bims-camemi Biomed News
on Mitochondrial metabolism in cancer
Issue of 2021–12–05
thirty-six papers selected by
Christian Frezza, , University of Cambridge, MRC Cancer Unit
  1. Serine catabolism generates liver NADPH and supports hepatic lipogenesis.
  2. Cysteine 253 of UCP1 regulates energy expenditure and sex-dependent adipose tissue inflammation.
  3. Pathways shaping the mitochondrial inner membrane.
  4. The Circadian Clock Protein BMAL1 Acts as a Metabolic Sensor In Macrophages to Control the Production of Pro IL-1β.
  5. Quantitative subcellular acyl-CoA analysis reveals distinct nuclear metabolism and isoleucine-dependent histone propionylation.
  6. Mutant-IDH inhibits Interferon-TET2 signaling to promote immunoevasion and tumor maintenance in cholangiocarcinoma.
  7. Pharmacological reduction of mitochondrial iron triggers a non-canonical BAX/BAK dependent cell death.
  8. Peroxisomal support of mitochondrial respiratory efficiency promotes ER stress survival.
  9. The potential of mitochondrial genome engineering.
  10. Metabolic design in a mammalian model of extreme metabolism, the North American least shrew (Cryptotis parva).
  11. ASS1 and ASL suppress growth in clear cell renal cell carcinoma via altered nitrogen metabolism.
  12. Mitochondrial sirtuins, metabolism, and aging.
  13. Targeting cancer metabolism in the era of precision oncology.
  14. Mitochondrial homeostasis is maintained in the absence of autophagy.
  15. Let-7a induces metabolic reprogramming in breast cancer cells via targeting mitochondrial encoded ND4.
  16. Stable Isotopes for Tracing Cardiac Metabolism in Diseases.
  17. Glutamine deprivation triggers NAGK-dependent hexosamine salvage.
  18. Single-molecule mitochondrial DNA sequencing shows no evidence of CpG methylation in human cells and tissues.
  19. Fumarate is a terminal electron acceptor in the mammalian electron transport chain.
  20. Cysteine is a limiting factor for glioma proliferation and survival.
  21. Mitochondrial TFAM as a Signaling Regulator between Cellular Organelles: A Perspective on Metabolic Diseases.
  22. Oncogenic dependency on STAT3 serine phosphorylation in KRAS mutant lung cancer.
  23. 1-deoxysphinganine initiates adaptive responses to serine and glycine starvation in cancer cells via proteolysis of sphingosine kinase.
  24. Local acetate inhibits brown adipose tissue function.
  25. Cysteine and iron accelerate the formation of ribose-5-phosphate, providing insights into the evolutionary origins of the metabolic network structure.
  26. Mitochondrial dysfunction as a trigger of programmed axon death.
  27. Metabolic reprogramming by driver mutation-tumor microenvironment interplay in pancreatic cancer: new therapeutic targets.
  28. Elucidating tumor-stromal metabolic crosstalk in colorectal cancer through integration of constraint-based models and LC-MS metabolomics.
  29. What do cellular responses to acidity tell us about cancer?
  30. Bend or break: how biochemically versatile molecules enable metabolic division of labor in clonal microbial communities.
  31. The nutrient sensor mTORC1 regulates insulin secretion by modulating ß-cell autophagy.
  32. NAD+ Metabolism in Cardiac Health, Aging, and Disease.
  33. Breaking the vicious circle: Extrachromosomal circular DNA as an emerging player in tumour evolution.
  34. A novel bi-allelic variant in the SDHB gene causes a severe mitochondrial complex II deficiency: a case report.
  35. The ongoing mystery of renal cell cancer.
  36. CRYPTOCHROMES promote daily protein homeostasis.
  1. Nat Metab. 2021 Nov 29.
    Serine catabolism generates liver NADPH and supports hepatic lipogenesis.
    Zhaoyue Zhang, Tara TeSlaa, Xincheng Xu, Xianfeng Zeng, Lifeng Yang, Gang Xing, Gregory J Tesz, Michelle F Clasquin, Joshua D Rabinowitz.
      Carbohydrate can be converted into fat by de novo lipogenesis, a process upregulated in fatty liver disease. Chemically, de novo lipogenesis involves polymerization and reduction of acetyl-CoA, using NADPH as the electron donor. The feedstocks used to generate acetyl-CoA and NADPH in lipogenic tissues remain, however, unclear. Here we show using stable isotope tracing in mice that de novo lipogenesis in adipose is supported by glucose and its catabolism via the pentose phosphate pathway to make NADPH. The liver, in contrast, derives acetyl-CoA for lipogenesis from acetate and lactate, and NADPH from folate-mediated serine catabolism. Such NADPH generation involves the cytosolic serine pathway in liver running in the opposite direction to that observed in most tissues and tumours, with NADPH made by the SHMT1-MTHFD1-ALDH1L1 reaction sequence. SHMT inhibition decreases hepatic lipogenesis. Thus, liver folate metabolism is distinctively wired to support cytosolic NADPH production and lipogenesis. More generally, while the same enzymes are involved in fat synthesis in liver and adipose, different substrates are used, opening the door to tissue-specific pharmacological interventions.
    DOI:  https://doi.org/10.1038/s42255-021-00487-4
  2. Cell Metab. 2021 Nov 24. pii: S1550-4131(21)00531-3. [Epub ahead of print]
    Cysteine 253 of UCP1 regulates energy expenditure and sex-dependent adipose tissue inflammation.
    Evanna L Mills, Cathal Harmon, Mark P Jedrychowski, Haopeng Xiao, Anja V Gruszczyk, Gary A Bradshaw, Nhien Tran, Ryan Garrity, Dina Laznik-Bogoslavski, John Szpyt, Hannah Prendeville, Lydia Lynch, Michael P Murphy, Steven P Gygi, Bruce M Spiegelman, Edward T Chouchani.
      Uncoupling protein 1 (UCP1) is a major regulator of brown and beige adipocyte energy expenditure and metabolic homeostasis. However, the widely employed UCP1 loss-of-function model has recently been shown to have a severe deficiency in the entire electron transport chain of thermogenic fat. As such, the role of UCP1 in metabolic regulation in vivo remains unclear. We recently identified cysteine-253 as a regulatory site on UCP1 that elevates protein activity upon covalent modification. Here, we examine the physiological importance of this site through the generation of a UCP1 cysteine-253-null (UCP1 C253A) mouse, a precise genetic model for selective disruption of UCP1 in vivo. UCP1 C253A mice exhibit significantly compromised thermogenic responses in both males and females but display no measurable effect on fat accumulation in an obesogenic environment. Unexpectedly, we find that a lack of C253 results in adipose tissue redox stress, which drives substantial immune cell infiltration and systemic inflammatory pathology in adipose tissues and liver of male, but not female, mice. Elevation of systemic estrogen reverses this male-specific pathology, providing a basis for protection from inflammation due to loss of UCP1 C253 in females. Together, our results establish the UCP1 C253 activation site as a regulator of acute thermogenesis and sex-dependent tissue inflammation.
    Keywords:  UCP1; cysteine; inflammation; metabolism; reactive oxygen species; sex differences
    DOI:  https://doi.org/10.1016/j.cmet.2021.11.003
  3. Open Biol. 2021 Dec;11(12): 210238
    Pathways shaping the mitochondrial inner membrane.
    Till Klecker, Benedikt Westermann.
      Mitochondria are complex organelles with two membranes. Their architecture is determined by characteristic folds of the inner membrane, termed cristae. Recent studies in yeast and other organisms led to the identification of four major pathways that cooperate to shape cristae membranes. These include dimer formation of the mitochondrial ATP synthase, assembly of the mitochondrial contact site and cristae organizing system (MICOS), inner membrane remodelling by a dynamin-related GTPase (Mgm1/OPA1), and modulation of the mitochondrial lipid composition. In this review, we describe the function of the evolutionarily conserved machineries involved in mitochondrial cristae biogenesis with a focus on yeast and present current models to explain how their coordinated activities establish mitochondrial membrane architecture.
