bims-mibica 2021-05-23 papers

bims-mibica

Biomed News

on Mitochondrial bioenergetics in cancer

Issue of 2021–05–23
forty-two papers selected by
Kelsey Fisher-Wellman, East Carolina University

Early-life mitochondrial DNA damage results in lifelong deficits in energy production mediated by redox signaling in Caenorhabditis elegans.
Inhibition of glycolysis and mitochondrial respiration promotes radiosensitisation of neuroblastoma and glioma cells.
Hyperpolarized mitochondria accumulate in Drosophila Hipk-overexpressing cells to drive tumor-like growth.
Mitochondrial survivin reduces oxidative phosphorylation in cancer cells by inhibiting mitophagy.
Metabolic Response to the Mitochondrial Toxin 1-Methyl-4-phenylpyridinium (MPP+) in LDH-A/B Double-knockout LS174T Colon Cancer Cells.
SMYD2 suppresses p53 activity to promote glucose metabolism in cervical cancer.
SUCLA2-coupled regulation of GLS succinylation and activity counteracts oxidative stress in tumor cells.
BCAT1 affects mitochondrial metabolism independently of leucine transamination in activated human macrophages.
Drosophila MICOS knockdown impairs mitochondrial structure and function and promotes mitophagy in muscle tissue.
ING2 tumor suppressive protein translocates into mitochondria and is involved in cellular metabolism homeostasis.
Increased supra-organization is a dynamic multistep remodelling of respiratory complexes against proteostasis stress.
A new brain mitochondrial sodium-sensitive potassium channel: effect of sodium ions on respiratory chain activity.
Skeletal muscle metabolism in sea-acclimatized king penguins: II. Improved efficiency of mitochondrial bioenergetics.
Metformin treatment response is dependent on glucose growth conditions and metabolic phenotype in colorectal cancer cells.
High-throughput screening identifies suppressors of mitochondrial fragmentation in OPA1 fibroblasts.
Adhesion-mediated mechanosignaling forces mitohormesis.
SIRT3 overexpression and epigenetic silencing of catalase regulate ROS accumulation in CLL cells activating AXL signaling axis.
Improved mitochondrial coupling as a response to high mass-specific metabolic rate in extremely small mammals.
Media composition and O2 levels determine effects of 17β-Estradiol on mitochondrial bioenergetics and cellular reactive oxygen species.
Yap regulates skeletal muscle fatty acid oxidation and adiposity in metabolic disease.
Sexual dimorphism in adipose tissue mitochondrial function and metabolic flexibility in obesity.
A flow-cytometry-based protocol for detection of mitochondrial ROS production under hypoxia.
The Use of the Patch-Clamp Technique to Study the Thermogenic Capacity of Mitochondria.
Vmp1, Vps13D, and Marf/Mfn2 function in a conserved pathway to regulate mitochondria and ER contact in development and disease.
Targeting the mitochondrial chaperone TRAP1: strategies and therapeutic perspectives.
Mesenchymal stromal cell mitochondrial transfer to human induced T-regulatory cells mediates FOXP3 stability.
A PKD-MFF signaling axis couples mitochondrial fission to mitotic progression.
Rapamycin facilitates differentiation of regulatory T cells via enhancement of oxidative phosphorylation.
Oncogenic KRAS mutations enhance amino acid uptake by colorectal cancer cells via the hippo signaling effector YAP1.
Longitudinal single-cell profiling reveals molecular heterogeneity and tumor-immune evolution in refractory mantle cell lymphoma.
Muscle mitochondrial capacity in high- and low-fitness females using near-infrared spectroscopy.
Mitochondrial Control of Stem Cell State and Fate: Lessons From Drosophila.
SLC45A4 Promotes Glycolysis and Prevents AMPK/ULK1-induced Autophagy in TP53 Mutant Pancreatic Ductal Adenocarcinoma.
UBQLN1 mediates sorafenib resistance through regulating mitochondrial biogenesis and ROS homeostasis by targeting PGC1β in hepatocellular carcinoma.
Cell of Origin Influences Pancreatic Cancer Subtype.
Organ-specific cholesterol metabolic aberration fuels liver metastasis of colorectal cancer.
TSP50 promotes the Warburg effect and hepatocyte proliferation via regulating PKM2 acetylation.
Curcumin reverses doxorubicin resistance in colon cancer cells at the metabolic level.
An atlas of mitochondrial DNA genotype-phenotype associations in the UK Biobank.
A novel selective mitochondrial-targeted curcumin analog with remarkable cytotoxicity in glioma cells.
A method for benchmarking genetic screens reveals a predominant mitochondrial bias.
Different Tumor Microenvironments Lead to Different Metabolic Phenotypes.

Redox Biol. 2021 May 05. pii: S2213-2317(21)00158-0. [Epub ahead of print]43 102000

Early-life mitochondrial DNA damage results in lifelong deficits in energy production mediated by redox signaling in Caenorhabditis elegans.

Kathleen A Hershberger, John P Rooney, Elena A Turner, Lauren J Donoghue, Rakesh Bodhicharla, Laura L Maurer, Ian T Ryde, Jina J Kim, Rashmi Joglekar, Jonathan D Hibshman, Latasha L Smith, Dhaval P Bhatt, Olga R Ilkayeva, Matthew D Hirschey, Joel N Meyer.

  The consequences of damage to the mitochondrial genome (mtDNA) are poorly understood, although mtDNA is more susceptible to damage resulting from some genotoxicants than nuclear DNA (nucDNA), and many environmental toxicants target the mitochondria. Reports from the toxicological literature suggest that exposure to early-life mitochondrial damage could lead to deleterious consequences later in life (the "Developmental Origins of Health and Disease" paradigm), but reports from other fields often report beneficial ("mitohormetic") responses to such damage. Here, we tested the effects of low (causing no change in lifespan) levels of ultraviolet C (UVC)-induced, irreparable mtDNA damage during early development in Caenorhabditis elegans. This exposure led to life-long reductions in mtDNA copy number and steady-state ATP levels, accompanied by increased oxygen consumption and altered metabolite profiles, suggesting inefficient mitochondrial function. Exposed nematodes were also developmentally delayed, reached smaller adult size, and were rendered more susceptible to subsequent exposure to chemical mitotoxicants. Metabolomic and genetic analysis of key signaling and metabolic pathways supported redox and mitochondrial stress-response signaling during early development as a mechanism for establishing these persistent alterations. Our results highlight the importance of early-life exposures to environmental pollutants, especially in the context of exposure to chemicals that target mitochondria.

Keywords:  Bioenergetics; Developmental exposures; Environmental toxicants; Mitochondrial DNA damage; Mitochondrial function; Redox signaling

DOI:  https://doi.org/10.1016/j.redox.2021.102000
Cancer Metab. 2021 May 19. 9(1): 24

Inhibition of glycolysis and mitochondrial respiration promotes radiosensitisation of neuroblastoma and glioma cells.

Donna L Nile, Colin Rae, David J Walker, Joe Canning Waddington, Isabel Vincent, Karl Burgess, Mark N Gaze, Robert J Mairs, Anthony J Chalmers.

   BACKGROUND: Neuroblastoma accounts for 7% of paediatric malignancies but is responsible for 15% of all childhood cancer deaths. Despite rigorous treatment involving chemotherapy, surgery, radiotherapy and immunotherapy, the 5-year overall survival rate of high-risk disease remains < 40%, highlighting the need for improved therapy. Since neuroblastoma cells exhibit aberrant metabolism, we determined whether their sensitivity to radiotherapy could be enhanced by drugs affecting cancer cell metabolism.
METHODS: Using a panel of neuroblastoma and glioma cells, we determined the radiosensitising effects of inhibitors of glycolysis (2-DG) and mitochondrial function (metformin). Mechanisms underlying radiosensitisation were determined by metabolomic and bioenergetic profiling, flow cytometry and live cell imaging and by evaluating different treatment schedules.
RESULTS: The radiosensitising effects of 2-DG were greatly enhanced by combination with the antidiabetic biguanide, metformin. Metabolomic analysis and cellular bioenergetic profiling revealed this combination to elicit severe disruption of key glycolytic and mitochondrial metabolites, causing significant reductions in ATP generation and enhancing radiosensitivity. Combination treatment induced G2/M arrest that persisted for at least 24 h post-irradiation, promoting apoptotic cell death in a large proportion of cells.
CONCLUSION: Our findings demonstrate that the radiosensitising effect of 2-DG was significantly enhanced by its combination with metformin. This clearly demonstrates that dual metabolic targeting has potential to improve clinical outcomes in children with high-risk neuroblastoma by overcoming radioresistance.

Keywords:  131I-MIBG; 2-DG; Metabolism; Metformin; Neuroblastoma; Radiation

DOI:  https://doi.org/10.1186/s40170-021-00258-5
J Cell Sci. 2020 Jan 01. pii: jcs.250944. [Epub ahead of print]

Hyperpolarized mitochondria accumulate in Drosophila Hipk-overexpressing cells to drive tumor-like growth.

Kenneth Kin Lam Wong, Jenny Zhe Liao, Claire R Y Shih, Nicholas Harden, Esther M Verheyen.

  Both functional and dysfunctional mitochondria are known to underlie tumor progression. Here, we establish use of the proto-oncogene Drosophila Homeodomain-interacting protein kinase (Hipk) as a new tool to address this paradox. We find that, in Hipk-overexpressing tumor-like cells, mitochondria accumulate and switch from fragmented to highly fused interconnected morphologies. Moreover, elevated Hipk promotes mitochondrial membrane hyperpolarization. These mitochondrial changes are at least in part driven by the upregulation of Myc. Furthermore, we show that the altered mitochondrial energetics, but not morphology, is required for Hipk tumor-like growth as knockdown of pdsw (NDUFB10 in mammals; a Complex I subunit) abrogates the growth. Knockdown of ATPsynβ (a Complex V subunit), which produces higher levels of reactive oxygen species (ROS) than pdsw knockdown, instead synergizes with Hipk to potentiate JNK activation and the downstream induction of Matrix metalloproteinases. Accordingly, ATPsynβ knockdown suppresses Hipk tumor-like growth only when ROS scavengers are co-expressed. Altogether, our work presents an in vivo tumor model featuring the accumulation of hyperfused and hyperpolarized mitochondria, and reveals respiratory Complex subunit-dependent, opposing effects on tumorigenic outcomes.

