bims-apauto 2022-10-30 papers

bims-apauto

Biomed News

on Apoptosis and autophagy

Issue of 2022–10–30
eight papers selected by
Su Hyun Lee, Seoul National University

A method for the isolation and characterization of autophagic bodies from yeast provides a key tool to investigate cargos of autophagy.
Phospholipid imbalance impairs autophagosome completion.
LC3-dependent EV loading and secretion (LDELS) promotes TFRC (transferrin receptor) secretion via extracellular vesicles.
Digest it all: the lysosomal turnover of cytoplasmic aggregates.
Autophagy in Cancer: A Metabolic Perspective.
Mitochondrial proteotoxicity: implications and ubiquitin-dependent quality control mechanisms.
Targeting Apoptosis in AML: Where Do We Stand?
Editorial: Apoptosis, autophagy, and mitophagy dysfunction in Alzheimer's disease: Evolving emergence and mechanisms.

J Biol Chem. 2022 Oct 25. pii: S0021-9258(22)01084-5. [Epub ahead of print] 102641

A method for the isolation and characterization of autophagic bodies from yeast provides a key tool to investigate cargos of autophagy.

Tomoko Kawamata, Shiho Makino, Yoko Kagohashi, Michiko Sasaki, Yoshinori Ohsumi.

  Autophagy is a major cellular degradation pathway that is highly conserved among eukaryotes. The identification of cargos captured by autophagosomes is critical to our understanding of the physiological significance of autophagy in cells, but these studies can be challenging because autophagosomes disintegrate easily. In the yeast S. cerevisiae, cells deficient in the vacuolar lipase Atg15 accumulate autophagic bodies (ABs) within the vacuole following the induction of autophagy. As ABs contain cytosolic components including proteins, RNAs, and lipids, their purification allows the identification of material targeted by autophagy for degradation. In this study, we demonstrate a method to purify intact ABs using isolated vacuoles from atg15Δ cells. Taking advantage of the size discrepancy between the vacuoles and ABs, the vacuolar membrane was disrupted by filtration to release ABs. Filtered vacuolar lysates were subjected to density gradient centrifugation to obtain AB fractions. Purified ABs retain membrane integrity and contain autophagic cargos. This technique offers a valuable tool for the identification of the cargos of autophagy, examination of autophagic cargo selectivity, and biochemical characterization of autophagosome membranes.

Keywords:  autophagic bodies; autophagy; degradation; starvation; yeast

DOI:  https://doi.org/10.1016/j.jbc.2022.102641
EMBO J. 2022 Oct 27. e110771

Phospholipid imbalance impairs autophagosome completion.

Alexandra Polyansky, Oren Shatz, Milana Fraiberg, Eyal Shimoni, Tali Dadosh, Muriel Mari, Fulvio M Reggiori, Chao Qin, Xianlin Han, Zvulun Elazar.

  Autophagy, a conserved eukaryotic intracellular catabolic pathway, maintains cell homeostasis by lysosomal degradation of cytosolic material engulfed in double membrane vesicles termed autophagosomes, which form upon sealing of single-membrane cisternae called phagophores. While the role of phosphatidylinositol 3-phosphate (PI3P) and phosphatidylethanolamine (PE) in autophagosome biogenesis is well-studied, the roles of other phospholipids in autophagy remain rather obscure. Here we utilized budding yeast to study the contribution of phosphatidylcholine (PC) to autophagy. We reveal for the first time that genetic loss of PC biosynthesis via the CDP-DAG pathway leads to changes in lipid composition of autophagic membranes, specifically replacement of PC by phosphatidylserine (PS). This impairs closure of the autophagic membrane and autophagic flux. Consequently, we show that choline-dependent recovery of de novo PC biosynthesis via the CDP-choline pathway restores autophagosome formation and autophagic flux in PC-deficient cells. Our findings therefore implicate phospholipid metabolism in autophagosome biogenesis.

Keywords:  autophagosome biogenesis; autophagy; phagophore; phospholipids

DOI:  https://doi.org/10.15252/embj.2022110771
Autophagy. 2022 Oct 26.

LC3-dependent EV loading and secretion (LDELS) promotes TFRC (transferrin receptor) secretion via extracellular vesicles.

Jackson O Gardner, Andrew M Leidal, Tan A Nguyen, Jayanta Debnath.

  LC3-dependent EV loading and secretion (LDELS) is a secretory autophagy pathway in which the macroautophagy/autophagy machinery facilitates the packaging of cytosolic cargos, such as RNA-binding proteins, into extracellular vesicles (EVs) for secretion outside of the cell. Here, we identify TFRC (transferrin receptor), one of the first proteins found to be secreted via EVs, as a transmembrane cargo of the LDELS pathway. Similar to other LDELS targets, TFRC secretion via EVs genetically requires components of the MAP1LC3/LC3-conjugation machinery but is independent of other ATGs involved in classical autophagosome formation. Furthermore, the packaging and secretion of this transmembrane protein into EVs depends on multiple ESCRT pathway components and the small GTPase RAB27A. Based on these results, we propose that the LDELS pathway promotes TFRC incorporation into EVs and its secretion outside the cell.

Keywords:  ATG7; ATG8; LC3-conjugation; extracellular vesicles; secretory autophagy; transferrin receptor

DOI:  https://doi.org/10.1080/15548627.2022.2140557
Trends Biochem Sci. 2022 Oct 21. pii: S0968-0004(22)00271-7. [Epub ahead of print]

Digest it all: the lysosomal turnover of cytoplasmic aggregates.

Mario Mauthe, Harm H Kampinga, Mark S Hipp, Fulvio Reggiori.

