bims-apauto Biomed News
on Apoptosis and autophagy
Issue of 2022–01–16
nine papers selected by
Su Hyun Lee, Seoul National University
  1. Autophagy facilitates age-related cell apoptosis-a new insight from senile cataract.
  2. Structural basis of BAK activation in mitochondrial apoptosis initiation.
  3. Degradation of the NOTCH intracellular domain by elevated autophagy in osteoblasts promotes osteoblast differentiation and alleviates osteoporosis.
  4. Structure of UBE2K-Ub/E3/polyUb reveals mechanisms of K48-linked Ub chain extension.
  5. Alternative mitophagy is a major form of mitophagy in the chronically stressed heart.
  6. Secretory Autophagy Forges a Therapy Resistant Microenvironment in Melanoma.
  7. USP10 inhibits aberrant cytoplasmic aggregation of TDP-43 by promoting stress granule clearance.
  8. A Notch inhibitor plus Resveratrol induced blockade of autophagy drives glioblastoma cell death by promoting a switch to apoptosis.
  9. Structural basis of K63-ubiquitin chain formation by the Gordon-Holmes syndrome RBR E3 ubiquitin ligase RNF216.
  1. Cell Death Dis. 2022 01 10. 13(1): 37
    Autophagy facilitates age-related cell apoptosis-a new insight from senile cataract.
    Jiani Huang, Wangshu Yu, Qin He, Xiaoying He, Ming Yang, Wei Chen, Wei Han.
      Age-related cell loss underpins many senescence-associated diseases. Apoptosis of lens epithelial cells (LECs) is the important cellular basis of senile cataract resulted from prolonged exposure to oxidative stress, although the specific mechanisms remain elusive. Our data indicated the concomitance of high autophagy activity, low SQSTM1/p62 protein level and apoptosis in the same LEC from senile cataract patients. Meanwhile, in primary cultured LECs model, more durable autophagy activation and more obvious p62 degradation under oxidative stress were observed in LECs from elder healthy donors, compared with that from young healthy donors. Using autophagy-deficiency HLE-B3 cell line, autophagy adaptor p62 was identified as the critical scaffold protein sustaining the pro-survival signaling PKCι-IKK-NF-κB cascades, which antagonized the pro-apoptotic signaling. Moreover, the pharmacological inhibitor of autophagy, 3-MA, significantly inhibited p62 degradation and rescued oxidative stress-induced apoptosis in elder LECs. Collectively, this study demonstrated that durable activation of autophagy promoted age-related cell death in LECs. Our work contributes to better understanding the pathogenesis of senescence-associated diseases.
    DOI:  https://doi.org/10.1038/s41419-021-04489-8
  2. Nat Commun. 2022 Jan 11. 13(1): 250
    Structural basis of BAK activation in mitochondrial apoptosis initiation.
    Geetika Singh, Cristina D Guibao, Jayaraman Seetharaman, Anup Aggarwal, Christy R Grace, Dan E McNamara, Sivaraja Vaithiyalingam, M Brett Waddell, Tudor Moldoveanu.
      BCL-2 proteins regulate mitochondrial poration in apoptosis initiation. How the pore-forming BCL-2 Effector BAK is activated remains incompletely understood mechanistically. Here we investigate autoactivation and direct activation by BH3-only proteins, which cooperate to lower BAK threshold in membrane poration and apoptosis initiation. We define in trans BAK autoactivation as the asymmetric "BH3-in-groove" triggering of dormant BAK by active BAK. BAK autoactivation is mechanistically similar to direct activation. The structure of autoactivated BAK BH3-BAK complex reveals the conformational changes leading to helix α1 destabilization, which is a hallmark of BAK activation. Helix α1 is destabilized and restabilized in structures of BAK engaged by rationally designed, high-affinity activating and inactivating BID-like BH3 ligands, respectively. Altogether our data support the long-standing hit-and-run mechanism of BAK activation by transient binding of BH3-only proteins, demonstrating that BH3-induced structural changes are more important in BAK activation than BH3 ligand affinity.
    DOI:  https://doi.org/10.1038/s41467-021-27851-y
  3. Autophagy. 2022 Jan 13. 1-10
    Degradation of the NOTCH intracellular domain by elevated autophagy in osteoblasts promotes osteoblast differentiation and alleviates osteoporosis.