Keywords:  Drosophila; Energetics; Hipk; Mitochondria; Myc; ROS

DOI:  https://doi.org/10.1242/jcs.250944
J Cell Sci. 2020 Jan 01. pii: jcs.247379. [Epub ahead of print]

Mitochondrial survivin reduces oxidative phosphorylation in cancer cells by inhibiting mitophagy.

Amelia R Townley, Sally P Wheatley.

  Survivin is a cancer-associated protein that is pivotal for cellular life and death: it is an essential mitotic protein and an inhibitor of apoptosis. In cancer cells, a small pool of survivin localises to the mitochondria, the function of which remains to be elucidated. Here, we report that mitochondrial survivin inhibits the selective form of autophagy, called "mitophagy", causing an accumulation of respiratory defective mitochondria. Mechanistically the data reveal that survivin prevents recruitment of the E3-ubiquitin ligase Parkin to mitochondria and their subsequent recognition by the autophagosome. The data also demonstrate that cells in which mitophagy has been blocked by survivin expression have an increased dependency on glycolysis. As these effects were found exclusively in cancer cells they suggest that the primary act of mitochondrial survivin is to steer cells towards the implementation of the Warburg transition by inhibiting mitochondrial turnover, which enables them to adapt and survive.

Keywords:  Cancer; Mitochondria; Mitophagy; Respiration; Survivin

DOI:  https://doi.org/10.1242/jcs.247379
Cancer Genomics Proteomics. 2021 May-Jun;18(3 Suppl):18(3 Suppl): 385-405

Metabolic Response to the Mitochondrial Toxin 1-Methyl-4-phenylpyridinium (MPP+) in LDH-A/B Double-knockout LS174T Colon Cancer Cells.

Nzinga Mack, Elizabeth Mazzio, Ramesh Badisa, Karam F A Soliman.

   BACKGROUND/AIM: Rapid glycolytic substrate-level phosphorylation (SLP) and accumulation of lactic acid are characteristics of diverse cancers. Recent advances in drug discovery have included the use of glycolytic inhibitors with mitochondrial targeting drugs to attempt to invoke an energy crisis in aggressive metabolically active chemo-resistant cancers. In this work, we examine the consequences of inhibiting mitochondrial oxidative phosphorylation (OXPHOS) with 1-methyl-4-phenylpyridinium (MPP+) in LS14T colon cancer cells containing a genetic double knock out (DKO) of lactic acid dehydrogenase (LDHA and LDHB).
MATERIALS AND METHODS: Several metabolic parameters were evaluated concomitant to whole transcriptomic (WT) mRNA, microRNA, and long intergenic non-coding RNAs using Affymetrix 2.1 human ST arrays.
RESULTS: MPP+ effectively blocked OXPHOS where a compensatory shift toward anaerobic SLP was only observed in the control vector (CV), and not observed in the LDH-A/B DKOs (lacking the ability to produce lactic acid). Despite this, there was an unexpected resilience to MPP+ in the latter in terms of energy, which displayed significantly higher resting baseline respiratory OXPHOS capacity relative to controls. At the transcriptome level, MPP+ invoked 1738 differential expressed genes (DEGs) out of 48,226; LDH-A/B DKO resulted in 855 DEGs while 349 DEGs were found to be overlapping in both groups versus respective controls, including loss of mitochondrial complex I (subunits 3 and 6), cell cycle transcripts and fluctuations in epigenetic chromatin remodeling systems. In terms of energy, the effects of MPP+ in the CV transcripts reflect the funneling of carbon intermediates toward glycolysis. The LDH-A/B DKO transcripts reflect a flow of carbons away from glycolysis toward the production of acetyl-CoA.
CONCLUSION: The findings from this study suggest a metabolic resilience to MPP+ in cancer cells devoid of LDH-A/B, explainable in-part by higher baseline OXPHOS respiratory ATP production, necessitating more toxin to suppress the electron transport chain.

Keywords:  LDH; cancer cells; glycolysis; mitochondria

DOI:  https://doi.org/10.21873/cgp.20267
Exp Cell Res. 2021 May 17. pii: S0014-4827(21)00181-6. [Epub ahead of print] 112649

SMYD2 suppresses p53 activity to promote glucose metabolism in cervical cancer.

Ying Wang, Ge Jin, Yunfeng Guo, Yuan Cao, Shuhuai Niu, Xiaomei Fan, Jun Zhang.

  Reprogrammed energy metabolism, especially the Warburg effect, is emerged as a hallmark of cancer. The protein lysine methyltransferase SMYD2 functions as an oncogene and is implicated in various malignant phenotypes of human cancers. However, the role of SMYD2 in tumor metabolism is still largely unknown. Here, we report that SMYD2 is highly expressed in human cervical cancer and its aberrant expression is linked to a poor prognosis. Bioinformatic analysis revealed a novel link between SMYD2 expression and aerobic glycolysis. Through loss-of-function experiments, we demonstrated that SMYD2 knockdown or inhibition induced a metabolic shift from aerobic glycolysis to oxidative phosphorylation, as evidenced by glucose uptake, lactate production, extracellular acidification, and the oxygen consumption rate. In contrast, SMYD2 overexpression promoted glycolytic metabolism in cervical cancer cells. Moreover, SMYD2 was required for tumor growth in cervical cancer and this oncogenic activity was largely glycolysis-dependent. Mechanistically, SMYD2 altered the methylation status of p53 and inhibited its transcriptional activity. Genetic silencing of p53 largely abrogated the effects of SMYD2 in promoting aerobic glycolysis. Taken together, our findings reveal a novel function of SMYD2 in regulating the Warburg effect in cervical cancer.

Keywords:  Cervical cancer; Oxidative phosphorylation; SMYD2; TP53; Warburg effect

DOI:  https://doi.org/10.1016/j.yexcr.2021.112649
Mol Cell. 2021 May 08. pii: S1097-2765(21)00269-0. [Epub ahead of print]

SUCLA2-coupled regulation of GLS succinylation and activity counteracts oxidative stress in tumor cells.

Yingying Tong, Dong Guo, Shu-Hai Lin, Jiazhen Liang, Dianqiang Yang, Chunmin Ma, Fei Shao, Min Li, Qiujing Yu, Yuhui Jiang, Lei Li, Jing Fang, Rilei Yu, Zhimin Lu.

  Glutaminase regulates glutaminolysis to promote cancer cell proliferation. However, the mechanism underlying glutaminase activity regulation is largely unknown. Here, we demonstrate that kidney-type glutaminase (GLS) is highly expressed in human pancreatic ductal adenocarcinoma (PDAC) specimens with correspondingly upregulated glutamine dependence for PDAC cell proliferation. Upon oxidative stress, the succinyl-coenzyme A (CoA) synthetase ADP-forming subunit β (SUCLA2) phosphorylated by p38 mitogen-activated protein kinase (MAPK) at S79 dissociates from GLS, resulting in enhanced GLS K311 succinylation, oligomerization, and activity. Activated GLS increases glutaminolysis and the production of nicotinamide adenine dinucleotide phosphate (NADPH) and glutathione, thereby counteracting oxidative stress and promoting tumor cell survival and tumor growth in mice. In addition, the levels of SUCLA2 pS79 and GLS K311 succinylation, which were mutually correlated, were positively associated with advanced stages of PDAC and poor prognosis for patients. Our findings reveal critical regulation of GLS by SUCLA2-coupled GLS succinylation regulation and underscore the regulatory role of metabolites in glutaminolysis and PDAC development.

Keywords:  GLS; GSH; NADPH; SUCLA2; glutaminolysis; p38; phosphorylation; succinyl-CoA; succinylation; tumorigenesis

DOI:  https://doi.org/10.1016/j.molcel.2021.04.002
J Cell Sci. 2020 Jan 01. pii: jcs.247957. [Epub ahead of print]

BCAT1 affects mitochondrial metabolism independently of leucine transamination in activated human macrophages.

Jeong-Hun Ko, Antoni Olona, Adonia E Papathanassiu, Norzawani Buang, Kwon-Sik Park, Ana S H Costa, Claudio Mauro, Christian Frezza, Jacques Behmoaras.

  In response to environmental stimuli, macrophages change their nutrient consumption and undergo an early metabolic adaptation that progressively shapes their polarization state. During the transient, early phase of pro-inflammatory macrophage activation, an increase in tricarboxylic acid (TCA) cycle activity has been reported but the relative contribution of branched chain amino acid (BCAA) leucine remain to be determined. Here we show that glucose but not glutamine is a major contributor of the increase in TCA cycle metabolites during early macrophage activation in humans. We then show that, although BCAA uptake is not altered, their transamination by BCAT1 is increased following 8h lipopolysaccharide (LPS) stimulation. Of note, leucine is not metabolized to integrate the TCA cycle in neither basal nor stimulated human macrophages. Surprisingly, the pharmacological inhibition of BCAT1 reduced glucose-derived itaconate, α-ketoglutarate, and 2-hydroxyglutarate levels, without affecting succinate and citrate levels, indicating a partial inhibition of TCA cycle. This indirect effect is associated with NRF2 activation and anti-oxidant responses. These results suggest a moonlighting role of BCAT1 through redox-mediated control of mitochondrial function during early macrophage activation.

