bims-apauto 2021-04-18 papers

bims-apauto

Biomed News

on Apoptosis and autophagy

Issue of 2021–04–18
ten papers selected by
Su Hyun Lee, Seoul National University

The AMBRA1 E3 ligase adaptor regulates the stability of cyclin D.
AMBRA1 regulates cyclin D to guard S-phase entry and genomic integrity.
Augmenting ATG14 alleviates atherosclerosis and inhibits inflammation via promotion of autophagosome-lysosome fusion in macrophages.
p62/SQSTM1 droplets initiate autophagosome biogenesis and oxidative stress control.
Ferritinophagy is involved in the zinc oxide nanoparticles-induced ferroptosis of vascular endothelial cells.
The deubiquitinase TRABID stabilizes the K29/K48-specific E3 ubiquitin ligase HECTD1.
Direct homophilic interaction of LAMP2A with the two-domain architecture revealed by site-directed photo-crosslinks and steric hindrances in mammalian cells.
Autophagy and senescence in cancer therapy.
Beyond cancer cells: Targeting the tumour microenvironment with gene therapy and armed oncolytic virus.
Regulation of the SIAH2-HIF-1 Axis by Protein Kinases and Its Implication in Cancer Therapy.

Nature. 2021 Apr 14.

The AMBRA1 E3 ligase adaptor regulates the stability of cyclin D.

Andrea C Chaikovsky, Chuan Li, Edwin E Jeng, Samuel Loebell, Myung Chang Lee, Christopher W Murray, Ran Cheng, Janos Demeter, Danielle L Swaney, Si-Han Chen, Billy W Newton, Jeffrey R Johnson, Alexandros P Drainas, Yan Ting Shue, Jose A Seoane, Preethi Srinivasan, Andy He, Akihiro Yoshida, Susan Q Hipkins, Edel McCrea, Carson D Poltorack, Nevan J Krogan, J Alan Diehl, Christina Kong, Peter K Jackson, Christina Curtis, Dmitri A Petrov, Michael C Bassik, Monte M Winslow, Julien Sage.

The initiation of cell division integrates a large number of intra- and extracellular inputs. D-type cyclins (hereafter, cyclin D) couple these inputs to the initiation of DNA replication1. Increased levels of cyclin D promote cell division by activating cyclin-dependent kinases 4 and 6 (hereafter, CDK4/6), which in turn phosphorylate and inactivate the retinoblastoma tumour suppressor. Accordingly, increased levels and activity of cyclin D-CDK4/6 complexes are strongly linked to unchecked cell proliferation and cancer2,3. However, the mechanisms that regulate levels of cyclin D are incompletely understood4,5. Here we show that autophagy and beclin 1 regulator 1 (AMBRA1) is the main regulator of the degradation of cyclin D. We identified AMBRA1 in a genome-wide screen to investigate the genetic basis of the response to CDK4/6 inhibition. Loss of AMBRA1 results in high levels of cyclin D in cells and in mice, which promotes proliferation and decreases sensitivity to CDK4/6 inhibition. Mechanistically, AMBRA1 mediates ubiquitylation and proteasomal degradation of cyclin D as a substrate receptor for the cullin 4 E3 ligase complex. Loss of AMBRA1 enhances the growth of lung adenocarcinoma in a mouse model, and low levels of AMBRA1 correlate with worse survival in patients with lung adenocarcinoma. Thus, AMBRA1 regulates cellular levels of cyclin D, and contributes to cancer development and the response of cancer cells to CDK4/6 inhibitors.

DOI: https://doi.org/10.1038/s41586-021-03474-7
Nature. 2021 Apr 14.

AMBRA1 regulates cyclin D to guard S-phase entry and genomic integrity.

