bims-apauto 2022-08-21 papers

Issue of 2022–08–21
eight papers selected by
Su Hyun Lee, Seoul National University

Autophagy. 2022 Aug 13. 1-3

The role of LC3B in autophagy as an RNA-binding protein.

The hallmark of cellular events observed upon macroautophagic/autophagic induction is the conjugation of LC3B, one of the mammalian Atg8 homologs, with phosphatidylethanolamine. This conversion from LC3B-I (an unconjugated form) to LC3B-II (a conjugated form) is essential for phagophore expansion and formation of autophagosomes. Our recent study revealed that LC3B binds to RNAs with a preference for the consensus AAUAAA motif and recruits the CCR4-NOT deadenylase complex. Consequently, LC3B elicits rapid degradation of mRNAs, which we have termed as LC3B-mediated mRNA decay (LMD). LMD requires the conversion of LC3B-I to LC3B-II and occurs before the formation of autolysosomes. Furthermore, we identified PRMT1 mRNA, which encodes a protein that functions as a negative regulator of autophagy, as an LMD substrate. A failure of rapid degradation of PRMT1 mRNA via LMD results in inefficient autophagy. Thus, our study unravels an important role of LC3B in autophagy as an RNA-binding protein for efficient mRNA decay.

Keywords: ATG8; CCR4-NOT deadenylase; LC3B; PRMT1; autophagy; mRNA decay

DOI: https://doi.org/10.1080/15548627.2022.2111083

EMBO J. 2022 Aug 15. e110398

Endosome maturation links PI3Kα signaling to lysosome repopulation during basal autophagy.

Samuel J Rodgers, Emily I Jones, Senthil Arumugam, Sabryn A Hamila, Jill Danne, Rajendra Gurung, Matthew J Eramo, Randini Nanayakkara, Georg Ramm, Meagan J McGrath, Christina A Mitchell.

Autophagy depends on the repopulation of lysosomes to degrade intracellular components and recycle nutrients. How cells co-ordinate lysosome repopulation during basal autophagy, which occurs constitutively under nutrient-rich conditions, is unknown. Here, we identify an endosome-dependent phosphoinositide pathway that links PI3Kα signaling to lysosome repopulation during basal autophagy. We show that PI3Kα-derived PI(3)P generated by INPP4B on late endosomes was required for basal but not starvation-induced autophagic degradation. PI(3)P signals were maintained as late endosomes matured into endolysosomes, and served as the substrate for the 5-kinase, PIKfyve, to generate PI(3,5)P2 . The SNX-BAR protein, SNX2, was recruited to endolysosomes by PI(3,5)P2 and promoted lysosome reformation. Inhibition of INPP4B/PIKfyve-dependent lysosome reformation reduced autophagic clearance of protein aggregates during proteotoxic stress leading to increased cytotoxicity. Therefore under nutrient-rich conditions, PI3Kα, INPP4B, and PIKfyve sequentially contribute to basal autophagic degradation and protection from proteotoxic stress via PI(3,5)P2 -dependent lysosome reformation from endolysosomes. These findings reveal that endosome maturation couples PI3Kα signaling to lysosome reformation during basal autophagy.

Keywords: INPP4B; PI3Kα; PIKfyve; autophagy; lysosome

DOI: https://doi.org/10.15252/embj.2021110398

Autophagy. 2022 Aug 18. 1-18

Use of acidic nanoparticles to rescue macrophage lysosomal dysfunction in atherosclerosis.

Xiangyu Zhang, Santosh Kumar Misra, Parikshit Moitra, Xiuli Zhang, Se-Jin Jeong, Jeremiah Stitham, Astrid Rodriguez-Velez, Arick Park, Yu-Sheng Yeh, William E Gillanders, Daping Fan, Abhinav Diwan, Jaehyung Cho, Slava Epelman, Irfan J Lodhi, Dipanjan Pan, Babak Razani.

