bims-camemi 2020-06-21 papers

bims-camemi

Biomed News

on Mitochondrial metabolism in cancer

Issue of 2020–06–21
35 papers selected by
Christian Frezza, , University of Cambridge, MRC Cancer Unit

Metabolic Fingerprinting Links Oncogenic PIK3CA with Enhanced Arachidonic Acid-Derived Eicosanoids.
PHGDH supports liver ceramide synthesis and sustains lipid homeostasis.
Targeting DGAT1 Ameliorates Glioblastoma by Increasing Fat Catabolism and Oxidative Stress.
Mitochondrial respiratory chain composition and organization in response to changing oxygen levels.
Multi-omics analysis delineates the distinct functions of sub-cellular acetyl-CoA pools in Toxoplasma gondii.
Homogeneous Oligomers of Pro-apoptotic BAX Reveal Structural Determinants of Mitochondrial Membrane Permeabilization.
The genomic and epigenomic evolutionary history of papillary renal cell carcinomas.
Leucine regulates autophagy via acetylation of the mTORC1 component raptor.
Mitochondria in cancer.
Eicosapentaenoic acid attenuates renal lipotoxicity by restoring autophagic flux.
Mitochondria-adaptor TRAK1 promotes kinesin-1 driven transport in crowded environments.
Macrophage metabolic adaptation to heme detoxification involves CO-dependent activation of the pentose phosphate pathway.
Altered RNA Splicing by Mutant p53 Activates Oncogenic RAS Signaling in Pancreatic Cancer.
Critical role of mitochondrial ubiquitination and the OPTN-ATG9A axis in mitophagy.
Beyond the Warburg Effect: N-Myc Contributes to Metabolic Reprogramming in Cancer Cells.
Dysfunctional telomeres trigger cellular senescence mediated by cyclic GMP-AMP synthase.
Macrophage metabolic reprogramming presents a therapeutic target in lupus nephritis.
Ca2+ Fluxes and Cancer.
Thinking outside the nucleus: mitochondrial DNA copy number in health and disease.
Metabolic reprogramming as a feast for virus replication.
Psychological distress and lack of PINK1 promote bioenergetics alterations in peripheral blood mononuclear cells.
Resolving Metabolic Heterogeneity in Experimental Models of the Tumor Microenvironment from a Stable Isotope Resolved Metabolomics Perspective.
Lipids, inflammasomes, metabolism, and disease.
Mitochondrial Ion Channels and Transporters in Plants: Prediction and Facts.
Senescence as a therapeutically relevant response to CDK4/6 inhibitors.
Better to keep in touch: investigating inter-organelle cross-talk.
Targeting the Hippo pathway in cancer, fibrosis, wound healing and regenerative medicine.
A review of nutrition and dietary interventions in oncology.
Senolytic CAR T cells reverse senescence-associated pathologies.
Primordial emergence of a nucleic acid-binding protein via phase separation and statistical ornithine-to-arginine conversion.
Recurrent horizontal transfer identifies mitochondrial positive selection in a transmissible cancer.
Opa1 Deficiency Leads to Diminished Mitochondrial Bioenergetics With Compensatory Increased Mitochondrial Motility.
Iron chelation inhibits mTORC1 signaling involving activation of AMPK and REDD1/Bnip3 pathways.
Targeting Metabolism to Improve the Tumor Microenvironment for Cancer Immunotherapy.
Genomic profiling in renal cell carcinoma.

Cell. 2020 Jun 18. pii: S0092-8674(20)30686-3. [Epub ahead of print]

Metabolic Fingerprinting Links Oncogenic PIK3CA with Enhanced Arachidonic Acid-Derived Eicosanoids.

Nikos Koundouros, Evdoxia Karali, Aurelien Tripp, Adamo Valle, Paolo Inglese, Nicholas J S Perry, David J Magee, Sara Anjomani Virmouni, George A Elder, Adam L Tyson, Maria Luisa Dória, Antoinette van Weverwijk, Renata F Soares, Clare M Isacke, Jeremy K Nicholson, Robert C Glen, Zoltan Takats, George Poulogiannis.

  Oncogenic transformation is associated with profound changes in cellular metabolism, but whether tracking these can improve disease stratification or influence therapy decision-making is largely unknown. Using the iKnife to sample the aerosol of cauterized specimens, we demonstrate a new mode of real-time diagnosis, coupling metabolic phenotype to mutant PIK3CA genotype. Oncogenic PIK3CA results in an increase in arachidonic acid and a concomitant overproduction of eicosanoids, acting to promote cell proliferation beyond a cell-autonomous manner. Mechanistically, mutant PIK3CA drives a multimodal signaling network involving mTORC2-PKCζ-mediated activation of the calcium-dependent phospholipase A2 (cPLA2). Notably, inhibiting cPLA2 synergizes with fatty acid-free diet to restore immunogenicity and selectively reduce mutant PIK3CA-induced tumorigenicity. Besides highlighting the potential for metabolic phenotyping in stratified medicine, this study reveals an important role for activated PI3K signaling in regulating arachidonic acid metabolism, uncovering a targetable metabolic vulnerability that largely depends on dietary fat restriction.

Keywords:  PIK3CA; PKCζ; arachidonic acid; cPLA2; cancer metabolism; diet; eicosanoids; fat restriction; iKnife; mTORC2

DOI:  https://doi.org/10.1016/j.cell.2020.05.053
Cancer Metab. 2020 ;8 6

PHGDH supports liver ceramide synthesis and sustains lipid homeostasis.

Yun Pyo Kang, Aimee Falzone, Min Liu, Paloma González-Sánchez, Bo-Hyun Choi, Jonathan L Coloff, James J Saller, Florian A Karreth, Gina M DeNicola.

   Background: d-3-phosphoglycerate dehydrogenase (PHGDH), which encodes the first enzyme in serine biosynthesis, is overexpressed in human cancers and has been proposed as a drug target. However, whether PHGDH is critical for the proliferation or homeostasis of tissues following the postnatal period is unknown.
Methods: To study PHGDH inhibition in adult animals, we developed a knock-in mouse model harboring a PHGDH shRNA under the control of a doxycycline-inducible promoter. With this model, PHGDH depletion can be globally induced in adult animals, while sparing the brain due to poor doxycycline delivery.
Results: We found that PHGDH depletion is well tolerated, and no overt phenotypes were observed in multiple highly proliferative cell compartments. Further, despite detectable knockdown and impaired serine synthesis, liver and pancreatic functions were normal. Interestingly, diminished PHGDH expression reduced liver serine and ceramide levels without increasing the levels of deoxysphingolipids. Further, liver triacylglycerol profiles were altered, with an accumulation of longer chain, polyunsaturated tails upon PHGDH knockdown.
Conclusions: These results suggest that dietary serine is adequate to support the function of healthy, adult murine tissues, but PHGDH-derived serine supports liver ceramide synthesis and sustains general lipid homeostasis.

Keywords:  Ceramide; Mouse model; PHGDH; Serine; Triacylglycerol

DOI:  https://doi.org/10.1186/s40170-020-00212-x
Cell Metab. 2020 Jun 09. pii: S1550-4131(20)30303-X. [Epub ahead of print]

Targeting DGAT1 Ameliorates Glioblastoma by Increasing Fat Catabolism and Oxidative Stress.

Xiang Cheng, Feng Geng, Meixia Pan, Xiaoning Wu, Yaogang Zhong, Chunyan Wang, Zhihua Tian, Chunming Cheng, Rui Zhang, Vinay Puduvalli, Craig Horbinski, Xiaokui Mo, Xianlin Han, Arnab Chakravarti, Deliang Guo.