Emiliano Maiani, Giacomo Milletti, Francesca Nazio, Søs Grønbæk Holdgaard, Jirina Bartkova, Salvatore Rizza, Valentina Cianfanelli, Mar Lorente, Daniele Simoneschi, Miriam Di Marco, Pasquale D'Acunzo, Luca Di Leo, Rikke Rasmussen, Costanza Montagna, Marilena Raciti, Cristiano De Stefanis, Estibaliz Gabicagogeascoa, Gergely Rona, Nélida Salvador, Emanuela Pupo, Joanna Maria Merchut-Maya, Colin J Daniel, Marianna Carinci, Valeriana Cesarini, Alfie O'sullivan, Yeon-Tae Jeong, Matteo Bordi, Francesco Russo, Silvia Campello, Angela Gallo, Giuseppe Filomeni, Letizia Lanzetti, Rosalie C Sears, Petra Hamerlik, Armando Bartolazzi, Robert E Hynds, David R Pearce, Charles Swanton, Michele Pagano, Guillermo Velasco, Elena Papaleo, Daniela De Zio, Apolinar Maya-Mendoza, Franco Locatelli, Jiri Bartek, Francesco Cecconi.

Mammalian development, adult tissue homeostasis and the avoidance of severe diseases including cancer require a properly orchestrated cell cycle, as well as error-free genome maintenance. The key cell-fate decision to replicate the genome is controlled by two major signalling pathways that act in parallel-the MYC pathway and the cyclin D-cyclin-dependent kinase (CDK)-retinoblastoma protein (RB) pathway1,2. Both MYC and the cyclin D-CDK-RB axis are commonly deregulated in cancer, and this is associated with increased genomic instability. The autophagic tumour-suppressor protein AMBRA1 has been linked to the control of cell proliferation, but the underlying molecular mechanisms remain poorly understood. Here we show that AMBRA1 is an upstream master regulator of the transition from G1 to S phase and thereby prevents replication stress. Using a combination of cell and molecular approaches and in vivo models, we reveal that AMBRA1 regulates the abundance of D-type cyclins by mediating their degradation. Furthermore, by controlling the transition from G1 to S phase, AMBRA1 helps to maintain genomic integrity during DNA replication, which counteracts developmental abnormalities and tumour growth. Finally, we identify the CHK1 kinase as a potential therapeutic target in AMBRA1-deficient tumours. These results advance our understanding of the control of replication-phase entry and genomic integrity, and identify the AMBRA1-cyclin D pathway as a crucial cell-cycle-regulatory mechanism that is deeply interconnected with genomic stability in embryonic development and tumorigenesis.

DOI: https://doi.org/10.1038/s41586-021-03422-5
Autophagy. 2021 Apr 14.

Augmenting ATG14 alleviates atherosclerosis and inhibits inflammation via promotion of autophagosome-lysosome fusion in macrophages.

Hui Zhang, Song Ge, Buqing Ni, Keshuai He, Pengcheng Zhu, Xiaohong Wu, Yongfeng Shao.

  Dysfunction of macroautophagy/autophagy in macrophages contributes to atherosclerosis. Impaired autophagy-lysosomal degradation system leads to lipid accumulation, facilitating atherosclerotic plaque. ATG14 is an essential regulator for the fusion of autophagosomes with lysosomes. Whether ATG14 plays a role in macrophage autophagy dysfunction in atherosclerosis is unknown. To investigate the effects of ATG14 on macrophage autophagy, human atherosclerotic plaque, apoe-/- mice and cultured mouse macrophages were evaluated. Overexpression of ATG14 by adenovirus was used to reveal its function in autophagy, inflammation and atherosclerotic plaque formation. Results showed that impaired autophagy function with reduction of ATG14 expression existed in macrophages of human and mouse atherosclerotic plaques. Ox-LDL impaired autophagosome-lysosome fusion with reduction of ATG14 expression in macrophages. Overexpression of ATG14 in macrophages enhanced fusion of autophagosomes with lysosomes and promoted lipid degradation, decreasing Ox-LDL-induced apoptosis and inflammatory response. Augmenting ATG14 expression reversed the autophagy dysfunction in macrophages of apoe-/- mice plaque, blunted SQSTM1/p62 accumulation, inhibited inflammation, and upregulated the population of Treg cells, resulting in alleviating atherosclerotic lesions.

Keywords:  ATG14; atherosclerosis; autophagy; inflammation; lipid degradation

DOI:  https://doi.org/10.1080/15548627.2021.1909833
Mol Cell Oncol. 2021 Mar 09. 8(2): 1890990

p62/SQSTM1 droplets initiate autophagosome biogenesis and oxidative stress control.

Eeva-Liisa Eskelinen, Shun Kageyama, Masaaki Komatsu.