    Gota Yoshida, Tsuyoshi Kawabata, Hyota Takamatsu, Shotaro Saita, Shuhei Nakamura, Keizo Nishikawa, Mari Fujiwara, Yusuke Enokidani, Tadashi Yamamuro, Keisuke Tabata, Maho Hamasaki, Masaru Ishii, Atsushi Kumanogoh, Tamotsu Yoshimori.
      Maintenance of bone integrity is mediated by the balanced actions of osteoblasts and osteoclasts. Because macroautophagy/autophagy regulates osteoblast mineralization, osteoclast differentiation, and their secretion from osteoclast cells, autophagy deficiency in osteoblasts or osteoclasts can disrupt this balance. However, it remains unclear whether upregulation of autophagy becomes beneficial for suppression of bone-associated diseases. In this study, we found that genetic upregulation of autophagy in osteoblasts facilitated bone formation. We generated mice in which autophagy was specifically upregulated in osteoblasts by deleting the gene encoding RUBCN/Rubicon, a negative regulator of autophagy. The rubcnflox/flox;Sp7/Osterix-Cre mice showed progressive skeletal abnormalities in femur bones. Consistent with this, RUBCN deficiency in osteoblasts resulted in elevated differentiation and mineralization, as well as an increase in the elevated expression of key transcription factors involved in osteoblast function such as Runx2 and Bglap/Osteocalcin. Furthermore, RUBCN deficiency in osteoblasts accelerated autophagic degradation of NOTCH intracellular domain (NICD) and downregulated the NOTCH signaling pathway, which negatively regulates osteoblast differentiation. Notably, osteoblast-specific deletion of RUBCN alleviated the phenotype in a mouse model of osteoporosis. We conclude that RUBCN is a key regulator of bone homeostasis. On the basis of these findings, we propose that medications targeting RUBCN or autophagic degradation of NICD could be used to treat age-related osteoporosis and bone fracture.Abbreviations: ALPL: alkaline phosphatase, liver/bone/kidney; BCIP/NBT: 5-bromo-4-chloro-3'-indolyl phosphate/nitro blue tetrazolium; BMD: bone mineral density; BV/TV: bone volume/total bone volume; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MTOR: mechanistic target of rapamycin kinase; NICD: NOTCH intracellular domain; RB1CC1/FIP200: RB1-inducible coiled-coil 1; RUBCN/Rubicon: RUN domain and cysteine-rich domain containing, Beclin 1-interacting protein; SERM: selective estrogen receptor modulator; TNFRSF11B/OCIF: tumor necrosis factor receptor superfamily, member 11b (osteoprotegerin).
    Keywords:  Bone remodeling; NICD; RUBCN; Rubicon; differentiation; mineralization; osteoblast
    DOI:  https://doi.org/10.1080/15548627.2021.2017587
  4. Nat Chem Biol. 2022 Jan 13.
    Structure of UBE2K-Ub/E3/polyUb reveals mechanisms of K48-linked Ub chain extension.
    Mark A Nakasone, Karolina A Majorek, Mads Gabrielsen, Gary J Sibbet, Brian O Smith, Danny T Huang.
      Ubiquitin (Ub) chain types govern distinct biological processes. K48-linked polyUb chains target substrates for proteasomal degradation, but the mechanism of Ub chain synthesis remains elusive due to the transient nature of Ub handover. Here, we present the structure of a chemically trapped complex of the E2 UBE2K covalently linked to donor Ub and acceptor K48-linked di-Ub, primed for K48-linked Ub chain synthesis by a RING E3. The structure reveals the basis for acceptor Ub recognition by UBE2K active site residues and the C-terminal Ub-associated (UBA) domain, to impart K48-linked Ub specificity and catalysis. Furthermore, the structure unveils multiple Ub-binding surfaces on the UBA domain that allow distinct binding modes for K48- and K63-linked Ub chains. This multivalent Ub-binding feature serves to recruit UBE2K to ubiquitinated substrates to overcome weak acceptor Ub affinity and thereby promote chain elongation. These findings elucidate the mechanism of processive K48-linked polyUb chain formation by UBE2K.