  Glioblastoma (GBM), a mostly lethal brain tumor, acquires large amounts of free fatty acids (FAs) to promote cell growth. But how the cancer avoids lipotoxicity is unknown. Here, we identify that GBM upregulates diacylglycerol-acyltransferase 1 (DGAT1) to store excess FAs into triglycerides and lipid droplets. Inhibiting DGAT1 disrupted lipid homeostasis and resulted in excessive FAs moving into mitochondria for oxidation, leading to the generation of high levels of reactive oxygen species (ROS), mitochondrial damage, cytochrome c release, and apoptosis. Adding N-acetyl-cysteine or inhibiting FA shuttling into mitochondria decreased ROS and cell death induced by DGAT1 inhibition. We show in xenograft models that targeting DGAT1 blocked lipid droplet formation, induced tumor cell apoptosis, and markedly suppressed GBM growth. Together, our study demonstrates that DGAT1 upregulation protects GBM from oxidative damage and maintains lipid homeostasis by facilitating storage of excess FAs. Targeting DGAT1 could be a promising therapeutic approach for GBM.

Keywords:  DGAT1; ROS; acylcarnitine; fatty acids; glioblastoma; lipid droplets; lipotoxicity; mitochondria; oxidative stress; triglycerides

DOI:  https://doi.org/10.1016/j.cmet.2020.06.002
J Life Sci (Westlake Village). 2020 Jun;2(2):

Mitochondrial respiratory chain composition and organization in response to changing oxygen levels.

Alba Timón-Gómez, Antoni Barrientos.

  Mitochondria are the major consumer of oxygen in eukaryotic cells, owing to the requirement of oxygen to generate ATP through the mitochondrial respiratory chain (MRC) and the oxidative phosphorylation system (OXPHOS). This aerobic energy transduction is more efficient than anaerobic processes such as glycolysis. Hypoxia, a condition in which environmental or intracellular oxygen levels are below the standard range, triggers an adaptive signaling pathway within the cell. When oxygen concentrations are low, hypoxia-inducible factors (HIFs) become stabilized and activated to mount a transcriptional response that triggers modulation of cellular metabolism to adjust to hypoxic conditions. Mitochondrial aerobic metabolism is one of the main targets of the hypoxic response to regulate its functioning and efficiency in the presence of decreased oxygen levels. During evolution, eukaryotic cells and tissues have increased the plasticity of their mitochondrial OXPHOS system to cope with metabolic needs in different oxygen contexts. In mammalian mitochondria, two factors contribute to this plasticity. First, several subunits of the multimeric MRC complexes I and IV exist in multiple tissue-specific and condition-specific isoforms. Second, the MRC enzymes can coexist organized as individual entities or forming supramolecular structures known as supercomplexes, perhaps in a dynamic manner to respond to environmental conditions and cellular metabolic demands. In this review, we will summarize the information currently available on oxygen-related changes in MRC composition and organization and will discuss gaps of knowledge and research opportunities in the field.

Keywords:  Hypoxia; MRC; Mitochondrial OXPHOS; hypoxia-inducible factors (HIFs)

DOI:  https://doi.org/10.36069/JoLS/20200601
BMC Biol. 2020 Jun 16. 18(1): 67

Multi-omics analysis delineates the distinct functions of sub-cellular acetyl-CoA pools in Toxoplasma gondii.

Joachim Kloehn, Rebecca D Oppenheim, Ghizal Siddiqui, Pieter-Jan De Bock, Sunil Kumar Dogga, Yohann Coute, Mohamed-Ali Hakimi, Darren J Creek, Dominique Soldati-Favre.

   BACKGROUND: Acetyl-CoA is a key molecule in all organisms, implicated in several metabolic pathways as well as in transcriptional regulation and post-translational modification. The human pathogen Toxoplasma gondii possesses at least four enzymes which generate acetyl-CoA in the nucleo-cytosol (acetyl-CoA synthetase (ACS); ATP citrate lyase (ACL)), mitochondrion (branched-chain α-keto acid dehydrogenase-complex (BCKDH)) and apicoplast (pyruvate dehydrogenase complex (PDH)). Given the diverse functions of acetyl-CoA, we know very little about the role of sub-cellular acetyl-CoA pools in parasite physiology.
RESULTS: To assess the importance and functions of sub-cellular acetyl-CoA-pools, we measured the acetylome, transcriptome, proteome and metabolome of parasites lacking ACL/ACS or BCKDH. We demonstrate that ACL/ACS constitute a synthetic lethal pair. Loss of both enzymes causes a halt in fatty acid elongation, hypo-acetylation of nucleo-cytosolic and secretory proteins and broad changes in gene expression. In contrast, loss of BCKDH results in an altered TCA cycle, hypo-acetylation of mitochondrial proteins and few specific changes in gene expression. We provide evidence that changes in the acetylome, transcriptome and proteome of cells lacking BCKDH enable the metabolic adaptations and thus the survival of these parasites.
CONCLUSIONS: Using multi-omics and molecular tools, we obtain a global and integrative picture of the role of distinct acetyl-CoA pools in T. gondii physiology. Cytosolic acetyl-CoA is essential and is required for the synthesis of parasite-specific fatty acids. In contrast, loss of mitochondrial acetyl-CoA can be compensated for through metabolic adaptations implemented at the transcriptional, translational and post-translational level.

Keywords:  ATP citrate lyase (ACL); Acetyl-CoA; Acetyl-CoA synthetase (ACS); Acetylome; Branched-chain α-keto acid dehydrogenase-complex (BCKDH); Formate/nitrite transporter (FNT); Metabolism; Multi-omics; Phosphoenolpyruvate carboxykinase (PEPCK); Toxoplasma gondii

DOI:  https://doi.org/10.1186/s12915-020-00791-7
Mol Cell. 2020 Jun 09. pii: S1097-2765(20)30349-X. [Epub ahead of print]

Homogeneous Oligomers of Pro-apoptotic BAX Reveal Structural Determinants of Mitochondrial Membrane Permeabilization.

Zachary J Hauseman, Edward P Harvey, Catherine E Newman, Thomas E Wales, Joel C Bucci, Julian Mintseris, Devin K Schweppe, Liron David, Lixin Fan, Daniel T Cohen, Henry D Herce, Rida Mourtada, Yael Ben-Nun, Noah B Bloch, Scott B Hansen, Hao Wu, Steven P Gygi, John R Engen, Loren D Walensky.

  BAX is a pro-apoptotic protein that transforms from a cytosolic monomer into a toxic oligomer that permeabilizes the mitochondrial outer membrane. How BAX monomers assemble into a higher-order conformation, and the structural determinants essential to membrane permeabilization, remain a mechanistic mystery. A key hurdle has been the inability to generate a homogeneous BAX oligomer (BAXO) for analysis. Here, we report the production and characterization of a full-length BAXO that recapitulates physiologic BAX activation. Multidisciplinary studies revealed striking conformational consequences of oligomerization and insight into the macromolecular structure of oligomeric BAX. Importantly, BAXO enabled the assignment of specific roles to particular residues and α helices that mediate individual steps of the BAX activation pathway, including unexpected functionalities of BAX α6 and α9 in driving membrane disruption. Our results provide the first glimpse of a full-length and functional BAXO, revealing structural requirements for the elusive execution phase of mitochondrial apoptosis.

Keywords:  BAX; BCL-2 family; activation; alpha-helix; apoptosis; membrane permeabilization; mitochondria; monomer; oligomer; structure

DOI:  https://doi.org/10.1016/j.molcel.2020.05.029
Nat Commun. 2020 Jun 18. 11(1): 3096

The genomic and epigenomic evolutionary history of papillary renal cell carcinomas.

