bims-apauto Biomed News
on Apoptosis and autophagy
Issue of 2022–02–20
nine papers selected by
Su Hyun Lee, Seoul National University
  1. Vps30/Atg6/BECN1 at the crossroads between cell metabolism and DNA damage response.
  2. Circadian remodeling of the proteome by chaperone-mediated autophagy.
  3. The AUTOTAC chemical biology platform for targeted protein degradation via the autophagy-lysosome system.
  4. CDK6 increases glycolysis and suppresses autophagy by mTORC1-HK2 pathway activation in cervical cancer cells.
  5. Studying the ubiquitin code through biotin-based labelling methods.
  6. Spatiotemporal dynamics of clonal selection and diversification in normal endometrial epithelium.
  7. Deubiquitinases in Neurodegeneration.
  8. An AMPKα2-specific phospho-switch controls lysosomal targeting for activation.
  9. CARD9 Regulation and its Role in Cardiovascular Diseases.
  1. Autophagy. 2022 Feb 15. 1-3
    Vps30/Atg6/BECN1 at the crossroads between cell metabolism and DNA damage response.
    Arta Ajazi, Marco Foiani.
      Several cytotoxic agents used in cancer therapy cause DNA damage and replication stress. Understanding the metabolic determinants of the cell response to replication stress-inducing agents could have relevant implications for cancer treatment. In a recent study, we showed that cell survival during replication stress is influenced by the availability of amino acids, as well as by TORC1 and Gcn2-mediated amino acid sensing pathways. Amino acid starvation, or TORC1 inhibition, sensitizes cells to replication stress conditions, whereas Gcn2 ablation promotes cell survival by stimulating protein synthesis. The Vps34-Vps15-Vps30/Atg6/BECN1-Vps38/UVRAG phosphatidylinositol-3-phosphate (PtdIns3P) complex at the endosomes sets the balance between survival and death signals during replication stress and amino acid starvation. The Vps34-Vps15-Vps30/Atg6/BECN1-Vps38/UVRAG axis promotes the degradation of amino acid transporters, thus sensitizing cells to amino acid starvation, while Vps34-Vps15-Vps30/Atg6/BECN1-Vps38/UVRAG inactivation promotes cell survival by enabling synthesis of stress response proteins mediating survival under replication stress conditions. Our study unravels an autophagy-independent mechanism through which Vps34-Vps30/Atg6/BECN1 promotes lethal events during replication stress.
    Keywords:  Amino acids; Atg6; DNA damage; Gcn2; TORC1; autophagy; endosomal trafficking; phosphatidylinositol-3 phosphate; replication stress
    DOI:  https://doi.org/10.1080/15548627.2022.2038502
  2. Autophagy. 2022 Feb 15. 1-3
    Circadian remodeling of the proteome by chaperone-mediated autophagy.
    Susmita Kaushik, Yves R Juste, Ana Maria Cuervo.
      The circadian clock drives daily cycles of physiology and behavioral outputs to keep organisms in tune with the environment. Cyclic oscillations in levels of the clock proteins maintain circadian rhythmicity. In our recent work, we have discovered the interdependence of the circadian clock and chaperone-mediated autophagy (CMA), a selective form of lysosomal protein degradation. Central and peripheral degradation of core clock proteins by CMA (selective chronophagy) modulates circadian rhythm. Loss of CMA in vivo disrupts physiological circadian cycling, resembling defects observed in aging, a condition with reduced CMA. Conversely, the circadian clock temporally regulates CMA activity in a tissue-specific manner, contributing to remodeling of a distinct subproteome at different circadian times. This timely remodeling cannot be sustained when CMA fails, despite rerouting of some CMA substrates to other degradation pathways.
    Keywords:  Central clock; chaperones; circadian rhythms; lysosomes; organelle proteomics; peripheral clock
    DOI:  https://doi.org/10.1080/15548627.2022.2038503
  3. Nat Commun. 2022 Feb 16. 13(1): 904
    The AUTOTAC chemical biology platform for targeted protein degradation via the autophagy-lysosome system.