    Keywords:  ATP synthase; MICOS; Mgm1; Saccharomyces cerevisiae; cristae; mitochondrial lipids
    DOI:  https://doi.org/10.1098/rsob.210238
  4. Front Immunol. 2021 ;12 700431
    The Circadian Clock Protein BMAL1 Acts as a Metabolic Sensor In Macrophages to Control the Production of Pro IL-1β.
    George A Timmons, Richard G Carroll, James R O'Siorain, Mariana P Cervantes-Silva, Lauren E Fagan, Shannon L Cox, Eva Palsson-McDermott, David K Finlay, Emma E Vincent, Nicholas Jones, Annie M Curtis.
      The transcription factor BMAL1 is a clock protein that generates daily or circadian rhythms in physiological functions including the inflammatory response of macrophages. Intracellular metabolic pathways direct the macrophage inflammatory response, however whether the clock is impacting intracellular metabolism to direct this response is unclear. Specific metabolic reprogramming of macrophages controls the production of the potent pro-inflammatory cytokine IL-1β. We now describe that the macrophage molecular clock, through Bmal1, regulates the uptake of glucose, its flux through glycolysis and the Krebs cycle, including the production of the metabolite succinate to drive Il-1β production. We further demonstrate that BMAL1 modulates the level and localisation of the glycolytic enzyme PKM2, which in turn activates STAT3 to further drive Il-1β mRNA expression. Overall, this work demonstrates that BMAL1 is a key metabolic sensor in macrophages, and its deficiency leads to a metabolic shift of enhanced glycolysis and mitochondrial respiration, leading to a heightened pro-inflammatory state. These data provide insight into the control of macrophage driven inflammation by the molecular clock, and the potential for time-based therapeutics against a range of chronic inflammatory diseases.
    Keywords:  IL-1β; macrophage inflammation; metabolism; molecular clock; pSTAT3
    DOI:  https://doi.org/10.3389/fimmu.2021.700431
  5. Mol Cell. 2021 Nov 22. pii: S1097-2765(21)00956-4. [Epub ahead of print]
    Quantitative subcellular acyl-CoA analysis reveals distinct nuclear metabolism and isoleucine-dependent histone propionylation.
    Sophie Trefely, Katharina Huber, Joyce Liu, Michael Noji, Stephanie Stransky, Jay Singh, Mary T Doan, Claudia D Lovell, Eliana von Krusenstiern, Helen Jiang, Anna Bostwick, Hannah L Pepper, Luke Izzo, Steven Zhao, Jimmy P Xu, Kenneth C Bedi, J Eduardo Rame, Juliane G Bogner-Strauss, Clementina Mesaros, Simone Sidoli, Kathryn E Wellen, Nathaniel W Snyder.
      Quantitative subcellular metabolomic measurements can explain the roles of metabolites in cellular processes but are subject to multiple confounding factors. We developed stable isotope labeling of essential nutrients in cell culture-subcellular fractionation (SILEC-SF), which uses isotope-labeled internal standard controls that are present throughout fractionation and processing to quantify acyl-coenzyme A (acyl-CoA) thioesters in subcellular compartments by liquid chromatography-mass spectrometry. We tested SILEC-SF in a range of sample types and examined the compartmentalized responses to oxygen tension, cellular differentiation, and nutrient availability. Application of SILEC-SF to the challenging analysis of the nuclear compartment revealed a nuclear acyl-CoA profile distinct from that of the cytosol, with notable nuclear enrichment of propionyl-CoA. Using isotope tracing, we identified the branched chain amino acid isoleucine as a major metabolic source of nuclear propionyl-CoA and histone propionylation, thus revealing a new mechanism of crosstalk between metabolism and the epigenome.
    Keywords:  acyl-CoA; branched chain amino acids; histone; internal standard; isoleucine; matrix effects; metabolomics; mitochondria; nucleus; propionylation; subcellular
    DOI:  https://doi.org/10.1016/j.molcel.2021.11.006
  6. Cancer Discov. 2021 Nov 30. pii: candisc.1077.2021. [Epub ahead of print]
    Mutant-IDH inhibits Interferon-TET2 signaling to promote immunoevasion and tumor maintenance in cholangiocarcinoma.
    Meng-Ju Wu, Lei Shi, Juan Dubrot, Joshua Merritt, Vindhya Vijay, Ting-Yu Wei, Emily Kessler, Kira E Olander, Ramzi Adil, Amaya Pankaj, Krishna Seshu Tummala, Vajira Weeresekara, Yuanli Zhen, Qibiao Wu, Meiqi Luo, William Shen, Maria Garcia-Beccaria, Mirian Fernandez-Vaquero, Christine Hudson, Sebastien Ronseaux, Yi Sun, Rodrigo Saad-Berreta, Russell W Jenkins, Tong Wang, Mathias Heikenwalder, Cristina R Ferrone, Lipika Goyal, Brandon Nicolay, Vikram Deshpande, Rahul M Kohli, Hongwu Zheng, Robert T Manguso, Nabeel Bardeesy.
      Isocitrate dehydrogenase 1 mutations (mIDH1) are common in cholangiocarcinoma. (R)-2-hydroxyglutarate generated by the mIDH1 enzyme inhibits multiple a-ketoglutarate-dependent enzymes, altering epigenetics and metabolism. Here, by developing mIDH1-driven genetically engineered mouse models, we show that mIDH1 supports cholangiocarcinoma tumor maintenance through an immunoevasion program centered on dual (R)-2-hydroxyglutarate-mediated mechanisms - suppression of CD8+ T cell activity and tumor cell-autonomous inactivation of TET2 DNA demethylase. Pharmacological mIDH1 inhibition stimulates CD8+ T cell recruitment and IFN-y expression and promotes TET2-dependent induction of IFN-y response genes in tumor cells. CD8+ T cell depletion or tumor cell-specific ablation of TET2 or Interferon-gamma receptor 1 causes treatment resistance. Whereas immune checkpoint activation limits mIDH1 inhibitor efficacy, CTLA4 blockade overcomes immunosuppression, providing therapeutic synergy. The findings in this mouse model of cholangiocarcinoma demonstrate that immune function and the IFN-y-TET2 axis are essential for response to mIDH1 inhibition and suggest a novel strategy for harnessing these inhibitors therapeutically.
    DOI:  https://doi.org/10.1158/2159-8290.CD-21-1077
  7. Cancer Discov. 2021 Dec 03. pii: candisc.0522.2021. [Epub ahead of print]
    Pharmacological reduction of mitochondrial iron triggers a non-canonical BAX/BAK dependent cell death.
    Sylvain Garciaz, Andrew A Guirguis, Sebastian Muller, Fiona C Brown, Yih-Chih Chan, Ali Motazedian, Caitlin L Rowe, James A Kuzich, Kah Lok Chan, Kevin Tran, Lorey Smith, Laura MacPherson, Brian Liddicoat, Enid Y N Lam, Tatiana Caneque, Marian L Burr, Veronique Litalien, Giovanna Pomilio, Mathilde Poplineau, Estelle Duprez, Sarah-Jane Dawson, Georg Ramm, Andrew G Cox, Kristin K Brown, David C S Huang, Andrew H Wei, Kate McArthur, Raphael Rodriguez, Mark A Dawson.