Bin Zhu, Maria Luana Poeta, Manuela Costantini, Tongwu Zhang, Jianxin Shi, Steno Sentinelli, Wei Zhao, Vincenzo Pompeo, Maurizio Cardelli, Boian S Alexandrov, Burcak Otlu, Xing Hua, Kristine Jones, Seth Brodie, Malgorzata Ewa Dabrowska, Jorge R Toro, Meredith Yeager, Mingyi Wang, Belynda Hicks, Ludmil B Alexandrov, Kevin M Brown, David C Wedge, Stephen Chanock, Vito Michele Fazio, Michele Gallucci, Maria Teresa Landi.

Intratumor heterogeneity (ITH) and tumor evolution have been well described for clear cell renal cell carcinomas (ccRCC), but they are less studied for other kidney cancer subtypes. Here we investigate ITH and clonal evolution of papillary renal cell carcinoma (pRCC) and rarer kidney cancer subtypes, integrating whole-genome sequencing and DNA methylation data. In 29 tumors, up to 10 samples from the center to the periphery of each tumor, and metastatic samples in 2 cases, enable phylogenetic analysis of spatial features of clonal expansion, which shows congruent patterns of genomic and epigenomic evolution. In contrast to previous studies of ccRCC, in pRCC, driver gene mutations and most arm-level somatic copy number alterations (SCNAs) are clonal. These findings suggest that a single biopsy would be sufficient to identify the important genetic drivers and that targeting large-scale SCNAs may improve pRCC treatment, which is currently poor. While type 1 pRCC displays near absence of structural variants (SVs), the more aggressive type 2 pRCC and the rarer subtypes have numerous SVs, which should be pursued for prognostic significance.

DOI: https://doi.org/10.1038/s41467-020-16546-5
Nat Commun. 2020 Jun 19. 11(1): 3148

Leucine regulates autophagy via acetylation of the mTORC1 component raptor.

Sung Min Son, So Jung Park, Eleanna Stamatakou, Mariella Vicinanza, Fiona M Menzies, David C Rubinsztein.

Macroautophagy ("autophagy") is the main lysosomal catabolic process that becomes activated under nutrient-depleted conditions, like amino acid (AA) starvation. The mechanistic target of rapamycin complex 1 (mTORC1) is a well-conserved negative regulator of autophagy. While leucine (Leu) is a critical mTORC1 regulator under AA-starved conditions, how Leu regulates autophagy is poorly understood. Here, we describe that in most cell types, including neurons, Leu negatively regulates autophagosome biogenesis via its metabolite, acetyl-coenzyme A (AcCoA). AcCoA inhibits autophagy by enhancing EP300-dependent acetylation of the mTORC1 component raptor, with consequent activation of mTORC1. Interestingly, in Leu deprivation conditions, the dominant effects on autophagy are mediated by decreased raptor acetylation causing mTORC1 inhibition, rather than by altered acetylation of other autophagy regulators. Thus, in most cell types we examined, Leu regulates autophagy via the impact of its metabolite AcCoA on mTORC1, suggesting that AcCoA and EP300 play pivotal roles in cell anabolism and catabolism.

DOI: https://doi.org/10.1038/s41467-020-16886-2
Cell Stress. 2020 May 11. 4(6): 114-146

Mitochondria in cancer.

Debora Grasso, Luca X Zampieri, Tânia Capelôa, Justine A Van de Velde, Pierre Sonveaux.

  The rediscovery and reinterpretation of the Warburg effect in the year 2000 occulted for almost a decade the key functions exerted by mitochondria in cancer cells. Until recent times, the scientific community indeed focused on constitutive glycolysis as a hallmark of cancer cells, which it is not, largely ignoring the contribution of mitochondria to the malignancy of oxidative and glycolytic cancer cells, being Warburgian or merely adapted to hypoxia. In this review, we highlight that mitochondria are not only powerhouses in some cancer cells, but also dynamic regulators of life, death, proliferation, motion and stemness in other types of cancer cells. Similar to the cells that host them, mitochondria are capable to adapt to tumoral conditions, and probably to evolve to 'oncogenic mitochondria' capable of transferring malignant capacities to recipient cells. In the wider quest of metabolic modulators of cancer, treatments have already been identified targeting mitochondria in cancer cells, but the field is still in infancy.

Keywords:  apoptosis; mitochondrial biogenesis; mitophagy; oxidative phosphorylation (OXPHOS); reactive oxygen species (ROS); tricarboxylic acid (TCA) cycle; tumor metabolism

DOI:  https://doi.org/10.15698/cst2020.06.221
Autophagy. 2020 Jun 16.

Eicosapentaenoic acid attenuates renal lipotoxicity by restoring autophagic flux.

Takeshi Yamamoto, Yoshitsugu Takabatake, Satoshi Minami, Shinsuke Sakai, Ryuta Fujimura, Atsushi Takahashi, Tomoko Namba-Hamano, Jun Matsuda, Tomonori Kimura, Isao Matsui, Jun-Ya Kaimori, Hiroaki Takeda, Masatomo Takahashi, Yoshihiro Izumi, Takeshi Bamba, Taiji Matsusaka, Fumio Niimura, Motoko Yanagita, Yoshitaka Isaka.

  Recently, we identified a novel mechanism of lipotoxicity in the kidney proximal tubular cells (PTECs); lipid overload stimulates macroautophagy/autophagy for the renovation of plasma and organelle membranes to maintain the integrity of the PTECs. However, this autophagic activation places a burden on the lysosomal system, leading to a downstream suppression of autophagy, which manifests as phospholipid accumulation and inadequate acidification in lysosomes. Here, we investigated whether pharmacological correction by eicosapentaenoic acid (EPA) supplementation could restore autophagic flux and alleviate renal lipotoxicity. EPA supplementation to high-fat diet (HFD)-fed mice reduced several hallmarks of lipotoxicity in the PTECs, such as phospholipid accumulation in the lysosome, mitochondrial dysfunction, inflammation, and fibrosis. In addition to improving the metabolic syndrome, EPA alleviated renal lipotoxicity via several mechanisms. EPA supplementation to HFD-fed mice or the isolated PTECs cultured in palmitic acid (PA) restored lysosomal function with significant improvements in the autophagic flux. The PA-induced redistribution of phospholipids from cellular membranes into lysosomes and the HFD-induced accumulation of SQSTM1/p62 (sequestosome 1), an autophagy substrate, during the temporal and genetic ablation of autophagy were significantly reduced by EPA, indicating that EPA attenuated the HFD-mediated increases in autophagy demand. Moreover, a fatty acid pulse-chase assay revealed that EPA promoted lipid droplet (LD) formation and transfer from LDs to the mitochondria for beta-oxidation. Noteworthy, the efficacy of EPA on lipotoxicity is autophagy-dependent and cell-intrinsic. In conclusion, EPA counteracts lipotoxicity in the proximal tubule by alleviating autophagic numbness, making it potentially suitable as a novel treatment for obesity-related kidney diseases.

Keywords:  autophagic flux; autophagy; lipid droplet; lysosome; mitochondria

DOI:  https://doi.org/10.1080/15548627.2020.1782034
Nat Commun. 2020 Jun 19. 11(1): 3123

Mitochondria-adaptor TRAK1 promotes kinesin-1 driven transport in crowded environments.

Verena Henrichs, Lenka Grycova, Cyril Barinka, Zuzana Nahacka, Jiri Neuzil, Stefan Diez, Jakub Rohlena, Marcus Braun, Zdenek Lansky.

