial Redox Signaling with MitoQ Prevents Metastasis of Human Pancreatic Cancer in Mice.

Tania Capeloa, Justine A Van de Velde, Donatienne d'Hose, Sara G Lipari, Françoise Derouane, Loïc Hamelin, Marie Bedin, Thibaut Vazeille, François P Duhoux, Michael P Murphy, Paolo E Porporato, Bernard Gallez, Pierre Sonveaux.

  At diagnosis, about 35% of pancreatic cancers are at the locally invasive yet premetastatic stage. Surgical resection is not a treatment option, leaving patients with a largely incurable disease that often evolves to the polymetastatic stage despite chemotherapeutic interventions. In this preclinical study, we hypothesized that pancreatic cancer metastasis can be prevented by inhibiting mitochondrial redox signaling with MitoQ, a mitochondria-targeted antioxidant. Using four different cancer cell lines, we report that, at clinically relevant concentrations (100-500 nM), MitoQ selectively repressed mesenchymal pancreatic cancer cell respiration, which involved the inhibition of the expression of PGC-1α, NRF1 and a reduced expression of electron-transfer-chain complexes I to III. MitoQ consequently decreased the mitochondrial membrane potential and mitochondrial superoxide production by these cells. Phenotypically, MitoQ further inhibited pancreatic cancer cell migration, invasion, clonogenicity and the expression of stem cell markers. It reduced by ~50% the metastatic homing of human MIA PaCa-2 cells in the lungs of mice. We further show that combination treatments with chemotherapy are conceivable. Collectively, this study indicates that the inhibition of mitochondrial redox signaling is a possible therapeutic option to inhibit the metastatic progression of pancreatic cancer.

Keywords:  MitoQ; cancer metabolism; cancer metastasis; mitochondria; pancreatic ductal adenocarcinoma (PDAC); reactive oxygen species (ROS); redox signaling

DOI:  https://doi.org/10.3390/cancers14194918
Sci Rep. 2022 Oct 11. 12(1): 17035

Mitochondrial transporter expression patterns distinguish tumor from normal tissue and identify cancer subtypes with different survival and metabolism.

Hartmut Wohlrab, Sabina Signoretti, Lucia E Rameh, Derrick K DeConti, Steen H Hansen.

Transporters of the inner mitochondrial membrane are essential to metabolism. We demonstrate that metabolism as represented by expression of genes encoding SLC25 transporters differentiates human cancers. Tumor to normal tissue expression ratios for clear cell renal cell carcinoma, colon adenocarcinoma, lung adenocarcinoma and breast invasive carcinoma were found to be highly significant. Affinity propagation trained on SLC25 gene expression patterns from 19 human cancer types (6825 TCGA samples) and normal tissues (2322 GTEx samples) was used to generate clusters. They differentiate cancers from normal tissues. They also indicate cancer subtypes with survivals distinct from the total patient population of the cancer type. Probing the kidney, colon, lung, and breast cancer clusters, subtype pairs of cancers were identified with distinct prognoses and differing in expression of protein coding genes from among 2080 metabolic enzymes assayed. We demonstrate that SLC25 expression clusters facilitate the identification of the tissue-of-origin, essential to efficacy of most cancer therapies, of CUPs (cancer-unknown-primary) known to have poor prognoses. Different cancer types within a single cluster have similar metabolic patterns and this raises the possibility that such cancers may respond similarly to existing and new anti-cancer therapies.

DOI: https://doi.org/10.1038/s41598-022-21411-0
Cells. 2022 Oct 10. pii: 3179. [Epub ahead of print]11(19):

Mitochondrial Distress in Methylmalonic Acidemia: Novel Pathogenic Insights and Therapeutic Perspectives.

Svenja Aline Keller, Alessandro Luciani.

  Mitochondria are highly dynamic, double-membrane-enclosed organelles that sustain cellular metabolism and, hence, cellular, and organismal homeostasis. Dysregulation of the mitochondrial network might, therefore, confer a potentially devastating vulnerability to high-energy-requiring cell types, contributing to a broad variety of hereditary and acquired diseases, which include inborn errors of metabolism, cancer, neurodegeneration, and aging-associated adversities. In this Review, we highlight the biological functions of mitochondria-localized enzymes, from the perspective of understanding the pathophysiology of the inherited disorders destroying mitochondrial homeostasis and cellular metabolism. Using methylmalonic acidemia (MMA) as a paradigm of mitochondrial dysfunction, we discuss how mitochondrial-directed signaling pathways sustain the physiological homeostasis of specialized cell types and how these may be disturbed in disease conditions. This Review also provides a critical analysis of molecular underpinnings, through which defects in the autophagy-mediated quality control and surveillance systems contribute to cellular dysfunction, and indicates potential therapeutic strategies for affected tissues. These insights might, ultimately, advance the discovery and development of new therapeutics, not only for methylmalonic acidemia but also for other currently intractable mitochondrial diseases, thus transforming our ability to modulate health and homeostasis.

Keywords:  epithelial cell distress; kidney tubule; metabolism; mitochondria; mitophagy; oxidative stress; signaling

DOI:  https://doi.org/10.3390/cells11193179
PLoS One. 2022 ;17(10): e0273520

Mitochondrial fitness and cancer risk.

Andrew V Kossenkov, Andrew Milcarek, Faiyaz Notta, Gun-Ho Jang, Julie M Wilson, Steven Gallinger, Daniel Cui Zhou, Li Ding, Jagadish C Ghosh, Michela Perego, Annamaria Morotti, Marco Locatelli, Marie E Robert, Valentina Vaira, Dario C Altieri.

Changes in metabolism are a hallmark of cancer, but molecular signatures of altered bioenergetics to aid in clinical decision-making do not currently exist. We recently identified a group of human tumors with constitutively reduced expression of the mitochondrial structural protein, Mic60, also called mitofilin or inner membrane mitochondrial protein (IMMT). These Mic60-low tumors exhibit severe loss of mitochondrial fitness, paradoxically accompanied by increased metastatic propensity and upregulation of a unique transcriptome of Interferon (IFN) signaling and Senescence-Associated Secretory Phenotype (SASP). Here, we show that an optimized, 11-gene signature of Mic60-low tumors is differentially expressed in multiple malignancies, compared to normal tissues, and correlates with poor patient outcome. When analyzed in three independent patient cohorts of pancreatic ductal adenocarcinoma (PDAC), the Mic60-low gene signature was associated with aggressive disease variants, local inflammation, FOLFIRINOX failure and shortened survival, independently of age, gender, or stage. Therefore, the 11-gene Mic60-low signature may provide an easily accessible molecular tool to stratify patient risk in PDAC and potentially other malignancies.

