bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2022–03–13
27 papers selected by
Kıvanç Görgülü, Technical University of Munich
  1. Indirect targeting of MYC sensitizes pancreatic cancer cells to mechanistic target of rapamycin (mTOR) inhibition.
  2. Ferrous iron-activatable drug conjugate achieves potent MAPK blockade in KRAS-driven tumors.
  3. A non-canonical tricarboxylic acid cycle underlies cellular identity.
  4. Proteolytic pan-RAS cleavage leads to tumor regression in patient-derived pancreatic cancer xenografts.
  5. The burning furnace: Alteration in lipid metabolism in cancer-associated cachexia.
  6. Confined migration promotes cancer metastasis through resistance to anoikis and increased invasiveness.
  7. RASGRF1 Fusions Activate Oncogenic RAS Signaling and Confer Sensitivity to MEK Inhibition.
  8. Fibrous stroma: Driver and passenger in cancer development.
  9. Mitochondrial respiration supports autophagy to provide stress resistance during quiescence.
  10. Autophagy-mediated plasma membrane removal promotes the formation of epithelial syncytia.
  11. On the origin of metastases: Induction of pro-metastatic states after impending cell death via ER stress, reprogramming, and a cytokine storm.
  12. Cancer progression as a learning process.
  13. Co-targeting of BAX and BCL-XL proteins broadly overcomes resistance to apoptosis in cancer.
  14. Protein methylation in mitochondria.
  15. Metabolic tricks of cancer cells.
  16. Iron Supplementation Delays Aging and Extends Cellular Lifespan through Potentiation of Mitochondrial Function.
  17. How many molecules of mitochondrial complex I are in a cell?
  18. CRISPR-Cas9 screen identifies oxidative phosphorylation as essential for cancer cell survival at low extracellular pH.
  19. Co-translational assembly orchestrates competing biogenesis pathways.
  20. Targeting metabolic adaptations in the breast cancer-liver metastatic niche using dietary approaches to improve endocrine therapy efficacy.
  21. Regulation of liver subcellular architecture controls metabolic homeostasis.
  22. Results of a Phase II Study on the use of Neoadjuvant Chemotherapy (FOLFIRINOX or Gemcitabine with nab-paclitaxel) for Borderline-Resectable Pancreatic Cancer (NUPAT-01).
  23. Liquid biopsies to monitor and direct cancer treatment in colorectal cancer.
  24. A saturation-mutagenesis analysis of the interplay between stability and activation in Ras.
  25. Clinical translation of patient-derived tumour organoids- bottlenecks and strategies.
  26. Mendelian randomization suggests a bidirectional, causal relationship between physical inactivity and adiposity.
  27. Biological mechanisms of aging predict age-related disease co-occurrence in patients.
  1. Cancer Commun (Lond). 2022 Mar 07.
    Indirect targeting of MYC sensitizes pancreatic cancer cells to mechanistic target of rapamycin (mTOR) inhibition.
    Christian Schneeweis, Zonera Hassan, Katja Ascherl, Matthias Wirth, Stella Koutsouli, Felix Orben, Lukas Krauß, Carolin Schneider, Rupert Öllinger, Oliver H Krämer, Roland Rad, Maximilian Reichert, Maria S Robles, Dieter Saur, Günter Schneider.
      
    DOI:  https://doi.org/10.1002/cac2.12280
  2. J Exp Med. 2022 Apr 04. pii: e20210739. [Epub ahead of print]219(4):
    Ferrous iron-activatable drug conjugate achieves potent MAPK blockade in KRAS-driven tumors.
    Honglin Jiang, Ryan K Muir, Ryan L Gonciarz, Adam B Olshen, Iwei Yeh, Byron C Hann, Ning Zhao, Yung-Hua Wang, Spencer C Behr, James E Korkola, Michael J Evans, Eric A Collisson, Adam R Renslo.
      KRAS mutations drive a quarter of cancer mortality, and most are undruggable. Several inhibitors of the MAPK pathway are FDA approved but poorly tolerated at the doses needed to adequately extinguish RAS/RAF/MAPK signaling in the tumor cell. We found that oncogenic KRAS signaling induced ferrous iron (Fe2+) accumulation early in and throughout mutant KRAS-mediated transformation. We converted an FDA-approved MEK inhibitor into a ferrous iron-activatable drug conjugate (FeADC) and achieved potent MAPK blockade in tumor cells while sparing normal tissues. This innovation allowed sustainable, effective treatment of tumor-bearing animals, with tumor-selective drug activation, producing superior systemic tolerability. Ferrous iron accumulation is an exploitable feature of KRAS transformation, and FeADCs hold promise for improving the treatment of KRAS-driven solid tumors.
    DOI:  https://doi.org/10.1084/jem.20210739
  3. Nature. 2022 Mar 09.
    A non-canonical tricarboxylic acid cycle underlies cellular identity.
    Paige K Arnold, Benjamin T Jackson, Katrina I Paras, Julia S Brunner, Madeleine L Hart, Oliver J Newsom, Sydney P Alibeckoff, Jennifer Endress, Esther Drill, Lucas B Sullivan, Lydia W S Finley.
      The tricarboxylic acid (TCA) cycle is a central hub of cellular metabolism, oxidizing nutrients to generate reducing equivalents for energy production and critical metabolites for biosynthetic reactions. Despite the importance of the products of the TCA cycle for cell viability and proliferation, mammalian cells display diversity in TCA-cycle activity1,2. How this diversity is achieved, and whether it is critical for establishing cell fate, remains poorly understood. Here we identify a non-canonical TCA cycle that is required for changes in cell state. Genetic co-essentiality mapping revealed a cluster of genes that is sufficient to compose a biochemical alternative to the canonical TCA cycle, wherein mitochondrially derived citrate exported to the cytoplasm is metabolized by ATP citrate lyase, ultimately regenerating mitochondrial oxaloacetate to complete this non-canonical TCA cycle. Manipulating the expression of ATP citrate lyase or the canonical TCA-cycle enzyme aconitase 2 in mouse myoblasts and embryonic stem cells revealed that changes in the configuration of the TCA cycle accompany cell fate transitions. During exit from pluripotency, embryonic stem cells switch from canonical to non-canonical TCA-cycle metabolism. Accordingly, blocking the non-canonical TCA cycle prevents cells from exiting pluripotency. These results establish a context-dependent alternative to the traditional TCA cycle and reveal that appropriate TCA-cycle engagement is required for changes in cell state.