    Chang Hoon Ji, Hee Yeon Kim, Min Ju Lee, Ah Jung Heo, Daniel Youngjae Park, Sungsu Lim, Seulgi Shin, Woo Seung Yang, Chang An Jung, Kun Young Kim, Eun Hye Jeong, Sun Ho Park, Su Bin Kim, Su Jin Lee, Jeong Eun Na, Ji In Kang, Hyung Min Chi, Hyun Tae Kim, Yun Kyung Kim, Bo Yeon Kim, Yong Tae Kwon.
      Targeted protein degradation allows targeting undruggable proteins for therapeutic applications as well as eliminating proteins of interest for research purposes. While several degraders that harness the proteasome or the lysosome have been developed, a technology that simultaneously degrades targets and accelerates cellular autophagic flux is still missing. In this study, we develop a general chemical tool and platform technology termed AUTOphagy-TArgeting Chimera (AUTOTAC), which employs bifunctional molecules composed of target-binding ligands linked to autophagy-targeting ligands. AUTOTACs bind the ZZ domain of the otherwise dormant autophagy receptor p62/Sequestosome-1/SQSTM1, which is activated into oligomeric bodies in complex with targets for their sequestration and degradation. We use AUTOTACs to degrade various oncoproteins and degradation-resistant aggregates in neurodegeneration at nanomolar DC50 values in vitro and in vivo. AUTOTAC provides a platform for selective proteolysis in basic research and drug development.
    DOI:  https://doi.org/10.1038/s41467-022-28520-4
  4. Cell Cycle. 2022 Feb 15. 1-19
    CDK6 increases glycolysis and suppresses autophagy by mTORC1-HK2 pathway activation in cervical cancer cells.
    Xiaoxi Zhang, Yunxia Sun, Siyao Cheng, Yanjing Yao, Xintao Hua, Yueyue Shi, Xiaoqin Jin, Jieli Pan, Miaofen G Hu, Pian Ying, Xiaoli Hou, Daozong Xia.
      Cervical carcinoma is a leading malignant tumor among women worldwide, characterized by the dysregulation of cell cycle. Cyclin-dependent kinase 6 (CDK6) plays important roles in the cell cycle progression, cell differentiation, and tumorigenesis. However, the role of CDK6 in cervical cancer remains controversial. Here, we found that loss of CDK6 in cervical adenocarcinoma HeLa cell line inhibited cell proliferation but induced apoptosis as well as autophagy, accompanied by attenuated expression of mammalian target of rapamycin complex 1 (mTORC1) and hexokinase 2 (HK2), reduced glycolysis, and production of protein, nucleotide, and lipid. Similarly, we showed that CDK6 knockout inhibited the survival of CDK6-high CaSki but not CDK6-low SiHa cervical cancer cells by regulation of glycolysis and autophagy process. Collectively, our studies indicate that CDK6 is a critical regulator of human cervical cancer cells, especially with high CDK6 level, through its ability to regulate cellular apoptosis and metabolism. Thus, inhibition of CDK6 kinase activity could be a powerful therapeutic avenue used to treat cervical cancers.
    Keywords:  CDK6; Cervical carcinoma; apoptosis; autophagy; glycolysis; mTOR
    DOI:  https://doi.org/10.1080/15384101.2022.2039981
  5. Semin Cell Dev Biol. 2022 Feb 15. pii: S1084-9521(22)00047-7. [Epub ahead of print]
    Studying the ubiquitin code through biotin-based labelling methods.
    Orhi Barroso-Gomila, Veronica Muratore, Laura Merino-Cacho, Jose Antonio Rodriguez, Rosa Barrio, James D Sutherland.