DOI: https://doi.org/10.1371/journal.pone.0273520
Int J Mol Sci. 2022 Sep 21. pii: 11052. [Epub ahead of print]23(19):

Metabolic Reprogramming in Tumor Endothelial Cells.

Melissa García-Caballero, Liliana Sokol, Anne Cuypers, Peter Carmeliet.

  The dynamic crosstalk between the different components of the tumor microenvironment is critical to determine cancer progression, metastatic dissemination, tumor immunity, and therapeutic responses. Angiogenesis is critical for tumor growth, and abnormal blood vessels contribute to hypoxia and acidosis in the tumor microenvironment. In this hostile environment, cancer and stromal cells have the ability to alter their metabolism in order to support the high energetic demands and favor rapid tumor proliferation. Recent advances have shown that tumor endothelial cell metabolism is reprogrammed, and that targeting endothelial metabolic pathways impacts developmental and pathological vessel sprouting. Therefore, the use of metabolic antiangiogenic therapies to normalize the blood vasculature, in combination with immunotherapies, offers a clinical niche to treat cancer.

Keywords:  metabolic reprogramming; tumor angiogenesis; tumor endothelial cell metabolism; tumor microenvironment

DOI:  https://doi.org/10.3390/ijms231911052
Elife. 2022 Oct 10. pii: e74031. [Epub ahead of print]11

N-myc downstream regulated gene 1 (ndrg1) functions as a molecular switch for cellular adaptation to hypoxia.

Jong S Park, Austin M Gabel, Polina Kassir, Lois Kang, Prableen K Chowdhary, Afia Osei-Ntansah, Neil D Tran, Soujanya Viswanathan, Bryanna Canales, Pengfei Ding, Young-Sam Lee, Rachel Brewster.

  Lack of oxygen (hypoxia and anoxia) is detrimental to cell function and survival and underlies many disease conditions. Hence, metazoans have evolved mechanisms to adapt to low oxygen. One such mechanism, metabolic suppression, decreases the cellular demand for oxygen by downregulating ATP-demanding processes. However, the molecular mechanisms underlying this adaptation are poorly understood. Here, we report on the role of ndrg1a in hypoxia adaptation of the anoxia-tolerant zebrafish embryo. ndrg1a is expressed in the kidney and ionocytes, cell types that use large amounts of ATP to maintain ion homeostasis. ndrg1a mutants are viable and develop normally when raised under normal oxygen. However, their survival and kidney function is reduced relative to WT embryos following exposure to prolonged anoxia. We further demonstrate that Ndrg1a binds to the energy-demanding sodium-potassium ATPase (NKA) pump under anoxia and is required for its degradation, which may preserve ATP in the kidney and ionocytes and contribute to energy homeostasis. Lastly, we show that sodium azide treatment, which increases lactate levels under normoxia, is sufficient to trigger NKA degradation in an Ndrg1a-dependent manner. These findings support a model whereby Ndrg1a is essential for hypoxia adaptation and functions downstream of lactate signaling to induce NKA degradation, a process known to conserve cellular energy.

Keywords:  NDRG1; anoxia; cell biology; developmental biology; hypometabolism; hypoxia; lactate; sodium-potassium pump; zebrafish

DOI:  https://doi.org/10.7554/eLife.74031
Trends Immunol. 2022 Oct 01. pii: S1471-4906(22)00183-1. [Epub ahead of print]

Linking nutrient sensing, mitochondrial function, and PRR immune cell signaling in liver disease.

Claudia Kemper, Michael N Sack.

  Caloric overconsumption in vertebrates promotes adipose and liver fat accumulation while perturbing the gut microbiome. This triad triggers pattern recognition receptor (PRR)-mediated immune cell signaling and sterile inflammation. Moreover, immune system activation perpetuates metabolic consequences, including the progression of nonalcoholic fatty liver disease (NAFLD) to nonalcoholic hepatic steatohepatitis (NASH). Recent findings show that sensing of nutrient overabundance disrupts the activity and homeostasis of the central cellular energy-generating organelle, the mitochondrion. In parallel, whether caloric excess-initiated PRR signaling and mitochondrial perturbations are coordinated to amplify this inflammatory process in NASH progression remains in question. We hypothesize that altered mitochondrial function, classic PRR signaling, and complement activation in response to nutrient overload together play an integrated role across the immune cell landscape, leading to liver inflammation and NASH progression.

Keywords:  cardiometabolic disease; complement; liver; mitochondria; pattern recognition receptors

DOI:  https://doi.org/10.1016/j.it.2022.09.002
Nat Commun. 2022 Oct 13. 13(1): 6058

Mitochondrial network configuration influences sarcomere and myosin filament structure in striated muscles.

Prasanna Katti, Alexander S Hall, Hailey A Parry, Peter T Ajayi, Yuho Kim, T Bradley Willingham, Christopher K E Bleck, Han Wen, Brian Glancy.

Sustained muscle contraction occurs through interactions between actin and myosin filaments within sarcomeres and requires a constant supply of adenosine triphosphate (ATP) from nearby mitochondria. However, it remains unclear how different physical configurations between sarcomeres and mitochondria alter the energetic support for contractile function. Here, we show that sarcomere cross-sectional area (CSA) varies along its length in a cell type-dependent manner where the reduction in Z-disk CSA relative to the sarcomere center is closely coordinated with mitochondrial network configuration in flies, mice, and humans. Further, we find myosin filaments near the sarcomere periphery are curved relative to interior filaments with greater curvature for filaments near mitochondria compared to sarcoplasmic reticulum. Finally, we demonstrate variable myosin filament lattice spacing between filament ends and filament centers in a cell type-dependent manner. These data suggest both sarcomere structure and myofilament interactions are influenced by the location and orientation of mitochondria within muscle cells.

DOI: https://doi.org/10.1038/s41467-022-33678-y
Cancers (Basel). 2022 Oct 05. pii: 4879. [Epub ahead of print]14(19):

PGC-1β and ERRα Promote Glutamine Metabolism and Colorectal Cancer Survival via Transcriptional Upregulation of PCK2.