    DOI:  https://doi.org/10.1038/s41586-022-04475-w
  4. Mol Cancer Ther. 2022 Feb 28. pii: molcanther.0550.2021. [Epub ahead of print]
    Proteolytic pan-RAS cleavage leads to tumor regression in patient-derived pancreatic cancer xenografts.
    Vania Vidimar, Minyoung Park, Caleb Kawun Stubbs, Nana Kwame Ingram, Wenan Qiang, Shanshan Zhang, Demirkan B Gursel, Roman A Melnyk, Karla J Satchell.
      The lack of effective RAS inhibition represents a major unmet medical need in the treatment of pancreatic ductal adenocarcinoma (PDAC). Here, we investigate the anticancer activity of RRSP-DTB, an engineered biologic that cleaves the Switch I of all RAS isoforms, in KRAS-mutant PDAC cell lines and patient-derived xenografts (PDXs). We first demonstrate that RRSP-DTB effectively engages RAS and impacts downstream ERK signaling in multiple KRAS-mutant PDAC cell lines inhibiting cell proliferation at picomolar concentrations. We next tested RRSP-DTB in immunodeficient mice bearing KRAS-mutant PDAC PDXs. Treatment with RRSP-DTB led to 95% tumor regression after 29 days. Residual tumors exhibited disrupted tissue architecture, increased fibrosis and fewer proliferating cells compared to controls. Intratumoral levels of phospho-ERK were also significantly lower, indicating in vivo target engagement. Importantly, tumors that started to regrow without RRSP-DTB shrank when treatment resumed, demonstrating resistance to RRSP-DTB had not developed. Tracking persistence of the toxin activity following intraperitoneal injection showed that RRSP-DTB is active in sera from immunocompetent mice for at least one hour, but absent after 16 hours, justifying use of daily dosing. Overall, we report that RRSP-DTB strongly regresses hard-to-treat KRAS-mutant PDX models of pancreatic cancer, warranting further development of this pan-RAS biologic for the management of RAS-addicted tumors.
    DOI:  https://doi.org/10.1158/1535-7163.MCT-21-0550
  5. Mol Cell Biochem. 2022 Mar 07.
    The burning furnace: Alteration in lipid metabolism in cancer-associated cachexia.
    Mit Joshi, Bhoomika M Patel.
      Cancer cachexia can be defined as a complex metabolic syndrome characterized by weight loss, anorexia, and emaciation due to the wasting of adipose tissue and skeletal muscle. In the last decade, much research has been done to decipher the role of lipid metabolism in cancer cachexia. Tumors, as well as host-derived factors, cause major metabolic changes in the body. Metabolic changes lead to higher energy expenditure by the host. To meet the high energy demand, the host utilizes fat depots stored in adipose tissues by a process known as lipolysis. High catabolic and low anabolic response leads to loss of adipose tissue. A significant insight has been made regarding adipose tissue "browning" bestow on thermogenic activities of adipocytes that result in catabolic energy expenditure. Both lipolysis and WAT browning play an important role in exhaustion adipose tissue. The goal of this review is to summarise what is currently known and about altered lipid metabolism and its utilization in cancer cachexia.
    Keywords:  Adipose tissue; Browning; Cancer; Cancer cachexia; Lipid metabolism; Lipolysis
    DOI:  https://doi.org/10.1007/s11010-022-04398-0
  6. Elife. 2022 Mar 08. pii: e73150. [Epub ahead of print]11
    Confined migration promotes cancer metastasis through resistance to anoikis and increased invasiveness.
    Deborah Fanfone, Zhichong Wu, Jade Mammi, Kevin Berthenet, David Neves, Kathrin Weber, Andrea Halaburkova, François Virard, Félix Bunel, Catherine Jamard, Hector Hernandez-Vargas, Stephen W G Tait, Ana Hennino, Gabriel Ichim.
      Mechanical stress is known to fuel several hallmarks of cancer, ranging from genome instability to uncontrolled proliferation or invasion. Cancer cells are constantly challenged by mechanical stresses not only in the primary tumour but also during metastasis. However, this latter has seldom been studied with regards to mechanobiology, in particular resistance to anoikis, a cell death programme triggered by loss of cell adhesion. Here, we show in vitro that migrating breast cancer cells develop resistance to anoikis following their passage through microporous membranes mimicking confined migration (CM), a mechanical constriction that cancer cells encounter during metastasis. This CM-induced resistance was mediated by Inhibitory of Apoptosis Proteins, and sensitivity to anoikis could be restored after their inhibition using second mitochondria-derived activator of caspase (SMAC) mimetics. Anoikis-resistant mechanically stressed cancer cells displayed enhanced cell motility and evasion from natural killer cell-mediated immune surveillance, as well as a marked advantage to form lung metastatic lesions in mice. Our findings reveal that CM increases the metastatic potential of breast cancer cells.
    Keywords:  IAP; anoikis; cancer biology; caspases; cell biology; confinement; human; mechanobiology; metastasis; mouse
    DOI:  https://doi.org/10.7554/eLife.73150
  7. Clin Cancer Res. 2022 Mar 01. pii: clincanres.4291.2021. [Epub ahead of print]
    RASGRF1 Fusions Activate Oncogenic RAS Signaling and Confer Sensitivity to MEK Inhibition.
    Lisa Hunihan, Dejian Zhao, Heather Lazowski, Man Li, Yuping Qian, Laura Abriola, Yulia V Surovtseva, Viswanathan Muthusamy, Lynn T Tanoue, Bonnie E Gould Rothberg, Kurt A Schalper, Roy S Herbst, Frederick H Wilson.