    DOI:  https://doi.org/10.1038/s41589-021-00952-x
  5. Autophagy. 2022 Jan 13. 1-2
    Alternative mitophagy is a major form of mitophagy in the chronically stressed heart.
    Junichi Sadoshima.
      Mitochondrial dysfunction is a key determinant of the development of cardiomyopathy in patients with obesity and diabetes. We recently reported that mitophagy is activated in the mouse heart during the chronic phase of high-fat diet (HFD) consumption, despite downregulation of general macroautophagy/autophagy. This form of mitophagy is mediated by a mechanism distinct from that of conventional autophagy and is termed alternative mitophagy. We here discuss the underlying mechanisms of alternative mitophagy and its functional significance in heart disease.
    Keywords:  Mitophagy; Rab9; cardiomyopathy; diabetes; heart; obesity
    DOI:  https://doi.org/10.1080/15548627.2022.2025573
  6. Cancers (Basel). 2022 Jan 04. pii: 234. [Epub ahead of print]14(1):
    Secretory Autophagy Forges a Therapy Resistant Microenvironment in Melanoma.
    Silvina Odete Bustos, Nathalia Leal Santos, Roger Chammas, Luciana Nogueira de Sousa Andrade.
      Melanoma is the most aggressive skin cancer characterized by high mutational burden and large heterogeneity. Cancer cells are surrounded by a complex environment, critical to tumor establishment and progression. Thus, tumor-associated stromal components can sustain tumor demands or impair cancer cell progression. One way to manage such processes is through the regulation of autophagy, both in stromal and tumor cells. Autophagy is a catabolic mechanism that provides nutrients and energy, and it eliminates damaged organelles by degradation and recycling of cellular elements. Besides this primary function, autophagy plays multiple roles in the tumor microenvironment capable of affecting cell fate. Evidence demonstrates the existence of novel branches in the autophagy system related to cytoplasmic constituent's secretion. Hence, autophagy-dependent secretion assembles a tangled network of signaling that potentially contributes to metabolism reprogramming, immune regulation, and tumor progression. Here, we summarize the current awareness regarding secretory autophagy and the intersection with exosome biogenesis and release in melanoma and their role in tumor resistance. In addition, we present and discuss data from public databases concerning autophagy and exosome-related genes as important mediators of melanoma behavior. Finally, we will present the main challenges in the field and strategies to translate most of the pre-clinical findings to clinical practice.
    Keywords:  exosomes; melanoma; secretion; secretory autophagy; tumor microenvironment; tumor resistance
    DOI:  https://doi.org/10.3390/cancers14010234
  7. Mol Cell Biol. 2022 Jan 10. MCB0039321
    USP10 inhibits aberrant cytoplasmic aggregation of TDP-43 by promoting stress granule clearance.
    Masahiko Takahashi, Hiroki Kitaura, Akiyoshi Kakita, Taichi Kakihana, Yoshinori Katsuragi, Osamu Onodera, Yuriko Iwakura, Hiroyuki Nawa, Masaaki Komatsu, Masahiro Fujii.
      TDP-43 is a causative factor of amyotrophic lateral sclerosis (ALS). Cytoplasmic TDP-43 aggregates in neurons are a hallmark pathology of ALS. Under various stress conditions, TDP-43 localizes sequentially to two cytoplasmic protein aggregates: stress granules (SGs) first, and then aggresomes. Accumulating evidence suggests that delayed clearance of TDP-43-positive SGs is associated with pathological TDP-43 aggregates in ALS. We found that USP10 promotes the clearance of TDP-43-positive SGs in cells treated with proteasome inhibitor, thereby promoting the formation of TDP-43-positive aggresomes, and the depletion of USP10 increases the amount of insoluble TDP-35, a cleaved product of TDP-43, in the cytoplasm. TDP-35 interacted with USP10 in an RNA-binding dependent manner; however, impaired RNA-binding of TDP-35 reduced the localization in SGs and aggresomes and induced USP10-negative TDP-35 aggregates. Immunohistochemistry showed that most of the cytoplasmic TDP-43/TDP-35-aggregates in the neurons of ALS patients were USP10-negative. Our findings suggest that USP10 inhibits aberrant aggregation of TDP-43/TDP-35 in the cytoplasm of neuronal cells by promoting the clearance of TDP-43/TDP-35-positive SGs and facilitating the formation of TDP-43/TDP-35-positive aggresomes.