  Selective autophagy contributes to the degradation of condensates, such as sequestosome 1-bodies, also called p62/SQSTM1-bodies. We showed that endogenous p62 forms gel-like structures, which serve as platforms for autophagosome formation and nuclear factor erythroid 2-related factor 2 (NRF2) activation. Further, p62-mediated NRF2 activation is not cytotoxic, but combination of NRF2 activation with impaired bulk and selective autophagy causes liver injury.

Keywords:  GABARAP; KEAP1; LC3; NRF2; autophagy; liquid-liquid phase separation; oxidative stress; p62/SQSTM1

DOI:  https://doi.org/10.1080/23723556.2021.1890990
Autophagy. 2021 Apr 12. 1-20

Ferritinophagy is involved in the zinc oxide nanoparticles-induced ferroptosis of vascular endothelial cells.

Xia Qin, Jun Zhang, Bin Wang, Ge Xu, Xi Yang, Zhen Zou, Chao Yu.

  Zinc oxide nanoparticles (ZnONPs) hold great promise for biomedical applications. Previous studies have revealed that ZnONPs exposure can induce toxicity in endothelial cells, but the underlying mechanisms have not been fully elucidated. In this study, we report that ZnONPs can induce ferroptosis of both HUVECs and EA.hy926 cells, as evidenced by the elevation of intracellular iron levels, lipid peroxidation and cell death in a dose- and time-dependent manner. In addition, both the lipid reactive oxygen species (ROS) scavenger ferrostatin-1 and the iron chelator deferiprone attenuated ZnONPs-induced cell death. Intriguingly, we found that ZnONPs-induced ferroptosis is macroautophagy/autophagy-dependent, because the inhibition of autophagy with a pharmacological inhibitor or by ATG5 gene knockout profoundly mitigated ZnONPs-induced ferroptosis. We further demonstrated that NCOA4 (nuclear receptor coactivator 4)-mediated ferritinophagy (autophagic degradation of the major intracellular iron storage protein ferritin) was required for the ferroptosis induced by ZnONPs, by showing that NCOA4 knockdown can reduce the intracellular iron level and lipid peroxidation, and subsequently alleviate ZnONPs-induced cell death. Furthermore, we showed that ROS originating from mitochondria (mtROS) probably activated the AMPK-ULK1 axis to trigger ferritinophagy. Most importantly, pulmonary ZnONPs exposure caused vascular inflammation and ferritinophagy in mice, and ferrostatin-1 supplementation significantly reversed the vascular injury induced by pulmonary ZnONPs exposure. Overall, our study indicates that ferroptosis is a novel mechanism for ZnONPs-induced endothelial cytotoxicity, and that NCOA4-mediated ferritinophagy is required for ZnONPs-induced ferroptotic cell death.

Keywords:  Autophagy; ferritinophagy; ferroptosis; vascular endothelial cell; zinc oxide nanoparticles

DOI:  https://doi.org/10.1080/15548627.2021.1911016
J Biol Chem. 2021 Jan 08. pii: S0021-9258(21)00011-9. [Epub ahead of print]296 100246

The deubiquitinase TRABID stabilizes the K29/K48-specific E3 ubiquitin ligase HECTD1.

Lee D Harris, Janic Le Pen, Nico Scholz, Juliusz Mieszczanek, Natalie Vaughan, Simon Davis, Georgina Berridge, Benedikt M Kessler, Mariann Bienz, Julien D F Licchesi.

  Ubiquitin is a versatile posttranslational modification, which is covalently attached to protein targets either as a single moiety or as a ubiquitin chain. In contrast to K48 and K63-linked chains, which have been extensively studied, the regulation and function of most atypical ubiquitin chains are only starting to emerge. The deubiquitinase TRABID/ZRANB1 is tuned for the recognition and cleavage of K29 and K33-linked chains. Yet, substrates of TRABID and the cellular functions of these atypical ubiquitin signals remain unclear. We determined the interactome of two TRABID constructs rendered catalytic dead either through a point mutation in the catalytic cysteine residue or through removal of the OTU catalytic domain. We identified 50 proteins trapped by both constructs and which therefore represent candidate substrates of TRABID. The E3 ubiquitin ligase HECTD1 was then validated as a substrate of TRABID and used UbiCREST and Ub-AQUA proteomics to show that HECTD1 preferentially assembles K29- and K48-linked ubiquitin chains. Further in vitro autoubiquitination assays using ubiquitin mutants established that while HECTD1 can assemble short homotypic K29 and K48-linked chains, it requires branching at K29/K48 in order to achieve its full ubiquitin ligase activity. We next used transient knockdown and genetic knockout of TRABID in mammalian cells in order to determine the functional relationship between TRABID and HECTD1. This revealed that upon TRABID depletion, HECTD1 is readily degraded. Thus, this study identifies HECTD1 as a mammalian E3 ligase that assembles branched K29/K48 chains and also establishes TRABID-HECTD1 as a DUB/E3 pair regulating K29 linkages.