      Cancer cell metabolism is increasingly recognised as providing an exciting therapeutic opportunity. However, a drug that directly couples targeting of a metabolic dependency with the induction of cell death in cancer cells has largely remained elusive. Here we report that the drug-like small molecule ironomycin (AM5) reduces the mitochondrial iron load, resulting in the potent disruption of mitochondrial metabolism. Ironomycin promotes the recruitment and activation of BAX/BAK but the resulting mitochondrial outer membrane permeabilization (MOMP) does not lead to potent activation of the apoptotic caspases, nor is the ensuing cell death prevented by inhibiting the previously established pathways of programmed cell death. Consistent with the fact that ironomycin and BH3 mimetics induce MOMP through independent non-redundant pathways, we find that ironomycin exhibits marked in vitro and in vivo synergy with venetoclax and overcomes venetoclax resistance in primary patient samples.
    DOI:  https://doi.org/10.1158/2159-8290.CD-21-0522
  8. J Cell Sci. 2021 Dec 02. pii: jcs.259254. [Epub ahead of print]
    Peroxisomal support of mitochondrial respiratory efficiency promotes ER stress survival.
    Imadeddin Hijazi, Emily Wang, Michelle Orozco, Sarah Pelton, Amy Chang.
      Endoplasmic reticulum stress (ERS) occurs when cellular demand for protein folding exceeds the capacity of the organelle. Adaptation and cell survival in response to ERS requires a critical contribution by mitochondria and peroxisomes. During ERS response, mitochondrial respiration increases to ameliorate reactive oxygen species (ROS) accumulation; we now show in yeast that peroxisome abundance also increases to promote an adaptive response. In pox1▵ cells, defective in peroxisomal ß oxidation of fatty acids, respiratory response to ERS is impaired, and ROS accrues. However, respiratory response to ERS is rescued, and ROS production is mitigated in pox1▵ cells by overexpression of Mpc1, the mitochondrial pyruvate carrier that provides another source of acetyl CoA to fuel the TCA cycle and oxidative phosphorylation. Using proteomics, select mitochondrial proteins were identified that undergo upregulation by ERS to remodel respiratory machinery. Several peroxisome-based proteins were also increased, corroborating the peroxisomal role in ERS adaptation. Finally, ERS stimulates assembly of respiratory complexes into higher order supercomplexes, underlying increased electron transfer efficiency. Our results highlight peroxisomal and mitochondrial support for ERS adaptation to favor cell survival.
    Keywords:  Endoplasmic reticulum; Mitochondria; Stress survival
    DOI:  https://doi.org/10.1242/jcs.259254
  9. Nat Rev Genet. 2021 Dec 02.
    The potential of mitochondrial genome engineering.
    Pedro Silva-Pinheiro, Michal Minczuk.
      Mitochondria are subject to unique genetic control by both nuclear DNA and their own genome, mitochondrial DNA (mtDNA), of which each mitochondrion contains multiple copies. In humans, mutations in mtDNA can lead to devastating, heritable, multi-system diseases that display different tissue-specific presentation at any stage of life. Despite rapid advances in nuclear genome engineering, for years, mammalian mtDNA has remained resistant to genetic manipulation, hampering our ability to understand the mechanisms that underpin mitochondrial disease. Recent developments in the genetic modification of mammalian mtDNA raise the possibility of using genome editing technologies, such as programmable nucleases and base editors, for the treatment of hereditary mitochondrial disease.
    DOI:  https://doi.org/10.1038/s41576-021-00432-x
  10. J Physiol. 2021 Nov 27.
    Metabolic design in a mammalian model of extreme metabolism, the North American least shrew (Cryptotis parva).
    Dillon J Chung, Grey P Madison, Angel M Aponte, Komudi Singh, Yuesheng Li, Mehdi Pirooznia, Christopher K E Bleck, Nissar A Darmani, Robert S Balaban.
       KEY POINTS: Least shrews were studied to explore the relationship between metabolic function, mitochondrial morphology and protein content in different tissues. Liver and kidney mitochondrial content and enzymatic activity approaches the heart indicating similar metabolic demand among tissues that contribute to basal and maximum metabolism. This allows examination of mitochondrial structure and composition in tissues with similar maximum metabolic demands. Mitochondrial networks only occur in striated muscle. In contrast, the liver and kidney maintain individual mitochondria with limited reticulation. Muscle mitochondrial reticulation is the result of dense ATPase activity and cell-spanning myofibrils which require networking for adequate metabolic support. In contrast, liver and kidney ATPase activity is localized to the endoplasmic reticulum and basolateral membrane respectively, generating a locally balanced energy conversion and utilization Mitochondrial morphology is not driven by maximum metabolic demand, but by the cytosolic distribution of energy utilizing systems set by the functions of the tissue.
    ABSTRACT: Mitochondrial adaptations are fundamental to differentiated function and energetic homeostasis in mammalian cells. But the mechanisms that underlie these relationships remain poorly understood. Here, we investigated organ-specific mitochondrial morphology, connectivity and protein composition in a model of extreme mammalian metabolism, the Least shrew (Cryptotis parva). This was achieved through a combination of high-resolution 3D focused-ion-beam EM imaging and tandem-mass-tag MS proteomics. We demonstrate that liver and kidney mitochondrial content are equivalent to the heart permitting assessment of mitochondrial adaptations in different organs with similar metabolic demand. Muscle mitochondrial networks (cardiac and skeletal) are extensive, with a high incidence of nanotunnels - which collectively support the metabolism of large muscle cells. Mitochondrial networks were not detected in the liver and kidney as individual mitochondria are localized with sites of ATP consumption. This configuration is not observed in striated muscle, likely due to a homogenous ATPase distribution and the structural requirements of contraction. These results demonstrate distinct, fundamental mitochondrial structural adaptations for similar metabolic demand that are dependent on the topology of energy utilization process in a mammalian model of extreme metabolism. Abstract figure. This study investigates the role of mitochondrial morphology and protein composition in setting the extreme metabolic rates of one of the smallest extant mammals - the North American least shrew (Cryptotis parva). To do this, mitochondrial characteristics from liver, kidney, skeletal muscle and heart tissues were compared as these tissues are major contributors to basal and maximum metabolic states. Liver and kidney mitochondrial volume density and protein content approach levels observed in the heart - indicating that these former tissues are major contributors to the high basal metabolic rates of small mammals. Despite this high mitochondrial content, the liver and kidney do not exhibit mitochondrial networking - structures that are proposed to conduct mitochondrial proton motive force at the scale of the cell. Shrew skeletal muscle and cardiac mitochondrial network organization is consistent with networks observed in larger mammals while also exhibiting increased connectivity at the nm-scale. Instead of forming networks, kidney and liver mitochondria are directly associated with sites of ATP utilization. These results identify conditions that dictate the formation of mitochondrial networks and processes that drive mammalian allometric scaling of metabolic rates. This article is protected by copyright. All rights reserved.
    Keywords:   
    DOI:  https://doi.org/10.1113/JP282153
  11. Cancer Metab. 2021 Dec 03. 9(1): 40
    ASS1 and ASL suppress growth in clear cell renal cell carcinoma via altered nitrogen metabolism.
    Sanika Khare, Laura C Kim, Graham Lobel, Paschalis-Thomas Doulias, Harry Ischiropoulos, Itzhak Nissim, Brian Keith, M Celeste Simon.
       BACKGROUND: Kidney cancer is a common adult malignancy in the USA. Clear cell renal cell carcinoma (ccRCC), the predominant subtype of kidney cancer, is characterized by widespread metabolic changes. Urea metabolism is one such altered pathway in ccRCC. The aim of this study was to elucidate the contributions of urea cycle enzymes, argininosuccinate synthase 1 (ASS1), and argininosuccinate lyase (ASL) towards ccRCC progression.
    METHODS: We employed a combination of computational, genetic, and metabolomic tools along with in vivo animal models to establish a tumor-suppressive role for ASS1 and ASL in ccRCC.