       PURPOSE: The identification of actionable oncogenic alterations has enabled targeted therapeutic strategies for subsets of patients with advanced malignancies including lung adenocarcinoma (LUAD). We sought to assess the frequency of known drivers and identify new candidate drivers in a cohort of LUAD from patients with minimal smoking history.
    EXPERIMENTAL DESIGN: We performed genomic characterization of 103 LUADs from patients with {less than or equal to}10 pack-year smoking history. Tumors were subjected to targeted molecular profiling and/or whole-exome sequencing and RNA-seq in search of established and previously uncharacterized candidate drivers.
    RESULTS: We identified an established oncogenic driver in 98 of 103 tumors (95%). From one tumor lacking a known driver, we identified a novel gene rearrangement between OCLN and RASGRF1. The encoded OCLN-RASGRF1 chimera fuses the membrane-spanning portion of the tight junction protein occludin with the catalytic RAS-GEF domain of the RAS activator RASGRF1. We identified a similar SLC4A4-RASGRF1 fusion in a pancreatic ductal adenocarcinoma (PDAC) cell line lacking an activating KRAS mutation and an IQGAP1-RASGRF1 fusion from a sarcoma in The Cancer Genome Atlas. We demonstrate these fusions increase cellular levels of active GTP-RAS, induce cellular transformation, and promote in vivo tumorigenesis. Cells driven by RASGRF1 fusions are sensitive to targeting of the RAF-MEK-ERK pathway in vitro and in vivo.
    CONCLUSIONS: Our findings credential RASGRF1 fusions as a therapeutic target in multiple malignancies and implicate RAF-MEK-ERK inhibition as a potential treatment strategy for advanced tumors harboring these alterations.
    DOI:  https://doi.org/10.1158/1078-0432.CCR-21-4291
  8. Sci Signal. 2022 Mar 08. 15(724): eabg3449
    Fibrous stroma: Driver and passenger in cancer development.
    Vandana Sharma, Joshua Letson, Saori Furuta.
      Cumulative evidence shows that fibrogenic stroma and stiff extracellular matrix (ECM) not only result from tumor growth but also play pivotal roles in cellular transformation and tumor initiation. This emerging concept may largely account for the increased cancer risk associated with environmental fibrogenic agents, such as asbestos and silica, and with chronic conditions that are fibrogenic, such as obesity and diabetes. It may also contribute to poor outcomes in patients treated with certain chemotherapeutics that can promote fibrosis, such as bleomycin and methotrexate. Although the mechanistic details of this phenomenon are still being unraveled, we provide an overview of the experimental evidence linking fibrogenic stroma and tumor initiation. In this Review, we will summarize the causes and consequences of fibrous stroma and how this stromal cue is transmitted to the nuclei of parenchymal cells through a physical continuum from the ECM to chromatin, as well as ECM-dependent biochemical signaling that contributes to cellular transformation.
    DOI:  https://doi.org/10.1126/scisignal.abg3449
  9. Autophagy. 2022 Mar 08. 1-18
    Mitochondrial respiration supports autophagy to provide stress resistance during quiescence.
    Silvia Magalhaes-Novais, Jan Blecha, Ravindra Naraine, Jana Mikesova, Pavel Abaffy, Alena Pecinova, Mirko Milosevic, Romana Bohuslavova, Jan Prochazka, Shawez Khan, Eliska Novotna, Radek Sindelka, Radek Machan, Mieke Dewerchin, Erik Vlcak, Joanna Kalucka, Sona Stemberkova Hubackova, Ales Benda, Jermaine Goveia, Tomas Mracek, Cyril Barinka, Peter Carmeliet, Jiri Neuzil, Katerina Rohlenova, Jakub Rohlena.
      Mitochondrial oxidative phosphorylation (OXPHOS) generates ATP, but OXPHOS also supports biosynthesis during proliferation. In contrast, the role of OXPHOS during quiescence, beyond ATP production, is not well understood. Using mouse models of inducible OXPHOS deficiency in all cell types or specifically in the vascular endothelium that negligibly relies on OXPHOS-derived ATP, we show that selectively during quiescence OXPHOS provides oxidative stress resistance by supporting macroautophagy/autophagy. Mechanistically, OXPHOS constitutively generates low levels of endogenous ROS that induce autophagy via attenuation of ATG4B activity, which provides protection from ROS insult. Physiologically, the OXPHOS-autophagy system (i) protects healthy tissue from toxicity of ROS-based anticancer therapy, and (ii) provides ROS resistance in the endothelium, ameliorating systemic LPS-induced inflammation as well as inflammatory bowel disease. Hence, cells acquired mitochondria during evolution to profit from oxidative metabolism, but also built in an autophagy-based ROS-induced protective mechanism to guard against oxidative stress associated with OXPHOS function during quiescence.Abbreviations: AMPK: AMP-activated protein kinase; AOX: alternative oxidase; Baf A: bafilomycin A1; CI, respiratory complexes I; DCF-DA: 2',7'-dichlordihydrofluorescein diacetate; DHE: dihydroethidium; DSS: dextran sodium sulfate; ΔΨmi: mitochondrial inner membrane potential; EdU: 5-ethynyl-2'-deoxyuridine; ETC: electron transport chain; FA: formaldehyde; HUVEC; human umbilical cord endothelial cells; IBD: inflammatory bowel disease; LC3B: microtubule associated protein 1 light chain 3 beta; LPS: lipopolysaccharide; MEFs: mouse embryonic fibroblasts; MTORC1: mechanistic target of rapamycin kinase complex 1; mtDNA: mitochondrial DNA; NAC: N-acetyl cysteine; OXPHOS: oxidative phosphorylation; PCs: proliferating cells; PE: phosphatidylethanolamine; PEITC: phenethyl isothiocyanate; QCs: quiescent cells; ROS: reactive oxygen species; PLA2: phospholipase A2, WB: western blot.
