Anastasia I, Ilacqua N, Raimondi A, Lemieux P, Ghandehari-Alavijeh R, Faure G, et al. Mitochondria-rough-ER contacts in the liver regulate systemic lipid homeostasis. Cell Rep. 2021;34:108873.
Article
CAS
PubMed
Google Scholar
Hurtley SM. It’s a wrap(pER). Ash Jesse CS, editor. Science (80- ) [Internet]. 2021;372:142–3. http://science.sciencemag.org/content/372/6538/142.5.abstract.
Ilacqua N, Anastasia I, Raimondi A, Lemieux P, de Aguiar Vallim TQ, Toth K, et al. A three-organelle complex made by wrappER contacts with peroxisomes and mitochondria responds to liver lipid flux changes. J Cell Sci. 2021;135:1–11.
Google Scholar
Bergey CM. Western diet shifts immune cell balance. Elife. 2021;10:1–3.
Article
Google Scholar
Furman D, Campisi J, Verdin E, Carrera-Bastos P, Targ S, Franceschi C, et al. Chronic inflammation in the etiology of disease across the life span. Nat Med [Internet]. 2019;25:1822–32. https://doi.org/10.1038/s41591-019-0675-0.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang Y, Li S, Li F, Lv C, Yang Q. High-fat diet impairs ferroptosis and promotes cancer invasiveness via downregulating tumor suppressor ACSL4 in lung adenocarcinoma. Biol Direct. 2021;16:1–13.
Article
PubMed
PubMed Central
Google Scholar
Augusto-Oliveira M, Verkhratsky A. Lifestyle-dependent microglial plasticity: training the brain guardians. Biol Direct [Internet]. 2021;16:1–14. https://doi.org/10.1186/s13062-021-00297-4.
Article
Google Scholar
Piccolis M, Bond LM, Kampmann M, Pulimeno P, Chitraju C, Jayson CBK, et al. Probing the global cellular responses to lipotoxicity caused by saturated fatty acids. Mol Cell [Internet]. 2019;74:32-44.e8. https://doi.org/10.1016/j.molcel.2019.01.036.
Article
CAS
PubMed
Google Scholar
Miller LL, Bly CG, Watson ML, Bale WF. The dominant role of the liver in plasma protein synthesis. J Exp Med. 1951;94:431–53.
Article
CAS
PubMed
PubMed Central
Google Scholar
Walther TC, Farese RV. Lipid droplets and cellular lipid metabolism. Annu Rev Biochem. 2012;81:687–714.
Article
CAS
PubMed
PubMed Central
Google Scholar
Heeren J, Scheja L. Metabolic-associated fatty liver disease and lipoprotein metabolism. Mol Metab [Internet]. 2021;50:101238. https://doi.org/10.1016/j.molmet.2021.101238.
Article
CAS
PubMed
Google Scholar
Darwisch W, von Spangenberg M, Lehmann J, Singin Ö, Deubert G, Kühl S, et al. Cerebellar and hepatic alterations in ACBD5-deficient mice are associated with unexpected, distinct alterations in cellular lipid homeostasis. Commun Biol [Internet]. 2020;3:1–19. https://doi.org/10.1038/s42003-020-01442-x.
Article
CAS
Google Scholar
Hanrahan BR, Tank JL, Speir SL, Matt T, Christopher SF, Mahl UH, et al. Altered SYNJ2BP-mediated mitochondrial-ER contacts in motor neuron disease. Neurobiol Dis [Internet]. 2022. https://doi.org/10.1016/j.scitotenv.2021.149501.
Article
Google Scholar
Chang BHJ, Liao W, Li L, Nakamuta M, Mack D, Chan L. Liver-specific inactivation of the abetalipoproteinemia gene completely abrogates very low density lipoprotein/low density lipoprotein production in a viable conditional knockout mouse. J Biol Chem. 1999;274:6051–5.
Article
CAS
PubMed
Google Scholar
Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O, et al. Highly accurate protein structure prediction with AlphaFold. Nature [Internet]. 2021;596:583–9. https://doi.org/10.1038/s41586-021-03819-2.
Article
CAS
PubMed
Google Scholar
Hung V, Lam SS, Udeshi ND, Svinkina T, Guzman G, Mootha VK, et al. Proteomic mapping of cytosol-facing outer mitochondrial and ER membranes in living human cells by proximity biotinylation. Elife [Internet]. 2017;6:e24463.