Intracellular trafficking of organelles, driven by kinesin-1 stepping along microtubules, underpins essential cellular processes. In absence of other proteins on the microtubule surface, kinesin-1 performs micron-long runs. Under crowding conditions, however, kinesin-1 motility is drastically impeded. It is thus unclear how kinesin-1 acts as an efficient transporter in intracellular environments. Here, we demonstrate that TRAK1 (Milton), an adaptor protein essential for mitochondrial trafficking, activates kinesin-1 and increases robustness of kinesin-1 stepping on crowded microtubule surfaces. Interaction with TRAK1 i) facilitates kinesin-1 navigation around obstacles, ii) increases the probability of kinesin-1 passing through cohesive islands of tau and iii) increases the run length of kinesin-1 in cell lysate. We explain the enhanced motility by the observed direct interaction of TRAK1 with microtubules, providing an additional anchor for the kinesin-1-TRAK1 complex. Furthermore, TRAK1 enables mitochondrial transport in vitro. We propose adaptor-mediated tethering as a mechanism regulating kinesin-1 motility in various cellular environments.

DOI: https://doi.org/10.1038/s41467-020-16972-5
Blood. 2020 Jun 18. pii: blood.2020004964. [Epub ahead of print]

Macrophage metabolic adaptation to heme detoxification involves CO-dependent activation of the pentose phosphate pathway.

Gael Fp Bories, Scott Yeudall, Vlad Serbulea, Todd E Fox, Brant E Isakson, Norbert Leitinger.

Heme is an essential cofactor for numerous cellular functions, but release of free heme during hemolysis results in oxidative tissue damage, vascular dysfunction, and inflammation. Macrophages play a key protective role in heme clearance; however, the mechanisms that regulate metabolic adaptations that are required for effective heme degradation remain unclear. Here we demonstrate that heme loading drives a unique bioenergetic switch in macrophages, which involves a metabolic shift from oxidative phosphorylation toward glucose consumption. Metabolomic and transcriptional analysis of heme-loaded macrophages revealed that glucose is funneled into the pentose phosphate pathway (PPP), which is indispensable for efficient heme detoxification and required to maintain redox homeostasis. We demonstrate that the metabolic shift to the PPP is controlled by heme oxygenase-dependent generation of carbon monoxide. Finally, we show that PPP upregulation occurs in vivo in organ systems central to heme clearance and that PPP activity correlates with heme levels in mouse SCD. Together, our findings demonstrate that metabolic adaptation to heme detoxification in macrophages requires a shift to the PPP that is induced by heme-derived carbon monoxide, suggesting pharmacological targeting of macrophage metabolism as a novel therapeutic strategy to improve heme clearance in patients with hemolytic disorders.

DOI: https://doi.org/10.1182/blood.2020004964
Cancer Cell. 2020 Jun 02. pii: S1535-6108(20)30260-9. [Epub ahead of print]

Altered RNA Splicing by Mutant p53 Activates Oncogenic RAS Signaling in Pancreatic Cancer.

Luisa F Escobar-Hoyos, Alex Penson, Ram Kannan, Hana Cho, Chun-Hao Pan, Rohit K Singh, Lisa H Apken, G Aaron Hobbs, Renhe Luo, Nicolas Lecomte, Sruthi Babu, Fong Cheng Pan, Direna Alonso-Curbelo, John P Morris, Gokce Askan, Olivera Grbovic-Huezo, Paul Ogrodowski, Jonathan Bermeo, Joseph Saglimbeni, Cristian D Cruz, Yu-Jui Ho, Sharon A Lawrence, Jerry P Melchor, Grant A Goda, Karen Bai, Alessandro Pastore, Simon J Hogg, Srivatsan Raghavan, Peter Bailey, David K Chang, Andrew Biankin, Kenneth R Shroyer, Brian M Wolpin, Andrew J Aguirre, Andrea Ventura, Barry Taylor, Channing J Der, Daniel Dominguez, Daniel Kümmel, Andrea Oeckinghaus, Scott W Lowe, Robert K Bradley, Omar Abdel-Wahab, Steven D Leach.

  Pancreatic ductal adenocarcinoma (PDAC) is driven by co-existing mutations in KRAS and TP53. However, how these mutations collaborate to promote this cancer is unknown. Here, we uncover sequence-specific changes in RNA splicing enforced by mutant p53 which enhance KRAS activity. Mutant p53 increases expression of splicing regulator hnRNPK to promote inclusion of cytosine-rich exons within GTPase-activating proteins (GAPs), negative regulators of RAS family members. Mutant p53-enforced GAP isoforms lose cell membrane association, leading to heightened KRAS activity. Preventing cytosine-rich exon inclusion in mutant KRAS/p53 PDACs decreases tumor growth. Moreover, mutant p53 PDACs are sensitized to inhibition of splicing via spliceosome inhibitors. These data provide insight into co-enrichment of KRAS and p53 mutations and therapeutics targeting this mechanism in PDAC.

Keywords:  GAP17; GTPase signaling; KRAS; RNA splicing; SF3B1; hnRNPK; oncogenes; p53; pancreatic cancer; splicing inhibitors

DOI:  https://doi.org/10.1016/j.ccell.2020.05.010
J Cell Biol. 2020 Sep 07. pii: e201912144. [Epub ahead of print]219(9):

Critical role of mitochondrial ubiquitination and the OPTN-ATG9A axis in mitophagy.

Koji Yamano, Reika Kikuchi, Waka Kojima, Ryota Hayashida, Fumika Koyano, Junko Kawawaki, Takuji Shoda, Yosuke Demizu, Mikihiko Naito, Keiji Tanaka, Noriyuki Matsuda.

Damaged mitochondria are selectively eliminated in a process called mitophagy. Parkin and PINK1, proteins mutated in Parkinson's disease, amplify ubiquitin signals on damaged mitochondria with the subsequent activation of autophagic machinery. Autophagy adaptors are thought to link ubiquitinated mitochondria and autophagy through ATG8 protein binding. Here, we establish methods for inducing mitophagy by mitochondria-targeted ubiquitin chains and chemical-induced mitochondrial ubiquitination. Using these tools, we reveal that the ubiquitin signal is sufficient for mitophagy and that PINK1 and Parkin are unnecessary for autophagy activation per se. Furthermore, using phase-separated fluorescent foci, we show that the critical autophagy adaptor OPTN forms a complex with ATG9A vesicles. Disruption of OPTN-ATG9A interactions does not induce mitophagy. Therefore, in addition to binding ATG8 proteins, the critical autophagy adaptors also bind the autophagy core units that contribute to the formation of multivalent interactions in the de novo synthesis of autophagosomal membranes near ubiquitinated mitochondria.

DOI: https://doi.org/10.1083/jcb.201912144
Front Oncol. 2020 ;10 791

Beyond the Warburg Effect: N-Myc Contributes to Metabolic Reprogramming in Cancer Cells.

Go J Yoshida.

  Cancer cells generate large amounts of lactate derived from glucose regardless of the available oxygen level. Cancer cells finely control ATP synthesis by modulating the uptake of substrates and the activity of enzymes involved in aerobic glycolysis (Warburg effect), which enables them to adapt to the tumor microenvironment. However, increasing evidence suggests that mitochondrial metabolism, including the tricarboxylic acid (TCA) cycle, oxidative phosphorylation (OXPHOS), and glutaminolysis, is paradoxically activated in MYCN-amplified malignancies. Unlike non-amplified cells, MYCN-amplified cancer cells significantly promote OXPHOS-dependent ATP synthesis. Furthermore, tumor cells are differentially dependent on fatty acid β-oxidation (FAO) according to N-Myc status. Therefore, upregulation of FAO-associated enzymes is positively correlated with both N-Myc expression level and poor clinical outcome. This review explores therapeutic strategies targeting cancer stem-like cells for the treatment of tumors associated with MYCN amplification.

Keywords:  N-Myc; TCA cycle; acyclic retinoid; amino acid transporter; cancer stem-like cells; fatty acid β-oxidation; glutaminolysis; mitochondria

DOI:  https://doi.org/10.3389/fonc.2020.00791
J Biol Chem. 2020 Jun 15. pii: jbc.RA120.012962. [Epub ahead of print]

Dysfunctional telomeres trigger cellular senescence mediated by cyclic GMP-AMP synthase.