Keywords:  E3 ubiquitin ligase; HECTD1; K29/K48-linked polyubiquitin chain; TRABID; deubiquitination; polyubiquitin chain; protein degradation; ubiquitin; ubiquitin thioesterase

DOI:  https://doi.org/10.1074/jbc.RA120.015162
Autophagy. 2021 Apr 14. 1-19

Direct homophilic interaction of LAMP2A with the two-domain architecture revealed by site-directed photo-crosslinks and steric hindrances in mammalian cells.

Kazue Terasawa, Yuji Kato, Yuta Ikami, Kensaku Sakamoto, Kazumasa Ohtake, Seisuke Kusano, Yuri Tomabechi, Mutsuko Kukimoto-Niino, Mikako Shirouzu, Jun-Lin Guan, Toshihide Kobayashi, Takanori Iwata, Tetsuro Watabe, Shigeyuki Yokoyama, Miki Hara-Yokoyama.

  LAMP1 (lysosomal-associated membrane protein 1) and LAMP2 are the most abundant protein components of lysosome membranes. Both LAMPs have common structures consisting of a large lumenal domain composed of two domains (N-domain and C-domain, which are membrane-distal and -proximal, respectively), both with the β-prism fold, a transmembrane domain, and a short cytoplasmic tail. LAMP2 is involved in various aspects of autophagy, and reportedly forms high-molecular weight complexes at the lysosomal membrane. We previously showed that LAMP2 molecules coimmunoprecipitated with each other, but whether the homophilic interaction is direct or indirect has remained to be elucidated. In the present study, we demonstrated the direct homophilic interaction of mouse LAMP2A molecules, using expanded genetic code technologies that generate photo-crosslinking and/or steric hindrance at specified interfaces. Specifically, the results suggested that LAMP2A molecules assemble by facing each other with one side of the β-prism (defined as side A) of the C-domains. The N-domain truncation, which increased the coimmunoprecipitation of LAMP2A molecules in our previous study, permitted the nonspecific involvement of both sides of the β-prism (side A and side B). Thus, the presence of the N-domain restricts the LAMP2A interactions to side A-specific. The truncation of LAMP2A impaired the recruitment of GAPDH (a CMA-substrate) fused to the HaloTag protein to the surface of late endosomes/lysosomes (LE/Lys) and affected a process that generates LE/Lys. The present study revealed that the homophilic interaction of LAMP2A is direct, and the side A-specific, homophilic interaction of LAMP2A is required for the functional aspects of LAMP2A.Abbreviations:Aloc-Lys: Nε-allyloxycarbonyl-l-lysine; CMA: chaperone-mediated autophagy; FFE: free-flow electrophoresis; GAPDH-HT: glyceraldehyde-3-phosphate dehydrogenase fused to HaloTag protein; LAMP1: lysosomal-associated membrane protein 1; LAMP2A: lysosomal-associated membrane protein 2A; LBPA: lysobisphosphatidic acid; LE/Lys: late endosome/lysosomes; MEFs: mouse embryonic fibroblasts; pBpa: p-benzoyl- l-phenylalanine.

Keywords:  Chaperone-mediated autophagy; GAPDH-HT; expanded genetic codes; lysosomes; photo-crosslinking; protein assembly

DOI:  https://doi.org/10.1080/15548627.2021.1911017
Adv Cancer Res. 2021 ;pii: S0065-230X(21)00002-6. [Epub ahead of print]150 1-74

Autophagy and senescence in cancer therapy.

Nipa H Patel, Sarah Bloukh, Enas Alwohosh, Ahmad Alhesa, Tareq Saleh, David A Gewirtz.