    Keywords:  ATG4B; biosynthesis; cell death; electron transport chain; endothelial cells; mitochondria; oxidative phosphorylation; oxidative stress; reactive oxygen species
    DOI:  https://doi.org/10.1080/15548627.2022.2038898
  10. EMBO J. 2022 Mar 09. e109992
    Autophagy-mediated plasma membrane removal promotes the formation of epithelial syncytia.
    Parisa Kakanj, Sourabh Bhide, Bernard Moussian, Maria Leptin.
      Epithelial wound healing in Drosophila involves the formation of multinucleate cells surrounding the wound. We show that autophagy, a cellular degradation process often deployed in stress responses, is required for the formation of a multinucleated syncytium during wound healing, and that autophagosomes that appear near the wound edge acquire plasma membrane markers. In addition, uncontrolled autophagy in the unwounded epidermis leads to the degradation of endo-membranes and the lateral plasma membrane, while apical and basal membranes and epithelial barrier function remain intact. Proper functioning of TORC1 is needed to prevent destruction of the larval epidermis by autophagy, in a process that depends on phagophore initiation and expansion but does not require autophagosomes fusion with lysosomes. Autophagy induction can also affect other sub-cellular membranes, as shown by its suppression of experimentally induced laminopathy-like nuclear defects. Our findings reveal a function for TORC1-mediated regulation of autophagy in maintaining membrane integrity and homeostasis in the epidermis and during wound healing.
    Keywords:  cell junction; gut barrier; myosin; nuclear morphology; wound healing
    DOI:  https://doi.org/10.15252/embj.2021109992
  11. Cell Rep. 2022 Mar 08. pii: S2211-1247(22)00223-6. [Epub ahead of print]38(10): 110490
    On the origin of metastases: Induction of pro-metastatic states after impending cell death via ER stress, reprogramming, and a cytokine storm.
    Arwen Conod, Marianna Silvano, Ariel Ruiz I Altaba.
      How metastatic cells arise is unclear. Here, we search for the induction of recently characterized pro-metastatic states as a surrogate for the origin of metastasis. Since cell-death-inducing therapies can paradoxically promote metastasis, we ask if such treatments induce pro-metastatic states in human colon cancer cells. We find that post-near-death cells acquire pro-metastatic states (PAMEs) and form distant metastases in vivo. These PAME ("let's go" in Greek) cells exhibit a multifactorial cytokine storm as well as signs of enhanced endoplasmic reticulum (ER) stress and nuclear reprogramming, requiring CXCL8, INSL4, IL32, PERK-CHOP, and NANOG. PAMEs induce neighboring tumor cells to become PAME-induced migratory cells (PIMs): highly migratory cells that re-enact the storm and enhance PAME migration. Metastases are thus proposed to originate from the induction of pro-metastatic states through intrinsic and extrinsic cues in a pro-metastatic tumoral ecosystem, driven by an impending cell-death experience involving ER stress modulation, metastatic reprogramming, and paracrine recruitment via a cytokine storm.
    Keywords:  ER stress; PAME; apoptosis; colon cancer; cytokine storm; metastasis; metastasis-initiating cells; metastatic reprogramming; primary heterogeneity; regulated cell death
    DOI:  https://doi.org/10.1016/j.celrep.2022.110490
  12. iScience. 2022 Mar 18. 25(3): 103924
    Cancer progression as a learning process.
    Aseel Shomar, Omri Barak, Naama Brenner.
      Drug resistance and metastasis-the major complications in cancer-both entail adaptation of cancer cells to stress, whether a drug or a lethal new environment. Intriguingly, these adaptive processes share similar features that cannot be explained by a pure Darwinian scheme, including dormancy, increased heterogeneity, and stress-induced plasticity. Here, we propose that learning theory offers a framework to explain these features and may shed light on these two intricate processes. In this framework, learning is performed at the single-cell level, by stress-driven exploratory trial-and-error. Such a process is not contingent on pre-existing pathways but on a random search for a state that diminishes the stress. We review underlying mechanisms that may support this search, and show by using a learning model that such exploratory learning is feasible in a high-dimensional system as the cell. At the population level, we view the tissue as a network of exploring agents that communicate, restraining cancer formation in health. In this view, disease results from the breakdown of homeostasis between cellular exploratory drive and tissue homeostasis.
    Keywords:  Cancer systems biology; Evolutionary theories
    DOI:  https://doi.org/10.1016/j.isci.2022.103924
  13. Nat Commun. 2022 Mar 07. 13(1): 1199
    Co-targeting of BAX and BCL-XL proteins broadly overcomes resistance to apoptosis in cancer.
    Andrea Lopez, Denis E Reyna, Nadege Gitego, Felix Kopp, Hua Zhou, Miguel A Miranda-Roman, Lars Ulrik Nordstrøm, Swathi-Rao Narayanagari, Ping Chi, Eduardo Vilar, Aristotelis Tsirigos, Evripidis Gavathiotis.
      Deregulation of the BCL-2 family interaction network ensures cancer resistance to apoptosis and is a major challenge to current treatments. Cancer cells commonly evade apoptosis through upregulation of the BCL-2 anti-apoptotic proteins; however, more resistant cancers also downregulate or inactivate pro-apoptotic proteins to suppress apoptosis. Here, we find that apoptosis resistance in a diverse panel of solid and hematological malignancies is mediated by both overexpression of BCL-XL and an unprimed apoptotic state, limiting direct and indirect activation mechanisms of pro-apoptotic BAX. Both survival mechanisms can be overcome by the combination of an orally bioavailable BAX activator, BTSA1.2 with Navitoclax. The combination demonstrates synergistic efficacy in apoptosis-resistant cancer cells, xenografts, and patient-derived tumors while sparing healthy tissues. Additionally, functional assays and genomic markers are identified to predict sensitive tumors to the combination treatment. These findings advance the understanding of apoptosis resistance mechanisms and demonstrate a novel therapeutic strategy for cancer treatment.
    DOI:  https://doi.org/10.1038/s41467-022-28741-7
  14. J Biol Chem. 2022 Mar 02. pii: S0021-9258(22)00231-9. [Epub ahead of print] 101791
    Protein methylation in mitochondria.
