bims-apauto Biomed News
on Apoptosis and autophagy
Issue of 2023–01–15
ten papers selected by
Su Hyun Lee, Seoul National University
  1. Where is the field of autophagy research heading?
  2. The autophagy in ischemic stroke: A regulatory role of non-coding-RNAs.
  3. RIPosomes are targets of IRGM-SQSTM1-dependent autophagy.
  4. Copper-dependent autophagic degradation of GPX4 drives ferroptosis.
  5. YWHAE/14-3-3ε crotonylation regulates leucine deprivation-induced autophagy.
  6. TTR (transthyretin) leads the autophagy disaster relief team against TARDBP/TDP-43 proteinopathy.
  7. Decoding of the ubiquitin code for clearance of colliding ribosomes by the RQT complex.
  8. LYSET/TMEM251/GCAF is critical for autophagy and lysosomal function by regulating the mannose-6-phosphate (M6P) pathway.
  9. An E3 ligase network engages GCN1 to promote the degradation of translation factors on stalled ribosomes.
  10. Drug and apoptosis resistance in cancer stem cells: a puzzle with many pieces.
  1. Autophagy. 2023 Jan 10.
    Where is the field of autophagy research heading?
    Hagai Abeliovich, Jayanta Debnath, Wen-Xing Ding, William T Jackson, Do-Hyung Kim, Daniel J Klionsky, Nicholas Ktistakis, Marta Margeta, Christian Münz, Morten Petersen, Junichi Sadoshima, Isabelle Vergne.
      In this editors' corner, the section editors were asked to indicate where they see the autophagy field heading and to suggest what they consider to be key unanswered questions in their specialty area.
    Keywords:  Ideas for your grant proposal; suggestions; the big picture; the grand scheme; thoughts; yada yada yada
    DOI:  https://doi.org/10.1080/15548627.2023.2166301
  2. Cell Signal. 2023 Jan 03. pii: S0898-6568(22)00348-5. [Epub ahead of print]104 110586
    The autophagy in ischemic stroke: A regulatory role of non-coding-RNAs.
    Su Xiaoqing, Chen Yinghua, Yuan Xingxing.
      Ischemic stroke (IS) is a central nervous system neurological disorder ascribed to an acute focal trauma, with high mortality and disability, leading to a heavy burden on family and society. Autophagy is a self-digesting process by which damaged organelles and useless proteins are recycled to maintain cellular homeostasis, and plays a pivotal role in the process of IS. Non-coding RNAs (ncRNAs), mainly contains microRNA, long non-coding RNA and circular RNA, have been extensively investigated on regulation of autophagy in human diseases. Recent studies have implied that ncRNAs-regulating autophagy participates in pathophysiological process of IS, including cell apoptosis, inflammation, oxidative stress, blood-brain barrier damage and glial activation, which indicates that regulating autophagy by ncRNAs may be beneficial for IS treatment. This review summarizes the role of autophagy in IS, as well as focuses on the role of ncRNAs-mediated autophagy in IS, for the development of potential therapeutic strategies in this disease.
    Keywords:  Autophagy; Ischemic stroke; Neuroprotection; Non-coding RNA; Therapy
    DOI:  https://doi.org/10.1016/j.cellsig.2022.110586
  3. Autophagy. 2023 Jan 10.
    RIPosomes are targets of IRGM-SQSTM1-dependent autophagy.
    Subhash Mehto, Soumya Kundu, Swati Chauhan, Santosh Chauhan.
      The NOD1-NOD2-RIPK2-NFKB/NF-κB pro-inflammatory axis plays a significant role in regulating the immune response to bacterial infection. However, an excess of NFKB-dependent cytokine response can be detrimental and, thus, should be kept under control to maintain the innate immune balance. In our recent study, first, we showed that bacterial infection induces the biogenesis of RIPK2 oligomers (RIPosomes) that are recruited around the bacteria to enhance an NFKB-dependent pro-inflammatory response. Next, we showed that SQSTM1- and IRGM-dependent selective macroautophagy/autophagy degrades RIPosomes and their components to limit NOD1-NOD2-RIPK2-NFKB pro-inflammatory signaling. Consistently, depletion of IRGM results in an augmented RIPK2-dependent pro-inflammatory cytokine response induced by Shigella flexneri and Salmonella typhimurium. Further, bacterial infection- and DSS-induced gut inflammation in irgm1KO mice is dampened upon therapeutic inhibition of RIPK2. Taken together, we showed that autophagy selectively degrades RIPosomes to suppress inflammation and maintain innate immune homeostasis.