Article
PubMed
Google Scholar
Antonicka H, Lin ZY, Janer A, Aaltonen MJ, Weraarpachai W, Gingras AC, et al. A high-density human mitochondrial proximity interaction network. Cell Metab [Internet]. 2020;32:479-497.e9. https://doi.org/10.1016/j.cmet.2020.07.017.
Article
CAS
PubMed
Google Scholar
Nemoto Y, De Camilli P. Recruitment of an alternatively spliced form of synaptojanin 2 to mitochondria by the interaction with the PDZ domain of a mitochondrial outer membrane protein. EMBO J [Internet]. 1999;18:2991–3006. https://doi.org/10.1093/emboj/18.11.2991.
Article
CAS
PubMed
Google Scholar
Horie C, Suzuki H, Sakaguchi M, Mihara K. Characterization of signal that directs C-tail–anchored proteins to mammalian mitochondrial outer membrane. Mol Biol Cell. 2002;13:1615–25.
Article
CAS
PubMed
PubMed Central
Google Scholar
De Brito OM, Scorrano L. Mitofusin 2 tethers endoplasmic reticulum to mitochondria. Nature. 2008;456:605–10.
Article
PubMed
Google Scholar
Hua R, Cheng D, Coyaud É, Freeman S, Di Pietro E, Wang Y, et al. VAPs and ACBD5 tether peroxisomes to the ER for peroxisome maintenance and lipid homeostasis. J Cell Biol. 2017;216:367–77.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhao YG, Liu N, Miao G, Chen Y, Zhao H, Zhang H. The ER contact proteins VAPA/B interact with multiple autophagy proteins to modulate autophagosome biogenesis. Curr Biol [Internet]. 2018;28:1234-1245.e4. https://doi.org/10.1016/j.cub.2018.03.002.
Article
CAS
PubMed
Google Scholar
Sebastián D, Hernández-Alvarez MI, Segalés J, Sorianello E, Muñoz JP, Sala D, et al. Mitofusin 2 (Mfn2) links mitochondrial and endoplasmic reticulum function with insulin signaling and is essential for normal glucose homeostasis. Proc Natl Acad Sci U S A. 2012;109:5523–8.
Article
PubMed
PubMed Central
Google Scholar
Ho J, Tumkaya T, Aryal S, Choi H, Claridge-Chang A. Moving beyond P values: data analysis with estimation graphics. Nat Methods [Internet]. 2019;16:565–6. https://doi.org/10.1038/s41592-019-0470-3.
Article
CAS
PubMed
Google Scholar
Calin-Jageman RJ, Cumming G. The new statistics for better science: ask how much, how uncertain, and what else is known. Am Stat. 2019;73:271–80.
Article
PubMed
PubMed Central
Google Scholar
Arruda AP, Pers BM, Parlakgül G, Güney E, Inouye K, Hotamisligil GS. Chronic enrichment of hepatic endoplasmic reticulum-mitochondria contact leads to mitochondrial dysfunction in obesity. Nat Med. 2014;20:1427–35.
Article
CAS
PubMed
PubMed Central
Google Scholar
Giacomello M, Pellegrini L. The coming of age of the mitochondria–ER contact: a matter of thickness. Cell Death Differ [Internet]. 2016;23:1417–27. https://doi.org/10.1038/cdd.2016.52.
Article
CAS
PubMed
Google Scholar
Sood A, Jeyaraju DV, Prudent J, Caron A, Lemieux P, McBride HM, et al. A Mitofusin-2–dependent inactivating cleavage of Opa1 links changes in mitochondria cristae and ER contacts in the postprandial liver. Proc Natl Acad Sci. 2014;11:16017–22.
Article
Google Scholar
Hamilton RL, Wong JS, Cham CM, Nielsen LB, Young SG. Chylomicron-sized lipid particles are formed in the setting of apolipoprotein B deficiency. J Lipid Res [Internet]. 1998;39:1543–57. https://doi.org/10.1016/S0022-2275(20)32183-0.