  Tumor cells can undergo diverse responses to cancer therapy. While apoptosis represents the most desirable outcome, tumor cells can alternatively undergo autophagy and senescence. Both autophagy and senescence have the potential to make complex contributions to tumor cell survival via both cell autonomous and cell non-autonomous pathways. The induction of autophagy and senescence in tumor cells, preclinically and clinically, either individually or concomitantly, has generated interest in the utilization of autophagy modulating and senolytic therapies to target autophagy and senescence, respectively. This chapter summarizes the current evidence for the promotion of autophagy and senescence as fundamental responses to cancer therapy and discusses the complexity of their functional contributions to cell survival and disease outcomes. We also highlight current modalities designed to exploit autophagy and senescence in efforts to improve the efficacy of cancer therapy.

Keywords:  Apoptosis; Autophagy; Cancer; Chemotherapy; Cytoprotective; Dormancy; Durable growth arrest; Radiation; SASP; Senescence; Senolytics

DOI:  https://doi.org/10.1016/bs.acr.2021.01.002
Mol Ther. 2021 Apr 09. pii: S1525-0016(21)00202-1. [Epub ahead of print]

Beyond cancer cells: Targeting the tumour microenvironment with gene therapy and armed oncolytic virus.

Peter Kt Wan, Anderson J Ryan, Leonard W Seymour.

  Cancer gene therapies are usually designed either to express wild type copies of tumour suppressor genes or to exploit tumour-associated phenotypic changes to endow selective cytotoxicity. However, these approaches become less relevant to cancers that contain many independent mutations and the situation is made more complex by our increased understanding of clonal evolution of tumours, meaning that different metastases and even regions of the same tumour mass have distinct mutational and phenotypic profiles. In contrast, the relatively genetically stable tumour microenvironment (TME) therefore provides an appealing therapeutic target, particular since it plays an essential role in promoting cancer growth, immune tolerance and acquired resistance to many therapies. Recently, a variety of different TME-targeted gene therapy and armed oncolytic strategies have been explored, with particular success observed in strategies targeting the cancer stroma, reducing tumour vasculature and repolarising the immunosuppressive microenvironment. Here we review the progress of these TME-targeting approaches and try to highlight those showing the greatest promise.

Keywords:  combination therapy; gene therapy; immunotherapy; oncolytic virus; tumour microenvironment

DOI:  https://doi.org/10.1016/j.ymthe.2021.04.015
Front Cell Dev Biol. 2021 ;9 646687

Regulation of the SIAH2-HIF-1 Axis by Protein Kinases and Its Implication in Cancer Therapy.

Dazhong Xu, Cen Li.

  The cellular response to hypoxia is a key biological process that facilitates adaptation of cells to oxygen deprivation (hypoxia). This process is critical for cancer cells to adapt to the hypoxic tumor microenvironment resulting from rapid tumor growth. Hypoxia-inducible factor 1 (HIF-1) is a transcription factor and a master regulator of the cellular response to hypoxia. The activity of HIF-1 is dictated primarily by its alpha subunit (HIF-1α), whose level and/or activity are largely regulated by an oxygen-dependent and ubiquitin/proteasome-mediated process. Prolyl hydroxylases (PHDs) and the E3 ubiquitin ligase Von Hippel-Lindau factor (VHL) catalyze hydroxylation and subsequent ubiquitin-dependent degradation of HIF-1α by the proteasome. Seven in Absentia Homolog 2 (SIAH2), a RING finger-containing E3 ubiquitin ligase, stabilizes HIF-1α by targeting PHDs for ubiquitin-mediated degradation by the proteasome. This SIAH2-HIF-1 signaling axis is important for maintaining the level of HIF-1α under both normoxic and hypoxic conditions. A number of protein kinases have been shown to phosphorylate SIAH2, thereby regulating its stability, activity, or substrate binding. In this review, we will discuss the regulation of the SIAH2-HIF-1 axis via phosphorylation of SIAH2 by these kinases and the potential implication of this regulation in cancer biology and cancer therapy.

Keywords:  HIF-1; SIAH2; cancer; hypoxia; protein kinases; therapy

DOI:  https://doi.org/10.3389/fcell.2021.646687