Danielle E Frodyma, Thomas C Troia, Chaitra Rao, Robert A Svoboda, Jordan A Berg, Dhananjay D Shinde, Vinai C Thomas, Robert E Lewis, Kurt W Fisher.

   BACKGROUND: Previous studies have shown that Peroxisome Proliferator-Activated Receptor Gamma, Coactivator 1 Beta (PGC-1β) and Estrogen-Related Receptor Alpha (ERRα) are over-expressed in colorectal cancer and promote tumor survival.
METHODS: In this study, we use immunoprecipitation of epitope tagged endogenous PGC-1β and inducible PGC-1β mutants to show that amino acid motif LRELL on PGC-1β is responsible for the physical interaction with ERRα and promotes ERRα mRNA and protein expression. We use RNAsequencing to determine the genes regulated by both PGC-1β & ERRα and find that mitochondrial Phosphoenolpyruvate Carboxykinase 2 (PCK2) is the gene that decreased most significantly after depletion of both genes.
RESULTS: Depletion of PCK2 in colorectal cancer cells was sufficient to reduce anchorage-independent growth and inhibit glutamine utilization by the TCA cycle. Lastly, shRNA-mediated depletion of ERRα decreased anchorage-independent growth and glutamine metabolism, which could not be rescued by plasmid derived expression of PCK2.
DISCUSSION: These findings suggest that transcriptional control of PCK2 is one mechanism used by PGC-1β and ERRα to promote glutamine metabolism and colorectal cancer cell survival.

Keywords:  ERRα; K-Ras; PCK2; PGC-1β; colorectal cancer; metabolism; precision medicine

DOI:  https://doi.org/10.3390/cancers14194879
N Engl J Med. 2022 Oct 13. 387(15): 1395-1403

Congenital Hypermetabolism and Uncoupled Oxidative Phosphorylation.

Rebecca D Ganetzky, Andrew L Markhard, Irene Yee, Sheila Clever, Alan Cahill, Hardik Shah, Zenon Grabarek, Tsz-Leung To, Vamsi K Mootha.

We describe the case of identical twin boys who presented with low body weight despite excessive caloric intake. An evaluation of their fibroblasts showed elevated oxygen consumption and decreased mitochondrial membrane potential. Exome analysis revealed a de novo heterozygous variant in ATP5F1B, which encodes the β subunit of mitochondrial ATP synthase (also called complex V). In yeast, mutations affecting the same region loosen coupling between the proton motive force and ATP synthesis, resulting in high rates of mitochondrial respiration. Expression of the mutant allele in human cell lines recapitulates this phenotype. These data support an autosomal dominant mitochondrial uncoupling syndrome with hypermetabolism. (Funded by the National Institutes of Health.).

DOI: https://doi.org/10.1056/NEJMoa2202949
Cancer Res. 2022 Oct 10. pii: CAN-22-2217. [Epub ahead of print]

Cell competition in carcinogenesis.

Esha Madan, António M Palma, Vignesh Vudatha, Jose G Trevino, Kedar Nath Natarajan, Robert A Winn, Kyoung Jae Won, Trevor A Graham, Ronny Drapkin, Stuart Ac McDonald, Paul B Fisher, Rajan Gogna.

The majority of human cancers evolve over time through the stepwise accumulation of somatic mutations followed by clonal selection akin to Darwinian evolution. However, the in-depth mechanisms that govern clonal dynamics and selection remain elusive, particularly during the earliest stages of tissue transformation. Cell competition, often referred to as 'survival of the fittest' at the cellular level, results in the elimination of less fit cells by their more fit neighbors supporting optimal organism health and function. Alternatively, cell competition may allow an uncontrolled expansion of super-fit cancer cells to outcompete their less fit neighbors thereby fueling tumorigenesis. Recent research discussed herein highlights the various non-cell autonomous principles, including inter-clonal competition and cancer-microenvironment competition supporting the ability of a tumor to progress from the initial stages to tissue colonization. Additionally, we extend current insights from cell competition-mediated clonal interactions and selection in normal tissues to better comprehend those factors that contribute to cancer development.

DOI: https://doi.org/10.1158/0008-5472.CAN-22-2217
Cancer Cell. 2022 Oct 12. pii: S1535-6108(22)00443-3. [Epub ahead of print]

Spatial epitope barcoding reveals clonal tumor patch behaviors.

Xavier Rovira-Clavé, Alexandros P Drainas, Sizun Jiang, Yunhao Bai, Maya Baron, Bokai Zhu, Alec E Dallas, Myung Chang Lee, Theresa P Chu, Alessandra Holzem, Ramya Ayyagari, Debadrita Bhattacharya, Erin F McCaffrey, Noah F Greenwald, Maxim Markovic, Garry L Coles, Michael Angelo, Michael C Bassik, Julien Sage, Garry P Nolan.

  Intratumoral heterogeneity is a seminal feature of human tumors contributing to tumor progression and response to treatment. Current technologies are still largely unsuitable to accurately track phenotypes and clonal evolution within tumors, especially in response to genetic manipulations. Here, we developed epitopes for imaging using combinatorial tagging (EpicTags), which we coupled to multiplexed ion beam imaging (EpicMIBI) for in situ tracking of barcodes within tissue microenvironments. Using EpicMIBI, we dissected the spatial component of cell lineages and phenotypes in xenograft models of small cell lung cancer. We observed emergent properties from mixed clones leading to the preferential expansion of clonal patches for both neuroendocrine and non-neuroendocrine cancer cell states in these models. In a tumor model harboring a fraction of PTEN-deficient cancer cells, we observed a non-autonomous increase of clonal patch size in PTEN wild-type cancer cells. EpicMIBI facilitates in situ interrogation of cell-intrinsic and cell-extrinsic processes involved in intratumoral heterogeneity.

Keywords:  MIBI; PTEN; SCLC; multiplex imaging; neuroendocrine; spatial barcoding; tumor heterogeneity

DOI:  https://doi.org/10.1016/j.ccell.2022.09.014
Cancers (Basel). 2022 Sep 27. pii: 4696. [Epub ahead of print]14(19):

The "Sweet Spot" of Targeting Tumor Metabolism in Ovarian Cancers.

Katelyn Tondo-Steele, Karen McLean.