Article
CAS
PubMed
Google Scholar
Pekmezovic M, Hovhannisyan H, Gresnigt MS, Iracane E, Oliveira-Pacheco J, Siscar-Lewin S, et al. Candida pathogens induce protective mitochondria-associated type I interferon signalling and a damage-driven response in vaginal epithelial cells. Nat Microbiol [Internet]. 2021;6:643–57. https://doi.org/10.1038/s41564-021-00875-2.
Article
CAS
PubMed
Google Scholar
Cheng X, Geng F, Pan M, Wu X, Zhong Y, Wang C, et al. Targeting DGAT1 ameliorates glioblastoma by increasing fat catabolism and oxidative stress. Cell Metab. 2020;32:229-242.e8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Solsona-Vilarrasa E, Fucho R, Torres S, Nuñez S, Nuño-Lámbarri N, Enrich C, et al. Cholesterol enrichment in liver mitochondria impairs oxidative phosphorylation and disrupts the assembly of respiratory supercomplexes. Redox Biol [Internet]. 2019;24:101214. https://doi.org/10.1016/j.redox.2019.101214.
Article
CAS
PubMed
Google Scholar
Wei E, Ben Ali Y, Lyon J, Wang H, Nelson R, Dolinsky VW, et al. Loss of TGH/Ces3 in mice decreases blood lipids, improves glucose tolerance, and increases energy expenditure. Cell Metab. 2010;11:183–93.
Article
CAS
PubMed
Google Scholar
Shelness GS, Sellers JA. Very-low-density lipoprotein assembly and secretion. Curr Opin Lipidol. 2001;12:151–7.
Article
CAS
PubMed
Google Scholar
Lindner K, Beckenbauer K, van Ek LC, Titeca K, de Leeuw SM, Awwad K, et al. Isoform- and cell-state-specific lipidation of ApoE in astrocytes. Cell Rep [Internet]. 2022;38:110435. https://doi.org/10.1016/j.celrep.2022.110435.
Article
CAS
PubMed
Google Scholar
Syed GH, Khan M, Yang S, Siddiqui A. Hepatitis C virus lipoviroparticles assemble in the endoplasmic reticulum (ER) and bud off from the ER to the Golgi compartment in COPII vesicles. J Virol. 2017;91:e00499-e517.
Article
CAS
PubMed
PubMed Central
Google Scholar
Loomba R, Friedman SL, Shulman GI. Mechanisms and disease consequences of nonalcoholic fatty liver disease. Cell [Internet]. 2021;184:2537–64.
Article
CAS
PubMed
Google Scholar
Vance JE. Phospholipid synthesis in a membrane fraction associated with mitochondria. J Biol Chem. 1990;265:7248–56.
Article
CAS
PubMed
Google Scholar
Vance JE. Inter-organelle membrane contact sites: implications for lipid metabolism. Biol Direct. 2020;15:1–8.
Article
Google Scholar
Raabe M, Véniant MM, Sullivan MA, Zlot CH, Björkegren J, Nielsen LB, et al. Analysis of the role of microsomal triglyceride transfer protein in the liver of tissue-specific knockout mice. J Clin Invest. 1999;103:1287–98.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rizzuto R, Pinton P, Carrington W, Fay FS, Fogarty KE, Lifshitz LM, et al. Close contacts with the endoplasmic reticulum as determinants of mitochondrial Ca2+ responses. Science (80- ). 1998;280:1763–6.
Article
CAS
Google Scholar
Ilacqua N, Anastasia I, Pellegrini L. Isolation and analysis of fractions enriched in WrappER-associated mitochondria from mouse liver. STAR Protoc. 2021;2:100752.
Article
CAS
PubMed
PubMed Central
Google Scholar
Grassian AR, Metallo CM, Coloff JL, Stephanopoulos G, Brugge JS. Erk regulation of pyruvate dehydrogenase flux through PDK4 modulates cell proliferation. Genes Dev [Internet]. 2011;25:1716–33.
Article
CAS
PubMed
Google Scholar
Harbauer AB, Hees JT, Wanderoy S, Segura I, Gibbs W, Cheng Y, et al. Neuronal mitochondria transport Pink1 mRNA via synaptojanin 2 to support local mitophagy. Neuron [Internet]. 2022;110:1516-1531.e9. https://doi.org/10.1016/j.neuron.2022.01.035.