      Post-translational modifications of cellular substrates by members of the ubiquitin (Ub) and ubiquitin-like (UbL) family are crucial for regulating protein homeostasis in organisms. The term "ubiquitin code" encapsulates how this diverse family of modifications, via adding single UbLs or different types of UbL chains, leads to specific fates for substrates. Cancer, neurodegeneration and other conditions are sometimes linked to underlying errors in this code. Studying these modifications in cells is particularly challenging since they are usually transient, scarce, and compartment-specific. Advances in the use of biotin-based methods to label modified proteins, as well as their proximally-located interactors, facilitate isolation and identification of substrates, modification sites, and the enzymes responsible for writing and erasing these modifications, as well as factors recruited as a consequence of the substrate being modified. In this review, we discuss site-specific and proximity biotinylation approaches being currently applied for studying modifications by UbLs, highlighting the pros and cons, with mention of complementary methods when possible. Future improvements may come from bioengineering and chemical biology but even now, biotin-based technology is uncovering new substrates and regulators, expanding potential therapeutic targets to manipulate the Ub code.
    Keywords:  Biotin; BirA; Proximity proteomics; SUMO; Ubiquitin
    DOI:  https://doi.org/10.1016/j.semcdb.2022.02.009
  6. Nat Commun. 2022 Feb 17. 13(1): 943
    Spatiotemporal dynamics of clonal selection and diversification in normal endometrial epithelium.
    Manako Yamaguchi, Hirofumi Nakaoka, Kazuaki Suda, Kosuke Yoshihara, Tatsuya Ishiguro, Nozomi Yachida, Kyota Saito, Haruka Ueda, Kentaro Sugino, Yutaro Mori, Kaoru Yamawaki, Ryo Tamura, Sundaramoorthy Revathidevi, Teiichi Motoyama, Kazuki Tainaka, Roel G W Verhaak, Ituro Inoue, Takayuki Enomoto.
      It has become evident that somatic mutations in cancer-associated genes accumulate in the normal endometrium, but spatiotemporal understanding of the evolution and expansion of mutant clones is limited. To elucidate the timing and mechanism of the clonal expansion of somatic mutations in cancer-associated genes in the normal endometrium, we sequence 1311 endometrial glands from 37 women. By collecting endometrial glands from different parts of the endometrium, we show that multiple glands with the same somatic mutations occupy substantial areas of the endometrium. We demonstrate that "rhizome structures", in which the basal glands run horizontally along the muscular layer and multiple vertical glands rise from the basal gland, originate from the same ancestral clone. Moreover, mutant clones detected in the vertical glands diversify by acquiring additional mutations. These results suggest that clonal expansions through the rhizome structures are involved in the mechanism by which mutant clones extend their territories. Furthermore, we show clonal expansions and copy neutral loss-of-heterozygosity events occur early in life, suggesting such events can be tolerated many years in the normal endometrium. Our results of the evolutionary dynamics of mutant clones in the human endometrium will lead to a better understanding of the mechanisms of endometrial regeneration during the menstrual cycle and the development of therapies for the prevention and treatment of endometrium-related diseases.
    DOI:  https://doi.org/10.1038/s41467-022-28568-2
  7. Cells. 2022 Feb 05. pii: 556. [Epub ahead of print]11(3):
    Deubiquitinases in Neurodegeneration.
    Abudu I Bello, Rituparna Goswami, Shelby L Brown, Kara Costanzo, Taylor Shores, Shefaa Allan, Revan Odah, Ryan D Mohan.
      Ubiquitination refers to the conjugation of the ubiquitin protein (a small protein highly conserved among eukaryotes) to itself or to other proteins through differential use of ubiquitin's seven internal linkage sites or the amino-terminal amino group. By creating different chain lengths, an enormous proteomic diversity may be formed. This creates a signaling system that is central to controlling almost every conceivable protein function, from proteostasis to regulating enzyme function and everything in between. Protein ubiquitination is reversed through the activity of deubiquitinases (DUBs), enzymes that function to deconjugate ubiquitin from itself and protein substrates. DUBs are regulated through several mechanisms, from controlled subcellular localization within cells to developmental and tissue specific expression. Misregulation of DUBs has been implicated in several diseases including cancer and neurodegeneration. Here we present a brief overview of the role of DUBs in neurodegeneration, and as potential therapeutic targets.