Salim Abdisalaam, Souparno Bhattacharya, Shibani Mukherjee, Debapriya Sinha, Kalayarasan Srinivasan, Mingrui Zhu, Esra A Akbay, Hesham A Sadek, Jerry W Shay, Asaithamby Aroumougame.

  Defective DNA damage response (DDR) signaling is a common mechanism that initiates and maintains the cellular senescence phenotype. Dysfunctional telomeres activate DDR signaling, genomic instability, and cellular senescence, but the links among these events remains unclear. Here, using an array of biochemical and imaging techniques, including a highly regulatable CRISPR/Cas9 strategy to induce DNA double-strand breaks specifically in the telomeres, chromatin immunoprecipitation, telomere immunofluorescence, fluorescence in situ hybridization (FISH), micronuclei imaging, and the telomere shortest length assay (TeSLA), we show that chromosome mis-segregation due to imperfect DDR signaling in response to dysfunctional telomeres creates a preponderance of chromatin fragments in the cytosol, which leads to a premature senescence phenotype. We found that this phenomenon is caused not by telomere shortening, but by cyclic GMP-AMP synthase (cGAS) recognizing cytosolic chromatin fragments and then activating the stimulator of interferon genes (STING) cytosolic DNA-sensing pathway and downstream interferon signaling. Significantly, genetic and pharmacological manipulation of cGAS not only attenuated immune signaling, but also prevented premature cellular senescence in response to dysfunctional telomeres. The findings of our study uncover a cellular intrinsic mechanism involving the cGAS-mediated cytosolic self-DNA-sensing pathway that initiates premature senescence independently of telomere shortening.

Keywords:  CRISPR/Cas; DNA damage; DNA damage response; chromatin; cyclic GMP-AMP synthase (cGAS); genome maintenance; micronuclei; senescence; telomere

DOI:  https://doi.org/10.1074/jbc.RA120.012962
Proc Natl Acad Sci U S A. 2020 Jun 15. pii: 202000943. [Epub ahead of print]

Macrophage metabolic reprogramming presents a therapeutic target in lupus nephritis.

Chenzhi Jing, Tomas Castro-Dopico, Nathan Richoz, Zewen K Tuong, John R Ferdinand, Laurence S C Lok, Kevin W Loudon, Gemma D Banham, Rebeccah J Mathews, Zaeem Cader, Susan Fitzpatrick, Kathleen R Bashant, Mariana J Kaplan, Arthur Kaser, Randall S Johnson, Michael P Murphy, Richard M Siegel, Menna R Clatworthy.

  IgG antibodies cause inflammation and organ damage in autoimmune diseases such as systemic lupus erythematosus (SLE). We investigated the metabolic profile of macrophages isolated from inflamed tissues in immune complex (IC)-associated diseases, including SLE and rheumatoid arthritis, and following IgG Fcγ receptor cross-linking. We found that human and mouse macrophages undergo a switch to glycolysis in response to IgG IC stimulation, mirroring macrophage metabolic changes in inflamed tissue in vivo. This metabolic reprogramming was required to generate a number of proinflammatory mediators, including IL-1β, and was dependent on mTOR and hypoxia-inducible factor (HIF)1α. Inhibition of glycolysis, or genetic depletion of HIF1α, attenuated IgG IC-induced activation of macrophages in vitro, including primary human kidney macrophages. In vivo, glycolysis inhibition led to a reduction in kidney macrophage IL-1β and reduced neutrophil recruitment in a murine model of antibody-mediated nephritis. Together, our data reveal the molecular mechanisms underpinning FcγR-mediated metabolic reprogramming in macrophages and suggest a therapeutic strategy for autoantibody-induced inflammation, including lupus nephritis.

Keywords:  Fcγ receptors; lupus nephritis; metabolism

DOI:  https://doi.org/10.1073/pnas.2000943117
Mol Cell. 2020 Jun 18. pii: S1097-2765(20)30259-8. [Epub ahead of print]78(6): 1055-1069

Ca2+ Fluxes and Cancer.

Saverio Marchi, Carlotta Giorgi, Lorenzo Galluzzi, Paolo Pinton.

  Ca2+ ions are key second messengers in both excitable and non-excitable cells. Owing to the rather pleiotropic nature of Ca2+ transporters and other Ca2+-binding proteins, however, Ca2+ signaling has attracted limited attention as a potential target of anticancer therapy. Here, we discuss cancer-associated alterations of Ca2+ fluxes at specific organelles as we identify novel candidates for the development of drugs that selectively target Ca2+ signaling in malignant cells.

Keywords:  IP(3)R; MCU complex; ORAI; TRP channels; mitochondrial permeability transition; store-operated calcium entry

DOI:  https://doi.org/10.1016/j.molcel.2020.04.017
Mitochondrion. 2020 Jun 13. pii: S1567-7249(20)30065-9. [Epub ahead of print]

Thinking outside the nucleus: mitochondrial DNA copy number in health and disease.

Christina A Castellani, Ryan J Longchamps, Jing Sun, Eliseo Guallar, Dan E Arking.

  Mitochondrial DNA copy number (mtDNA-CN) is a biomarker of mitochondrial function and levels of mtDNA-CN have been reproducibly associated with overall mortality and a number of age-related diseases, including cardiovascular disease, chronic kidney disease, and cancer. Recent advancements in techniques for estimating mtDNA-CN, in particular the use of DNA microarrays and next-generation sequencing data, have led to the comprehensive assessment of mtDNA-CN across these and other diseases and traits. The importance of mtDNA-CN measures to disease and these advancing technologies suggest the potential for mtDNA-CN to be a useful biomarker in the clinic. While the exact mechanism(s) underlying the association of mtDNA-CN with disease remain to be elucidated, we review the existing literature which supports roles for inflammatory dynamics, immune function and alterations to cell signaling as consequences of variation in mtDNA-CN. We propose that future studies should focus on characterizing longitudinal, cell-type and cross-tissue profiles of mtDNA-CN as well as improving methods for measuring mtDNA-CN which will expand the potential for its use as a clinical biomarker.

Keywords:  clinical biomarker; complex disease; mitochondrial DNA; mtDNA

DOI:  https://doi.org/10.1016/j.mito.2020.06.004
Acta Virol. 2020 ;64(2): 201-215

Metabolic reprogramming as a feast for virus replication.

K Polcicova, L Badurova, J Tomaskova.

Viral replication depends entirely on the energy and biosynthetic precursors supplied by the host cell metabolic network. Viruses actively reprogram host cell metabolism to establish optimal environment for their replication and spread. They stimulate the uptake of extracellular nutrients and predominantly modulate glucose, glutamine, and fatty acid metabolism to support anabolic metabolic pathways. Some viruses activate the process of aerobic glycolysis, divert the glycolytic carbon for biosynthetic reactions, and stimulate glutamine utilization to replenish tricarboxylic cycle intermediates. Others use glutamine carbon to promote de novo fatty acid synthesis, amino acid supply or glutathione production. The unique metabolic signature and different dependence of viral life cycle on the individual metabolic processes is therefore characteristic feature of almost each virus. Deeper understanding of how viruses alter cellular metabolic pathways or their upstream regulatory circuits may lead to development of more effective antiviral treatment strategies based on targeted metabolic inhibition. Keywords: virus infection; metabolism; glycolysis; glutamine metabolism; fatty acid synthesis; metabolic reprogramming; virus-host interaction.

DOI: https://doi.org/10.4149/av_2020_210
Sci Rep. 2020 Jun 17. 10(1): 9820

Psychological distress and lack of PINK1 promote bioenergetics alterations in peripheral blood mononuclear cells.