    Jędrzej M Małecki, Erna Davydova, Pål Ø Falnes.
      Many proteins are modified by post-translational methylation, introduced by a number of methyltransferases (MTases). Protein methylation plays important roles in modulating protein function, and thus in optimizing and regulating cellular and physiological processes. Research has mainly focused on nuclear and cytosolic protein methylation, but it has been known for many years that also mitochondrial proteins are methylated. During the last decade, significant progress has been made on identifying the MTases responsible for mitochondrial protein methylation and addressing its functional significance. In particular, several novel human MTases have been uncovered that methylate lysine, arginine, histidine, and glutamine residues in various mitochondrial substrates. Several of these substrates are key components of the bioenergetics machinery, e.g. respiratory Complex I, citrate synthase and the ATP synthase. In the present review we report the status of the field of mitochondrial protein methylation, with a particular emphasis on recently discovered human MTases. We also discuss evolutionary aspects and functional significance of mitochondrial protein methylation, and present an outlook for this emergent research field.
    Keywords:  ATP synthase; bioenergetics; electron transport chain; methyltransferase; mitochondria; oxidative phosphorylation; protein methylation
    DOI:  https://doi.org/10.1016/j.jbc.2022.101791
  15. Biochim Biophys Acta Rev Cancer. 2022 Mar 08. pii: S0304-419X(22)00030-0. [Epub ahead of print] 188705
    Metabolic tricks of cancer cells.
    Katerina Hönigova, Jiri Navratil, Barbora Peltanova, Hana Holcova Polanska, Martina Raudenska, Michal Masarik.
      One of the characteristics of cancer cells important for tumorigenesis is their metabolic plasticity. Indeed, in various stress conditions, cancer cells can reshape their metabolic pathways to support the increased energy request due to continuous growth and rapid proliferation. Moreover, selective pressures in the tumor microenvironment, such as hypoxia, acidosis, and competition for resources, force cancer cells to adapt by complete reorganization of their metabolism. In this review, we highlight the characteristics of cancer metabolism and discuss its clinical significance, since overcoming metabolic plasticity of cancer cells is a key objective of modern cancer therapeutics and a better understanding of metabolic reprogramming may lead to the identification of possible targets for cancer therapy.
    Keywords:  Cancer metabolism; Cell death; Glutaminolysis; Metabolic symbiosis; Mitochondrial bioenergetics; Warburg effect
    DOI:  https://doi.org/10.1016/j.bbcan.2022.188705
  16. Cells. 2022 Mar 02. pii: 862. [Epub ahead of print]11(5):
    Iron Supplementation Delays Aging and Extends Cellular Lifespan through Potentiation of Mitochondrial Function.
    Jovian Lin Jing, Trishia Cheng Yi Ning, Federica Natali, Frank Eisenhaber, Mohammad Alfatah.
      Aging is the greatest challenge to humankind worldwide. Aging is associated with a progressive loss of physiological integrity due to a decline in cellular metabolism and functions. Such metabolic changes lead to age-related diseases, thereby compromising human health for the remaining life. Thus, there is an urgent need to identify geroprotectors that regulate metabolic functions to target the aging biological processes. Nutrients are the major regulator of metabolic activities to coordinate cell growth and development. Iron is an important nutrient involved in several biological functions, including metabolism. In this study using yeast as an aging model organism, we show that iron supplementation delays aging and increases the cellular lifespan. To determine how iron supplementation increases lifespan, we performed a gene expression analysis of mitochondria, the main cellular hub of iron utilization. Quantitative analysis of gene expression data reveals that iron supplementation upregulates the expression of the mitochondrial tricarboxylic acid (TCA) cycle and electron transport chain (ETC) genes. Furthermore, in agreement with the expression profiles of mitochondrial genes, ATP level is elevated by iron supplementation, which is required for increasing the cellular lifespan. To confirm, we tested the role of iron supplementation in the AMPK knockout mutant. AMPK is a highly conserved controller of mitochondrial metabolism and energy homeostasis. Remarkably, iron supplementation rescued the short lifespan of the AMPK knockout mutant and confirmed its anti-aging role through the enhancement of mitochondrial functions. Thus, our results suggest a potential therapeutic use of iron supplementation to delay aging and prolong healthspan.
    Keywords:  AMPK; Saccharomyces cerevisiae; cellular lifespan extension; chronological aging; iron; mitochondria
    DOI:  https://doi.org/10.3390/cells11050862
  17. Anal Biochem. 2022 Mar 05. pii: S0003-2697(22)00102-6. [Epub ahead of print] 114646
    How many molecules of mitochondrial complex I are in a cell?
    Fariha Ansari, Belem Yoval, Zoya Niatsetskaya, Vadim Ten, Ilka Wittig, Alexander Galkin.
      Mitochondrial complex I is the only enzyme responsible for oxidation of matrix NADH and regeneration of NAD+ for catabolism. Nuclear and mtDNA mutations, assembly impairments, and enzyme damage are implicated in inherited diseases, ischemia-reperfusion injury, neurodegeneration, and tumorogenesis. Here we introduce a novel method to measure the absolute content of complex I. The method is based on flavin fluorescence scanning of a polyacrylamide gel after separation of complexes by Clear Native electrophoresis. Using mouse primary astrocytes as an example, we calculated an average value of 2.2 × 105 complex I molecules/cell. Our method can be used for accurate quantification of complex I content.
    Keywords:  Astrocytes; Flavin mononucleotide; Fluorescence; Mitochondrial complex I; Respiratory chain
    DOI:  https://doi.org/10.1016/j.ab.2022.114646
  18. Cell Rep. 2022 Mar 08. pii: S2211-1247(22)00226-1. [Epub ahead of print]38(10): 110493
    CRISPR-Cas9 screen identifies oxidative phosphorylation as essential for cancer cell survival at low extracellular pH.
    Johanna Michl, Yunyi Wang, Stefania Monterisi, Wiktoria Blaszczak, Ryan Beveridge, Esther M Bridges, Jana Koth, Walter F Bodmer, Pawel Swietach.