    Keywords:  Autophagy; IRGM; NFKB; NOD1; NOD2; RIPK2; RIPosomes
    DOI:  https://doi.org/10.1080/15548627.2023.2166724
  4. Autophagy. 2023 Jan 12. 1-15
    Copper-dependent autophagic degradation of GPX4 drives ferroptosis.
    Qian Xue, Ding Yan, Xi Chen, Xiaofen Li, Rui Kang, Daniel J Klionsky, Guido Kroemer, Xin Chen, Daolin Tang, Jinbao Liu.
      Ferroptosis is a type of iron-dependent regulated cell death characterized by unrestricted lipid peroxidation and membrane damage. Although GPX4 (glutathione peroxidase 4) plays a master role in blocking ferroptosis by eliminating phospholipid hydroperoxides, the regulation of GPX4 remains poorly understood. Here, we report an unexpected role for copper in promoting ferroptotic cell death, but not cuproptosis, by inducing macroautophagic/autophagic degradation of GPX4. Copper chelators reduce ferroptosis sensitivity but do not inhibit other types of cell death, such as apoptosis, necroptosis, and alkaliptosis. Conversely, exogenous copper increases GPX4 ubiquitination and the formation of GPX4 aggregates by directly binding to GPX4 protein cysteines C107 and C148. TAX1BP1 (Tax1 binding protein 1) then acts as an autophagic receptor for GPX4 degradation and subsequent ferroptosis in response to copper stress. Consequently, copper enhances ferroptosis-mediated tumor suppression in a mouse model of pancreatic cancer tumor, whereas copper chelators attenuate experimental acute pancreatitis associated with ferroptosis. Taken together, these findings provide new insights into the link between metal stress and autophagy-dependent cell death.Abbreviations: CALCOCO2, calcium binding and coiled-coil domain 2; GPX4, glutathione peroxidase 4; MAP1LC3A/B, microtubule associated protein 1 light chain 3 alpha/beta; MPO, myeloperoxidase; NCOA4, nuclear receptor coactivator 4; OPTN, optineurin; PDAC, pancreatic ductal adenocarcinoma; RIPK1, receptor interacting serine/threonine kinase 1; ROS, reactive oxygen species; SLC40A1, solute carrier family 40 member 1; SQSTM1, sequestosome 1; TAX1BP1, Tax1 binding protein 1; TEPA, tetraethylenepentamine; TM, tetrathiomolybdate.
    Keywords:  Autophagy; GPX4; TAX1BP1; copper; cuproptosis; ferroptosis
    DOI:  https://doi.org/10.1080/15548627.2023.2165323
  5. Autophagy. 2023 Jan 10.
    YWHAE/14-3-3ε crotonylation regulates leucine deprivation-induced autophagy.
    Zilong Zheng, Qing Zhong, Xianghua Yan.
      Macroautophagy/autophagy is an important process responsible for protein turnover and cell survival in amino acid-deprived conditions, especially for leucine (Leu). With the dramatic advances in mass spectrometry, many new post-translational modifications (PTMs) have been identified. However, whether these PTMs regulate autophagy remains unclear. Here we found global lysine crotonylation levels are significantly upregulated during Leu-deprivation-induced autophagy. A comprehensive crotonylome profiling showed that YWHA/14-3-3 proteins are significantly enriched in the Leu regulated-crotonylome. The inhibition of YWHAE/14-3-3ε crotonylation by mutating two crotonylated sites to arginine, K73R K78R, significantly attenuates autophagy induced by Leu deprivation. Molecular dynamics suggest that YWHAE K73 and K78 crotonylations decrease protein conformation and thermodynamic stability. Moreover, we found crotonylation of YWHAE releases PPM1B to dephosphorylate ULK1 and consequently activate autophagy. Decrotonylation of YWHAE is mediated by HDAC7 whose activity is inhibited significantly by Leu deprivation. Taken together, our finding reveals a critical role of YWHAE crotonylation in Leu deprivation-induced autophagy.
