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      Copper is an essential regulator of the autophagic kinases ULK1/2 to drive lung adenocarcinoma

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          Abstract

          While the transition metal copper (Cu) is an essential nutrient that is conventionally viewed as a static cofactor within enzyme active sites, a nontraditional role for Cu as a modulator of kinase signaling is emerging. We discovered that Cu is required for the activity of the autophagic kinases ULK1/2 through a direct Cu-ULK1/2 interaction. Genetic loss of the Cu transporter Ctr1 or mutations in ULK1 that disrupt Cu-binding reduced ULK1/2-dependent signaling and autophagosome complex formation. Elevated intracellular Cu levels are associated with starvation induced autophagy and sufficient to enhance ULK1 kinase activity and in turn autophagic flux. The growth and survival of lung tumors driven by KRAS G12D is diminished in the absence of Ctr1, depends on ULK1 Cu-binding, and is associated with reduced autophagy levels and signaling. These findings suggest a molecular basis for exploiting Cu-chelation therapy to forestall autophagy signaling to limit proliferation and survival in cancer.

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          Most cited references61

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          AMPK and mTOR regulate autophagy through direct phosphorylation of Ulk1.

          Autophagy is a process by which components of the cell are degraded to maintain essential activity and viability in response to nutrient limitation. Extensive genetic studies have shown that the yeast ATG1 kinase has an essential role in autophagy induction. Furthermore, autophagy is promoted by AMP activated protein kinase (AMPK), which is a key energy sensor and regulates cellular metabolism to maintain energy homeostasis. Conversely, autophagy is inhibited by the mammalian target of rapamycin (mTOR), a central cell-growth regulator that integrates growth factor and nutrient signals. Here we demonstrate a molecular mechanism for regulation of the mammalian autophagy-initiating kinase Ulk1, a homologue of yeast ATG1. Under glucose starvation, AMPK promotes autophagy by directly activating Ulk1 through phosphorylation of Ser 317 and Ser 777. Under nutrient sufficiency, high mTOR activity prevents Ulk1 activation by phosphorylating Ulk1 Ser 757 and disrupting the interaction between Ulk1 and AMPK. This coordinated phosphorylation is important for Ulk1 in autophagy induction. Our study has revealed a signalling mechanism for Ulk1 regulation and autophagy induction in response to nutrient signalling.
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            Is Open Access

            Comprehensive molecular profiling of lung adenocarcinoma

            Adenocarcinoma of the lung is the leading cause of cancer death worldwide. Here we report molecular profiling of 230 resected lung adenocarcinomas using messenger RNA, microRNA and DNA sequencing integrated with copy number, methylation and proteomic analyses. High rates of somatic mutation were seen (mean 8.9 mutations per megabase). Eighteen genes were statistically significantly mutated, including RIT1 activating mutations and newly described loss-of-function MGA mutations which are mutually exclusive with focal MYC amplification. EGFR mutations were more frequent in female patients, whereas mutations in RBM10 were more common in males. Aberrations in NF1, MET, ERBB2 and RIT1 occurred in 13% of cases and were enriched in samples otherwise lacking an activated oncogene, suggesting a driver role for these events in certain tumours. DNA and mRNA sequence from the same tumour highlighted splicing alterations driven by somatic genomic changes, including exon 14 skipping in MET mRNA in 4% of cases. MAPK and PI(3)K pathway activity, when measured at the protein level, was explained by known mutations in only a fraction of cases, suggesting additional, unexplained mechanisms of pathway activation. These data establish a foundation for classification and further investigations of lung adenocarcinoma molecular pathogenesis.
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              p62/SQSTM1 binds directly to Atg8/LC3 to facilitate degradation of ubiquitinated protein aggregates by autophagy.

              Protein degradation by basal constitutive autophagy is important to avoid accumulation of polyubiquitinated protein aggregates and development of neurodegenerative diseases. The polyubiquitin-binding protein p62/SQSTM1 is degraded by autophagy. It is found in cellular inclusion bodies together with polyubiquitinated proteins and in cytosolic protein aggregates that accumulate in various chronic, toxic, and degenerative diseases. Here we show for the first time a direct interaction between p62 and the autophagic effector proteins LC3A and -B and the related gamma-aminobutyrate receptor-associated protein and gamma-aminobutyrate receptor-associated-like proteins. The binding is mediated by a 22-residue sequence of p62 containing an evolutionarily conserved motif. To monitor the autophagic sequestration of p62- and LC3-positive bodies, we developed a novel pH-sensitive fluorescent tag consisting of a tandem fusion of the red, acid-insensitive mCherry and the acid-sensitive green fluorescent proteins. This approach revealed that p62- and LC3-positive bodies are degraded in autolysosomes. Strikingly, even rather large p62-positive inclusion bodies (2 microm diameter) become degraded by autophagy. The specific interaction between p62 and LC3, requiring the motif we have mapped, is instrumental in mediating autophagic degradation of the p62-positive bodies. We also demonstrate that the previously reported aggresome-like induced structures containing ubiquitinated proteins in cytosolic bodies are dependent on p62 for their formation. In fact, p62 bodies and these structures are indistinguishable. Taken together, our results clearly suggest that p62 is required both for the formation and the degradation of polyubiquitin-containing bodies by autophagy.
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                Author and article information

                Journal
                100890575
                21417
                Nat Cell Biol
                Nat Cell Biol
                Nature cell biology
                1465-7392
                1476-4679
                13 February 2020
                16 March 2020
                April 2020
                04 November 2020
                : 22
                : 4
                : 412-424
                Affiliations
                [1 ]Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
                [2 ]Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA, 19104, USA.
                [3 ]Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
                Author notes

                Author contributions. T.T. and J.M.P contributed equally to this work. T.T. contributed to the study design, generated cell lines and plasmids, prepared samples for ICP-MS, performed Western blot analysis, immunocomplex kinase assays, crystal violet growth assays, co-immunoprecipitations, qPCR, and in vivo xenograft mouse work, analyzed data, and prepared figures. J.M.P. generated cell lines, performed flow cytometry, immunofluorescence imaging, live cell imaging, immunohistochemical analysis, Western blot analysis, crystal violet growth assays, quantitative PCR (qPCR), and assisted in in vivo KRAS G12D mouse tumor model work. A.A.G. maintained in vivo KRAS G12D mouse tumor models and performed in vivo KRAS G12D mouse tumor model imaging. M.C. generated tumors in vivo KRAS G12D mouse model. D.M.F. contributed to the study design, provided expertise in vivo mouse tumor models, and facilitated data analysis. D.C.B conceived of the project, contributed to the study design, generated cell lines, plasmids, and recombinant proteins, performed Cu-binding assays, in vitro kinase assays, immunofluorescence imaging, and in vivo xenograft mouse work, analyzed data, prepared figures, and wrote the manuscript. All authors read and provided feedback on manuscript and figures.

                [4]

                These authors contributed equally to this work.

                [* ] Corresponding author. Correspondence and requests for materials should be addressed to Donita C. Brady ( bradyd@ 123456pennmedicine.upenn.edu ).
                Article
                NIHMS1557425
                10.1038/s41556-020-0481-4
                7610258
                32203415
                5eec3385-4943-4fdc-b00b-a601be6c1377

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                Cell biology
                Cell biology

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