  The objective of this review is to explore the metabolomic environment of epithelial ovarian cancer that contributes to chemoresistance and to use this knowledge to identify possible targets for therapeutic intervention. The Warburg effect describes increased glucose uptake and lactate production in cancer cells. In ovarian cancer, we require a better understanding of how cancer cells reprogram their glycogen metabolism to overcome their nutrient deficient environment and become chemoresistant. Glucose metabolism in ovarian cancer cells has been proposed to be influenced by altered fatty acid metabolism, oxidative phosphorylation, and acidification of the tumor microenvironment. We investigate several markers of altered metabolism in ovarian cancer including hypoxia-induced factor 1, VEGF, leptin, insulin-like growth factors, and glucose transporters. We also discuss the signaling pathways involved with these biomarkers including PI3K/AKT/mTOR, JAK/STAT and OXPHOS. This review outlines potential metabolic targets to overcome chemoresistance in ovarian cancer. Continued research of the metabolic changes in ovarian cancer is needed to identify and target these alterations to improve treatment approaches.

Keywords:  PI3K/AKT/mTOR; fatty acid oxidation; glucose; glycolysis; insulin; leptin; metabolism; metabolomics; ovarian cancer; oxidative phosphorylation

DOI:  https://doi.org/10.3390/cancers14194696
Cancer Lett. 2022 Oct 07. pii: S0304-3835(22)00435-9. [Epub ahead of print]550 215948

Metabolic and epigenetic orchestration of (CAR) T cell fate and function.

Behnia Akbari, Zahra Hosseini, Pardis Shahabinejad, Saba Ghassemi, Hamid Reza Mirzaei, Roddy S O'Connor.

  Longevity, functionality, and metabolic fitness are key determinants of chimeric antigen receptor (CAR) T cell efficacy. Activated T cells follow an ordered differentiation program which is facilitated by metabolic adaptations. In response to antigen, T cells undergo a highly-regulated shift to glycolysis. Committing to, and engaging in, glycolysis supports T cell expansion and effector function. Inside tumors, heightened tumor cell metabolism and dysregulated perfusion create a competition for nutrients. As local metabolism supports the differentiation of T cells into functionally-competent progeny, nutrient depletion coupled with persisting antigen can trigger T cell exhaustion. Emerging insights into the barriers impeding CAR T cell function in hostile tumor microenvironments (TME) reveal that metabolic intermediates shape the immune response by influencing epigenetic programs and the control of gene expression. In this review, we discuss recent progress connecting cellular metabolism with epigenetic states in CAR T cells. Given that CAR T cell metabolism can be dynamically regulated, we introduce the concepts of "metabolic-based epigenetic altering" and "epigenetic-based metabolism altering" to restore functional competence in CARTs traversing solid TMEs.

Keywords:  CAR T cell; Epigenetics; Immunotherapy; Metabolism; T cell exhaustion

DOI:  https://doi.org/10.1016/j.canlet.2022.215948
Mol Oncol. 2022 Oct 10.

MYC and therapy resistance in cancer: risks and opportunities.

Giulio Donati, Bruno Amati.

  The MYC transcription factor, encoded by the c-MYC proto-oncogene, is activated by growth-promoting signals, and is a key regulator of biosynthetic and metabolic pathways driving cell growth and proliferation. These same processes are deregulated in MYC-driven tumors, where they become critical for cancer cell proliferation and survival. As other oncogenic insults, overexpressed MYC induces a series of cellular stresses (metabolic, oxidative, replicative, etc.) collectively known as oncogenic stress, which impact not only on tumor progression, but also on the response to therapy, with profound, multifaceted consequences on clinical outcome. On one hand, recent evidence uncovered a widespread role for MYC in therapy resistance in multiple cancer types, with either standard chemotherapeutic or targeted regimens. Reciprocally, oncogenic MYC imparts a series of molecular and metabolic dependencies to cells, thus giving rise to cancer-specific vulnerabilities that may be exploited to obtain synthetic-lethal interactions with novel anticancer drugs. Here we will review the current knowledge on the links between MYC and therapeutic responses, and will discuss possible strategies to overcome resistance through new, targeted interventions.

Keywords:  Myc; synthetic lethality; targeted therapy; therapy resistance

DOI:  https://doi.org/10.1002/1878-0261.13319
Nat Chem Biol. 2022 Oct 10.

Parallel pathways for serotonin biosynthesis and metabolism in C. elegans.

Jingfang Yu, Merly C Vogt, Bennett W Fox, Chester J J Wrobel, Diana Fajardo Palomino, Brian J Curtis, Bingsen Zhang, Henry H Le, Arnaud Tauffenberger, Oliver Hobert, Frank C Schroeder.

The neurotransmitter serotonin plays a central role in animal behavior and physiology, and many of its functions are regulated via evolutionarily conserved biosynthesis and degradation pathways. Here we show that in Caenorhabditis elegans, serotonin is abundantly produced in nonneuronal tissues via phenylalanine hydroxylase, in addition to canonical biosynthesis via tryptophan hydroxylase in neurons. Combining CRISPR-Cas9 genome editing, comparative metabolomics and synthesis, we demonstrate that most serotonin in C. elegans is incorporated into N-acetylserotonin-derived glucosides, which are retained in the worm body and further modified via the carboxylesterase CEST-4. Expression patterns of CEST-4 suggest that serotonin or serotonin derivatives are transported between different tissues. Last, we show that bacterial indole production interacts with serotonin metabolism via CEST-4. Our results reveal a parallel pathway for serotonin biosynthesis in nonneuronal cell types and further indicate that serotonin-derived metabolites may serve distinct signaling functions and contribute to previously described serotonin-dependent phenotypes.

DOI: https://doi.org/10.1038/s41589-022-01148-7
Cancer Cell. 2022 Oct 10. pii: S1535-6108(22)00437-8. [Epub ahead of print]40(10): 1092-1094

Cold exposure as anti-cancer therapy.

Mariia Yuneva.

Seki et al. report in Nature that increasing glucose catabolism in brown adipose tissue by cold exposure lowers blood glucose and insulin tolerance. This systemic effect on body metabolism decreases glucose catabolism in tumors and arrests tumor progression, offering a novel alternative approach for metabolism-based cancer therapy.

DOI: https://doi.org/10.1016/j.ccell.2022.09.008
FEBS J. 2022 Oct 11.

Senescent cells in the brain and where to find them.

Noa Rachmian, Valery Krizhanovsky.