Keywords:  BCAT1; Immunometabolism; Macrophages; Mitochondria; Redox biology; TCA cycle

DOI:  https://doi.org/10.1242/jcs.247957
Biol Open. 2020 Jan 01. pii: bio.054262. [Epub ahead of print]

Drosophila MICOS knockdown impairs mitochondrial structure and function and promotes mitophagy in muscle tissue.

Li-Jie Wang, Tian Hsu, Hsiang-Ling Lin, Chi-Yu Fu.

  The mitochondrial contact site and cristae organizing system (MICOS) is a multi-protein interaction hub that helps define mitochondrial ultrastructure. While the functional importance of MICOS is mostly characterized in yeast and mammalian cells in culture, the contributions of MICOS to tissue homeostasis in vivo remain further elucidation. In this study, we examined how knocking down expression of Drosophila MICOS genes affects mitochondrial function and muscle tissue homeostasis. We found that CG5903/MIC26-MIC27 colocalizes and functions with Mitofilin/MIC60 and QIL1/MIC13 as a Drosophila MICOS component; knocking down expression of any of these three genes predictably altered mitochondrial morphology, causing loss of cristae junctions, and disruption of cristae packing. Furthermore, the knockdown flies exhibited low mitochondrial membrane potential, fusion/fission imbalances, increased mitophagy, and limited cell death. Reductions in climbing ability indicated deficits in muscle function. Knocking down MICOS genes also caused reduced mtDNA content and fragmented mitochondrial nucleoid structure in Drosophila. Together, our data demonstrate an essential role of Drosophila MICOS in maintaining proper homeostasis of mitochondrial structure and function to promote the function of muscle tissue.

Keywords:  Drosophila; MICOS; Mitochondria

DOI:  https://doi.org/10.1242/bio.054262
Oncogene. 2021 May 20.

ING2 tumor suppressive protein translocates into mitochondria and is involved in cellular metabolism homeostasis.

Charles Ricordel, Laura Chaillot, Alice Blondel, Jérôme Archambeau, Florence Jouan, Audrey Mouche, Marie Tiercin, Agnès Burel, Hervé Lena, Benoît Desrues, Thierry Guillaudeux, Rémy Pedeux.

ING2 (Inhibitor of Growth 2) is a tumor suppressor gene that has been implicated in critical biological functions (cell-cycle regulation, replicative senescence, DNA repair and DNA replication), most of which are recognized hallmarks of tumorigenesis occurring in the cell nucleus. As its close homolog ING1 has been recently observed in the mitochondrial compartment, we hypothesized that ING2 could also translocate into the mitochondria and be involved in new biological functions. In the present study, we demonstrate that ING2 is imported in the inner mitochondrial fraction in a redox-sensitive manner in human cells and that this mechanism is modulated by 14-3-3η protein expression. Remarkably, ING2 is necessary to maintain mitochondrial ultrastructure integrity without interfering with mitochondrial networks or polarization. We observed an interaction between ING2 and mtDNA under basal conditions. This interaction appears to be mediated by TFAM, a critical regulator of mtDNA integrity. The loss of mitochondrial ING2 does not impair mtDNA repair, replication or transcription but leads to a decrease in mitochondrial ROS production, suggesting a detrimental impact on OXPHOS activity. We finally show using multiple models that ING2 is involved in mitochondrial respiration and that its loss confers a protection against mitochondrial respiratory chain inhibition in vitro. Consequently, we propose a new tumor suppressor role for ING2 protein in the mitochondria as a metabolic shift gatekeeper during tumorigenesis.

DOI: https://doi.org/10.1038/s41388-021-01832-3
J Cell Sci. 2020 Jan 01. pii: jcs.248492. [Epub ahead of print]

Increased supra-organization is a dynamic multistep remodelling of respiratory complexes against proteostasis stress.

Shivali Rawat, Suparna Ghosh, Debodyuti Mondal, Valpadashi Anusha, Swasti Raychaudhuri.

  Proteasome-mediated degradation of misfolded proteins prevents aggregation inside and outside mitochondria. But how do cells safeguard mitochondrial proteome and function despite increased aggregation during proteasome-inactivation? Here, using a novel two-dimensional complexome profiling strategy, we report increased supra-organizations of respiratory complexes (RCs) in proteasome-inhibited cells simultaneous to pelletable aggregation of RC-subunits inside mitochondria. Complex-II (CII) and CV-subunits are increasingly incorporated into oligomers. CI, CIII and CIV-subunits are engaged into supercomplex formation. We unravel unique quinary-states of supercomplexes at early-stress that exhibit plasticity and inequivalence of constituent RCs. Core stoichiometry of CI and CIII is preserved whereas CIV-composition varies. These partially disintegrated supercomplexes remain functionally competent via conformational optimization. Subsequently, increased stepwise integration of RC-subunits into holocomplex and supercomplexes re-establish steady-state stoichiometry. Overall, the mechanism of increased supra-organization of RCs mimics the cooperative unfolding and folding pathways for protein-folding, restricted to RCs only and not observed for any other mitochondrial protein complexes.

Keywords:  Increased supercomplex; Multistep proteome remodelling; Proteostasis; Quinary supercomplex; Respiratory complex biogenesis; Two-dimensional complexome profiling

DOI:  https://doi.org/10.1242/jcs.248492
J Cell Sci. 2020 Jan 01. pii: jcs.242446. [Epub ahead of print]

A new brain mitochondrial sodium-sensitive potassium channel: effect of sodium ions on respiratory chain activity.

Javad Fahanik-Babaei, Bahareh Rezaee, Maryam Nazari, Nihad Torabi, Reza Saghiri, Remy Sauve, Afsaneh Eliassi.

  We have determined the electropharmacological properties of a new potassium channel from brain mitochondrial membrane by planar lipid bilayer method. Our results showed the presence of a channel with a conductance of 150 pS at potentials between 0 and -60 mV in 200 cis/50 trans mM KCl solutions. The channel was voltage-independent, with an open probability value ∼0.6 at different voltages. ATP did not affect current amplitude and Po at positive and negative voltages. Notably, adding iberiotoxin, charybdotoxin, lidocaine, and margatoxin had no effect on the channel behavior. Similarly, no changes were observed by decreasing the cis-pH to 6. Interestingly, the channel was inhibited by adding sodium in a dose dependent manner. Our results also indicated a significant increase in mitochondrial complex IV activity and membrane potential and decrease in complex I activity and mitochondrial ROS production in the presence of sodium ions. We propose that inhibition of mitochondrial K+ transport by Na ions on K+ channel opening may be important for cell protection and ATP synthesis.

Keywords:  Brain; Intracellular ion channel; Mitochondria; Mitochondrial respiratory chain; Potassium channels; Single channel

DOI:  https://doi.org/10.1242/jcs.242446
J Exp Biol. 2020 Jan 01. pii: jeb.233684. [Epub ahead of print]

Skeletal muscle metabolism in sea-acclimatized king penguins: II. Improved efficiency of mitochondrial bioenergetics.

Damien Roussel, Vincent Marmillot, Pierre-Axel Monternier, Aurore Bourguignon, Gaëlle Toullec, Caroline Romestaing, Claude Duchamp.

  At fledging, juvenile king penguins (Aptenodytes patagonicus) must overcome the tremendous energetic constraints imposed by their marine habitat, including during sustained extensive swimming activity and deep dives in cold seawater. Both endurance swimming and skeletal muscle thermogenesis require high mitochondrial respiratory capacity while the submerged part of dive cycles repeatedly and greatly reduce oxygen availability imposing a need for solutions to conserve oxygen. The aim of the present study was to determine in vitro whether skeletal muscle mitochondria become more "thermogenic" to sustain heat production or more "economical" to conserve oxygen in sea-acclimatized immature penguins as compared with terrestrial juveniles. Rates of mitochondrial oxidative phosphorylation were measured in permeabilized fibers and mitochondria from the pectoralis muscle. Mitochondrial ATP synthesis and coupling efficiency were measured in isolated muscle mitochondria. The mitochondrial activities of respiratory chain complexes and citrate synthase were also assessed. The results showed that respiration, ATP synthesis and respiratory chain complex activities in pectoralis muscles were increased by sea acclimatization. Further, muscle mitochondria were on average 30% to 45% more energy efficient in sea-acclimatized immatures than in pre-fledging juveniles, depending on the respiratory substrate used (pyruvate; palmitoyl-carnitine). Hence, sea acclimatization favors the development of economical management of oxygen, decreasing the oxygen needed to produce a given amount of ATP. This mitochondrial phenotype may improve dive performance during the early marine life of king penguins, by extending their aerobic dive limit.

Keywords:  Bioenergetics; Marine birds; Mitochondria; Oxidative phosphorylation.

DOI:  https://doi.org/10.1242/jeb.233684
Sci Rep. 2021 May 18. 11(1): 10487

Metformin treatment response is dependent on glucose growth conditions and metabolic phenotype in colorectal cancer cells.

Abdelnour H Alhourani, Tia R Tidwell, Ansooya A Bokil, Gro V Røsland, Karl Johan Tronstad, Kjetil Søreide, Hanne R Hagland.

Cancer cells exhibit altered metabolism, a phenomenon described a century ago by Otto Warburg. However, metabolic drug targeting is considered an underutilized and poorly understood area of cancer therapy. Metformin, a metabolic drug commonly used to treat type 2 diabetes, has been associated with lower cancer incidence, although studies are inconclusive concerning effectiveness of the drug in treatment or cancer prevention. The aim of this study was to determine how glucose concentration influences cancer cells' response to metformin, highlighting why metformin studies are inconsistent. We used two colorectal cancer cell lines with different growth rates and clinically achievable metformin concentrations. We found that fast growing SW948 are more glycolytic in terms of metabolism, while the slower growing SW1116 are reliant on mitochondrial respiration. Both cell lines show inhibitory growth after metformin treatment under physiological glucose conditions, but not in high glucose conditions. Furthermore, SW1116 converges with SW948 at a more glycolytic phenotype after metformin treatment. This metabolic shift is supported by changed GLUT1 expression. Thus, cells having different metabolic phenotypes, show a clear differential response to metformin treatment based on glucose concentration. This demonstrates the importance of growth conditions for experiments or clinical studies involving metabolic drugs such as metformin.