    DOI:  https://doi.org/10.1128/MCB.00393-21
  8. Am J Cancer Res. 2021 ;11(12): 5933-5950
    A Notch inhibitor plus Resveratrol induced blockade of autophagy drives glioblastoma cell death by promoting a switch to apoptosis.
    Francesca Giordano, Francesca Ida Montalto, Maria Luisa Panno, Sebastiano Andò, Francesca De Amicis.
      Glioblastoma multiforme (GBM) is the most common and aggressive form of brain tumors and the hardest type of cancer to treat. Therapies targeting developmental pathways, such as Notch, eliminate neoplastic glioma cells, but their efficacy can be limited by various mechanisms. Combination regimens may represent a good opportunity for effective therapies with durable effects. We used low doses of the γ-secretase inhibitor RO4929097 (GSI), to block the Notch pathway activity, in combination with Resveratrol (RSV) and we evidenced the mechanisms of autophagy/apoptosis transition in GBM cells. Resveratrol and GSI combination results in the synergistic induction of cell death together with the block of the autophagic flux evidenced by a sustained increase of LC3-II and p62 protein content, due to the dramatic reduction of CDK4, an important regulator of lysosomal function. The ectopic overexpression of the constitutive active CDK4 mutant, greatly counteracted the RSV+GSI induced block of the autophagy. Triggering autophagy in RSV+GSI-treated cells, which have impaired lysosomal function, caused the collapse of the system and a following apoptosis. For instance, by combining the CDK4 mutant as well as the early stage autophagy inhibitor, 3-methyladenina, abolished the RSV+GSI induced caspases activation. The initiator caspases (caspases-8 and -9), effector caspase (caspase-3) and its downstream substrate PARP were induced after RSV+GSI exposure as well as the percentage of the TUNEL positive cells. Moreover, the pro-apoptotic signaling MAPK p38 was activated while the pro-survival MAPK p42/p44 signaling was inhibited. In short, we establish the role of CDK4 in the regulation of autophagy/apoptosis transition induced by RSV and GSI in GBM cells. This new synergistic therapeutic combination, increasing the accumulation of autophagosomes, may have therapeutic value for GBM patients.
    Keywords:  Atg12; brain; cancer; cdk4; cell death; gamma secretase inhibitor
  9. Mol Cell. 2021 Dec 30. pii: S1097-2765(21)01067-4. [Epub ahead of print]
    Structural basis of K63-ubiquitin chain formation by the Gordon-Holmes syndrome RBR E3 ubiquitin ligase RNF216.
    Thomas R Cotton, Simon A Cobbold, Jonathan P Bernardini, Lachlan W Richardson, Xiangyi S Wang, Bernhard C Lechtenberg.
      An increasing number of genetic diseases are linked to deregulation of E3 ubiquitin ligases. Loss-of-function mutations in the RING-between-RING (RBR) family E3 ligase RNF216 (TRIAD3) cause Gordon-Holmes syndrome (GHS) and related neurodegenerative diseases. Functionally, RNF216 assembles K63-linked ubiquitin chains and has been implicated in regulation of innate immunity signaling pathways and synaptic plasticity. Here, we report crystal structures of key RNF216 reaction states including RNF216 in complex with ubiquitin and its reaction product, K63 di-ubiquitin. Our data provide a molecular explanation for chain-type specificity and reveal the molecular basis for disruption of RNF216 function by pathogenic GHS mutations. Furthermore, we demonstrate how RNF216 activity and chain-type specificity are regulated by phosphorylation and that RNF216 is allosterically activated by K63-linked di-ubiquitin. These molecular insights expand our understanding of RNF216 function and its role in disease and further define the mechanistic diversity of the RBR E3 ligase family.
    Keywords:  E3 ligases; Gordon-Holmes syndrome; RBR; RNF216; allostery; neurodegeneration; phosphorylation; structural biology; ubiquitin; zinc finger
    DOI:  https://doi.org/10.1016/j.molcel.2021.12.005
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