  Cellular senescence is a process in which cells change their characteristic phenotype in response to stress and enter a state of prolonged cell cycle arrest accompanied by a distinct secretory phenotype. Cellular senescence has both beneficial and detrimental outcomes. With age, senescent cells progressively accumulate in tissues and might be the bridge connecting ageing to many age-related pathologies. In recent years, evidence emerged supporting the accumulation of brain senescent cells during neurological disorders and ageing. Here, we will discuss the different brain cell populations that exhibit a senescent phenotype. Subsequently, we will explore several senolytic strategies which have been developed to eliminate senescent cells. Finally, we will examine their potential to directly eliminate these senescent brain cells.

Keywords:  Ageing; Blood-brain barrier; Cellular Senescence; Neurodegeneration; Senolytics

DOI:  https://doi.org/10.1111/febs.16649
Front Med (Lausanne). 2022 ;9 1017650

Rheumatoid arthritis and mitochondrial homeostasis: The crossroads of metabolism and immunity.

Liu Cui, Jing Weiyao, Su Chenghong, Liu Limei, Zhang Xinghua, Yuan Bo, Du Xiaozheng, Wang Haidong.

  Rheumatoid arthritis is an autoimmune disease characterized by chronic symmetric synovial inflammation and erosive bone destruction. Mitochondria are the main site of cellular energy supply and play a key role in the process of energy metabolism. They possess certain self-regulatory and repair capabilities. Mitochondria maintain relative stability in number, morphology, and spatial structure through biological processes, such as biogenesis, fission, fusion, and autophagy, which are collectively called mitochondrial homeostasis. An imbalance in the mitochondrial homeostatic environment will affect immune cell energy metabolism, synovial cell proliferation, apoptosis, and inflammatory signaling. These biological processes are involved in the onset and development of rheumatoid arthritis. In this review, we found that in rheumatoid arthritis, abnormal mitochondrial homeostasis can mediate various immune cell metabolic disorders, and the reprogramming of immune cell metabolism is closely related to their inflammatory activation. In turn, mitochondrial damage and homeostatic imbalance can lead to mtDNA leakage and increased mtROS production. mtDNA and mtROS are active substances mediating multiple inflammatory pathways. Several rheumatoid arthritis therapeutic agents regulate mitochondrial homeostasis and repair mitochondrial damage. Therefore, modulation of mitochondrial homeostasis would be one of the most attractive targets for the treatment of rheumatoid arthritis.

Keywords:  apoptosis and proliferation; energy metabolism; immune cells; inflammatory pathways; mitochondrial homeostasis; rheumatoid arthritis

DOI:  https://doi.org/10.3389/fmed.2022.1017650
Front Mol Biosci. 2022 ;9 991188

The metabolic plasticity of B cells.

Yurena Vivas-García, Alejo Efeyan.

  The humoral response requires rapid growth, biosynthetic capacity, proliferation and differentiation of B cells. These processes involve profound B-cell phenotypic transitions that are coupled to drastic changes in metabolism so as to meet the extremely different energetic requirements as B cells switch from resting to an activated, highly proliferative state and to plasma or memory cell fates. Thus, B cells execute a multi-step, energetically dynamic process of profound metabolic rewiring from low ATP production to transient and large increments of energy expenditure that depend on high uptake and consumption of glucose and fatty acids. Such metabolic plasticity is under tight transcriptional and post-transcriptional regulation. Alterations in B-cell metabolism driven by genetic mutations or by extrinsic insults impair B-cell functions and differentiation and may underlie the anomalous behavior of pathological B cells. Herein, we review molecular switches that control B-cell metabolism and fuel utilization, as well as the emerging awareness of the impact of dynamic metabolic adaptations of B cells throughout the different phases of the humoral response.

Keywords:  B-cell activation; Oxphos; anabolism; glycolysis; humoral response; metabolic plasticity

DOI:  https://doi.org/10.3389/fmolb.2022.991188
Methods Mol Biol. 2023 ;2553 417-439

Machine Learning and Hybrid Methods for Metabolic Pathway Modeling.

Miroslava Cuperlovic-Culf, Thao Nguyen-Tran, Steffany A L Bennett.

  Computational cell metabolism models seek to provide metabolic explanations of cell behavior under different conditions or following genetic alterations, help in the optimization of in vitro cell growth environments, or predict cellular behavior in vivo and in vitro. In the extremes, mechanistic models can include highly detailed descriptions of a small number of metabolic reactions or an approximate representation of an entire metabolic network. To date, all mechanistic models have required details of individual metabolic reactions, either kinetic parameters or metabolic flux, as well as information about extracellular and intracellular metabolite concentrations. Despite the extensive efforts and the increasing availability of high-quality data, required in vivo data are not available for the majority of known metabolic reactions; thus, mechanistic models are based primarily on ex vivo kinetic measurements and limited flux information. Machine learning approaches provide an alternative for derivation of functional dependencies from existing data. The increasing availability of metabolomic and lipidomic data, with growing feature coverage as well as sample set size, is expected to provide new data options needed for derivation of machine learning models of cell metabolic processes. Moreover, machine learning analysis of longitudinal data can lead to predictive models of cell behaviors over time. Conversely, machine learning models trained on steady-state data can provide descriptive models for the comparison of metabolic states in different environments or disease conditions. Additionally, inclusion of metabolic network knowledge in these analyses can further help in the development of models with limited data.This chapter will explore the application of machine learning to the modeling of cell metabolism. We first provide a theoretical explanation of several machine learning and hybrid mechanistic machine learning methods currently being explored to model metabolism. Next, we introduce several avenues for improving these models with machine learning. Finally, we provide protocols for specific examples of the utilization of machine learning in the development of predictive cell metabolism models using metabolomic data. We describe data preprocessing, approaches for training of machine learning models for both descriptive and predictive models, and the utilization of these models in synthetic and systems biology. Detailed protocols provide a list of software tools and libraries used for these applications, step-by-step modeling protocols, troubleshooting, as well as an overview of existing limitations to these approaches.

Keywords:  Hybrid modeling; Lipidomics, Flux analysis; Machine learning; Metabolism modeling; Metabolomics

DOI:  https://doi.org/10.1007/978-1-0716-2617-7_18
EMBO Rep. 2022 Oct 10. e54685

Lactate induces metabolic and epigenetic reprogramming of pro-inflammatory Th17 cells.