Mariana Grigoruţă, Ruben K Dagda, Ángel G Díaz-Sánchez, Alejandro Martínez-Martínez.

Psychological distress induces oxidative stress and alters mitochondrial metabolism in the nervous and immune systems. Psychological distress promotes alterations in brain metabolism and neurochemistry in wild-type (WT) rats in a similar manner as in Parkinsonian rats lacking endogenous PTEN-induced kinase 1 (PINK1), a serine/threonine kinase mutated in a recessive forms of Parkinson's disease. PINK1 has been extensively studied in the brain, but its physiological role in peripheral tissues and the extent to which it intersects with the neuroimmune axis is not clear. We surmised that PINK1 modulates the bioenergetics of peripheral blood mononuclear cells (PBMCs) under basal conditions or in situations that promote oxidative stress as psychological distress. By using an XF metabolic bioanalyzer, PINK1-KO-PBMCs showed significantly increased oxidative phosphorylation and basal glycolysis compared to WT cells and correlated with motor dysfunction. In addition, psychological distress enhanced the glycolytic capacity in PINK1-KO-PBMCs but not in WT-PBMCs. The level of antioxidant markers and brain-derived neurotrophic factor were altered in PINK1-KO-PBMCs and by psychological distress. In summary, our data suggest that PINK1 is critical for modulating the bioenergetics and antioxidant responses in PBMCs whereas lack of PINK1 upregulates compensatory glycolysis in response to oxidative stress induced by psychological distress.

DOI: https://doi.org/10.1038/s41598-020-66745-9
Metabolites. 2020 Jun 15. pii: E249. [Epub ahead of print]10(6):

Resolving Metabolic Heterogeneity in Experimental Models of the Tumor Microenvironment from a Stable Isotope Resolved Metabolomics Perspective.

Teresa W-M Fan, Richard M Higashi, Yelena Chernayavskaya, Andrew N Lane.

  The tumor microenvironment (TME) comprises complex interactions of multiple cell types that determines cell behavior and metabolism such as nutrient competition and immune suppression. We discuss the various types of heterogeneity that exist in solid tumors, and the complications this invokes for studies of TME. As human subjects and in vivo model systems are complex and difficult to manipulate, simpler 3D model systems that are compatible with flexible experimental control are necessary for studying metabolic regulation in TME. Stable Isotope Resolved Metabolomics (SIRM) is a valuable tool for tracing metabolic networks in complex systems, but at present does not directly address heterogeneous metabolism at the individual cell level. We compare the advantages and disadvantages of different model systems for SIRM experiments, with a focus on lung cancer cells, their interactions with macrophages and T cells, and their response to modulators in the immune microenvironment. We describe the experimental set up, illustrate results from 3D cultures and co-cultures of lung cancer cells with human macrophages, and outline strategies to address the heterogeneous TME.

Keywords:  3D cultures; stable isotope resolved metabolomics; tissue slices; tumor microenvironment

DOI:  https://doi.org/10.3390/metabo10060249
Immunol Rev. 2020 Jun 20.

Lipids, inflammasomes, metabolism, and disease.

Paras K Anand.

  Inflammasomes are multi-protein complexes that regulate the cleavage of cysteine protease caspase-1, secretion of inflammatory cytokines, and induction of inflammatory cell death, pyroptosis. Several members of the nod-like receptor family assemble inflammasome in response to specific ligands. An exception to this is the NLRP3 inflammasome which is activated by structurally diverse entities. Recent studies have suggested that NLRP3 might be a sensor of cellular homeostasis, and any perturbation in distinct metabolic pathways results in the activation of this inflammasome. Lipid metabolism is exceedingly important in maintaining cellular homeostasis, and it is recognized that cells and tissues undergo extensive lipid remodeling during activation and disease. Some lipids are involved in instigating chronic inflammatory diseases, and new studies have highlighted critical upstream roles for lipids, particularly cholesterol, in regulating inflammasome activation implying key functions for inflammasomes in diseases with defective lipid metabolism. The focus of this review is to highlight how lipids regulate inflammasome activation and how this leads to the progression of inflammatory diseases. The key roles of cholesterol metabolism in the activation of inflammasomes have been comprehensively discussed. Besides, the roles of oxysterols, fatty acids, phospholipids, and lipid second messengers are also summarized in the context of inflammasomes. The overriding theme is that lipid metabolism has numerous but complex functions in inflammasome activation. A detailed understanding of this area will help us develop therapeutic interventions for diseases where dysregulated lipid metabolism is the underlying cause.

Keywords:  NLRP3; cholesterol; homeostasis; inflammasome; lipids; metabolism

DOI:  https://doi.org/10.1111/imr.12891
Mitochondrion. 2020 Jun 12. pii: S1567-7249(20)30051-9. [Epub ahead of print]

Mitochondrial Ion Channels and Transporters in Plants: Prediction and Facts.

Ute C Vothknecht, Ildiko Szabo.

Mitochondria are crucial bioenergetic organelles for providing different metabolites, including ATP, to sustain cell growth both in animals and in plants. These organelles, delimited by two membranes (outer and inner mitochondrial membranes), maintain their function by an intensive communication with other organelles as well as with the cytosol. Transport of metabolites across the two membranes, but also that of inorganic ions, takes place through specific ion channels and transporters and plays a crucial role in ensuring an adequate ionic milieu within the mitochondria. In the present review we briefly summarize the current knowledge about plant mitochondrial ion channels and transporters in comparison to those of animal mitochondria and examine the possible molecular identity of the so far unidentified transport systems taking into account subcellular targeting predictions and data from literature.

DOI: https://doi.org/10.1016/j.mito.2020.05.007
Oncogene. 2020 Jun 15.

Senescence as a therapeutically relevant response to CDK4/6 inhibitors.

Verena Wagner, Jesús Gil.

Cyclin-dependent kinases 4 and 6 (CDK4/6) phosphorylate and inhibit retinoblastoma (RB) family proteins. Hyperphosphorylated RB releases E2F transcription factors, activating a transcriptional program that initiates S phase. Due to the critical role that this pathway has in regulating cell cycle progression, inhibiting CDK4/6 is an attractive therapeutic strategy. Indeed, CDK4/6 inhibitors in combination with antiestrogens produce a significant benefit in patients with ER+/HER2- breast cancer. Clinical trials are currently investigating if the use of CDK4/6 inhibitors alone or in combination can be extended to other cancer types. Inhibition of CDK4/6 can result in different cell fates such as quiescence, senescence, or apoptosis. Senescence is a stress response that can be induced by stimuli that include oncogenic activation, chemotherapy, irradiation, and targeted therapies such as CDK4/6 inhibitors. Senescent cells undergo a stable cell cycle arrest and produce a bioactive secretome that remodels their microenvironment and engages the immune system. In this review, we analyze the therapeutic relevance of senescence induction by CDK4/6 inhibitors. We also discuss how different therapies, including checkpoint inhibitors and drugs targeting MEK or PI3K, can be used in combination with CDK4/6 inhibitors to reinforce or exploit senescence. Recently, a lot of effort has been put into identifying compounds that selectively kill senescent cells (termed senolytics). Thus, sequential treatment with senolytics might be an additional strategy to potentiate the antitumor effects of CDK4/6 inhibitors.

DOI: https://doi.org/10.1038/s41388-020-1354-9
FEBS J. 2020 Jun 15.

Better to keep in touch: investigating inter-organelle cross-talk.

Michela Rossini, Paola Pizzo, Riccardo Filadi.