DOI: https://doi.org/10.1038/s41598-021-89861-6
EMBO Mol Med. 2021 May 20. e13579

High-throughput screening identifies suppressors of mitochondrial fragmentation in OPA1 fibroblasts.

Emma Cretin, Priscilla Lopes, Elodie Vimont, Takashi Tatsuta, Thomas Langer, Anastasia Gazi, Martin Sachse, Patrick Yu-Wai-Man, Pascal Reynier, Timothy Wai.

  Mutations in OPA1 cause autosomal dominant optic atrophy (DOA) as well as DOA+, a phenotype characterized by more severe neurological deficits. OPA1 deficiency causes mitochondrial fragmentation and also disrupts cristae, respiration, mitochondrial DNA (mtDNA) maintenance, and cell viability. It has not yet been established whether phenotypic severity can be modulated by genetic modifiers of OPA1. We screened the entire known mitochondrial proteome (1,531 genes) to identify genes that control mitochondrial morphology using a first-in-kind imaging pipeline. We identified 145 known and novel candidate genes whose depletion promoted elongation or fragmentation of the mitochondrial network in control fibroblasts and 91 in DOA+ patient fibroblasts that prevented mitochondrial fragmentation, including phosphatidyl glycerophosphate synthase (PGS1). PGS1 depletion reduces CL content in mitochondria and rebalances mitochondrial dynamics in OPA1-deficient fibroblasts by inhibiting mitochondrial fission, which improves defective respiration, but does not rescue mtDNA depletion, cristae dysmorphology, or apoptotic sensitivity. Our data reveal that the multifaceted roles of OPA1 in mitochondria can be functionally uncoupled by modulating mitochondrial lipid metabolism, providing novel insights into the cellular relevance of mitochondrial fragmentation.

Keywords:  OPA1; genetic modifiers; high-throughput screening; mitochondrial dynamics; phospholipid metabolism

DOI:  https://doi.org/10.15252/emmm.202013579
Cell Metab. 2021 May 17. pii: S1550-4131(21)00183-2. [Epub ahead of print]

Adhesion-mediated mechanosignaling forces mitohormesis.

Kevin M Tharp, Ryo Higuchi-Sanabria, Greg A Timblin, Breanna Ford, Carlos Garzon-Coral, Catherine Schneider, Jonathon M Muncie, Connor Stashko, Joseph R Daniele, Andrew S Moore, Phillip A Frankino, Stefan Homentcovschi, Sagar S Manoli, Hao Shao, Alicia L Richards, Kuei-Ho Chen, Johanna Ten Hoeve, Gregory M Ku, Marc Hellerstein, Daniel K Nomura, Karou Saijo, Jason Gestwicki, Alexander R Dunn, Nevan J Krogan, Danielle L Swaney, Andrew Dillin, Valerie M Weaver.

  Mitochondria control eukaryotic cell fate by producing the energy needed to support life and the signals required to execute programed cell death. The biochemical milieu is known to affect mitochondrial function and contribute to the dysfunctional mitochondrial phenotypes implicated in cancer and the morbidities of aging. However, the physical characteristics of the extracellular matrix are also altered in cancerous and aging tissues. Here, we demonstrate that cells sense the physical properties of the extracellular matrix and activate a mitochondrial stress response that adaptively tunes mitochondrial function via solute carrier family 9 member A1-dependent ion exchange and heat shock factor 1-dependent transcription. Overall, our data indicate that adhesion-mediated mechanosignaling may play an unappreciated role in the altered mitochondrial functions observed in aging and cancer.

Keywords:  UPRmt; adhesion; aging; cancer; extracellular matrix; mechanical stress; mechanotabolism; metabolism; oxidative stress; tension

DOI:  https://doi.org/10.1016/j.cmet.2021.04.017
Blood Cancer J. 2021 May 17. 11(5): 93

SIRT3 overexpression and epigenetic silencing of catalase regulate ROS accumulation in CLL cells activating AXL signaling axis.

Guru P Maiti, Sutapa Sinha, Hasan Mahmud, Justin Boysen, Mariana T Mendez, Sara K Vesely, Jennifer Holter-Chakrabarty, Neil E Kay, Asish K Ghosh.

Mitochondrial metabolism is the key source for abundant ROS in chronic lymphocytic leukemia (CLL) cells. Here, we detected significantly lower superoxide anion (O2-) levels with increased accumulation of hydrogen peroxide (H2O2) in CLL cells vs. normal B-cells. Further analysis indicated that mitochondrial superoxide dismutase (SOD)2, which converts O2- into H2O2 remained deacetylated in CLL cells due to SIRT3 overexpression resulting its constitutive activation. In addition, catalase expression was also reduced in CLL cells suggesting impairment of H2O2-conversion into water and O2 which may cause H2O2-accumulation. Importantly, we identified two CpG-islands in the catalase promoter and discovered that while the distal CpG-island (-3619 to -3765) remained methylated in both normal B-cells and CLL cells, variable degrees of methylation were discernible in the proximal CpG-island (-174 to -332) only in CLL cells. Finally, treatment of CLL cells with a demethylating agent increased catalase mRNA levels. Functionally, ROS accumulation in CLL cells activated the AXL survival axis while upregulated SIRT3, suggesting that CLL cells rapidly remove highly reactive O2- to avoid its cytotoxic effect but maintain increased H2O2-level to promote cell survival. Therefore, abrogation of aberrantly activated cell survival pathways using antioxidants can be an effective intervention in CLL therapy in combination with conventional agents.

DOI: https://doi.org/10.1038/s41408-021-00484-6
J Exp Biol. 2020 Jan 01. pii: jeb.215558. [Epub ahead of print]

Improved mitochondrial coupling as a response to high mass-specific metabolic rate in extremely small mammals.

Boël Mélanie, Romestaing Caroline, Duchamp Claude, Veyrunes Frédéric, Renaud Sabrina, Roussel Damien, Voituron Yann.

  Mass-specific metabolic rate negatively co-varies with body mass from the whole-animal to the mitochondrial levels. Mitochondria are the mainly consumers of oxygen inspired by mammals to generate ATP or compensate energetic losses dissipated as the form of heat (proton leak) during oxidative phosphorylation. Consequently, ATP synthesis and proton leak thus compete for the same electrochemical gradient. Because proton leak co-varies negatively with body mass, it is unknown if extremely small mammals further decouple their mitochondria to maintain their body temperature or if they implement metabolic innovations to ensure cellular homeostasis. The present study investigates the impact of body mass variation on cellular and mitochondrial functioning in small mammals, comparing the two extremely small African pygmy mice (Mus mattheyi, approx. 5 g and Mus minutoides, approx. 7 g) with the larger house mouse (Mus musculus, approx. 22 g). Oxygen consumption rates were measured from the animal to the mitochondrial levels. We also measured mitochondrial ATP synthesis in order to appreciate the mitochondrial efficiency (ATP/O). At the whole-animal scale, mass- and surface-specific metabolic rates co-varied negatively with body mass, whereas this was not necessarily the case at cellular and mitochondrial levels. M. mattheyi had generally the lowest cellular and mitochondrial fluxes, depending on the tissue considered (liver or skeletal muscle), as well as having higher efficient muscle mitochondria than the other two species. M. mattheyi presents metabolic innovations to ensure its homeostasis, by generating more ATP per oxygen consumed.

Keywords:  Allometry; Liver; Mitochondrial efficiency; Mus; Muscles; Oxidative phosphorylation

DOI:  https://doi.org/10.1242/jeb.215558
Am J Physiol Cell Physiol. 2021 05 19.

Media composition and O2 levels determine effects of 17β-Estradiol on mitochondrial bioenergetics and cellular reactive oxygen species.

Feresteh Moradi, Marco Fiocchetti, Maria Marino, Christopher Moffatt, Jeffrey A Stuart.

  Estradiol (E2) and selective estrogen receptor modulators (SERMs) have broad-ranging cellular effects that include mitochondrial respiration and reactive oxygen species (ROS) metabolism. Many of these effects have been studied using cell culture models. Recent advances have revealed the extent to which cellular metabolism is affected by the culture environment. Cell culture media with metabolite composition similar to blood plasma (e.g. Plasmax, HPLM) alter cellular behaviours including responses to drugs. Similar effects have been observed with respect to O2 levels in cell culture. Given these observations, we set out to determine whether the effects of E2 and SERMs are also influenced by media composition and O2 level during cell culture experiments. We analyzed mitochondrial network characteristics, cellular oxygen consumption rates, and cellular H2O2 production in C2C12 myoblasts growing in physiologic (5%) or standard cell culture (18%) O2 and in physiologic (Plasmax) or standard cell culture (DMEM) media. The cell culture conditions affected all measured parameters under basal conditions and changed how cells responded to E2 or SERMs. These results indicate that the effects of E2 and SERMs on various aspects of cell physiology strongly depends on growth conditions, which in turn emphasizes the need to consider this carefully in cell culture experiments.

Keywords:  Bioenergetics; Cell culture; Estradiol; Mitochondria; ROS

DOI:  https://doi.org/10.1152/ajpcell.00080.2021
Nat Commun. 2021 05 17. 12(1): 2887

Yap regulates skeletal muscle fatty acid oxidation and adiposity in metabolic disease.