Aleksandra Lopez Krol, Hannah P Nehring, Felix F Krause, Anne Wempe, Hartmann Raifer, Andrea Nist, Thorsten Stiewe, Wilhelm Bertrams, Bernd Schmeck, Maik Luu, Hanna Leister, Ho-Ryun Chung, Uta-Maria Bauer, Till Adhikary, Alexander Visekruna.

  Increased lactate levels in the tissue microenvironment are a well-known feature of chronic inflammation. However, the role of lactate in regulating T cell function remains controversial. Here, we demonstrate that extracellular lactate predominantly induces deregulation of the Th17-specific gene expression program by modulating the metabolic and epigenetic status of Th17 cells. Following lactate treatment, Th17 cells significantly reduced their IL-17A production and upregulated Foxp3 expression through ROS-driven IL-2 secretion. Moreover, we observed increased levels of genome-wide histone H3K18 lactylation, a recently described marker for active chromatin in macrophages, in lactate-treated Th17 cells. In addition, we show that high lactate concentrations suppress Th17 pathogenicity during intestinal inflammation in mice. These results indicate that lactate is capable of reprogramming pro-inflammatory T cell phenotypes into regulatory T cells.

Keywords:  Th17 cells; Tregs; histone lactylation; immunometabolism; lactate

DOI:  https://doi.org/10.15252/embr.202254685
Proc Natl Acad Sci U S A. 2022 Oct 18. 119(42): e2210844119

Epigenetic factor competition reshapes the EMT landscape.

M Ali Al-Radhawi, Shubham Tripathi, Yun Zhang, Eduardo D Sontag, Herbert Levine.

  The emergence of and transitions between distinct phenotypes in isogenic cells can be attributed to the intricate interplay of epigenetic marks, external signals, and gene-regulatory elements. These elements include chromatin remodelers, histone modifiers, transcription factors, and regulatory RNAs. Mathematical models known as gene-regulatory networks (GRNs) are an increasingly important tool to unravel the workings of such complex networks. In such models, epigenetic factors are usually proposed to act on the chromatin regions directly involved in the expression of relevant genes. However, it has been well-established that these factors operate globally and compete with each other for targets genome-wide. Therefore, a perturbation of the activity of a regulator can redistribute epigenetic marks across the genome and modulate the levels of competing regulators. In this paper, we propose a conceptual and mathematical modeling framework that incorporates both local and global competition effects between antagonistic epigenetic regulators, in addition to local transcription factors, and show the counterintuitive consequences of such interactions. We apply our approach to recent experimental findings on the epithelial-mesenchymal transition (EMT). We show that it can explain the puzzling experimental data, as well as provide verifiable predictions.

Keywords:  EMT; epigenetic; gene network

DOI:  https://doi.org/10.1073/pnas.2210844119
Front Aging. 2021 ;2 690686

An NRF2 Perspective on Stem Cells and Ageing.

Matthew Dodson, Annadurai Anandhan, Donna D Zhang, Lalitha Madhavan.

  Redox and metabolic mechanisms lie at the heart of stem cell survival and regenerative activity. NRF2 is a major transcriptional controller of cellular redox and metabolic homeostasis, which has also been implicated in ageing and lifespan regulation. However, NRF2's role in stem cells and their functioning with age is only just emerging. Here, focusing mainly on neural stem cells, which are core to adult brain plasticity and function, we review recent findings that identify NRF2 as a fundamental player in stem cell biology and ageing. We also discuss NRF2-based molecular programs that may govern stem cell state and function with age, and implications of this for age-related pathologies.

Keywords:  NRF2; ageing; metabolism; neural stem cells; redox

DOI:  https://doi.org/10.3389/fragi.2021.690686
Cancer Res. 2022 Oct 10. pii: CAN-21-4369. [Epub ahead of print]

Mono- and diunsaturated fatty acids sensitize cervical cancer to radiation therapy.

Naoshad Muhammad, Fiona Ruiz, Jennifer Stanley, Ramachandran Rashmi, Kevin Cho, Kay Jayachandran, Michael C Zahner, Yi Huang, Jin Zhang, Stephanie Markovina, Gary J Patti, Julie K Schwarz.

Obesity induces numerous physiological changes that can impact cancer risk and patient response to therapy. Obese patients with cervical cancer have been reported to have superior outcomes following chemoradiation, suggesting that free fatty acids (FFAs) might enhance response to radiation. Here, using preclinical models, we show that mono- and diunsaturated FFAs (uPPAs) radiosensitize cervical cancer through a novel p53-dependent mechanism. UFFAs signaled through PPARγ and p53 to promote lipid uptake, storage, and metabolism after radiation. Stable isotope labeling confirmed that cervical cancer cells increase both catabolic and anabolic oleate metabolism in response to radiation, with associated increases in dependence on mitochondrial fatty acid oxidation for survival. In vivo, supplementation with exogenous oleate suppressed tumor growth in xenografts after radiation, an effect which could be partially mimicked in tumors from high fat diet-induced obese mice. These results suggest that supplementation with uFFAs may improve tumor responses to radiation therapy, particularly in p53 wild type tumors.

DOI: https://doi.org/10.1158/0008-5472.CAN-21-4369
Biochim Biophys Acta Gen Subj. 2022 Oct 10. pii: S0304-4165(22)00168-4. [Epub ahead of print] 130250

Dysregulation of hexosamine biosynthetic pathway wiring metabolic signaling circuits in cancer.

Naoki Itano, Shungo Iwamoto.

  Metabolite sensing, a fundamental biological process, plays a key role in metabolic signaling circuit rewiring. Hexosamine biosynthetic pathway (HBP) is a glucose metabolic pathway essential for the synthesis of uridine diphosphate N-acetylglucosamine (UDP-GlcNAc), which senses key nutrients and integrally maintains cellular homeostasis. UDP-GlcNAc dynamically regulates protein N-glycosylation and O-linked-N-acetylglucosamine modification (O-GlcNAcylation). Dysregulated HBP flux leads to abnormal protein glycosylation, and contributes to cancer development and progression by affecting protein function and cellular signaling. Furthermore, O-GlcNAcylation regulates cellular signaling pathways, and its alteration is linked to various cancer characteristics. Additionally, recent findings have suggested a close association between HBP stimulation and cancer stemness; an elevated HBP flux promotes cancer cell conversion to cancer stem cells and enhances chemotherapy resistance via downstream signal activation. In this review, we highlight the prominent roles of HBP in metabolic signaling and summarize the recent advances in HBP and its downstream signaling, relevant to cancer.