  The strategic importance for cellular organelles of being in contact with each other, exchanging messenger molecules, is nowadays well established. Different inter-organelle crosstalk pathways finely regulate multiple physiological cellular mechanisms and their dysregulation has been found to underlie different pathological conditions. In the last years, a great effort has been made to study such organelle interactions, to understand their functional roles within the cell and the molecules involved in their formation and/or modulation. In this contribution, some examples of organelle cross-talk and their contributions in regulating physiological processes are presented. Moreover, the pro and cons of the available methods for a proper, reliable investigation of membrane contact sites are described.

Keywords:  calcium; endoplasmic reticulum; intracellular signalling; lipids; membrane contact sites; microscopy; mitochondria; organelle contacts; organelles

DOI:  https://doi.org/10.1111/febs.15451
Nat Rev Drug Discov. 2020 Jun 17.

Targeting the Hippo pathway in cancer, fibrosis, wound healing and regenerative medicine.

Anwesha Dey, Xaralabos Varelas, Kun-Liang Guan.

The Hippo pathway is an evolutionarily conserved signalling pathway with key roles in organ development, epithelial homeostasis, tissue regeneration, wound healing and immune modulation. Many of these roles are mediated by the transcriptional effectors YAP and TAZ, which direct gene expression via control of the TEAD family of transcription factors. Dysregulated Hippo pathway and YAP/TAZ-TEAD activity is associated with various diseases, most notably cancer, making this pathway an attractive target for therapeutic intervention. This Review highlights the key findings from studies of Hippo pathway signalling across biological processes and diseases, and discusses new strategies and therapeutic implications of targeting this pathway.

DOI: https://doi.org/10.1038/s41573-020-0070-z
SAGE Open Med. 2020 ;8 2050312120926877

A review of nutrition and dietary interventions in oncology.

Ashley Gray, Brian N Dang, Theodore B Moore, Roger Clemens, Peter Pressman.

  The complex cellular mechanisms and inter-related pathways of cancer proliferation, evasion, and metastasis remain an emerging field of research. Over the last several decades, nutritional research has prominent role in identifying emerging adjuvant therapies in our fight against cancer. Nutritional and dietary interventions are being explored to improve the morbidity and mortality for cancer patients worldwide. In this review, we examine several dietary interventions and their proposed mechanisms against cancer as well as identifying limitations in the currently available literature. This review provides a comprehensive review of the cancer metabolism, dietary interventions used during cancer treatment, anti metabolic drugs, and their impact on nutritional deficiencies along with a critical review of the following diets: caloric restriction, intermittent fasting, ketogenic diet, Mediterranean diet, Japanese diet, and vegan diet.

Keywords:  Diet; caloric restriction; intermittent fasting; ketogenic diet; oncology

DOI:  https://doi.org/10.1177/2050312120926877
Nature. 2020 Jun 17.

Senolytic CAR T cells reverse senescence-associated pathologies.

Corina Amor, Judith Feucht, Josef Leibold, Yu-Jui Ho, Changyu Zhu, Direna Alonso-Curbelo, Jorge Mansilla-Soto, Jacob A Boyer, Xiang Li, Theodoros Giavridis, Amanda Kulick, Shauna Houlihan, Ellinor Peerschke, Scott L Friedman, Vladimir Ponomarev, Alessandra Piersigilli, Michel Sadelain, Scott W Lowe.

Cellular senescence is characterized by stable cell-cycle arrest and a secretory program that modulates the tissue microenvironment1,2. Physiologically, senescence serves as a tumour-suppressive mechanism that prevents the expansion of premalignant cells3,4 and has a beneficial role in wound-healing responses5,6. Pathologically, the aberrant accumulation of senescent cells generates an inflammatory milieu that leads to chronic tissue damage and contributes to diseases such as liver and lung fibrosis, atherosclerosis, diabetes and osteoarthritis1,7. Accordingly, eliminating senescent cells from damaged tissues in mice ameliorates the symptoms of these pathologies and even promotes longevity1,2,8-10. Here we test the therapeutic concept that chimeric antigen receptor (CAR) T cells that target senescent cells can be effective senolytic agents. We identify the urokinase-type plasminogen activator receptor (uPAR)11 as a cell-surface protein that is broadly induced during senescence and show that uPAR-specific CAR T cells efficiently ablate senescent cells in vitro and in vivo. CAR T cells that target uPAR extend the survival of mice with lung adenocarcinoma that are treated with a senescence-inducing combination of drugs, and restore tissue homeostasis in mice in which liver fibrosis is induced chemically or by diet. These results establish the therapeutic potential of senolytic CAR T cells for senescence-associated diseases.

DOI: https://doi.org/10.1038/s41586-020-2403-9
Proc Natl Acad Sci U S A. 2020 Jun 19. pii: 202001989. [Epub ahead of print]

Primordial emergence of a nucleic acid-binding protein via phase separation and statistical ornithine-to-arginine conversion.

Liam M Longo, Dragana Despotović, Orit Weil-Ktorza, Matthew J Walker, Jagoda Jabłońska, Yael Fridmann-Sirkis, Gabriele Varani, Norman Metanis, Dan S Tawfik.

  De novo emergence demands a transition from disordered polypeptides into structured proteins with well-defined functions. However, can polypeptides confer functions of evolutionary relevance, and how might such polypeptides evolve into modern proteins? The earliest proteins present an even greater challenge, as they were likely based on abiotic, spontaneously synthesized amino acids. Here we asked whether a primordial function, such as nucleic acid binding, could emerge with ornithine, a basic amino acid that forms abiotically yet is absent in modern-day proteins. We combined ancestral sequence reconstruction and empiric deconstruction to unravel a gradual evolutionary trajectory leading from a polypeptide to a ubiquitous nucleic acid-binding protein. Intermediates along this trajectory comprise sequence-duplicated functional proteins built from 10 amino acid types, with ornithine as the only basic amino acid. Ornithine side chains were further modified into arginine by an abiotic chemical reaction, improving both structure and function. Along this trajectory, function evolved from phase separation with RNA (coacervates) to avid and specific double-stranded DNA binding. Our results suggest that phase-separating polypeptides may have been an evolutionary resource for the emergence of early proteins, and that ornithine, together with its postsynthesis modification to arginine, could have been the earliest basic amino acids.

Keywords:  abiotic amino acids; helix-hairpin-helix; prebiotic chemistry; protein evolution; protein synthesis

DOI:  https://doi.org/10.1073/pnas.2001989117
Nat Commun. 2020 Jun 16. 11(1): 3059

Recurrent horizontal transfer identifies mitochondrial positive selection in a transmissible cancer.

Andrea Strakova, Thomas J Nicholls, Adrian Baez-Ortega, Máire Ní Leathlobhair, Alexander T Sampson, Katherine Hughes, Isobelle A G Bolton, Kevin Gori, Jinhong Wang, Ilona Airikkala-Otter, Janice L Allen, Karen M Allum, Clara L Arnold, Leontine Bansse-Issa, Thinlay N Bhutia, Jocelyn L Bisson, Kelli Blank, Cristóbal Briceño, Artemio Castillo Domracheva, Anne M Corrigan, Hugh R Cran, Jane T Crawford, Stephen M Cutter, Eric Davis, Karina F de Castro, Andrigo B De Nardi, Anna P de Vos, Laura Delgadillo Keenan, Edward M Donelan, Adela R Espinoza Huerta, Ibikunle A Faramade, Mohammed Fazil, Eleni Fotopoulou, Skye N Fruean, Fanny Gallardo-Arrieta, Olga Glebova, Pagona G Gouletsou, Rodrigo F Häfelin Manrique, Joaquim J G P Henriques, Rodrigo S Horta, Natalia Ignatenko, Yaghouba Kane, Cathy King, Debbie Koenig, Ada Krupa, Steven J Kruzeniski, Marta Lanza-Perea, Mihran Lazyan, Adriana M Lopez Quintana, Thibault Losfelt, Gabriele Marino, Simón Martínez Castañeda, Mayra F Martínez-López, Bedan M Masuruli, Michael Meyer, Edward J Migneco, Berna Nakanwagi, Karter B Neal, Winifred Neunzig, Sally J Nixon, Antonio Ortega-Pacheco, Francisco Pedraza-Ordoñez, Maria C Peleteiro, Katherine Polak, Ruth J Pye, Juan C Ramirez-Ante, John F Reece, Jose Rojas Gutierrez, Haleema Sadia, Sheila K Schmeling, Olga Shamanova, Alan G Sherlock, Audrey E Steenland-Smit, Alla Svitich, Lester J Tapia Martínez, Ismail Thoya Ngoka, Cristian G Torres, Elizabeth M Tudor, Mirjam G van der Wel, Bogdan A Vițălaru, Sevil A Vural, Oliver Walkinton, Alvaro S Wehrle-Martinez, Sophie A E Widdowson, Irina Zvarich, Patrick F Chinnery, Maria Falkenberg, Claes M Gustafsson, Elizabeth P Murchison.