K I Watt, D C Henstridge, M Ziemann, C B Sim, M K Montgomery, D Samocha-Bonet, B L Parker, G T Dodd, S T Bond, T M Salmi, R S Lee, R E Thomson, A Hagg, J R Davey, H Qian, R Koopman, A El-Osta, J R Greenfield, M J Watt, M A Febbraio, B G Drew, A G Cox, E R Porrello, K F Harvey, P Gregorevic.

Obesity is a major risk factor underlying the development of metabolic disease and a growing public health concern globally. Strategies to promote skeletal muscle metabolism can be effective to limit the progression of metabolic disease. Here, we demonstrate that the levels of the Hippo pathway transcriptional co-activator YAP are decreased in muscle biopsies from obese, insulin-resistant humans and mice. Targeted disruption of Yap in adult skeletal muscle resulted in incomplete oxidation of fatty acids and lipotoxicity. Integrated 'omics analysis from isolated adult muscle nuclei revealed that Yap regulates a transcriptional profile associated with metabolic substrate utilisation. In line with these findings, increasing Yap abundance in the striated muscle of obese (db/db) mice enhanced energy expenditure and attenuated adiposity. Our results demonstrate a vital role for Yap as a mediator of skeletal muscle metabolism. Strategies to enhance Yap activity in skeletal muscle warrant consideration as part of comprehensive approaches to treat metabolic disease.

DOI: https://doi.org/10.1038/s41467-021-23240-7
Int J Obes (Lond). 2021 May 17.

Sexual dimorphism in adipose tissue mitochondrial function and metabolic flexibility in obesity.

Amanda D V MacCannell, T Simon Futers, Anna Whitehead, Amy Moran, Klaus K Witte, Lee D Roberts.

OBJECTIVE: The prevalence of obesity is growing globally. Adiposity increases the risk for metabolic syndrome, type 2 diabetes and cardiovascular disease. Adipose tissue distribution influences systemic metabolism and impacts metabolic disease risk. The link between sexual dimorphisms of adiposity and metabolism is poorly defined. We hypothesise that depot-specific adipose tissue mitochondrial function contributes to the sexual dimorphism of metabolic flexibility in obesity.
METHODS: Male and female mice fed high fat diet (HFD) or standard diet (STD) from 8-18 weeks of age underwent whole animal calorimetry and high-resolution mitochondrial respirometry analysis on adipose tissue depots. To determine translatability we used RT-qPCR to examine key brown adipocyte-associated gene expression: peroxisome proliferator-activated receptor co-activator 1α, Uncoupling protein 1 and cell death inducing DFFA like effector a in brown adipose tissue (BAT) and subcutaneous adipose tissue (sWAT) of 18-week-old mice and sWAT from human volunteers.
RESULTS: Male mice exhibited greater weight gain compared to female mice when challenged with HFD. Relative to increased body mass, the adipose to body weight ratio for BAT and sWAT depots was increased in HFD-fed males compared to female HFD-fed mice. Oxygen consumption, energy expenditure, respiratory exchange ratio and food consumption did not differ between males and females fed HFD. BAT mitochondria from obese females showed increased Complex I & II respiration and maximal respiration compared to lean females whereas obese males did not exhibit adaptive mitochondrial BAT respiration. Sexual dimorphism in BAT-associated gene expression in sWAT was also associated with Body Mass Index in humans.
CONCLUSIONS: We show that sexual dimorphism of weight gain is reflected in mitochondrial respiration analysis. Female mice have increased metabolic flexibility to adapt to changes in energy intake by regulating energy expenditure through increased complex II and maximal mitochondrial respiration within BAT when HFD challenged and increased proton leak in sWAT mitochondria.

DOI: https://doi.org/10.1038/s41366-021-00843-0
STAR Protoc. 2021 Jun 18. 2(2): 100466

A flow-cytometry-based protocol for detection of mitochondrial ROS production under hypoxia.

Yun Yang, Guimin Zhang, Tao Yang, Jia Gan, Lin Xu, Hanshuo Yang.

  Hypoxia is known to stimulate mitochondrial reactive oxygen species (mROS) in cells. Here, we present a detailed protocol to detect mROS using MitoSOX staining in live cells under normoxia and hypoxia. Flow cytometry allows sensitive and reliable quantification of mROS by FlowJo software. We optimized several aspects of the procedure including hypoxic treatment, working concentrations of the staining buffer, and quantitative analyses. Here, we use HepG2 cells, but the protocol can be applied to other cell lines. For complete details on the use and execution of this protocol, please refer to Yang et al. (2020).

Keywords:  Cell Biology; Cell-based Assays; Flow Cytometry/Mass Cytometry; Molecular/Chemical Probes

DOI:  https://doi.org/10.1016/j.xpro.2021.100466
J Vis Exp. 2021 May 03.

The Use of the Patch-Clamp Technique to Study the Thermogenic Capacity of Mitochondria.

Ambre M Bertholet.

Mitochondrial thermogenesis (also known as mitochondrial uncoupling) is one of the most promising targets for increasing energy expenditure to combat metabolic syndrome. Thermogenic tissues such as brown and beige fats develop highly specialized mitochondria for heat production. Mitochondria of other tissues, which primarily produce ATP, also convert up to 25% of the total mitochondrial energy production into heat and can, therefore, have a considerable impact on the physiology of the whole body. Mitochondrial thermogenesis is not only essential for maintaining the body temperature, but also prevents diet-induced obesity and reduces the production of reactive oxygen species (ROS) to protect cells from oxidative damage. Since mitochondrial thermogenesis is a key regulator of cellular metabolism, a mechanistic understanding of this fundamental process will help in the development of therapeutic strategies to combat many pathologies associated with mitochondrial dysfunction. Importantly, the precise molecular mechanisms that control acute activation of thermogenesis in mitochondria are poorly defined. This lack of information is largely due to a dearth of methods for the direct measurement of uncoupling proteins. The recent development of patch-clamp methodology applied to mitochondria enabled, for the first time, the direct study of the phenomenon at the origin of mitochondrial thermogenesis, H+ leak through the IMM, and the first biophysical characterization of mitochondrial transporters responsible for it, the uncoupling protein 1 (UCP1), specific of brown and beige fats, and the ADP/ATP transporter (AAC) for all other tissues. This unique approach will provide new insights into the mechanisms that control H+ leak and mitochondrial thermogenesis and how they can be targeted to combat metabolic syndrome. This paper describes the patch-clamp methodology applied to mitochondria to study their thermogenic capacity by directly measuring H+ currents through the IMM.

DOI: https://doi.org/10.3791/62618
Curr Biol. 2021 May 14. pii: S0960-9822(21)00609-6. [Epub ahead of print]

Vmp1, Vps13D, and Marf/Mfn2 function in a conserved pathway to regulate mitochondria and ER contact in development and disease.

James L Shen, Tina M Fortier, Yan G Zhao, Ruoxi Wang, Margit Burmeister, Eric H Baehrecke.

  Mutations in Vps13D cause defects in autophagy, clearance of mitochondria, and human movement disorders. Here, we discover that Vps13D functions in a pathway downstream of Vmp1 and upstream of Marf/Mfn2. Like vps13d, vmp1 mutant cells exhibit defects in autophagy, mitochondrial size, and clearance. Through the relationship between vmp1 and vps13d, we reveal a novel role for Vps13D in the regulation of mitochondria and endoplasmic reticulum (ER) contact. Significantly, the function of Vps13D in mitochondria and ER contact is conserved between fly and human cells, including fibroblasts derived from patients suffering from VPS13D mutation-associated neurological symptoms. vps13d mutants have increased levels of Marf/MFN2, a regulator of mitochondrial fusion. Importantly, loss of marf/MFN2 suppresses vps13d mutant phenotypes, including mitochondria and ER contact. These findings indicate that Vps13d functions at a regulatory point between mitochondria and ER contact, mitochondrial fusion and autophagy, and help to explain how Vps13D contributes to disease.

Keywords:  Drosophila; Vmp1; Vps13D; autophagy; membrane contact; mitochondria

DOI:  https://doi.org/10.1016/j.cub.2021.04.062
Trends Pharmacol Sci. 2021 May 12. pii: S0165-6147(21)00072-9. [Epub ahead of print]

Targeting the mitochondrial chaperone TRAP1: strategies and therapeutic perspectives.

Stefano A Serapian, Carlos Sanchez-Martín, Elisabetta Moroni, Andrea Rasola, Giorgio Colombo.

  TRAP1, the mitochondrial isoform of heat shock protein (Hsp)90 chaperones, is a key regulator of metabolism and organelle homeostasis in diverse pathological states. While selective TRAP1 targeting is an attractive goal, classical active-site-directed strategies have proved difficult, due to high active site conservation among Hsp90 paralogs. Here, we discuss advances in developing TRAP1-directed strategies, from lead modification with mitochondria delivery groups to the computational discovery of allosteric sites and ligands. Specifically, we address the unique opportunities that targeting TRAP1 opens up in tackling fundamental questions on its biology and in unveiling new therapeutic approaches. Finally, we show how crucial to this endeavor is our ability to predict the activities of TRAP1-selective allosteric ligands and to optimize target engagement to avoid side effects.

Keywords:  drug design; mitochondrial proteostasis; molecular chaperones; molecular dynamics

DOI:  https://doi.org/10.1016/j.tips.2021.04.003
Sci Rep. 2021 May 21. 11(1): 10676

Mesenchymal stromal cell mitochondrial transfer to human induced T-regulatory cells mediates FOXP3 stability.

Jeong-Su Do, Daniel Zwick, Jonathan D Kenyon, Fei Zhong, David Askew, Alex Y Huang, Wouter Van't Hof, Marcie Finney, Mary J Laughlin.