    RESULTS: We show that the mRNA and protein expression of urea cycle enzymes ASS1 and ASL are reduced in ccRCC tumors when compared to the normal kidney. Furthermore, the loss of ASL in HK-2 cells (immortalized renal epithelial cells) promotes growth in 2D and 3D growth assays, while combined re-expression of ASS1 and ASL in ccRCC cell lines suppresses growth in 2D, 3D, and in vivo xenograft models. We establish that this suppression is dependent on their enzymatic activity. Finally, we demonstrate that conservation of cellular aspartate, regulation of nitric oxide synthesis, and pyrimidine production play pivotal roles in ASS1+ASL-mediated growth suppression in ccRCC.
    CONCLUSIONS: ccRCC tumors downregulate the components of the urea cycle including the enzymes argininosuccinate synthase 1 (ASS1) and argininosuccinate lyase (ASL). These cytosolic enzymes lie at a critical metabolic hub in the cell and are involved in aspartate catabolism and arginine and nitric oxide biosynthesis. Loss of ASS1 and ASL helps cells redirect aspartate towards pyrimidine synthesis and support enhanced proliferation. Additionally, reduced levels of ASS1 and ASL might help regulate nitric oxide (NO) generation and mitigate its cytotoxic effects. Overall, our work adds to the understanding of urea cycle enzymes in a context-independent of ureagenesis, their role in ccRCC progression, and uncovers novel potential metabolic vulnerabilities in ccRCC.
    Keywords:  Argininosuccinate lyase; Argininosuccinate synthase 1; Aspartate; DNA synthesis; Nitric oxide metabolism; Urea cycle; ccRCC
    DOI:  https://doi.org/10.1186/s40170-021-00271-8
  12. J Genet Genomics. 2021 Nov 29. pii: S1673-8527(21)00358-1. [Epub ahead of print]
    Mitochondrial sirtuins, metabolism, and aging.
    Zhejun Ji, Guang-Hui Liu, Jing Qu.
      Maintaining metabolic homeostasis is essential for cellular and organismal health throughout life. Of the multiple signaling pathways that regulate metabolism, such as PI3K/AKT, mTOR, AMPK, and sirtuins, mammalian sirtuins also play unique roles in aging. By understanding how sirtuins regulate metabolic processes, we can start to understand how they slow down or accelerate biological aging. Here, we review the biology of SIRT3, SIRT4, and SIRT5, known as the mitochondrial sirtuins due to their localization in the mitochondrial matrix. First, we will focus on canonical pathways that regulate metabolism more broadly and how these are integrated with aging regulation. Then, we will summarize the current knowledge about functional differences between SIRT3, SIRT4, and SIRT5 in metabolic control and integration in signaling networks. Finally, we will discuss how mitochondrial sirtuins regulate processes associated with aging and oxidative stress, calorie restriction and disease.
    Keywords:  Metabolism and aging regulation; Mitochondrial sirtuins; SIRT3; SIRT4; SIRT5; age-related diseases
    DOI:  https://doi.org/10.1016/j.jgg.2021.11.005
  13. Nat Rev Drug Discov. 2021 Dec 03.
    Targeting cancer metabolism in the era of precision oncology.
    Zachary E Stine, Zachary T Schug, Joseph M Salvino, Chi V Dang.
      One hundred years have passed since Warburg discovered alterations in cancer metabolism, more than 70 years since Sidney Farber introduced anti-folates that transformed the treatment of childhood leukaemia, and 20 years since metabolism was linked to oncogenes. However, progress in targeting cancer metabolism therapeutically in the past decade has been limited. Only a few metabolism-based drugs for cancer have been successfully developed, some of which are in - or en route to - clinical trials. Strategies for targeting the intrinsic metabolism of cancer cells often did not account for the metabolism of non-cancer stromal and immune cells, which have pivotal roles in tumour progression and maintenance. By considering immune cell metabolism and the clinical manifestations of inborn errors of metabolism, it may be possible to isolate undesirable off-tumour, on-target effects of metabolic drugs during their development. Hence, the conceptual framework for drug design must consider the metabolic vulnerabilities of non-cancer cells in the tumour immune microenvironment, as well as those of cancer cells. In this Review, we cover the recent developments, notable milestones and setbacks in targeting cancer metabolism, and discuss the way forward for the field.
    DOI:  https://doi.org/10.1038/s41573-021-00339-6
  14. Mol Cell Oncol. 2021 ;8(5): 1984162
    Mitochondrial homeostasis is maintained in the absence of autophagy.
    Christina G Towers.
      Autophagy is a central recycling process, and it plays a complex role in cancer. We discovered that when autophagy is blocked, cancer cells compensate by increasing mitochondrial-derived vesicles. However, there are many unanswered questions remaining, particularly in the context of the dual roles of autophagy in cancer.
    Keywords:  Autophagy; cancer; mitochondria; mitochondrial derived vesicles; mitophagy
    DOI:  https://doi.org/10.1080/23723556.2021.1984162
  15. Cancer Cell Int. 2021 Nov 27. 21(1): 629
    Let-7a induces metabolic reprogramming in breast cancer cells via targeting mitochondrial encoded ND4.
    Praveen Sharma, Vibhuti Sharma, Tarunveer Singh Ahluwalia, Nilambra Dogra, Santosh Kumar, Sandeep Singh.
       BACKGROUND AND OBJECTIVES: MicroRNA (miRNA) that translocate from the nucleus to mitochondria are referred to as mitochondrial microRNA (mitomiR). Albeit mitomiRs have been shown to modulate gene expression, their functional impact within mitochondria is unknown. The main objective of this study is to investigate whether the mitochondrial genome is regulated by miR present inside the mitochondria.
    METHODS AND RESULTS: Here, we report mitomiR let-7a regulates mitochondrial transcription in breast cancer cells and reprogram the metabolism accordingly. These effects were mediated through the interaction of let-7a with mtDNA, as studied by RNA pull-down assays, altering the activity of Complex I in a cell line-specific manner. Our study, for the first time, identifies the role of mitomiR (let-7a) in regulating the mitochondrial genome by transcriptional repression and its contribution to regulating mitochondrial metabolism of breast cancer cells.
    CONCLUSION: These findings uncover a novel mechanism by which mitomiR regulates mitochondrial transcription.
    Keywords:  Cancer; Glycolysis; Metabolic reprogramming; Mito-miRs; Mitochondria
    DOI:  https://doi.org/10.1186/s12935-021-02339-3
  16. Front Cardiovasc Med. 2021 ;8 734364
    Stable Isotopes for Tracing Cardiac Metabolism in Diseases.
    Anja Karlstaedt.
      Although metabolic remodeling during cardiovascular diseases has been well-recognized for decades, the recent development of analytical platforms and mathematical tools has driven the emergence of assessing cardiac metabolism using tracers. Metabolism is a critical component of cellular functions and adaptation to stress. The pathogenesis of cardiovascular disease involves metabolic adaptation to maintain cardiac contractile function even in advanced disease stages. Stable-isotope tracer measurements are a powerful tool for measuring flux distributions at the whole organism level and assessing metabolic changes at a systems level in vivo. The goal of this review is to summarize techniques and concepts for in vivo or ex vivo stable isotope labeling in cardiovascular research, to highlight mathematical concepts and their limitations, to describe analytical methods at the tissue and single-cell level, and to discuss opportunities to leverage metabolic models to address important mechanistic questions relevant to all patients with cardiovascular disease.
    Keywords:  cardiovascular disease; metabolic flux analysis; metabolism; stable-isotope tracer; systems biology
    DOI:  https://doi.org/10.3389/fcvm.2021.734364
  17. Elife. 2021 11 30. pii: e62644. [Epub ahead of print]10
    Glutamine deprivation triggers NAGK-dependent hexosamine salvage.