Dysfunction in the macrophage lysosomal system including reduced acidity and diminished degradative capacity is a hallmark of atherosclerosis, leading to blunted clearance of excess cellular debris and lipids in plaques and contributing to lesion progression. Devising strategies to rescue this macrophage lysosomal dysfunction is a novel therapeutic measure. Nanoparticles have emerged as an effective platform to both target specific tissues and serve as drug delivery vehicles. In most cases, administered nanoparticles are taken up non-selectively by the mononuclear phagocyte system including monocytes/macrophages leading to the undesirable degradation of cargo in lysosomes. We took advantage of this default route to target macrophage lysosomes to rectify their acidity in disease states such as atherosclerosis. Herein, we develop and test two commonly used acidic nanoparticles, poly-lactide-co-glycolic acid (PLGA) and polylactic acid (PLA), both in vitro and in vivo. Our results in cultured macrophages indicate that the PLGA-based nanoparticles are the most effective at trafficking to and enhancing acidification of lysosomes. PLGA nanoparticles also provide functional benefits including enhanced lysosomal degradation, promotion of macroautophagy/autophagy and protein aggregate removal, and reduced apoptosis and inflammasome activation. We demonstrate the utility of this system in vivo, showing nanoparticle accumulation in, and lysosomal acidification of, macrophages in atherosclerotic plaques. Long-term administration of PLGA nanoparticles results in significant reductions in surrogates of plaque complexity with reduced apoptosis, necrotic core formation, and cytotoxic protein aggregates and increased fibrous cap formation. Taken together, our data support the use of acidic nanoparticles to rescue macrophage lysosomal dysfunction in the treatment of atherosclerosis.Abbreviations: BCA: brachiocephalic arteries; FACS: fluorescence activated cell sorting; FITC: fluorescein-5-isothiocyanatel; IL1B: interleukin 1 beta; LAMP: lysosomal associated membrane protein; LIPA/LAL: lipase A, lysosomal acid type; LSDs: lysosomal storage disorders; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MFI: mean fluorescence intensity; MPS: mononuclear phagocyte system; PEGHDE: polyethylene glycol hexadecyl ether; PLA: polylactic acid; PLGA: poly-lactide-co-glycolic acid; SQSTM1/p62: sequestosome 1.

Keywords: Acidic nanoparticles; PLGA; atherosclerosis; lysosomal dysfunction; macrophage

DOI: https://doi.org/10.1080/15548627.2022.2108252

EMBO Rep. 2022 Aug 18. e54859

UBXD8 mediates mitochondria-associated degradation to restrain apoptosis and mitophagy.

Jing Zheng, Yu Cao, Jun Yang, Hui Jiang.

The hexameric AAA-ATPase valosin-containing protein (VCP) is essential for mitochondrial protein quality control. How VCP is recruited to mammalian mitochondria remains obscure. Here we report that UBXD8, an ER- and lipid droplet-localized VCP adaptor, also localizes to mitochondria and locally recruits VCP. UBXD8 associates with mitochondrial and ER ubiquitin E3 ligases and targets their substrates for degradation. Remarkably, both mitochondria- and ER-localized UBXD8 can degrade mitochondrial and ER substrates in cis and in trans. UBXD8 also associates with the TOM complex but is dispensable for translocation-associated degradation. UBXD8 knockout impairs the degradation of the pro-survival protein Mcl1 but surprisingly sensitizes cells to apoptosis and mitochondrial stresses. UBXD8 knockout also hyperactivates mitophagy. We identify pro-apoptotic BH3-only proteins Noxa, Bik, and Bnip3 as novel UBXD8 substrates and determine that UBXD8 inhibits apoptosis via degrading Noxa and restrains mitophagy via degrading Bnip3. Collectively, our characterizations reveal UBXD8 as the major mitochondrial adaptor of VCP and unveil its role in apoptosis and mitophagy regulation.

Keywords: UBXD8; VCP; apoptosis; mitochondria-associated degradation; mitophagy

DOI: https://doi.org/10.15252/embr.202254859

Autophagy. 2022 Aug 13.

Targeting Mitophagy to Promote Apoptosis is a Potential Therapeutic Strategy for Cancer.

Yancheng Tang, Liming Wang, Jiangjiang Qin, Ying-Ying Lu, Han-Ming Shen, Hu-Biao Chen.

Many anticancer agents exert cytotoxicity and trigger apoptosis through the induction of mitochondrial dysfunction. Mitophagy, as the key mitochondrial quality control mechanism, can remove damaged mitochondria in an effective and timely manner, which may result in drug resistance. Although the implication of mitophagy in neurodegenerative diseases has been extensively studied, the role and mechanism of mitophagy in tumorigenesis and cancer therapy are largely unknown. In a recent study, we found that the inhibition of PINK1-PRKN-mediated mitophagy can significantly enhance the anticancer efficacy of magnolol, a natural product with potential anticancer properties. On the one hand, magnolol can induce severe mitochondrial dysfunction, including mitochondrial depolarization, excessive mitochondrial fragmentation and the generation of mitochondrial ROS, leading to apoptosis. On the other hand, magnolol induces PINK1-PRKN-dependent mitophagy via activation of two rounds of feedforward amplification loops. The blockage of mitophagy through genetic or pharmacological approaches promotes rather than attenuates magnolol-induced cell death. Furthermore, inhibition of mitophagy by using distinct inhibitors targeting different mitophagic stages effectively enhances magnolol's anticancer efficacy in vivo. Taken together, our findings strongly indicate that manipulation of mitophagy in cancer treatment will be a promising therapeutic strategy for overcoming cancer drug resistance and improving the therapeutic efficacy of anticancer agents.