    Keywords:  14-3-3ε; HDAC7; PPM1B; autophagy; crotonylation; leucine deprivation
    DOI:  https://doi.org/10.1080/15548627.2023.2166276
  6. Autophagy. 2023 Jan 12.
    TTR (transthyretin) leads the autophagy disaster relief team against TARDBP/TDP-43 proteinopathy.
    Yuan-Ping Chu, Pei-Chuan Ho, Kuen-Jer Tsai.
      TTR (transthyretin) strikes a neuroprotective function in the prevention of amyloid-β (Aβ) deposition in Alzheimer disease (AD). Perturbation of the stringently controlled TARDBP/TDP-43 (TAR DNA binding protein) expression gives rise to cytoplasmic aggregation, characterized by TARDBP proteinopathy affiliated with several neurological disorders, including frontotemporal lobar degeneration with TARDBP pathology (FTLD-TDP) and amyotrophic lateral sclerosis/ALS. Proposedly, TTR can maintain cellular proteostasis susceptible to TARDBP aggregates and initiate its removal. Herein, we disclose that TTR upregulated in response to excessive TARDBP causes TARDBP aggregation in FTLD-TDP and co-accumulates with it. Moreover, TTR expression increases with age in FTLD-TDP but shows a downward decline in the elderly. TTR promotes macroautophagy/autophagy activity and facilitates aggregated TARDBP degradation via autophagy. Compellingly, TTR binds to ATF4 and boosts its nuclear import for autophagy upregulation. Therefore, TTR directs autophagy teamwork in bi-directional regulation through enhancing autophagy activity via ATF4 and chaperoning aggregated TARDBP to phagophores for degradation.
    Keywords:  ATF4; FTLD; TDP-43; TTR; autophagy; proteinopathy
    DOI:  https://doi.org/10.1080/15548627.2023.2167690
  7. Nat Commun. 2023 Jan 10. 14(1): 79
    Decoding of the ubiquitin code for clearance of colliding ribosomes by the RQT complex.
    Yoshitaka Matsuo, Takayuki Uchihashi, Toshifumi Inada.
      The collision sensor Hel2 specifically recognizes colliding ribosomes and ubiquitinates the ribosomal protein uS10, leading to noncanonical subunit dissociation by the ribosome-associated quality control trigger (RQT) complex. Although uS10 ubiquitination is essential for rescuing stalled ribosomes, its function and recognition steps are not fully understood. Here, we show that the RQT complex components Cue3 and Rqt4 interact with the K63-linked ubiquitin chain and accelerate the recruitment of the RQT complex to the ubiquitinated colliding ribosome. The CUE domain of Cue3 and the N-terminal domain of Rqt4 bind independently to the K63-linked ubiquitin chain. Their deletion abolishes ribosomal dissociation mediated by the RQT complex. High-speed atomic force microscopy (HS-AFM) reveals that the intrinsically disordered regions of Rqt4 enable the expansion of the searchable area for interaction with the ubiquitin chain. These findings provide mechanistic insight into the decoding of the ubiquitin code for clearance of colliding ribosomes by the RQT complex.
    DOI:  https://doi.org/10.1038/s41467-022-35608-4
  8. Autophagy. 2023 Jan 12.
    LYSET/TMEM251/GCAF is critical for autophagy and lysosomal function by regulating the mannose-6-phosphate (M6P) pathway.
    Bokai Zhang, Xi Yang, Ming Li.
      Vertebrate cells rely on mannose-6-phosphate (M6P) modifications to deliver most lumenal hydrolases to the lysosome. As a critical trafficking signal for lysosomal enzymes, the M6P biosynthetic pathway has been thoroughly investigated. However, its regulatory mechanism is largely unknown. Here, we summarize three recent studies that independently discovered LYSET/TMEM251/GCAF as a key regulator of the M6P pathway. LYSET/TMEM251 directly interacts with GNPT, the enzyme that catalyzes the transfer of M6P, and is critical for its activity and stability. Deleting LYSET/TMEM251 impairs the GNPT function and M6P modifications. Consequently, lysosomal enzymes are mistargeted for secretion. Defective lysosomes fail to degrade cargoes such as endocytic vesicles and autophagosomes, leading to a newly identified lysosomal storage disease in humans. These discoveries open up a new direction in the regulation of the M6P biosynthetic pathway.