    Sydney Campbell, Clementina Mesaros, Luke Izzo, Hayley Affronti, Michael Noji, Bethany E Schaffer, Tiffany Tsang, Kathryn Sun, Sophie Trefely, Salisa Kruijning, John Blenis, Ian A Blair, Kathryn E Wellen.
      Tumors frequently exhibit aberrant glycosylation, which can impact cancer progression and therapeutic responses. The hexosamine biosynthesis pathway (HBP) produces uridine diphosphate N-acetylglucosamine (UDP-GlcNAc), a major substrate for glycosylation in the cell. Prior studies have identified the HBP as a promising therapeutic target in pancreatic ductal adenocarcinoma (PDA). The HBP requires both glucose and glutamine for its initiation. The PDA tumor microenvironment is nutrient poor, however, prompting us to investigate how nutrient limitation impacts hexosamine synthesis. Here, we identify that glutamine limitation in PDA cells suppresses de novo hexosamine synthesis but results in increased free GlcNAc abundance. GlcNAc salvage via N-acetylglucosamine kinase (NAGK) is engaged to feed UDP-GlcNAc pools. NAGK expression is elevated in human PDA, and NAGK deletion from PDA cells impairs tumor growth in mice. Together, these data identify an important role for NAGK-dependent hexosamine salvage in supporting PDA tumor growth.
    Keywords:  N-acetylglucosamine kinase; cancer biology; glutamine; hexosamine; human; mouse; pancreatic cancer
    DOI:  https://doi.org/10.7554/eLife.62644
  18. Nucleic Acids Res. 2021 Nov 29. pii: gkab1179. [Epub ahead of print]
    Single-molecule mitochondrial DNA sequencing shows no evidence of CpG methylation in human cells and tissues.
    Iacopo Bicci, Claudia Calabrese, Zoe J Golder, Aurora Gomez-Duran, Patrick F Chinnery.
      Methylation on CpG residues is one of the most important epigenetic modifications of nuclear DNA, regulating gene expression. Methylation of mitochondrial DNA (mtDNA) has been studied using whole genome bisulfite sequencing (WGBS), but recent evidence has uncovered technical issues which introduce a potential bias during methylation quantification. Here, we validate the technical concerns of WGBS, and develop and assess the accuracy of a new protocol for mtDNA nucleotide variant-specific methylation using single-molecule Oxford Nanopore Sequencing (ONS). Our approach circumvents confounders by enriching for full-length molecules over nuclear DNA. Variant calling analysis against showed that 99.5% of homoplasmic mtDNA variants can be reliably identified providing there is adequate sequencing depth. We show that some of the mtDNA methylation signal detected by ONS is due to sequence-specific false positives introduced by the technique. The residual signal was observed across several human primary and cancer cell lines and multiple human tissues, but was always below the error threshold modelled using negative controls. We conclude that there is no evidence for CpG methylation in human mtDNA, thus resolving previous controversies. Additionally, we developed a reliable protocol to study epigenetic modifications of mtDNA at single-molecule and single-base resolution, with potential applications beyond CpG methylation.
    DOI:  https://doi.org/10.1093/nar/gkab1179
  19. Science. 2021 Dec 03. 374(6572): 1227-1237
    Fumarate is a terminal electron acceptor in the mammalian electron transport chain.
    Jessica B Spinelli, Paul C Rosen, Hans-Georg Sprenger, Anna M Puszynska, Jessica L Mann, Julian M Roessler, Andrew L Cangelosi, Antonia Henne, Kendall J Condon, Tong Zhang, Tenzin Kunchok, Caroline A Lewis, Navdeep S Chandel, David M Sabatini.
      [Figure: see text].
    DOI:  https://doi.org/10.1126/science.abi7495
  20. Mol Oncol. 2021 Dec 02.
    Cysteine is a limiting factor for glioma proliferation and survival.
    Victor Ruiz-Rodado, Tyrone Dowdy, Adrian Lita, Tamalee Kramp, Meili Zhang, Jinkyu Jung, Ana Dios-Esponera, Lumin Zhang, Christel C Herold-Mende, Kevin Camphausen, Mark R Gilbert, Mioara Larion.
      Nutritional intervention is becoming more prevalent as adjuvant therapy for many cancers in view of the tumor dependence on external sources for some nutrients. However, little is known about the mechanisms that render cancer cells dependent on certain nutrients from the microenvironment. Herein, we report the dependence of glioma cells on exogenous cysteine/cystine, despite this amino acid being nonessential. Using several 13 C-tracers and analysis of cystathionine synthase and cystathioninase levels, we revealed that glioma cells were not able to support GSH synthesis through the transsulfuration pathway, which allows methionine to be converted to cysteine in cysteine/cystine deprived conditions. Therefore, we explored the nutritional deprivation in a mouse model of glioma. Animals subjected to a cysteine/cystine-free diet survived longer, although this increase did not attain statistical significance, with concomitant reductions in plasma glutathione and cysteine levels. At the end point, however, tumors displayed the ability to synthesize glutathione, although higher levels of oxidative stress were detected. We observed a compensation from the nutritional intervention revealed as the recovery of cysteine-related metabolites levels in plasma. Our study highlights a time window where cysteine deprivation can be exploited for additional therapeutic strategies.
    Keywords:  Glioma; cysteine; diet; glutathione; metabolism
    DOI:  https://doi.org/10.1002/1878-0261.13148
  21. Diabetes Metab J. 2021 Nov;45(6): 853-865
    Mitochondrial TFAM as a Signaling Regulator between Cellular Organelles: A Perspective on Metabolic Diseases.
    Jin-Ho Koh, Yong-Woon Kim, Dae-Yun Seo, Tae-Seo Sohn.
      Tissues actively involved in energy metabolism are more likely to face metabolic challenges from bioenergetic substrates and are susceptible to mitochondrial dysfunction, leading to metabolic diseases. The mitochondria receive signals regarding the metabolic states in cells and transmit them to the nucleus or endoplasmic reticulum (ER) using calcium (Ca2+) for appropriate responses. Overflux of Ca2+ in the mitochondria or dysregulation of the signaling to the nucleus and ER could increase the incidence of metabolic diseases including insulin resistance and type 2 diabetes mellitus. Mitochondrial transcription factor A (Tfam) may regulate Ca2+ flux via changing the mitochondrial membrane potential and signals to other organelles such as the nucleus and ER. Since Tfam is involved in metabolic function in the mitochondria, here, we discuss the contribution of Tfam in coordinating mitochondria-ER activities for Ca2+ flux and describe the mechanisms by which Tfam affects mitochondrial Ca2+ flux in response to metabolic challenges.
    Keywords:  Calcium; Cell nucleus; Diabetes mellitus, type 2; Endoplasmic reticulum; Mitochondria; TFAM protein
    DOI:  https://doi.org/10.4093/dmj.2021.0138
  22. Oncogene. 2021 Dec 03.
    Oncogenic dependency on STAT3 serine phosphorylation in KRAS mutant lung cancer.
    Sultan Alhayyani, Louise McLeod, Alison C West, Jesse J Balic, Christopher Hodges, Liang Yu, Julian A Smith, Zdenka Prodanovic, Steven Bozinovski, Beena Kumar, Saleela M Ruwanpura, Mohamed I Saad, Brendan J Jenkins.