Article
CAS
PubMed
Google Scholar
Puchalska P, Crawford PA. Multi-dimensional roles of ketone bodies in fuel metabolism, signaling, and therapeutics. Cell Metab [Internet]. 2017;25:262–84. https://doi.org/10.1016/j.cmet.2016.12.022.
Article
CAS
PubMed
Google Scholar
Qin W, Myers SA, Carey DK, Carr SA, Ting AY. Spatiotemporally-resolved mapping of RNA binding proteins via functional proximity labeling reveals a mitochondrial mRNA anchor promoting stress recovery. Nat Commun [Internet]. 2021. https://doi.org/10.1038/s41467-021-25259-2.
Article
PubMed
PubMed Central
Google Scholar
Hallgren J, Tsirigos KD, Damgaard Pedersen M, Juan J, Armenteros A, Marcatili P, et al. DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks. bioRxiv [Internet]. 2022;2022.04.08.487609. https://doi.org/10.1101/2022.04.08.487609.abstract.
Ponting CP, Phillips C, Davies KE, Blake DJ. PDZ domains: targeting signalling molecules to sub-membraneous sites. BioEssays. 1997;19:469–79.
Article
CAS
PubMed
Google Scholar
Van Ham M, Hendriks W. PDZ domains: glue and guide. Mol Biol Rep. 2003;30:69–82.
Article
PubMed
Google Scholar
Bean C, Audano M, Varanita T, Favaretto F, Medaglia M, Gerdol M, et al. The mitochondrial protein Opa1 promotes adipocyte browning that is dependent on urea cycle metabolites. Nat Metab. 2021;3:1633–47.
Article
CAS
PubMed
Google Scholar
Haskins N, Bhuvanendran S, Anselmi C, Gams A, Kanholm T, Kocher KM, et al. Mitochondrial enzymes of the urea cycle cluster at the inner mitochondrial membrane. Front Physiol. 2021;11:1–17.
Article
Google Scholar
De Chiara F, Heebøll S, Marrone G, Montoliu C, Hamilton-Dutoit S, Ferrandez A, et al. Urea cycle dysregulation in non-alcoholic fatty liver disease. J Hepatol. 2018;69:905–15.
Article
PubMed
Google Scholar
Arnold L, Perrin H, de Chanville CB, Saclier M, Hermand P, Poupel L, et al. CX3CR1 deficiency promotes muscle repair and regeneration by enhancing macrophage ApoE production. Nat Commun [Internet]. 2015;6:8972.
Article
CAS
PubMed
PubMed Central
Google Scholar
Becker L, Gharib SA, Irwin AD, Wijsman E, Vaisar T, Oram JF, et al. A macrophage sterol-responsive network linked to atherogenesis. Cell Metab [Internet]. 2010;11:125–35.
Article
CAS
PubMed
Google Scholar
Garewal M, Zhang L, Ren G. Optimized negative-staining protocol for examining lipid-protein interactions by electron microscopy. Methods Mol Biol [Internet]. 2013 [cited 2019 May 16]. p. 111–8. http://www.ncbi.nlm.nih.gov/pubmed/23404274.
Pfaffl MW. A new mathematical model for relative quantification in real-time RT–PCR. Mon Not R Astron Soc. 2001;29:2002–7.
Google Scholar
Warrington JA, Nair A, Mahadevappa M, Tsyganskaya M. Comparison of human adult and fetal expression and identification of 535 housekeeping/maintenance genes. Physiol Genom. 2000;2000:143–7.
Article
Google Scholar
Bustin SA, Beaulieu JF, Huggett J, Jaggi R, Kibenge FSB, Olsvik PA, et al. MIQE précis: practical implementation of minimum standard guidelines for fluorescence-based quantitative real-time PCR experiments. BMC Mol Biol. 2010;11:1–5.
Article
Google Scholar
Cox J, Mann M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol. 2008;26:1367–72.
Article
CAS
PubMed
Google Scholar
Pascovici D, Handler DCL, Wu JX, Haynes PA. Multiple testing corrections in quantitative proteomics: a useful but blunt tool. Proteomics. 2016;16:2448–53.
Article
CAS
PubMed
Google Scholar
Raudvere U, Kolberg L, Kuzmin I, Arak T, Adler P, Peterson H, et al. G:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update). Nucleic Acids Res. 2019;47:W191–8.
Article
CAS
PubMed
PubMed Central
Google Scholar