Keywords:  Hexosamine biosynthetic pathway; Metabolic signaling; N-glycosylation; O-GlcNAcylation; cancer stem cells

DOI:  https://doi.org/10.1016/j.bbagen.2022.130250
Cell Rep. 2022 Oct 11. pii: S2211-1247(22)01317-1. [Epub ahead of print]41(2): 111467

An unusual mode of baseline translation adjusts cellular protein synthesis capacity to metabolic needs.

Cornelius Schneider, Florian Erhard, Beyenech Binotti, Alexander Buchberger, Jörg Vogel, Utz Fischer.

  In all domains of life, mechanisms exist that adjust translational capacity to nutrient restriction and other growth constraints. The mammalian target of rapamycin (mTOR) regulates the synthesis of ribosomal proteins and translation factors in mammalian cells via phosphorylation of the La-related protein 1 (LARP1). In the present model of starvation-induced translational silencing, LARP1 targets mRNAs carrying a 5' terminal oligopyrimidine (5'TOP) motif to shift these into subpolysomal ribonucleoprotein particles. However, how these mRNAs would be protected from degradation and rapidly made available to restore translation capacity when needed remained enigmatic. Here, to address this, we employ gradient profiling by sequencing (Grad-seq) and monosome footprinting. Challenging the above model, we find that 5'TOP mRNAs, instead of being translationally silenced during starvation, undergo low baseline translation with reduced initiation rates. This mode of regulation ensures a stable 5'TOP mRNA population under starvation and allows fast reversibility of the translational repression.

Keywords:  5'TOP; CP: Molecular biology; LARP1; TOP mRNAs; TOP response; baseline translation; mRNA; mTORC1; starvation; translation initiation; translation regulation

DOI:  https://doi.org/10.1016/j.celrep.2022.111467
Nat Metab. 2022 Oct 10.

The aldolase inhibitor aldometanib mimics glucose starvation to activate lysosomal AMPK.

Chen-Song Zhang, Mengqi Li, Yu Wang, Xiaoyang Li, Yue Zong, Shating Long, Mingliang Zhang, Jin-Wei Feng, Xiaoyan Wei, Yan-Hui Liu, Baoding Zhang, Jianfeng Wu, Cixiong Zhang, Wenhua Lian, Teng Ma, Xiao Tian, Qi Qu, Yaxin Yu, Jinye Xiong, Dong-Tai Liu, Zhenhua Wu, Mingxia Zhu, Changchuan Xie, Yaying Wu, Zheni Xu, Chunyan Yang, Junjie Chen, Guohong Huang, Qingxia He, Xi Huang, Lei Zhang, Xiufeng Sun, Qingfeng Liu, Abdul Ghafoor, Fu Gui, Kaili Zheng, Wen Wang, Zhi-Chao Wang, Yong Yu, Qingliang Zhao, Shu-Yong Lin, Zhi-Xin Wang, Hai-Long Piao, Xianming Deng, Sheng-Cai Lin.

The activity of 5'-adenosine monophosphate-activated protein kinase (AMPK) is inversely correlated with the cellular availability of glucose. When glucose levels are low, the glycolytic enzyme aldolase is not bound to fructose-1,6-bisphosphate (FBP) and, instead, signals to activate lysosomal AMPK. Here, we show that blocking FBP binding to aldolase with the small molecule aldometanib selectively activates the lysosomal pool of AMPK and has beneficial metabolic effects in rodents. We identify aldometanib in a screen for aldolase inhibitors and show that it prevents FBP from binding to v-ATPase-associated aldolase and activates lysosomal AMPK, thereby mimicking a cellular state of glucose starvation. In male mice, aldometanib elicits an insulin-independent glucose-lowering effect, without causing hypoglycaemia. Aldometanib also alleviates fatty liver and nonalcoholic steatohepatitis in obese male rodents. Moreover, aldometanib extends lifespan and healthspan in both Caenorhabditis elegans and mice. Taken together, aldometanib mimics and adopts the lysosomal AMPK activation pathway associated with glucose starvation to exert physiological roles, and might have potential as a therapeutic for metabolic disorders in humans.

DOI: https://doi.org/10.1038/s42255-022-00640-7
Annu Rev Physiol. 2022 Oct 13.

Intracellular Ion Control of WNK Signaling.

Elizabeth J Goldsmith, Aylin R Rodan.

The with no lysine (K) (WNK) kinases are an evolutionarily ancient group of kinases with atypical placement of the catalytic lysine and diverse physiological roles. Recent studies have shown that WNKs are directly regulated by chloride, potassium, and osmotic pressure. Here, we review the discovery of WNKs as chloride-sensitive kinases and discuss physiological contexts in which chloride regulation of WNKs has been demonstrated. These include the kidney, pancreatic duct, neurons, and inflammatory cells. We discuss the interdependent relationship of osmotic pressure and intracellular chloride in cell volume regulation. We review the recent demonstration of potassium regulation of WNKs and speculate on possible physiological roles. Finally, structural and mechanistic aspects of intracellular ion and osmotic pressure regulation of WNKs are discussed. Expected final online publication date for the Annual Review of Physiology, Volume 85 is February 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

DOI: https://doi.org/10.1146/annurev-physiol-031522-080651
Biochem Biophys Res Commun. 2022 Sep 29. pii: S0006-291X(22)01340-7. [Epub ahead of print]632 173-180

Fluid shear stress enhances proliferation of breast cancer cells via downregulation of the c-subunit of the F1FO ATP synthase.

Han-A Park, Spenser R Brown, Joseph Jansen, Tracie Dunn, Madison Scott, Nelli Mnatsakanyan, Elizabeth A Jonas, Yonghyun Kim.

  The presence of circulating cancer cells in the bloodstream is positively correlated with metastasis. We hypothesize that fluid shear stress (FSS) occurring during circulation alters mitochondrial function, enhancing metastatic behaviors of cancer cells. MCF7 and MDA-MB-231 human breast cancer cells subjected to FSS exponentially increased proliferation. Notably, FSS-treated cells consumed more oxygen but were resistant to uncoupler-mediated ATP loss. We found that exposure to FSS downregulated the F1FO ATP synthase c-subunit and overexpression of the c-subunit arrested cancer cell migration. Approaches that regulate c-subunit abundance may reduce the likelihood of breast cancer metastasis.