      The oncogenic potential of the latent transcription factor signal transducer and activator of transcription (STAT)3 in many human cancers, including lung cancer, has been largely attributed to its nuclear activity as a tyrosine-phosphorylated (pY705 site) transcription factor. By contrast, an alternate mitochondrial pool of serine phosphorylated (pS727 site) STAT3 has been shown to promote tumourigenesis by regulating metabolic processes, although this has been reported in only a restricted number of mutant RAS-addicted neoplasms. Therefore, the involvement of STAT3 serine phosphorylation in the pathogenesis of most cancer types, including mutant KRAS lung adenocarcinoma (LAC), is unknown. Here, we demonstrate that LAC is suppressed in oncogenic KrasG12D-driven mouse models engineered for pS727-STAT3 deficiency. The proliferative potential of the transformed KrasG12D lung epithelium, and mutant KRAS human LAC cells, was significantly reduced upon pS727-STAT3 deficiency. Notably, we uncover the multifaceted capacity of constitutive pS727-STAT3 to metabolically reprogramme LAC cells towards a hyper-proliferative state by regulating nuclear and mitochondrial (mt) gene transcription, the latter via the mtDNA transcription factor, TFAM. Collectively, our findings reveal an obligate requirement for the transcriptional activity of pS727-STAT3 in mutant KRAS-driven LAC with potential to guide future therapeutic targeting approaches.
    DOI:  https://doi.org/10.1038/s41388-021-02134-4
  23. J Lipid Res. 2021 Nov 24. pii: S0022-2275(21)00137-1. [Epub ahead of print] 100154
    1-deoxysphinganine initiates adaptive responses to serine and glycine starvation in cancer cells via proteolysis of sphingosine kinase.
    Jean-Philip Truman, Christian F Ruiz, Emily Montal, Monica Garcia-Barros, Izolda Mileva, Ashley J Snider, Yusuf A Hannun, Lina M Obeid, Cungui Mao.
      Cancer cells can become dependent on exogenous serine, depletion of which results in slower growth and activation of a number of adaptive metabolic changes. We previously demonstrated that serine and glycine (SG) deprivation causes loss of sphingosine kinase 1 (SK1) in cancer cells, thereby increasing levels of its lipid substrate, sphingosine (Sph), which mediates several adaptive biological responses. However, the signaling molecules that regulate levels of SK1 and Sph in response to SG deprivation have yet to be defined. Here, we identify 1-deoxysphinganine (dSA), a non-canonical sphingoid base generated in the absence of serine from the alternative condensation of alanine and palmitoyl CoA by serine palmitoyl transferase (SPT), as a proximal mediator of SG deprivation in SK1 loss and Sph level elevation in SG deprivation in cancer cells. SG starvation markedly increased dSA levels in vitro and in vivo, and in turn induced SK1 degradation through a SPT-dependent mechanism, resulting in an increase in SPH levels. Addition of exogenous dSA caused a moderate increase in intracellular reactive oxygen species (ROS), which in turn decreased pyruvate kinase PKM2 activity while increasing phosphoglycerate dehydrogenase (PHGDH) levels, and thereby promoted serine synthesis. We further showed that increased dSA induces the adaptive cellular and metabolic functions in the response of cells to decreased availability of serine likely by increasing Sph levels. Thus, we conclude that dSA functions as an initial sensor of serine loss, SK1 functions as its direct target, and Sph functions as a downstream effector of cellular and metabolic adaptations. These studies define a previously unrecognized 'physiological' non-toxic function for dSA.
    Keywords:  Sphingosine kinase; hereditary sensory and autonomic neuropathy (HSAN); mass spectrometry; phosphoglycerate dehydrogenase (PHGDH); pyruvate kinase (PKM2); reactive oxygen species (ROS); serine biosynthesis; serine palmitoyl transferase (SPT); sphingosine; ubiquitination
    DOI:  https://doi.org/10.1016/j.jlr.2021.100154
  24. Proc Natl Acad Sci U S A. 2021 Dec 07. pii: e2116125118. [Epub ahead of print]118(49):
    Local acetate inhibits brown adipose tissue function.
    Wenfei Sun, Hua Dong, Christian Wolfrum.
      Brown adipose tissue has been extensively studied in the last decade for its potential to counteract the obesity pandemic. However, the paracrine regulation within brown tissue is largely unknown. Here, we show that local acetate directly inhibits brown fat thermogenesis, without changing acetate levels in the circulation. We demonstrate that modulating acetate within brown tissue at physiological levels blunts its function and systemically decreases energy expenditure. Using a series of transcriptomic analyses, we identified genes related to the tricarboxylic acid cycle and brown adipocyte formation, which are down-regulated upon local acetate administration. Overall, these findings demonstrate that local acetate inhibits brown fat function.
    Keywords:  RNA-seq; acetate; brown adipose tissue; obesity
    DOI:  https://doi.org/10.1073/pnas.2116125118
  25. PLoS Biol. 2021 Dec 03. 19(12): e3001468
    Cysteine and iron accelerate the formation of ribose-5-phosphate, providing insights into the evolutionary origins of the metabolic network structure.
    Gabriel Piedrafita, Sreejith J Varma, Cecilia Castro, Christoph Messner, Lukasz Szyrwiel, Julian L Griffin, Markus Ralser.
      The structure of the metabolic network is highly conserved, but we know little about its evolutionary origins. Key for explaining the early evolution of metabolism is solving a chicken-egg dilemma, which describes that enzymes are made from the very same molecules they produce. The recent discovery of several nonenzymatic reaction sequences that topologically resemble central metabolism has provided experimental support for a "metabolism first" theory, in which at least part of the extant metabolic network emerged on the basis of nonenzymatic reactions. But how could evolution kick-start on the basis of a metal catalyzed reaction sequence, and how could the structure of nonenzymatic reaction sequences be imprinted on the metabolic network to remain conserved for billions of years? We performed an in vitro screening where we add the simplest components of metabolic enzymes, proteinogenic amino acids, to a nonenzymatic, iron-driven reaction network that resembles glycolysis and the pentose phosphate pathway (PPP). We observe that the presence of the amino acids enhanced several of the nonenzymatic reactions. Particular attention was triggered by a reaction that resembles a rate-limiting step in the oxidative PPP. A prebiotically available, proteinogenic amino acid cysteine accelerated the formation of RNA nucleoside precursor ribose-5-phosphate from 6-phosphogluconate. We report that iron and cysteine interact and have additive effects on the reaction rate so that ribose-5-phosphate forms at high specificity under mild, metabolism typical temperature and environmental conditions. We speculate that accelerating effects of amino acids on rate-limiting nonenzymatic reactions could have facilitated a stepwise enzymatization of nonenzymatic reaction sequences, imprinting their structure on the evolving metabolic network.
    DOI:  https://doi.org/10.1371/journal.pbio.3001468
  26. Trends Neurosci. 2021 Nov 29. pii: S0166-2236(21)00214-9. [Epub ahead of print]
    Mitochondrial dysfunction as a trigger of programmed axon death.
    Elisa Merlini, Michael P Coleman, Andrea Loreto.
      Mitochondrial failure has long been associated with programmed axon death (Wallerian degeneration, WD), a widespread and potentially preventable mechanism of axon degeneration. While early findings in axotomised axons indicated that mitochondria are involved during the execution steps of this pathway, recent studies suggest that in addition, mitochondrial dysfunction can initiate programmed axon death without physical injury. As mitochondrial dysfunction is associated with disorders involving early axon loss, including Parkinson's disease, peripheral neuropathies, and multiple sclerosis, the findings that programmed axon death is activated by mitochondrial impairment could indicate the involvement of druggable mechanisms whose disruption may protect axons in such diseases. Here, we review the latest developments linking mitochondrial dysfunction to programmed axon death and discuss their implications for injury and disease.
    Keywords:  Parkinson’s disease; SARM1; Wallerian degeneration; axon degeneration; mitochondrial dysfunction; programmed axon death
    DOI:  https://doi.org/10.1016/j.tins.2021.10.014
  27. Cancer Metastasis Rev. 2021 Dec 02.
    Metabolic reprogramming by driver mutation-tumor microenvironment interplay in pancreatic cancer: new therapeutic targets.