      Unlike most cell types, many cancer cells survive at low extracellular pH (pHe), a chemical signature of tumors. Genes that facilitate survival under acid stress are therefore potential targets for cancer therapies. We performed a genome-wide CRISPR-Cas9 cell viability screen at physiological and acidic conditions to systematically identify gene knockouts associated with pH-related fitness defects in colorectal cancer cells. Knockouts of genes involved in oxidative phosphorylation (NDUFS1) and iron-sulfur cluster biogenesis (IBA57, NFU1) grew well at physiological pHe, but underwent profound cell death under acidic conditions. We identified several small-molecule inhibitors of mitochondrial metabolism that can kill cancer cells at low pHe only. Xenografts established from NDUFS1-/- cells grew considerably slower than their wild-type controls, but growth could be stimulated with systemic bicarbonate therapy that lessens the tumoral acid stress. These findings raise the possibility of therapeutically targeting mitochondrial metabolism in combination with acid stress as a cancer treatment option.
    Keywords:  CRISPR-Cas9 screen; acidosis; oxidative phosphorylation; tumor acidity
    DOI:  https://doi.org/10.1016/j.celrep.2022.110493
  19. Nat Commun. 2022 Mar 09. 13(1): 1224
    Co-translational assembly orchestrates competing biogenesis pathways.
    Maximilian Seidel, Anja Becker, Filipa Pereira, Jonathan J M Landry, Nayara Trevisan Doimo de Azevedo, Claudia M Fusco, Eva Kaindl, Natalie Romanov, Janina Baumbach, Julian D Langer, Erin M Schuman, Kiran Raosaheb Patil, Gerhard Hummer, Vladimir Benes, Martin Beck.
      During the co-translational assembly of protein complexes, a fully synthesized subunit engages with the nascent chain of a newly synthesized interaction partner. Such events are thought to contribute to productive assembly, but their exact physiological relevance remains underexplored. Here, we examine structural motifs contained in nucleoporins for their potential to facilitate co-translational assembly. We experimentally test candidate structural motifs and identify several previously unknown co-translational interactions. We demonstrate by selective ribosome profiling that domain invasion motifs of beta-propellers, coiled-coils, and short linear motifs may act as co-translational assembly domains. Such motifs are often contained in proteins that are members of multiple complexes (moonlighters) and engage with closely related paralogs. Surprisingly, moonlighters and paralogs assemble co-translationally in only some but not all of the relevant biogenesis pathways. Our results highlight the regulatory complexity of assembly pathways.
    DOI:  https://doi.org/10.1038/s41467-022-28878-5
  20. Mol Cancer Res. 2022 Feb 23. pii: molcanres.MCR-21-0781-A.2021. [Epub ahead of print]
    Targeting metabolic adaptations in the breast cancer-liver metastatic niche using dietary approaches to improve endocrine therapy efficacy.
    Qianying Zuo, Ayca Nazli Mogol, Yu-Jeh Liu, Ashlie Santaliz Casiano, Christine Chien, Jenny Drnevich, Ozan Berk Imir, Eylem Kulkoyluoglu-Cotul, Nicole Hwajin Park, David J Shapiro, Ben Ho Park, Yvonne Ziegler, Benita S Katzenellenbogen, Evelyn Aranda, John D O'Neill, Akshara Singareeka Raghavendra, Debu Tripathy, Zeynep Madak Erdogan.
      Estrogen receptor-positive (ER+) metastatic tumors contribute to nearly 70% of breast cancer-related deaths. Most patients with ER+ metastatic breast cancer (MBC) undergo treatment with the estrogen receptor antagonist fulvestrant (Fulv) as standard-of-care. Yet, among such patients, metastasis in the liver is associated with reduced overall survival compared to other metastasis sites. The factors underlying the reduced responsiveness of liver metastases to ER-targeting agents remain unknown, impeding the development of more effective treatment approaches to improve outcomes for patients with ER+ liver metastases. We therefore evaluated site-specific changes in MBC cells and determined the mechanisms through which the liver metastatic niche specifically influences ER+ tumor metabolism and drug resistance. We characterized ER activity of MBC cells both in vitro, using a novel system of tissue-specific extracellular matrix hydrogels representing the stroma of ER+ tumor metastatic sites (liver, lung and bone), and in vivo, in liver and lung metastasis mouse models. ER+ metastatic liver tumors and MBC cells grown in liver hydrogels displayed upregulated expression of glucose metabolism enzymes in response to Fulv. Furthermore, differential ERα activity, but not expression, was detected in liver hydrogels. In vivo, increased glucose metabolism led to increased glycogen deposition in liver metastatic tumors, while a fasting-mimicking diet increased efficacy of Fulv treatment to reduce the metastatic burden. Our findings identify a novel mechanism of endocrine resistance driven by the liver tumor microenvironment. Implications: These results may guide the development of dietary strategies to circumvent drug resistance in liver metastasis, with potential applicability in other metastatic diseases.
    DOI:  https://doi.org/10.1158/1541-7786.MCR-21-0781
  21. Nature. 2022 Mar 09.
    Regulation of liver subcellular architecture controls metabolic homeostasis.
    Güneş Parlakgül, Ana Paula Arruda, Song Pang, Erika Cagampan, Nina Min, Ekin Güney, Grace Yankun Lee, Karen Inouye, Harald F Hess, C Shan Xu, Gökhan S Hotamışlıgil.
      Cells display complex intracellular organization by compartmentalization of metabolic processes into organelles, yet the resolution of these structures in the native tissue context and their functional consequences are not well understood. Here we resolved the three-dimensional structural organization of organelles in large (more than 2.8 × 105 µm3) volumes of intact liver tissue (15 partial or full hepatocytes per condition) at high resolution (8 nm isotropic pixel size) using enhanced focused ion beam scanning electron microscopy1,2 imaging followed by deep-learning-based automated image segmentation and 3D reconstruction. We also performed a comparative analysis of subcellular structures in liver tissue of lean and obese mice and found substantial alterations, particularly in hepatic endoplasmic reticulum (ER), which undergoes massive structural reorganization characterized by marked disorganization of stacks of ER sheets3 and predominance of ER tubules. Finally, we demonstrated the functional importance of these structural changes by monitoring the effects of experimental recovery of the subcellular organization on cellular and systemic metabolism. We conclude that the hepatic subcellular organization of the ER architecture are highly dynamic, integrated with the metabolic state and critical for adaptive homeostasis and tissue health.