  Aggrephagy describes the selective lysosomal transport and turnover of cytoplasmic protein aggregates by macro-autophagy. In this process, protein aggregates and conglomerates are polyubiquitinated and then sequestered by autophagosomes. Soluble selective autophagy receptors (SARs) are central to aggrephagy and physically bind to both ubiquitin and the autophagy machinery, thus linking the cargo to the forming autophagosomal membrane. Because the accumulation of protein aggregates is associated with cytotoxicity in several diseases, a better molecular understanding of aggrephagy might provide a conceptual framework to develop therapeutic strategies aimed at delaying the onset of these pathologies by preventing the buildup of potentially toxic aggregates. We review recent advances in our knowledge about the mechanism of aggrephagy.

Keywords:  cellular protein quality control; chaperone-mediated autophagy; macro-autophagy; micro-autophagy; p62 bodies; selective autophagy receptors

DOI:  https://doi.org/10.1016/j.tibs.2022.09.012
Subcell Biochem. 2022 ;100 143-172

Autophagy in Cancer: A Metabolic Perspective.

Sweta Sikder, Atanu Mondal, Chandrima Das, Tapas K Kundu.

  Autophagy is an intracellular catabolic degradative process in which damaged cellular organelles, unwanted proteins and different cytoplasmic components get recycled to maintain cellular homeostasis or metabolic balance. During autophagy, a double membrane vesicle is formed to engulf these cytosolic materials and fuse to lysosomes wherein the entire cargo degrades to be used again. Because of this unique recycling ability of cells, autophagy is a universal stress response mechanism. Dysregulation of autophagy leads to several diseases, including cancer, neurodegeneration and microbial infection. Thus, autophagy machineries have become targets for therapeutics. This chapter provides an overview of the paradoxical role of autophagy in tumorigenesis in the perspective of metabolism.

Keywords:  Autophagy; Cancer; Histone modifications; Metabolism

DOI:  https://doi.org/10.1007/978-3-031-07634-3_5
Cell Mol Life Sci. 2022 Oct 29. 79(11): 574

Mitochondrial proteotoxicity: implications and ubiquitin-dependent quality control mechanisms.

Mariusz Karbowski, Yumiko Oshima, Nicolas Verhoeven.

  Through their role in energy generation and regulation of several vital pathways, including apoptosis and inflammation, mitochondria are critical for the life of eukaryotic organisms. Mitochondrial dysfunction is a major problem implicated in the etiology of many pathologies, including neurodegenerative diseases, such as Parkinson's disease (PD), Alzheimer's disease (AD), Huntington's disease (HD), and amyotrophic lateral sclerosis (ALS), diabetes, cardiovascular diseases, and many others. Proteotoxic stress, here defined as a reduction in bioenergetic activity induced by the accumulation of aberrant proteins in the mitochondria, is likely to be implicated in disease-linked mitochondrial and cellular decline. Various quality control pathways, such as mitochondrial unfolded protein response (mtUPR), the ubiquitin (Ub)-dependent degradation of aberrant mitochondrial proteins, and mitochondria-specific autophagy (mitophagy), respond to proteotoxic stress and eliminate defective proteins or dysfunctional mitochondria. This work provides a concise review of mechanisms by which disease-linked aberrant proteins affect mitochondrial function and an overview of mitochondrial quality control pathways that counteract mitochondrial proteotoxicity. We focus on mitochondrial quality control mechanisms relying on the Ub-mediated protein degradation, such as mitochondria-specific autophagy and the mitochondrial arm of the Ub proteasome system (UPS). We highlight the importance of a widening perspective of how these pathways protect mitochondria from proteotoxic stress to better understand mitochondrial proteotoxicity in overlapping pathophysiological pathways. Implications of these mechanisms in disease development are also briefly summarized.

Keywords:  Mitochondria; Mitophagy; Proteotoxicity; Quality control; Ubiquitin

DOI:  https://doi.org/10.1007/s00018-022-04604-8
Cancers (Basel). 2022 Oct 12. pii: 4995. [Epub ahead of print]14(20):

Targeting Apoptosis in AML: Where Do We Stand?

Kinga Krawiec, Piotr Strzałka, Magdalena Czemerska, Aneta Wiśnik, Izabela Zawlik, Agnieszka Wierzbowska, Agnieszka Pluta.

  More than 97% of patients with acute myeloid leukemia (AML) demonstrate genetic mutations leading to excessive proliferation combined with the evasion of regulated cell death (RCD). The most prominent and well-defined form of RCD is apoptosis, which serves as a defense mechanism against the emergence of cancer cells. Apoptosis is regulated in part by the BCL-2 family of pro- and anti-apoptotic proteins, whose balance can significantly determine cell survival. Apoptosis evasion plays a key role in tumorigenesis and drug resistance, and thus in the development and progression of AML. Research on the structural and biochemical aspects of apoptosis proteins and their regulators offers promise for new classes of targeted therapies and strategies for therapeutic intervention. This review provides a comprehensive overview of current AML treatment options related to the mechanism of apoptosis, particularly its mitochondrial pathway, and other promising concepts such as neddylation. It pays particular attention to clinically-relevant aspects of current and future AML treatment approaches, highlighting the molecular basis of individual therapies.

Keywords:  BCL-2 family; acute myeloid leukemia; apoptosis; neddylation

DOI:  https://doi.org/10.3390/cancers14204995
Front Mol Neurosci. 2022 ;15 1049914

Editorial: Apoptosis, autophagy, and mitophagy dysfunction in Alzheimer's disease: Evolving emergence and mechanisms.

Rajkumar Singh Kalra, Ramesh Kandimalla, Binukumar Bk.



Keywords:  Alzheimer's disease; amyloid-β plaques; apoptosis; autophagy; mitophagy; neuro-fibrillary tangles; neurodegeneration; neuroinflammation

DOI:  https://doi.org/10.3389/fnmol.2022.1049914