    Keywords:  Autophagy; GNPT; M6P; TMEM251; lysosomal enzymes; lysosomal storage disease
    DOI:  https://doi.org/10.1080/15548627.2023.2167375
  9. Cell. 2023 Jan 05. pii: S0092-8674(22)01538-0. [Epub ahead of print]
    An E3 ligase network engages GCN1 to promote the degradation of translation factors on stalled ribosomes.
    Keely Oltion, Jordan D Carelli, Tangpo Yang, Stephanie K See, Hao-Yuan Wang, Martin Kampmann, Jack Taunton.
      Ribosomes frequently stall during mRNA translation, resulting in the context-dependent activation of quality control pathways to maintain proteostasis. However, surveillance mechanisms that specifically respond to stalled ribosomes with an occluded A site have not been identified. We discovered that the elongation factor-1α (eEF1A) inhibitor, ternatin-4, triggers the ubiquitination and degradation of eEF1A on stalled ribosomes. Using a chemical genetic approach, we unveiled a signaling network comprising two E3 ligases, RNF14 and RNF25, which are required for eEF1A degradation. Quantitative proteomics revealed the RNF14 and RNF25-dependent ubiquitination of eEF1A and a discrete set of ribosomal proteins. The ribosome collision sensor GCN1 plays an essential role by engaging RNF14, which directly ubiquitinates eEF1A. The site-specific, RNF25-dependent ubiquitination of the ribosomal protein RPS27A/eS31 provides a second essential signaling input. Our findings illuminate a ubiquitin signaling network that monitors the ribosomal A site and promotes the degradation of stalled translation factors, including eEF1A and the termination factor eRF1.
    Keywords:  CRISPRi screen; E3 ligase; K6-linked ubiquitin; RWD domain; diGly proteomics; natural product; protein synthesis; ribosomal ubiquitination; ribosome quality control; translation factor
    DOI:  https://doi.org/10.1016/j.cell.2022.12.025
  10. Cancer Drug Resist. 2022 ;5(4): 850-872
    Drug and apoptosis resistance in cancer stem cells: a puzzle with many pieces.
    Ahmad R Safa.
      Resistance to anticancer agents and apoptosis results in cancer relapse and is associated with cancer mortality. Substantial data have provided convincing evidence establishing that human cancers emerge from cancer stem cells (CSCs), which display self-renewal and are resistant to anticancer drugs, radiation, and apoptosis, and express enhanced epithelial to mesenchymal progression. CSCs represent a heterogeneous tumor cell population and lack specific cellular targets, which makes it a great challenge to target and eradicate them. Similarly, their close relationship with the tumor microenvironment creates greater complexity in developing novel treatment strategies targeting CSCs. Several mechanisms participate in the drug and apoptosis resistance phenotype in CSCs in various cancers. These include enhanced expression of ATP-binding cassette membrane transporters, activation of various cytoprotective and survival signaling pathways, dysregulation of stemness signaling pathways, aberrant DNA repair mechanisms, increased quiescence, autophagy, increased immune evasion, deficiency of mitochondrial-mediated apoptosis, upregulation of anti-apoptotic proteins including c-FLIP [cellular FLICE (FADD-like IL-1β-converting enzyme)-inhibitory protein], Bcl-2 family members, inhibitors of apoptosis proteins, and PI3K/AKT signaling. Studying such mechanisms not only provides mechanistic insights into these cells that are unresponsive to drugs, but may lead to the development of targeted and effective therapeutics to eradicate CSCs. Several studies have identified promising strategies to target CSCs. These emerging strategies may help target CSC-associated drug resistance and metastasis in clinical settings. This article will review the CSCs drug and apoptosis resistance mechanisms and how to target CSCs.
    Keywords:  Bcl-2 family; Cancer stem cells (CSCs); anti-apoptotic proteins; apoptosis; c-FLIP; death receptor pathways; drug resistance
    DOI:  https://doi.org/10.20517/cdr.2022.20
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