    DOI:  https://doi.org/10.1038/s41586-022-04488-5
  22. Ann Surg. 2022 Mar 03.
    Results of a Phase II Study on the use of Neoadjuvant Chemotherapy (FOLFIRINOX or Gemcitabine with nab-paclitaxel) for Borderline-Resectable Pancreatic Cancer (NUPAT-01).
    Junpei Yamaguchi, Yukihiro Yokoyama, Tsutomu Fujii, Suguru Yamada, Hideki Takami, Hiroki Kawashima, Eizaburo Ohno, Takuya Ishikawa, Osamu Maeda, Hiroshi Ogawa, Yasuhiro Kodera, Masato Nagino, Tomoki Ebata.
       OBJECTIVE: Given the frequent adverse events with multidrug chemotherapy, not only the survival benefit but also the feasibility of using neoadjuvant chemotherapy to treat pancreatic cancer need to be clarified.
    SUMMARY BACKGROUND DATA: Although the development of multidrug chemotherapy regimens has improved the survival outcomes of patients with unresectable pancreatic cancer, the benefits of these treatments in the neoadjuvant setting remain controversial.
    METHODS: Patients with borderline-resectable pancreatic cancer were enrolled and randomly assigned to receive neoadjuvant chemotherapy with either FOLFIRINOX or gemcitabine with nab-paclitaxel (GEM/nab-PTX). After the completion of chemotherapy, patients underwent surgical resection when feasible. This study (NUPAT-01) was a randomized phase II trial, and the primary endpoint was the R0 resection rate.
    RESULTS: Fifty-one patients were enrolled in this study (FOLFIRINOX (n = 26) and GEM/nab-PTX (n=25)). A total of 84.3% (n=43/51) of the patients eventually underwent surgery, and R0 resection was achieved in 67.4% (n=33/51) of the patients. Adverse events (grade >3) due to neoadjuvant treatment were observed in 45.1% of the patients (n=23/51), and major surgical complications occurred in 30.0% (n=13/43), with no mortality noted. The intention-to-treat analysis showed that the 3-year overall survival rate was 54.7%, with a median survival time of 39.4 months, and a significant difference in overall survival was not observed between the FOLFIRINOX and GEM/nab-PTX groups.
    CONCLUSIONS: These results indicate that neoadjuvant chemotherapy with FOLFIRINOX or GEM/nab-PTX is feasible and well tolerated, achieving an R0 resection rate of 67.4%. The survival of patients was even found to be favorable in the intention-to-treat analysis.
    DOI:  https://doi.org/10.1097/SLA.0000000000005430
  23. Br J Cancer. 2022 Mar 09.
    Liquid biopsies to monitor and direct cancer treatment in colorectal cancer.
    Gianluca Mauri, Pietro Paolo Vitiello, Alberto Sogari, Giovanni Crisafulli, Andrea Sartore-Bianchi, Silvia Marsoni, Salvatore Siena, Alberto Bardelli.
      Colorectal cancer (CRC) is one of the most prevalent and deadly cancers worldwide. Despite recent improvements in treatment and prevention, most of the current therapeutic options are weighted by side effects impacting patients' quality of life. Better patient selection towards systemic treatments represents an unmet clinical need. The recent multidisciplinary and molecular advancements in the treatment of CRC patients demand the identification of efficient biomarkers allowing to personalise patient care. Currently, core tumour biopsy specimens represent the gold-standard biological tissue to identify such biomarkers. However, technical feasibility, tumour heterogeneity and cancer evolution are major limitations of this single-snapshot approach. Genotyping circulating tumour DNA (ctDNA) has been addressed as potentially overcoming such limitations. Indeed, ctDNA has been retrospectively demonstrated capable of identifying minimal residual disease post-surgery and post-adjuvant treatment, as well as spotting druggable molecular alterations for tailoring treatments in metastatic disease. In this review, we summarise the available evidence on ctDNA applicability in CRC. Then, we review ongoing clinical trials assessing how liquid biopsy can be used interventionally to guide therapeutic choice in localised, locally advanced and metastatic CRC. Finally, we discuss how its widespread could transform CRC patients' management, dissecting its limitations while suggesting improvement strategies.
    DOI:  https://doi.org/10.1038/s41416-022-01769-8
  24. Elife. 2022 Mar 11. pii: e76595. [Epub ahead of print]11
    A saturation-mutagenesis analysis of the interplay between stability and activation in Ras.
    Frank Hidalgo, Laura M Nocka, Neel H Shah, Kent Gorday, Naomi R Latorraca, Pradeep Bandaru, Sage Templeton, David Lee, Deepti Karandur, Jeffrey G Pelton, Susan Marqusee, David Wemmer, John Kuriyan.
      Cancer mutations in Ras occur predominantly at three hotspots: Gly 12, Gly 13, and Gln 61. Previously, we reported that deep mutagenesis of H-Ras using a bacterial assay identified many other activating mutations (Bandaru et al., 2017). We now show that the results of saturation mutagenesis of H-Ras in mammalian Ba/F3 cells correlate well with the results of bacterial experiments in which H-Ras or K-Ras are co-expressed with a GTPase-activating protein (GAP). The prominent cancer hotspots are not dominant in the Ba/F3 data. We used the bacterial system to mutagenize Ras constructs of different stabilities and discovered a feature that distinguishes the cancer hotspots. While mutations at the cancer hotspots activate Ras regardless of construct stability, mutations at lower-frequency sites (e.g. at Val 14 or Asp 119) can be activating or deleterious, depending on the stability of the Ras construct. We characterized the dynamics of three non-hotspot activating Ras mutants by using NMR to monitor hydrogen-deuterium exchange (HDX). These mutations result in global increases in HDX rates, consistent with destabilization of Ras. An explanation for these observations is that mutations that destabilize Ras increase nucleotide dissociation rates, enabling activation by spontaneous nucleotide exchange. A further stability decrease can lead to insufficient levels of folded Ras - and subsequent loss of function. In contrast, the cancer hotspot mutations are mechanism-based activators of Ras that interfere directly with the action of GAPs. Our results demonstrate the importance of GAP surveillance and protein stability in determining the sensitivity of Ras to mutational activation.