The key obstacle to clinical application of human inducible regulatory T cells (iTreg) as an adoptive cell therapy in autoimmune disorders is loss of FOXP3 expression in an inflammatory milieu. Here we report human iTreg co-cultured with bone marrow-derived mesenchymal stromal cells (MSCs) during short-term ex vivo expansion enhances the stability of iTreg FOXP3 expression and suppressive function in vitro and in vivo, and further that a key mechanism of action is MSC mitochondrial (mt) transfer via tunneling nanotubules (TNT). MSC mt transfer is driven by mitochondrial metabolic function (CD39/CD73 signaling) in proliferating iTreg and promotes iTreg expression of FOXP3 stabilizing factors BACH2 and SENP3. These results elucidate cellular and molecular mechanisms underlying human MSC mt transfer to proliferating cells. MSC mt transfer stabilizes FOXP3 expression in iTregs, thereby enhancing and sustaining their suppressive function in inflammatory conditions in vitro and in vivo.

DOI: https://doi.org/10.1038/s41598-021-90115-8
Cell Rep. 2021 May 18. pii: S2211-1247(21)00468-X. [Epub ahead of print]35(7): 109129

A PKD-MFF signaling axis couples mitochondrial fission to mitotic progression.

Evanthia Pangou, Olga Bielska, Lucile Guerber, Stephane Schmucker, Arantxa Agote-Arán, Taozhi Ye, Yongrong Liao, Marta Puig-Gamez, Erwan Grandgirard, Charlotte Kleiss, Yansheng Liu, Emmanuel Compe, Zhirong Zhang, Ruedi Aebersold, Romeo Ricci, Izabela Sumara.

  Mitochondria are highly dynamic organelles subjected to fission and fusion events. During mitosis, mitochondrial fission ensures equal distribution of mitochondria to daughter cells. If and how this process can actively drive mitotic progression remains largely unknown. Here, we discover a pathway linking mitochondrial fission to mitotic progression in mammalian cells. The mitochondrial fission factor (MFF), the main mitochondrial receptor for the Dynamin-related protein 1 (DRP1), is directly phosphorylated by Protein Kinase D (PKD) specifically during mitosis. PKD-dependent MFF phosphorylation is required and sufficient for mitochondrial fission in mitotic but not in interphasic cells. Phosphorylation of MFF is crucial for chromosome segregation and promotes cell survival by inhibiting adaptation of the mitotic checkpoint. Thus, PKD/MFF-dependent mitochondrial fission is critical for the maintenance of genome integrity during cell division.

Keywords:  MFF; PKD; cell survival; fission; mitochondria; mitosis; mitotic checkpoint

DOI:  https://doi.org/10.1016/j.celrep.2021.109129
Cell Immunol. 2021 May 09. pii: S0008-8749(21)00097-6. [Epub ahead of print]365 104378

Rapamycin facilitates differentiation of regulatory T cells via enhancement of oxidative phosphorylation.

Xuelu Chen, Shengfu Li, Dan Long, Juan Shan, Youping Li.

  We explored the interplay between energy metabolism and the impact of rapamycin (Rapa) on regulatory T cell (Treg) differentiation. Naïve CD4+ T cells were stimulated under Treg-polarizing conditions with or without Rapa. Rapa promoted Treg induction, as the expression of Foxp3 and Treg phenotypic markers were enhanced. Rapa disrupts glycolysis while favoring mitochondrial metabolism in induced Tregs (iTregs). Metabolic profiling showed reduced glycolytic metabolites in Rapa-treated iTregs, in line with the downregulation of glucose uptake and the expression of glycolytic enzymes. Conversely, Rapa increased the ratios of ATP/ADP and ATP/AMP, the production of mitochondrial ATP, and the expression of ATP5A. Treatment with oxidative phosphorylation inhibitors suppressed Foxp3 expression in Rapa-treated cells. Moreover, Rapa decreased oleic acid and palmitoleic acid levels and increased l-carnitine and acetylcarnitine levels and CPT1A expression in iTregs, indicative of augmented fatty acid oxidation. In conclusion, Rapa induces metabolic reprogramming in Tregs, affecting their differentiation.

Keywords:  Glycolysis; Immunometabolism; Oxidative phosphorylation; Rapamycin; Regulatory T cells

DOI:  https://doi.org/10.1016/j.cellimm.2021.104378
Mol Oncol. 2021 May 18.

Oncogenic KRAS mutations enhance amino acid uptake by colorectal cancer cells via the hippo signaling effector YAP1.

Palanivel Kandasamy, Inti Zlobec, Damian T Nydegger, Jonai Pujol Giménez, Rajesh Bhardwaj, Senji Shirasawa, Toshiyuki Tsunoda, Matthias A Hediger.

  Oncogenic KRAS mutations develop unique metabolic dependencies on nutrients to support tumor metabolism and cell proliferation. In particular, KRAS mutant cancer cells exploit amino acids (AAs) such as glutamine and leucine, to accelerate energy metabolism, redox balance through glutathione (GSH) synthesis and macromolecule biosynthesis. However, the identities of the amino acid transporters (AATs) that are prominently upregulated in KRAS mutant cancer cells, and the mechanism regulating their expression have not yet been systematically investigated. Here we report that the majority of the KRAS mutant colorectal cancer (CRC) cells upregulate selected AATs (SLC7A5/LAT1, SLC38A2/SNAT2 and SLC1A5/ASCT2), which correlates with enhanced uptake of AAs such as glutamine and leucine. Consistently, knockdown of oncogenic KRAS downregulated the expression of AATs, thereby decreasing the levels of amino acids taken up by CRC cells. Moreover, overexpression of mutant KRAS upregulated the expression of AATs (SLC7A5/LAT1, SLC38A2/SNAT2 and SLC1A5/ASCT2) in KRAS wild-type CRC cells and mouse embryonic fibroblasts (MEFs). In addition, we show that the YAP1 (Yes-associated protein 1) transcriptional coactivator accounts for increased expression of AATs and mTOR activation in KRAS mutant CRC cells. Specific knockdown of AATs by shRNAs or pharmacological blockage of AATs effectively inhibited AA uptake, mTOR activation and cell proliferation. Collectively, we conclude that oncogenic KRAS mutations enhance the expression of AATs via the hippo effector YAP1, leading to mTOR activation and CRC cell proliferation.

Keywords:  Amino acid transporters; Oncogene; SLC1A5/ASCT2; SLC38A2/SNAT2; SLC7A5/LAT1; Solute carriers

DOI:  https://doi.org/10.1002/1878-0261.12999
Nat Commun. 2021 05 17. 12(1): 2877

Longitudinal single-cell profiling reveals molecular heterogeneity and tumor-immune evolution in refractory mantle cell lymphoma.

Shaojun Zhang, Vivian Changying Jiang, Guangchun Han, Dapeng Hao, Junwei Lian, Yang Liu, Rongjia Zhang, Joseph McIntosh, Ruiping Wang, Minghao Dang, Enyu Dai, Yuanxin Wang, David Santos, Maria Badillo, Angela Leeming, Zhihong Chen, Kimberly Hartig, John Bigcal, Jia Zhou, Rashmi Kanagal-Shamanna, Chi Young Ok, Hun Lee, Raphael E Steiner, Jianhua Zhang, Xingzhi Song, Ranjit Nair, Sairah Ahmed, Alma Rodriquez, Selvi Thirumurthi, Preetesh Jain, Nicolaus Wagner-Bartak, Holly Hill, Krystle Nomie, Christopher Flowers, Andrew Futreal, Linghua Wang, Michael Wang.

The mechanisms driving therapeutic resistance and poor outcomes of mantle cell lymphoma (MCL) are incompletely understood. We characterize the cellular and molecular heterogeneity within and across patients and delineate the dynamic evolution of tumor and immune cell compartments at single cell resolution in longitudinal specimens from ibrutinib-sensitive patients and non-responders. Temporal activation of multiple cancer hallmark pathways and acquisition of 17q are observed in a refractory MCL. Multi-platform validation is performed at genomic and cellular levels in PDX models and larger patient cohorts. We demonstrate that due to 17q gain, BIRC5/survivin expression is upregulated in resistant MCL tumor cells and targeting BIRC5 results in marked tumor inhibition in preclinical models. In addition, we discover notable differences in the tumor microenvironment including progressive dampening of CD8+ T cells and aberrant cell-to-cell communication networks in refractory MCLs. This study reveals diverse and dynamic tumor and immune programs underlying therapy resistance in MCL.

DOI: https://doi.org/10.1038/s41467-021-22872-z
Physiol Rep. 2021 May;9(9): e14838

Muscle mitochondrial capacity in high- and low-fitness females using near-infrared spectroscopy.

Bart Lagerwaard, Joëlle J E Janssen, Iris Cuijpers, Jaap Keijer, Vincent C J de Boer, Arie G Nieuwenhuizen.

  The recovery of muscle oxygen consumption (m V˙ O2 ) after exercise measured using near-infrared spectroscopy (NIRS) provides a measure of skeletal muscle mitochondrial capacity. Nevertheless, due to sex differences in factors that can influence scattering and thus penetration depth of the NIRS signal in the tissue, e.g., subcutaneous adipose tissue thickness and intramuscular myoglobin and hemoglobin, it is unknown whether results in males can be extrapolated to a female population. Therefore, the aim of this study was to measure skeletal muscle mitochondrial capacity in females at different levels of aerobic fitness to test whether NIRS can measure relevant differences in mitochondrial capacity. Mitochondrial capacity was analyzed in the gastrocnemius muscle and the wrist flexors of 32 young female adults, equally divided in relatively high ( V˙ O2 peak ≥ 47 ml/kg/min) and relatively low aerobic fitness group ( V˙ O2 peak ≤ 37 ml/kg/min). m V˙ O2 recovery was significantly faster in the high- compared to the low-fitness group in the gastrocnemius, but not in the wrist flexors (p = 0.009 and p = 0.0528, respectively). Furthermore, V˙ O2 peak was significantly correlated to m V˙ O2 recovery in both gastrocnemius (R2 = 0.27, p = 0.0051) and wrist flexors (R2 = 0.13, p = 0.0393). In conclusion, NIRS measurements can be used to assess differences in mitochondrial capacity within a female population and is correlated to V˙ O2 peak. This further supports NIRS assessment of muscle mitochondrial capacity providing additional evidence for NIRS as a promising approach to monitor mitochondrial capacity, also in an exclusively female population.