    Henriette Berg Andersen, Renata Ialchina, Stine Falsig Pedersen, Dominika Czaplinska.
      Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancers globally with a mortality rate exceeding 95% and very limited therapeutic options. A hallmark of PDAC is its acidic tumor microenvironment, further characterized by excessive fibrosis and depletion of oxygen and nutrients due to poor vascularity. The combination of PDAC driver mutations and adaptation to this hostile environment drives extensive metabolic reprogramming of the cancer cells toward non-canonical metabolic pathways and increases reliance on scavenging mechanisms such as autophagy and macropinocytosis. In addition, the cancer cells benefit from metabolic crosstalk with nonmalignant cells within the tumor microenvironment, including pancreatic stellate cells, fibroblasts, and endothelial and immune cells. Increasing evidence shows that this metabolic rewiring is closely related to chemo- and radioresistance and immunosuppression, causing extensive treatment failure. Indeed, stratification of human PDAC tumors into subtypes based on their metabolic profiles was shown to predict disease outcome. Accordingly, an increasing number of clinical trials target pro-tumorigenic metabolic pathways, either as stand-alone treatment or in conjunction with chemotherapy. In this review, we highlight key findings and potential future directions of pancreatic cancer metabolism research, specifically focusing on novel therapeutic opportunities.
    Keywords:  Acidosis; Clinical trials; Glycolysis; Lipid metabolism; Metabolic subtypes; PDAC
    DOI:  https://doi.org/10.1007/s10555-021-10004-4
  28. Metab Eng. 2021 Nov 25. pii: S1096-7176(21)00177-4. [Epub ahead of print]
    Elucidating tumor-stromal metabolic crosstalk in colorectal cancer through integration of constraint-based models and LC-MS metabolomics.
    Junmin Wang, Alireza Delfarah, Patrick Gelbach, Emma Fong, Paul Macklin, Shannon M Mumenthaler, Nicholas A Graham, Stacey Finley.
      Colorectal cancer (CRC) is a major cause of morbidity and mortality in the United States. Tumor-stromal metabolic crosstalk in the tumor microenvironment promotes CRC development and progression, but exactly how stromal cells, in particular cancer-associated fibroblasts (CAFs), affect the metabolism of tumor cells remains unknown. Here we take a data-driven approach to investigate the metabolic interactions between CRC cells and CAFs, integrating constraint-based modeling and metabolomic profiling. Using metabolomics data, we perform unsteady-state parsimonious flux balance analysis to infer flux distributions for central carbon metabolism in CRC cells treated with or without CAF-conditioned media. We find that CAFs reprogram CRC metabolism through stimulation of glycolysis, the oxidative arm of the pentose phosphate pathway (PPP), and glutaminolysis as well as inhibition of the tricarboxylic acid cycle. To identify potential therapeutic targets, we simulate enzyme knockouts and find that CAF-treated CRC cells are especially sensitive to inhibitions of hexokinase and glucose-6-phosphate, the rate limiting steps of glycolysis and oxidative PPP. Our work gives mechanistic insights into the metabolic interactions between CRC cells and CAFs and provides a framework for testing hypotheses towards CRC-targeted therapies.
    Keywords:  Flux balance analysis; Mathematical biosciences; Metabolomics; Systems biology; Tumor microenvironment
    DOI:  https://doi.org/10.1016/j.ymben.2021.11.006
  29. Cancer Metastasis Rev. 2021 Nov 30.
    What do cellular responses to acidity tell us about cancer?
    Wiktoria Blaszczak, Pawel Swietach.
      The notion that invasive cancer is a product of somatic evolution is a well-established theory that can be modelled mathematically and demonstrated empirically from therapeutic responses. Somatic evolution is by no means deterministic, and ample opportunities exist to steer its trajectory towards cancer cell extinction. One such strategy is to alter the chemical microenvironment shared between host and cancer cells in a way that no longer favours the latter. Ever since the first description of the Warburg effect, acidosis has been recognised as a key chemical signature of the tumour microenvironment. Recent findings have suggested that responses to acidosis, arising through a process of selection and adaptation, give cancer cells a competitive advantage over the host. A surge of research efforts has attempted to understand the basis of this advantage and seek ways of exploiting it therapeutically. Here, we review key findings and place these in the context of a mathematical framework. Looking ahead, we highlight areas relating to cellular adaptation, selection, and heterogeneity that merit more research efforts in order to close in on the goal of exploiting tumour acidity in future therapies.
    Keywords:  Acid–base; Adaptation; Cell lines; Evolution; Metabolism; Phenotype; Selection; Variation; pH
    DOI:  https://doi.org/10.1007/s10555-021-10005-3
  30. Genetics. 2021 Oct 02. pii: iyab109. [Epub ahead of print]219(2):
    Bend or break: how biochemically versatile molecules enable metabolic division of labor in clonal microbial communities.
    Sriram Varahan, Sunil Laxman.
      In fluctuating nutrient environments, isogenic microbial cells transition into "multicellular" communities composed of phenotypically heterogeneous cells, showing functional specialization. In fungi (such as budding yeast), phenotypic heterogeneity is often described in the context of cells switching between different morphotypes (e.g., yeast to hyphae/pseudohyphae or white/opaque transitions in Candida albicans). However, more fundamental forms of metabolic heterogeneity are seen in clonal Saccharomyces cerevisiae communities growing in nutrient-limited conditions. Cells within such communities exhibit contrasting, specialized metabolic states, and are arranged in distinct, spatially organized groups. In this study, we explain how such an organization can stem from self-organizing biochemical reactions that depend on special metabolites. These metabolites exhibit plasticity in function, wherein the same metabolites are metabolized and utilized for distinct purposes by different cells. This in turn allows cell groups to function as specialized, interdependent cross-feeding systems which support distinct metabolic processes. Exemplifying a system where cells exhibit either gluconeogenic or glycolytic states, we highlight how available metabolites can drive favored biochemical pathways to produce new, limiting resources. These new resources can themselves be consumed or utilized distinctly by cells in different metabolic states. This thereby enables cell groups to sustain contrasting, even apparently impossible metabolic states with stable transcriptional and metabolic signatures for a given environment, and divide labor in order to increase community fitness or survival. We speculate on possible evolutionary implications of such metabolic specialization and division of labor in isogenic microbial communities.
    Keywords:  cross-feeding systems; division of labor; gluconeogenesis; glycolysis; metabolic specialization; phenotypic heterogeneity
    DOI:  https://doi.org/10.1093/genetics/iyab109
  31. Diabetes. 2021 Dec 03. pii: db210281. [Epub ahead of print]
    The nutrient sensor mTORC1 regulates insulin secretion by modulating ß-cell autophagy.
    Tal Israeli, Yael Riahi, Perla Garzon, Ruy Andrade Louzada, Joao Pedro Werneck-de-Castro, Manuel Blandino-Rosano, Roni Yeroslaviz-Stolper, Liat Kadosh, Sharona Tornovsky-Babeay, Gilad Hacker, Nitzan Israeli, Orly Agmon, Boaz Tirosh, Erol Cerasi, Ernesto Bernal-Mizrachi, Gil Leibowitz.