Autonomous replication and segregation of mitochondrial DNA (mtDNA) creates the potential for evolutionary conflict driven by emergence of haplotypes under positive selection for 'selfish' traits, such as replicative advantage. However, few cases of this phenomenon arising within natural populations have been described. Here, we survey the frequency of mtDNA horizontal transfer within the canine transmissible venereal tumour (CTVT), a contagious cancer clone that occasionally acquires mtDNA from its hosts. Remarkably, one canine mtDNA haplotype, A1d1a, has repeatedly and recently colonised CTVT cells, recurrently replacing incumbent CTVT haplotypes. An A1d1a control region polymorphism predicted to influence transcription is fixed in the products of an A1d1a recombination event and occurs somatically on other CTVT mtDNA backgrounds. We present a model whereby 'selfish' positive selection acting on a regulatory variant drives repeated fixation of A1d1a within CTVT cells.

DOI: https://doi.org/10.1038/s41467-020-16765-w
Invest Ophthalmol Vis Sci. 2020 Jun 03. 61(6): 42

Opa1 Deficiency Leads to Diminished Mitochondrial Bioenergetics With Compensatory Increased Mitochondrial Motility.

Shanshan Sun, Irina Erchova, Frank Sengpiel, Marcela Votruba.

Purpose: Retinal ganglion cells (RGCs) are susceptible to mitochondrial deficits and also the major cell type affected in patients with mutations in the OPA1 gene in autosomal dominant optic atrophy (ADOA). Here, we characterized mitochondria in RGCs in vitro from a heterozygous B6; C3-Opa1Q285STOP (Opa1+/-) mouse model to investigate mitochondrial changes underlying the pathology in ADOA.
Methods: Mouse RGCs were purified from wild-type and Opa1+/- mouse retina by two-step immunopanning. The mitochondria in neurites of RGCs were labeled with MitoTracker Red for structure and motility measurement by time-lapse imaging. Mitochondrial bioenergetics were determined by the real-time measurement of oxygen consumption rate using a Seahorse XFe 96 Extracellular Flux Analyzer.
Results: We observed a significant decrease in mitochondrial length in Opa1+/- RGCs with a remarkably higher proportion and density of motile mitochondria along the neurites. We also observed an increased transport velocity with a higher number of contacts between mitochondria in Opa1+/- RGC neurites. The oxygen consumption assays showed a severe impairment in basal respiration, Adenosine triphosphate-linked (ATP-linked) oxygen consumption, as well as reserve respiratory capacity, in RGCs from Opa1+/- mouse retina.
Conclusions: Opa1 deficiency leads to significant fragmentation of mitochondrial morphology, activation of mitochondrial motility and impaired respiratory function in RGCs from the B6; C3-Opa1Q285STOP mouse model. This highlights the significant alterations in the intricate interplay between mitochondrial morphology, motility, and energy production in RGCs with Opa1 deficiency long before the onset of clinical symptoms of the pathology.

DOI: https://doi.org/10.1167/iovs.61.6.42
Oncogene. 2020 Jun 15.

Iron chelation inhibits mTORC1 signaling involving activation of AMPK and REDD1/Bnip3 pathways.

Chaowei Shang, Hongyu Zhou, Wang Liu, Tao Shen, Yan Luo, Shile Huang.

The mammalian target of rapamycin (mTOR) functions as two complexes (mTORC1 and mTORC2), regulating cell growth and metabolism. Aberrant mTOR signaling occurs frequently in cancers, so mTOR has become an attractive target for cancer therapy. Iron chelators have emerged as promising anticancer agents. However, the mechanisms underlying the anticancer action of iron chelation are not fully understood. Particularly, reports on the effects of iron chelation on mTOR complexes are inconsistent or controversial. Here, we found that iron chelators consistently inhibited mTORC1 signaling, which was blocked by pretreatment with ferrous sulfate. Mechanistically, iron chelation-induced mTORC1 inhibition was not related to ROS induction, copper chelation, or PP2A activation. Instead, activation of AMPK pathway mainly and activation of both HIF-1/REDD1 and Bnip3 pathways partially contribute to iron chelation-induced mTORC1 inhibition. Our findings indicate that iron chelation inhibits mTORC1 via multiple pathways and iron is essential for mTORC1 activation.

DOI: https://doi.org/10.1038/s41388-020-1366-5
Mol Cell. 2020 Jun 18. pii: S1097-2765(20)30355-5. [Epub ahead of print]78(6): 1019-1033

Targeting Metabolism to Improve the Tumor Microenvironment for Cancer Immunotherapy.

Jackie E Bader, Kelsey Voss, Jeffrey C Rathmell.

The growing field of immune metabolism has revealed promising indications for metabolic targets to modulate anti-cancer immunity. Combination therapies involving metabolic inhibitors with immune checkpoint blockade (ICB), chemotherapy, radiation, and/or diet now offer new approaches for cancer therapy. However, it remains uncertain how to best utilize these strategies in the context of the complex tumor microenvironment (TME). Oncogene-driven changes in tumor cell metabolism can impact the TME to limit immune responses and present barriers to cancer therapy. These changes also reveal opportunities to reshape the TME by targeting metabolic pathways to favor immunity. Here we explore current strategies that shift immune cell metabolism to pro-inflammatory states in the TME and highlight a need to better replicate physiologic conditions to select targets, clarify mechanisms, and optimize metabolic inhibitors. Unifying our understanding of these pathways and interactions within the heterogenous TME will be instrumental to advance this promising field and enhance immunotherapy.

DOI: https://doi.org/10.1016/j.molcel.2020.05.034
Nat Rev Nephrol. 2020 Jun 19.

Genomic profiling in renal cell carcinoma.

Nazli Dizman, Errol J Philip, Sumanta K Pal.

The treatment landscape of metastatic renal cell carcinoma (RCC) has been revolutionized over the past two decades, bringing forth an era in which more than a dozen therapeutic agents are now available to treat patients. As a consequence, personalized care has become a critical part of developing effective treatment guidelines and improving patient outcomes. One of the most important emerging aspects of precision medicine in cancer is matching patients and treatments based on the genomic characteristics of an individual and their tumour. Despite the lack of a single genomic predictor of treatment response or prognostication feature in RCC, emerging research suggests that the identification of such markers remains promising. Mutations in VHL and alterations in its downstream pathways are the mainstay of RCC development and progression. However, the predictive value of VHL mutations has been questioned. Further research has examined mutations in genes involved in chromosome remodelling (for example, PBRM1, BAP1 and SETD2), DNA methylation and DNA damage repair, all of which have been associated with clinical outcomes. Here, we provide a comprehensive overview of genomic evidence in the context of RCC and its potential predictive and prognostic value.

DOI: https://doi.org/10.1038/s41581-020-0301-x