Keywords:  V˙ O2peak; NIRS; fitness; mitochondria; oxidative metabolism

DOI:  https://doi.org/10.14814/phy2.14838
Front Cell Dev Biol. 2021 ;9 606639

Mitochondrial Control of Stem Cell State and Fate: Lessons From Drosophila.

Satish Kumar Tiwari, Sudip Mandal.

  Over the years, Drosophila has served as a wonderful genetically tractable model system to unravel various facets of tissue-resident stem cells in their microenvironment. Studies in different stem and progenitor cell types of Drosophila have led to the discovery of cell-intrinsic and extrinsic factors crucial for stem cell state and fate. Though initially touted as the ATP generating machines for carrying various cellular processes, it is now increasingly becoming clear that mitochondrial processes alone can override the cellular program of stem cells. The last few years have witnessed a surge in our understanding of mitochondria's contribution to governing different stem cell properties in their subtissular niches in Drosophila. Through this review, we intend to sum up and highlight the outcome of these in vivo studies that implicate mitochondria as a central regulator of stem cell fate decisions; to find the commonalities and uniqueness associated with these regulatory mechanisms.

Keywords:  Drosophila; differentiation; maintenance; metabolism; mitochondria; regulation; stem cell

DOI:  https://doi.org/10.3389/fcell.2021.606639
J Gene Med. 2021 May 19. e3364

SLC45A4 Promotes Glycolysis and Prevents AMPK/ULK1-induced Autophagy in TP53 Mutant Pancreatic Ductal Adenocarcinoma.

Wenying Chen, Fengting Huang, Jing Huang, Yuanhua Li, Juanfei Peng, Yanyan Zhuang, Xianxian Huang, Liting Lu, Zhe Zhu, Shineng Zhang.

   BACKGROUND: Somatic mutations of the TP53 gene occur frequently in pancreatic ductal adenocarcinoma (PDA). The solute carrier family 45 member A4 (SLC45A4) is a H+ - dependent sugar cotransporter. The role of SLC45A4 in PDA, especially in TP53 mutant PDA, remains poorly understood.
METHODS: We explored the TCGA datasets to identify oncogenes in TP53 mutant PDA. MTS, colony formation and Edu assays were performed to study the function of SLC45A4 in vitro. Glucose consumption, lactate production and ATP production were detected to evaluate glucose utilization. The ECAR and the OCR assay were used to evaluate glycolysis and oxidative phosphorylation. The subcutaneous xenotransplantation models were conducted to explore the function of SLC45A4 in vivo. RNA-seq and GSEA were employed to explore the biological alteration caused by SLC45A4 knockdown. Western blot was performed to evaluate the activation of glycolysis, AMPK pathway and autophagy.
RESULTS: SLC45A4 was overexpressed in PDA and whose expression was significantly higher in TP53 mutant PDA than that in wildtype PDA tissues. Moreover, high level of SLC45A4 expression was tightly associated with poor clinical outcomes in PDA patients. Silencing SLC45A4 inhibited proliferation in TP53 mutant PDA cells. Knockdown of SLC45A4 reduced glucose uptake and ATP production which led to activation of autophagy via AMPK/ULK1 pathway. Deleting SLC45A4 in TP53 mutant HPAF-II cells inhibited the growth of xenografts in nude mice.
CONCLUSION: Our study found that SLC45A4 prevents autophagy via AMPK/ULK1 axis in TP53 mutant PDA, which may be a promising biomarker and therapeutic target in TP53 mutant PDA.

Keywords:  AMPK pathway; SLC45A4; TP53 mutation; autophagy; glucose metabolism

DOI:  https://doi.org/10.1002/jgm.3364
Signal Transduct Target Ther. 2021 May 18. 6(1): 190

UBQLN1 mediates sorafenib resistance through regulating mitochondrial biogenesis and ROS homeostasis by targeting PGC1β in hepatocellular carcinoma.

Junjie Xu, Lin Ji, Yeling Ruan, Zhe Wan, Zhongjie Lin, Shunjie Xia, Liye Tao, Junhao Zheng, Liuxin Cai, Yifan Wang, Xiao Liang, Xiujun Cai.

The treatment for hepatocellular carcinoma (HCC) is promising in recent years, but still facing critical challenges. The first targeted therapy, sorafenib, prolonged the overall survival by months. However, resistance often occurs, largely limits its efficacy. Sorafenib was found to target the electron transport chain complexes, which results in the generation of reactive oxygen species (ROS). To maintain sorafenib resistance and further facilitate tumor progression, cancer cells develop strategies to overcome excessive ROS production and obtain resistance to oxidative stress-induced cell death. In the present study, we investigated the roles of ROS in sorafenib resistance, and found suppressed ROS levels and reductive redox states in sorafenib-resistant HCC cells. Mitochondria in sorafenib-resistant cells maintained greater functional and morphological integrity under the treatment of sorafenib. However, cellular oxygen consumption rate and mitochondria DNA content analyses revealed fewer numbers of mitochondria in sorafenib-resistant cells. Further investigation attributed this finding to decreased mitochondrial biogenesis, likely caused by the accelerated degradation of peroxisome proliferator-activated receptor γ coactivator 1β (PGC1β). Mechanistic dissection showed that upregulated UBQLN1 induced PGC1β degradation in a ubiquitination-independent manner to attenuate mitochondrial biogenesis and ROS production in sorafenib-resistant cells under sorafenib treatment. Furthermore, clinical investigations further indicated that the patients with higher UBQLN1 levels experienced worse recurrence-free survival. In conclusion, we propose a novel mechanism involving mitochondrial biogenesis and ROS homeostasis in sorafenib resistance, which may offer new therapeutic targets and strategies for HCC patients.

DOI: https://doi.org/10.1038/s41392-021-00594-4
Cancer Discov. 2021 Mar;11(3): 660-677

Cell of Origin Influences Pancreatic Cancer Subtype.

Brittany M Flowers, Hang Xu, Abigail S Mulligan, Kathryn J Hanson, Jose A Seoane, Hannes Vogel, Christina Curtis, Laura D Wood, Laura D Attardi.

Pancreatic ductal adenocarcinoma (PDAC) is a deadly disease with a 5-year survival rate of approximately 9%. An improved understanding of PDAC initiation and progression is paramount for discovering strategies to better detect and combat this disease. Although transcriptomic analyses have uncovered distinct molecular subtypes of human PDAC, the factors that influence subtype development remain unclear. Here, we interrogate the impact of cell of origin and different Trp53 alleles on tumor evolution, using a panel of tractable genetically engineered mouse models. Oncogenic KRAS expression, coupled with Trp53 deletion or point mutation, drives PDAC from both acinar and ductal cells. Gene-expression analysis reveals further that ductal cell-derived and acinar cell-derived tumor signatures are enriched in basal-like and classical subtypes of human PDAC, respectively. These findings highlight cell of origin as one factor that influences PDAC molecular subtypes and provide insight into the fundamental impact that the very earliest events in carcinogenesis can have on cancer evolution. SIGNIFICANCE: Although human PDAC has been classified into different molecular subtypes, the etiology of these distinct subtypes remains unclear. Using mouse genetics, we reveal that cell of origin is an important determinant of PDAC molecular subtype. Deciphering the biology underlying pancreatic cancer subtypes may reveal meaningful distinctions that could improve clinical intervention.This article is highlighted in the In This Issue feature, p. 521.

DOI: https://doi.org/10.1158/2159-8290.CD-20-0633
Theranostics. 2021 ;11(13): 6560-6572

Organ-specific cholesterol metabolic aberration fuels liver metastasis of colorectal cancer.

Kai-Li Zhang, Wen-Wei Zhu, Sheng-Hao Wang, Chao Gao, Jun-Jie Pan, Zun-Guo Du, Lu Lu, Hu-Liang Jia, Qiong-Zhu Dong, Jin-Hong Chen, Ming Lu, Lun-Xiu Qin.

  Rationale: Metastasis, the development of secondary malignant growth at a distance from a primary tumor, is the main cause of cancer-associated death. However, little is known about how metastatic cancer cells adapt to and colonize in the new organ environment. Here we sought to investigate the functional mechanism of cholesterol metabolic aberration in colorectal carcinoma (CRC) liver metastasis. Methods: The expression of cholesterol metabolism-related genes in primary colorectal tumors (PT) and paired liver metastases (LM) were examined by RT-PCR. The role of SREBP2-dependent cholesterol biosynthesis pathway in cell growth and CRC liver metastasis were determined by SREBP2 silencing in CRC cell lines and experimental metastasis models including, intra-splenic injection models and liver orthotropic injection model. Growth factors treatment and co-culture experiment were performed to reveal the mechanism underlying the up-regulation of SREBP2 in CRC liver metastases. The in vivo efficacy of inhibition of cholesterol biosynthesis pathway by betulin or simvastatin were evaluated in experimental metastasis models. Results: In the present study, we identify a colorectal cancer (CRC) liver metastasis-specific cholesterol metabolic pathway involving the activation of SREBP2-dependent cholesterol biosynthesis, which is required for the colonization and growth of metastatic CRC cells in the liver. Inhibiting this cholesterol biosynthesis pathway suppresses CRC liver metastasis. Mechanically, hepatocyte growth factor (HGF) from liver environment activates SREBP2-dependent cholesterol biosynthesis pathway by activating c-Met/PI3K/AKT/mTOR axis in CRC cells. Conclusion: Our findings support the notion that CRC liver metastases show a specific cholesterol metabolic aberration. Targeting this cholesterol biosynthesis pathway could be a promising treatment for CRC liver metastasis.