Keywords:  Breast cancer; F(1)F(O) ATP synthase; Fluid shear stress; Mitochondria

DOI:  https://doi.org/10.1016/j.bbrc.2022.09.084
Proc Natl Acad Sci U S A. 2022 Oct 25. 119(43): e2214263119

Experimental evolution reveals complex responses to environmental change.

Morgan W Kelly.

DOI: https://doi.org/10.1073/pnas.2214263119
Science. 2022 Oct 14. 378(6616): eabm5874

Cellular barcoding to decipher clonal dynamics in disease.

Vijay G Sankaran, Jonathan S Weissman, Leonard I Zon.

Cellular barcodes are distinct DNA sequences that enable one to track specific cells across time or space. Recent advances in our ability to detect natural or synthetic cellular barcodes, paired with single-cell readouts of cell state, have markedly increased our knowledge of clonal dynamics and genealogies of the cells that compose a variety of tissues and organs. These advances hold promise to redefine our view of human disease. Here, we provide an overview of cellular barcoding approaches, discuss applications to gain new insights into disease mechanisms, and provide an outlook on future applications. We discuss unanticipated insights gained through barcoding in studies of cancer and blood cell production and describe how barcoding can be applied to a growing array of medical fields, particularly with the increasing recognition of clonal contributions in human diseases.

DOI: https://doi.org/10.1126/science.abm5874
Nat Biotechnol. 2022 Oct 13.

Precision mitochondrial DNA editing with high-fidelity DddA-derived base editors.

Seonghyun Lee, Hyunji Lee, Gayoung Baek, Jin-Soo Kim.

Bacterial toxin DddA-derived cytosine base editors (DdCBEs)-composed of split DddAtox (a cytosine deaminase specific to double-stranded DNA), custom-designed TALE (transcription activator-like effector) DNA-binding proteins, and a uracil glycosylase inhibitor-enable mitochondrial DNA (mtDNA) editing in human cells, which may pave the way for therapeutic correction of pathogenic mtDNA mutations in patients. The utility of DdCBEs has been limited by off-target activity, which is probably caused by spontaneous assembly of the split DddAtox deaminase enzyme, independent of DNA-binding interactions. We engineered high-fidelity DddA-derived cytosine base editors (HiFi-DdCBEs) with minimal off-target activity by substituting alanine for amino acid residues at the interface between the split DddAtox halves. The resulting domains cannot form a functional deaminase without binding of their linked TALE proteins at adjacent sites on DNA. Whole mitochondrial genome sequencing shows that, unlike conventional DdCBEs, which induce hundreds of unwanted off-target C-to-T conversions in human mtDNA, HiFi-DdCBEs are highly efficient and precise, avoiding collateral off-target mutations, and as such, they will probably be desirable for therapeutic applications.

DOI: https://doi.org/10.1038/s41587-022-01486-w
EMBO J. 2022 Oct 12. e112415

Making liver cancer cells go ARGh!

Alessa L Henneberg, Christiane A Opitz.

A recent study by Missiaen et al (2022) uncovers hepatocellular carcinoma (HCC) cells to downregulate urea cycle enzymes and rely on the uptake of exogenous arginine and GCN2 kinase-dependent cell-cycle arrest for survival. These results offer new avenues for combinatorial targeting of liver cancer.

DOI: https://doi.org/10.15252/embj.2022112415
J Cell Biol. 2022 Nov 07. pii: e202109133. [Epub ahead of print]221(11):

Lysosomal solute and water transport.

Meiqin Hu, Nan Zhou, Weijie Cai, Haoxing Xu.

Lysosomes mediate hydrolase-catalyzed macromolecule degradation to produce building block catabolites for reuse. Lysosome function requires an osmo-sensing machinery that regulates osmolytes (ions and organic solutes) and water flux. During hypoosmotic stress or when undigested materials accumulate, lysosomes become swollen and hypo-functional. As a membranous organelle filled with cargo macromolecules, catabolites, ions, and hydrolases, the lysosome must have mechanisms that regulate its shape and size while coordinating content exchange. In this review, we discussed the mechanisms that regulate lysosomal fusion and fission as well as swelling and condensation, with a focus on solute and water transport mechanisms across lysosomal membranes. Lysosomal H+, Na+, K+, Ca2+, and Cl- channels and transporters sense trafficking and osmotic cues to regulate both solute flux and membrane trafficking. We also provide perspectives on how lysosomes may adjust the volume of themselves, the cytosol, and the cytoplasm through the control of lysosomal solute and water transport.

DOI: https://doi.org/10.1083/jcb.202109133
Cancer Discov. 2022 Oct 12. pii: CD-21-1661. [Epub ahead of print]

Disabling Uncompetitive Inhibition of Oncogenic IDH Mutations Drives Acquired Resistance.

Junhua Lyu, Yuxuan Liu, Lihu Gong, Mingyi Chen, Yazan F Madanat, Yuannyu Zhang, Feng Cai, Zhimin Gu, Hui Cao, Pranita Kaphle, Yoon Jung Kim, Fatma N Kalkan, Helen Stephens, Kathryn E Dickerson, Min Ni, Weina Chen, Prapti Patel, Alice S Mims, Uma Borate, Amy Burd, Sheng F Cai, C Cameron Yin, M James You, Stephen S Chung, Robert H Collins, Ralph J DeBerardinis, Xin Liu, Jian Xu.

Mutations in IDH genes occur frequently in acute myeloid leukemia (AML) and other human cancers to generate the oncometabolite R-2HG. Allosteric inhibition of mutant IDH suppresses R-2HG production in a subset of AML patients; however, acquired resistance emerges as a new challenge and the underlying mechanisms remain incompletely understood. Here we establish isogenic leukemia cells containing common IDH oncogenic mutations by CRISPR base editing. By mutational scanning of IDH single-amino acid variants in base-edited cells, we describe a repertoire of IDH second-site mutations responsible for therapy resistance through disabling uncompetitive enzyme inhibition. Recurrent mutations at NADPH binding sites within IDH heterodimers act in cis or trans to prevent the formation of stable enzyme-inhibitor complexes, restore R-2HG production in the presence of inhibitors, and drive therapy resistance in IDH-mutant AML cells and patients. We therefore uncover a new class of pathogenic mutations and mechanisms for acquired resistance to targeted cancer therapies.

DOI: https://doi.org/10.1158/2159-8290.CD-21-1661