      The dynamic regulation of autophagy in β-cells by cycles of fasting-feeding and its effects on insulin secretion are unknown. In β-cells mTORC1 is inhibited while fasting, and is rapidly stimulated during refeeding by a single amino acid, leucine, and glucose. Stimulation of mTORC1 by nutrients inhibited the autophagy initiator ULK1 and the transcription factor TFEB, thereby preventing autophagy when β-cells are continuously exposed to nutrients. Inhibition of mTORC1 by Raptor knockout mimicked the effects of fasting and stimulated autophagy while inhibiting insulin secretion, whereas moderate inhibition of autophagy under these conditions rescued insulin secretion. These results show that mTORC1 regulates insulin secretion through modulation of autophagy under different nutritional situations. In the fasting state, autophagy is regulated in an mTORC1-dependent manner and its stimulation is required to keep insulin levels low, thereby preventing hypoglycemia. Reciprocally, stimulation of mTORC1 by elevated leucine and glucose, which is common in obesity, may promote hyperinsulinemia by inhibiting autophagy.
    DOI:  https://doi.org/10.2337/db21-0281
  32. Circulation. 2021 Nov 30. 144(22): 1795-1817
    NAD+ Metabolism in Cardiac Health, Aging, and Disease.
    Mahmoud Abdellatif, Simon Sedej, Guido Kroemer.
      Nicotinamide adenine dinucleotide (NAD+) is a central metabolite involved in energy and redox homeostasis as well as in DNA repair and protein deacetylation reactions. Pharmacological or genetic inhibition of NAD+-degrading enzymes, external supplementation of NAD+ precursors, and transgenic overexpression of NAD+-generating enzymes have wide positive effects on metabolic health and age-associated diseases. NAD+ pools tend to decline with normal aging, obesity, and hypertension, which are all major risk factors for cardiovascular disease, and NAD+ replenishment extends healthspan, avoids metabolic syndrome, and reduces blood pressure in preclinical models. In addition, experimental elevation of NAD+ improves atherosclerosis, ischemic, diabetic, arrhythmogenic, hypertrophic, or dilated cardiomyopathies, as well as different modalities of heart failure. Here, we critically discuss cardiomyocyte-specific circuitries of NAD+ metabolism, comparatively evaluate distinct NAD+ precursors for their preclinical efficacy, and raise outstanding questions on the optimal design of clinical trials in which NAD+ replenishment or supraphysiological NAD+ elevations are assessed for the prevention or treatment of major cardiac diseases. We surmise that patients with hitherto intractable cardiac diseases such as heart failure with preserved ejection fraction may profit from the administration of NAD+ precursors. The development of such NAD+-centered treatments will rely on technological and conceptual progress on the fine regulation of NAD+ metabolism.
    Keywords:  NAD; cardiomyopathy; heart failure; human; nicotinamide; nicotinamide mononucleotide; obesity
    DOI:  https://doi.org/10.1161/CIRCULATIONAHA.121.056589
  33. Semin Cell Dev Biol. 2021 Nov 29. pii: S1084-9521(21)00291-3. [Epub ahead of print]
    Breaking the vicious circle: Extrachromosomal circular DNA as an emerging player in tumour evolution.
    Matius Robert, Karen Crasta.
      Extrachromosomal circular DNA (ecDNA) or double minutes have gained renewed interest since its discovery more than five decades ago, emerging as potent drivers of tumour evolution. This has largely been motivated by recent discovery that the tumour-exclusive ecDNA are highly prevalent in almost all cancers unlike previously thought. EcDNAs contribute to elevated oncogene expression, intratumoural heterogeneity, tumour adaptation and therapy resistance independently of canonical chromosomal alterations. Importantly, ecDNAs play a critical role in patient survival as ecDNA-based oncogene amplification adversely affects clinical outcome to a significantly greater extent than intrachromosomal amplification. Chromothripsis, a major driver of ecDNA biogenesis and gene amplification, is a mutational process characterised by chromosomal shattering and localised complex genome rearrangement. Chemotherapeutic drugs can lead to chromothriptic rearrangements and therapy resistance. In this review, we examine how ecDNAs mediate oncogene overexpression, facilitate accelerated tumour malignancy and enhance rapid adaptation independently of linear chromosomes. We delve into discoveries pertaining to mechanisms of biogenesis, distinctive features of ecDNA, gene regulation and topological interactions with active chromatin. We also discuss the critical role of chromothripsis in engendering ecDNA amplification and evolution. One envisions that insights into ecDNA biology not only hold importance for the cancer genome and tumour evolutionary dynamics, but could also inform prognostication and clinical intervention, particularly for cancers characterised by high oncogene amplification.
    Keywords:  Chromatin bridges; Chromothripsis; Double minutes; Extrachromosomal circular DNA; Micronuclei; Oncogene amplification
    DOI:  https://doi.org/10.1016/j.semcdb.2021.11.015
  34. Clin Neurol Neurosurg. 2021 Nov 20. pii: S0303-8467(21)00568-0. [Epub ahead of print]212 107039
    A novel bi-allelic variant in the SDHB gene causes a severe mitochondrial complex II deficiency: a case report.
    Asli Ece Solmaz, Erhan Pariltay, Beril Talim, Huseyin Onay.
      Isolated deficiency of complex II is a rare inborn error of metabolism, accounting for approximately 2% of mitochondrial diseases. Mitochondrial complex II deficiency is predominantly seen in cases with bi-allelic SDHA mutations. To our knowledge, only 11 patients and five pathogenic variants have been reported for the SDHB gene. Our patient had a severe clinical presentation with seizures and sepsis, and died at the age of 2 months. Muscle biopsy analysis was compatible with mitochondrial myopathy with complex II deficiency. The family was given a molecular diagnosis for their child 2 years after his death via a clinical exome test of a frozen muscle biopsy specimen and a novel homozygous missense variant c.592 A>G (p.Ser198Gly) in SDHB gene was detected by next-generation sequencing. Here, we present another patient with a novel homozygous SDHB variant causing severe complex II deficiency and early death.
    Keywords:  Mitochondrial complex II deficiency; Mitochondrial diseases; Next-Generation Sequencing; SDHB
    DOI:  https://doi.org/10.1016/j.clineuro.2021.107039
  35. Cell Rep Med. 2021 Nov 16. 2(11): 100445
    The ongoing mystery of renal cell cancer.
    James C Yang.
      Au et al. take an in-depth longitudinal look at tumor cells and T cells in patients with renal cancer undergoing anti-PD1 blockade.
    DOI:  https://doi.org/10.1016/j.xcrm.2021.100445
  36. EMBO J. 2021 Nov 29. e2021108883
    CRYPTOCHROMES promote daily protein homeostasis.
    David C S Wong, Estere Seinkmane, Aiwei Zeng, Alessandra Stangherlin, Nina M Rzechorzek, Andrew D Beale, Jason Day, Martin Reed, Sew Y Peak-Chew, Christine T Styles, Rachel S Edgar, Marrit Putker, John S O'Neill.
      The daily organisation of most mammalian cellular functions is attributed to circadian regulation of clock-controlled protein expression, driven by daily cycles of CRYPTOCHROME-dependent transcriptional feedback repression. To test this, we used quantitative mass spectrometry to compare wild-type and CRY-deficient fibroblasts under constant conditions. In CRY-deficient cells, we found that temporal variation in protein, phosphopeptide, and K+ abundance was at least as great as wild-type controls. Most strikingly, the extent of temporal variation within either genotype was much smaller than overall differences in proteome composition between WT and CRY-deficient cells. This proteome imbalance in CRY-deficient cells and tissues was associated with increased susceptibility to proteotoxic stress, which impairs circadian robustness, and may contribute to the wide-ranging phenotypes of CRY-deficient mice. Rather than generating large-scale daily variation in proteome composition, we suggest it is plausible that the various transcriptional and post-translational functions of CRY proteins ultimately act to maintain protein and osmotic homeostasis against daily perturbation.
    Keywords:  CRYPTOCHROME; circadian rhythm; clock mutant; protein homeostasis; proteotoxic stress
    DOI:  https://doi.org/10.15252/embj.2021108883
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