Keywords:  HGF; SREBP2; cholesterol biosynthesis; colorectal cancer; liver metastasis

DOI:  https://doi.org/10.7150/thno.55609
Cell Death Dis. 2021 May 20. 12(6): 517

TSP50 promotes the Warburg effect and hepatocyte proliferation via regulating PKM2 acetylation.

Feng Gao, Xiaojun Zhang, Shuyue Wang, Lihua Zheng, Ying Sun, Guannan Wang, Zhenbo Song, Yongli Bao.

Metabolic reprogramming is a hallmark of malignancy. Testes-specific protease 50 (TSP50), a newly identified oncogene, has been shown to play an important role in tumorigenesis. However, its role in tumor cell metabolism remains unclear. To investigate this issue, LC-MS/MS was employed to identify TSP50-binding proteins and pyruvate kinase M2 isoform (PKM2), a known key enzyme of aerobic glycolysis, was identified as a novel binding partner of TSP50. Further studies suggested that TSP50 promoted aerobic glycolysis in HCC cells by maintaining low pyruvate kinase activity of the PKM2. Mechanistically, TSP50 promoted the Warburg effect by increasing PKM2 K433 acetylation level and PKM2 acetylation site (K433R) mutation remarkably abrogated the TSP50-induced aerobic glycolysis, cell proliferation in vitro and tumor formation in vivo. Our findings indicate that TSP50-mediated low PKM2 pyruvate kinase activity is an important determinant for Warburg effect in HCC cells and provide a mechanistic link between TSP50 and tumor metabolism.

DOI: https://doi.org/10.1038/s41419-021-03782-w
J Pharm Biomed Anal. 2021 May 07. pii: S0731-7085(21)00240-5. [Epub ahead of print]201 114129

Curcumin reverses doxorubicin resistance in colon cancer cells at the metabolic level.

Nan Zhang, Ming Gao, Zihan Wang, Jingxian Zhang, Weiqi Cui, Jinjin Li, Xiaolin Zhu, Hang Zhang, Dong-Hua Yang, Xia Xu.

  Doxorubicin (Dox) is commonly used for the treatment of malignant tumors, including colon cancer. However, the development of P-glycoprotein (P-gp)-mediated multidrug resistance (MDR) in tumor chemotherapy has seriously reduced the therapeutic efficacy of Dox. Natural product curcumin (Cur) was demonstrated to have a variety of pharmacological effects, such as anti-tumor, anti-oxidation and anti-aging activities. Here, we examined the MDR reversal capability of Cur in drug sensitive-(SW620) and resistant-(SW620/Ad300) colon cancer cells, and elucidated the underlying molecular mechanisms at the metabolic level. It was found that Cur reversed P-gp-mediated resistance in SW620/Ad300 cells by enhancing the Dox-induced cytotoxicity and apoptosis. Further mechanistic studies indicated that Cur inhibited the ATP-dependent transport activity of P-gp, thereby increasing the intra-celluar accumulation of Dox in drug-resistant cells. Metabolomics analysis based on UPLC-MS/MS showed that the MDR phenomenon in SW620/Ad300 cells was closely correlated with the upregulation of spermine and spermidine synthesis and D-glutamine metabolism. Cur significantly inhibited the biosynthesis of spermine and spermidine by decreasing the expression of ornithine decarboxylase (ODC) and suppressed D-glutamine metabolism, which in turn decreased the anti-oxidative stress ability and P-gp transport activity of SW620/Ad300 cells, eventually reversed MDR. These findings indicated the MDR reversal activity and the related mechanism of action of Cur, suggesting that Cur could be a promising MDR reversal agent for cancer treatment.

Keywords:  Biosynthesis of polyamines; Colon cancer; Curcumin; D-glutamine metabolism; Metabolomics; P-glycoprotein

DOI:  https://doi.org/10.1016/j.jpba.2021.114129
Nat Genet. 2021 May 17.

An atlas of mitochondrial DNA genotype-phenotype associations in the UK Biobank.

Ekaterina Yonova-Doing, Claudia Calabrese, Aurora Gomez-Duran, Katherine Schon, Wei Wei, Savita Karthikeyan, Patrick F Chinnery, Joanna M M Howson.

Mitochondrial DNA (mtDNA) variation in common diseases has been underexplored, partly due to a lack of genotype calling and quality-control procedures. Developing an at-scale workflow for mtDNA variant analyses, we show correlations between nuclear and mitochondrial genomic structures within subpopulations of Great Britain and establish a UK Biobank reference atlas of mtDNA-phenotype associations. A total of 260 mtDNA-phenotype associations were new (P < 1 × 10-5), including rs2853822 /m.8655 C>T (MT-ATP6) with type 2 diabetes, rs878966690 /m.13117 A>G (MT-ND5) with multiple sclerosis, 6 mtDNA associations with adult height, 24 mtDNA associations with 2 liver biomarkers and 16 mtDNA associations with parameters of renal function. Rare-variant gene-based tests implicated complex I genes modulating mean corpuscular volume and mean corpuscular hemoglobin. Seven traits had both rare and common mtDNA associations, where rare variants tended to have larger effects than common variants. Our work illustrates the value of studying mtDNA variants in common complex diseases and lays foundations for future large-scale mtDNA association studies.

DOI: https://doi.org/10.1038/s41588-021-00868-1
Eur J Med Chem. 2021 May 12. pii: S0223-5234(21)00377-9. [Epub ahead of print]221 113528

A novel selective mitochondrial-targeted curcumin analog with remarkable cytotoxicity in glioma cells.

Lei Shi, Li-Li Gao, Shi-Zhong Cai, Qian-Wei Xiong, Zhou-Rui Ma.

  Naturally occurring polyphenol curcumin (4) or demethoxycurcumin (5) and their synthetic derivatives display promising anticancer activities. However, their further development is limited by low bioavailability and poor selectivity. Thus, a mitochondria-targeted compound 14 (DMC-TPP) was prepared in the present study by conjugating a triphenylphosphine moiety to the phenolic hydroxyl group of demethoxycurcumin to enhance its bioavailability and treatment efficacy. The in vitro biological experiments of DMC-TPP showed that it not only displayed higher cytotoxicity as compared with its parent compound 5, but also exhibited superior mitochondria accumulation ability. Glioma cells were more sensitive to DMC-TPP, which inhibited the proliferation of U251 cells with an IC50 of 0.42 μM. The mechanism studies showed that DMC-TPP triggers mitochondria-dependent apoptosis, caused by caspase activation, production of reactive oxygen species (ROS) and decrease of mitochondrial membrane potential (MMP). In addition, DMC-TPP efficiently inhibited cellular thioredoxin reductase, which contributed to its cytotoxicity. Significantly, DMC-TPP delayed tumor progression in a mouse xenograft model of human glioma cancer. Taken together, the potent in vitro and in vivo antitumor activity of DMC-TPP warrant further comprehensive evaluation as a novel anti-glioma agent.

Keywords:  Curcumin; Demethoxycurcumin; Glioma; Mitochondrial-targeting; Thioredoxin reductase

DOI:  https://doi.org/10.1016/j.ejmech.2021.113528
Mol Syst Biol. 2021 May;17(5): e10013

A method for benchmarking genetic screens reveals a predominant mitochondrial bias.

Mahfuzur Rahman, Maximilian Billmann, Michael Costanzo, Michael Aregger, Amy H Y Tong, Katherine Chan, Henry N Ward, Kevin R Brown, Brenda J Andrews, Charles Boone, Jason Moffat, Chad L Myers.

  We present FLEX (Functional evaluation of experimental perturbations), a pipeline that leverages several functional annotation resources to establish reference standards for benchmarking human genome-wide CRISPR screen data and methods for analyzing them. FLEX provides a quantitative measurement of the functional information captured by a given gene-pair dataset and a means to explore the diversity of functions captured by the input dataset. We apply FLEX to analyze data from the diverse cell line screens generated by the DepMap project. We identify a predominant mitochondria-associated signal within co-essentiality networks derived from these data and explore the basis of this signal. Our analysis and time-resolved CRISPR screens in a single cell line suggest that the variable phenotypes associated with mitochondria genes across cells may reflect screen dynamics and protein stability effects rather than genetic dependencies. We characterize this functional bias and demonstrate its relevance for interpreting differential hits in any CRISPR screening context. More generally, we demonstrate the utility of the FLEX pipeline for performing robust comparative evaluations of CRISPR screens or methods for processing them.

Keywords:  CRISPR screens; computational evaluation; electron transport chain

DOI:  https://doi.org/10.15252/msb.202010013
Adv Exp Med Biol. 2021 ;1311 137-147

Different Tumor Microenvironments Lead to Different Metabolic Phenotypes.

Marjorie Justine Antonio, Cissy Zhang, Anne Le.

  The beginning of the twenty-first century offered new advances in cancer research, including new knowledge about the tumor microenvironment (TME). Because TMEs provide the niches in which cancer cells, fibroblasts, lymphocytes, and immune cells reside, they play a crucial role in cancer cell development, differentiation, survival, and proliferation. Throughout cancer progression, the TME constantly evolves, causing cancer cells to adapt to the new conditions. The heterogeneity of cancer, evidenced by diverse proliferation rates, cellular structures, metabolisms, and gene expressions, presents challenges for cancer treatment despite the advances in research. This chapter discusses how different TMEs lead to specific metabolic adaptations that drive cancer progression.

Keywords:  Fatty acid oxidation; Heterogeneity of cancer; Metabolic phenotypes; Metabolic processes; Tumor microenvironments

DOI:  https://doi.org/10.1007/978-3-030-65768-0_10