DOI: https://doi.org/10.1080/15548627.2022.2112830

Cell Death Dis. 2022 Aug 16. 13(8): 712

USP21 promotes self-renewal and tumorigenicity of mesenchymal glioblastoma stem cells by deubiquitinating and stabilizing FOXD1.

Qixiang Zhang, Zhengxin Chen, Qikai Tang, Zhangjie Wang, Jiacheng Lu, Yongping You, Huibo Wang.

Recent studies suggest that Forkhead box D1 (FOXD1) plays an indispensable role in maintaining the mesenchymal (MES) properties of glioblastoma (GBM) stem cells (GSCs). Thus, understanding the mechanisms that control FOXD1 protein expression is critical for guiding GBM treatment, particularly in patients with therapy-resistant MES subtypes. In this study, we identify the ubiquitin-specific peptidase 21 (USP21) as a critical FOXD1 deubiquitinase in MES GSCs. We find that USP21 directly interacts with and stabilizes FOXD1 by reverting its proteolytic ubiquitination. Silencing of USP21 enhances polyubiquitination of FOXD1, promotes its proteasomal degradation, and ultimately attenuates MES identity in GSCs, while these effects could be largely restored by reintroduction of FOXD1. Remarkably, we show that disulfiram, a repurposed drug that could block the enzymatic activities of USP21, suppresses GSC tumorigenicity in MES GSC-derived GBM xenograft model. Additionally, we demonstrate that USP21 is overexpressed and positively correlated with FOXD1 protein levels in GBM tissues, and its expression is inversely correlated with patient survival. Collectively, our work reveals that USP21 maintains MES identity by antagonizing FOXD1 ubiquitination and degradation, suggesting that USP21 is a potential therapeutic target for the MES subtype of GBM.

DOI: https://doi.org/10.1038/s41419-022-05163-3

Life Sci. 2022 Aug 13. pii: S0024-3205(22)00584-7. [Epub ahead of print] 120884

All-trans retinoic acid-mediated miR-30a up-regulation suppresses autophagy and sensitizes gastric cancer cells to cisplatin.

Asadollah Abbasi, Mohammadali Hosseinpourfeizi, Reza Safaralizadeh.

AIMS: The potential of all-trans retinoic acid (ATRA) in regulating some microRNAs (miRNAs) involved in multiple cancer-related pathways, including resistance to chemotherapeutics, may be a valuable idea for overcoming the CDDP resistance of GC cells.
MAIN METHODS: Treatment of gastric AGS and MKN-45 cells with CDDP enriched the CDDP surviving cells (CDDP-SCs). The abilities of chemoresistance to CDDP drug, migration, either apoptosis or cell cycle distribution, spheroid body formation and changes at miRNA and protein levels were evaluated in vitro by MTT assay, colony formation assay, flow cytometry, tumor spheres culture, qRT-PCR and western blot assay in CDDP-SCs and ATRA-treated CDDP-SCs cells, respectively.
KEY FINDINGS: CDDP-based chemotherapy significantly reduced microRNA-30a (miR-30a) levels in GC cells. We also observed elevated autophagy activity in cancer cells that possess stem cell-like properties with overexpressed specific stem cell markers. Our extended study suggested that the reduction of miR-30a by CDDP treatment, is the possible underlying mechanism of enhanced autophagic activity, as demonstrated by enhancing autophagy-related protein beclin 1 and LC3-II/LC-I ratio. The addition of ATRA in the culture medium of GC cells increased the expression of miR-30a, and disturbed characteristic CSC-like properties. Additional studies revealed that the increased expression of miR-30a declined the expression level of its target gene, beclin 1, and beclin 1-mediated autophagy. This leads to promoted CDDP-induced GC cell apoptosis and G2/M cell cycle arrest.
SIGNIFICANCE: Overall, miR-30a/autophagy signaling has a critical role in regulating the chemoresistance of GC cells that ATRA could modulate.

Keywords: All-trans retinoic acid; Autophagy; CDDP; CSC-like; MiR-30a

DOI: https://doi.org/10.1016/j.lfs.2022.120884

Trends Biochem Sci. 2022 Aug 10. pii: S0968-0004(22)00189-X. [Epub ahead of print]

DUB-le vision: snapshots of the proteasome during substrate processing.

Helena M Schnell, John Hanna.

Covalent modification by the small protein ubiquitin can target proteins for destruction by the proteasome, but the ubiquitin signal itself is recycled. Surprisingly, proteasomes contain three different deubiquitinating enzymes (DUBs). Recent work by Zhang and Zou et al. reveals how one of these enzymes, Usp14, regulates, and is regulated by, the proteasome.

Keywords: Rpn11; Ubp6; Usp14; proteasome; ubiquitin

DOI: https://doi.org/10.1016/j.tibs.2022.07.007