    Keywords:  E. coli; ba/f3; cancer; cancer mutants; h-ras; high throughput screening; k-ras; molecular biophysics; ras; saturation-mutagenesis; signaling activation; structural biology
    DOI:  https://doi.org/10.7554/eLife.76595
  25. Biomark Res. 2022 Mar 10. 10(1): 10
    Clinical translation of patient-derived tumour organoids- bottlenecks and strategies.
    Malia Alexandra Foo, Mingliang You, Shing Leng Chan, Gautam Sethi, Glenn K Bonney, Wei-Peng Yong, Edward Kai-Hua Chow, Eliza Li Shan Fong, Lingzhi Wang, Boon-Cher Goh.
      Multiple three-dimensional (3D) tumour organoid models assisted by multi-omics and Artificial Intelligence (AI) have contributed greatly to preclinical drug development and precision medicine. The intrinsic ability to maintain genetic and phenotypic heterogeneity of tumours allows for the reconciliation of shortcomings in traditional cancer models. While their utility in preclinical studies have been well established, little progress has been made in translational research and clinical trials. In this review, we identify the major bottlenecks preventing patient-derived tumour organoids (PDTOs) from being used in clinical setting. Unsuitable methods of tissue acquisition, disparities in establishment rates and a lengthy timeline are the limiting factors for use of PDTOs in clinical application. Potential strategies to overcome this include liquid biopsies via circulating tumour cells (CTCs), an automated organoid platform and optical metabolic imaging (OMI). These proposed solutions accelerate and optimize the workflow of a clinical organoid drug screening. As such, PDTOs have the potential for potential applications in clinical oncology to improve patient outcomes. If remarkable progress is made, cancer patients can finally benefit from this revolutionary technology.
    Keywords:  Medicine; Organoid; Precision; Three-Dimensional (3D); Tumour
    DOI:  https://doi.org/10.1186/s40364-022-00356-6
  26. Elife. 2022 Mar 07. pii: e70386. [Epub ahead of print]11
    Mendelian randomization suggests a bidirectional, causal relationship between physical inactivity and adiposity.
    Germán Darío Carrasquilla, Mario García-Ureña, Tove Fall, Thorkild I A Sørensen, Tuomas Kilpeläinen.
      Physical inactivity and increased sedentary time are associated with excess weight gain in observational studies. However, some longitudinal studies indicate reverse causality where weight gain leads to physical inactivity and increased sedentary time. As observational studies suffer from reverse causality, it is challenging to assess the true causal directions. Here, we assess the bidirectional causality between physical inactivity, sedentary time and adiposity by bidirectional Mendelian randomization analysis. We assessed genetic liability using results from genome-wide association studies for accelerometer-based physical activity and sedentary time in 91,105 individuals and for body mass index (BMI) in 806,834 individuals. We implemented Mendelian randomization using CAUSE method that accounts for pleiotropy and sample overlap using full genome-wide data. We also applied inverse variance-weighted, MR-Egger, weighted median, and weighted mode methods using genome-wide significant variants only. We found evidence of bidirectional causality between sedentary time and BMI: longer sedentary time was causal for higher BMI [beta (95%CI) from CAUSE method: 0.11 (0.02, 0.2), P=0.02], and higher BMI was causal for longer sedentary time (0.13 (0.08, 0.17), P=6.3.x10-4). Our analyses suggest that higher moderate and vigorous physical activity are causal for lower BMI (moderate: -0.18 (-0.3,-0.05), P=0.006; vigorous: -0.16 (-0.24,-0.08), P=3.8x10-4), but indicate that the association between higher BMI and lower levels of physical activity is due to horizontal pleiotropy. The bidirectional, causal relationship between sedentary time and BMI suggests that decreasing sedentary time is beneficial for weight management, but also that targeting adiposity may lead to additional health benefits by reducing sedentary time.
    Keywords:  epidemiology; genetics; genomics; global health; none
    DOI:  https://doi.org/10.7554/eLife.70386
  27. Aging Cell. 2022 Mar 08. e13524
    Biological mechanisms of aging predict age-related disease co-occurrence in patients.
    Helen C Fraser, Valerie Kuan, Ronja Johnen, Magdalena Zwierzyna, Aroon D Hingorani, Andreas Beyer, Linda Partridge.
      Genetic, environmental, and pharmacological interventions into the aging process can confer resistance to multiple age-related diseases in laboratory animals, including rhesus monkeys. These findings imply that individual mechanisms of aging might contribute to the co-occurrence of age-related diseases in humans and could be targeted to prevent these conditions simultaneously. To address this question, we text mined 917,645 literature abstracts followed by manual curation and found strong, non-random associations between age-related diseases and aging mechanisms in humans, confirmed by gene set enrichment analysis of GWAS data. Integration of these associations with clinical data from 3.01 million patients showed that age-related diseases associated with each of five aging mechanisms were more likely than chance to be present together in patients. Genetic evidence revealed that innate and adaptive immunity, the intrinsic apoptotic signaling pathway and activity of the ERK1/2 pathway were associated with multiple aging mechanisms and diverse age-related diseases. Mechanisms of aging hence contribute both together and individually to age-related disease co-occurrence in humans and could potentially be targeted accordingly to prevent multimorbidity.
    Keywords:  age-related disease; aging; aging hallmarks; genetics; multimorbidity
    DOI:  https://doi.org/10.1111/acel.13524
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