    Keywords:  Drosophila; deubiquitinase; neurodegeneration; ubiquitin; ubiquitin-specific protease
    DOI:  https://doi.org/10.3390/cells11030556
  8. Cell Rep. 2022 02 15. pii: S2211-1247(22)00086-9. [Epub ahead of print]38(7): 110365
    An AMPKα2-specific phospho-switch controls lysosomal targeting for activation.
    Kaitlin R Morrison, William J Smiles, Naomi X Y Ling, Ashfaqul Hoque, Gabrielle Shea, Kevin R W Ngoei, Dingyi Yu, Lisa Murray-Segal, John W Scott, Sandra Galic, Bruce E Kemp, Janni Petersen, Jonathan S Oakhill.
      AMP-activated protein kinase (AMPK) and mechanistic target of rapamycin complex 1 (mTORC1) are metabolic kinases that co-ordinate nutrient supply with cell growth. AMPK negatively regulates mTORC1, and mTORC1 reciprocally phosphorylates S345/7 in both AMPK α-isoforms. We report that genetic or torin1-induced loss of α2-S345 phosphorylation relieves suppression of AMPK signaling; however, the regulatory effect does not translate to α1-S347 in HEK293T or MEF cells. Dephosphorylation of α2-S345, but not α1-S347, transiently targets AMPK to lysosomes, a cellular site for activation by LKB1. By mass spectrometry, we find that α2-S345 is basally phosphorylated at 2.5-fold higher stoichiometry than α1-S347 in HEK293T cells and, unlike α1, phosphorylation is partially retained after prolonged mTORC1 inhibition. Loss of α2-S345 phosphorylation in endogenous AMPK fails to sustain growth of MEFs under amino acid starvation conditions. These findings uncover an α2-specific mechanism by which AMPK can be activated at lysosomes in the absence of changes in cellular energy.
    Keywords:  AMPK; energy homeostasis; kinase; lysosome; mTORC1; metabolic signaling; phosphorylation
    DOI:  https://doi.org/10.1016/j.celrep.2022.110365
  9. Int J Biol Sci. 2022 ;18(3): 970-982
    CARD9 Regulation and its Role in Cardiovascular Diseases.
    Haina Zhang, Yeling Wang, Hongbo Men, Wenqian Zhou, Shanshan Zhou, Quan Liu, Lu Cai.
      Caspase recruitment domain-containing protein 9 (CARD9) is an adaptor protein expressed on myeloid cells and located downstream of pattern recognition receptors (PRRs), which transduces signals involved in innate immunity. CARD9 deficiency is associated with increased susceptibility to various fungal diseases. Increasing evidence shows that CARD9 mediates the activation of p38 MAPK, NF-κB, and NLRP3 inflammasome in various CVDs and then promotes the production of proinflammatory cytokines and chemokines, which contribute to cardiac remodeling and cardiac dysfunction in certain cardiovascular diseases (CVDs). Moreover, CARD9-mediated anti-apoptosis and autophagy are implicated in the progression of CVDs. Here, we summarize the structure and function of CARD9 in innate immunity and its various roles in inflammation, apoptosis, and autophagy in the pathogenesis of CVDs. Furthermore, we discuss the potential therapies targeting CARD9 to prevent CVDs and raise some issues for further exploring the role of CARD9 in CVDs.
    Keywords:  CARD9; apoptosis; autophagy; cardiovascular diseases; inflammation; innate immunity
    DOI:  https://doi.org/10.7150/ijbs.65979
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