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Zhang W, Zou M, Fu J, Xu Y, Zhu Y. Autophagy: A potential target for natural products in the treatment of ulcerative colitis. Biomed Pharmacother 2024; 176:116891. [PMID: 38865850 DOI: 10.1016/j.biopha.2024.116891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 05/16/2024] [Accepted: 06/05/2024] [Indexed: 06/14/2024] Open
Abstract
Ulcerative colitis (UC) is a chronic inflammatory bowel disease primarily affecting the mucosa of the colon and rectum. UC is characterized by recurrent episodes, often necessitating lifelong medication use, imposing a significant burden on patients. Current conventional and advanced treatments for UC have the disadvantages of insufficient efficiency, susceptibility to drug resistance, and notable adverse effects. Therefore, developing effective and safe drugs has become an urgent need. Autophagy is an intracellular degradation process that plays an important role in intestinal homeostasis. Emerging evidence suggests that aberrant autophagy is involved in the development of UC, and modulating autophagy can effectively alleviate experimental colitis. A growing number of studies have established that autophagy can interplay with endoplasmic reticulum stress, gut microbiota, apoptosis, and the NLRP3 inflammasome, all of which contribute to the pathogenesis of UC. In addition, a variety of intestinal epithelial cells, including absorptive cells, goblet cells, and Paneth cells, as well as other cell types like neutrophils, antigen-presenting cells, and stem cells in the gut, mediate the development of UC through autophagy. To date, many studies have found that natural products hold the potential to exert therapeutic effects on UC by regulating autophagy. This review focuses on the possible effects and pharmacological mechanisms of natural products to alleviate UC with autophagy as a potential target in recent years, aiming to provide a basis for new drug development.
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Affiliation(s)
- Wei Zhang
- The First Clinical College of Traditional Chinese Medicine, Hunan University of Chinese Medicine, Changsha, Hunan 410208, China
| | - Menglong Zou
- The First Clinical College of Traditional Chinese Medicine, Hunan University of Chinese Medicine, Changsha, Hunan 410208, China
| | - Jia Fu
- Department of Gastroenterology, The First Hospital of Hunan University of Chinese Medicine, Changsha, Hunan 410007, China
| | - Yin Xu
- Department of Gastroenterology, The First Hospital of Hunan University of Chinese Medicine, Changsha, Hunan 410007, China.
| | - Ying Zhu
- Department of Gastroenterology, The First Hospital of Hunan University of Chinese Medicine, Changsha, Hunan 410007, China.
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2
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Baumann V, Achleitner S, Tulli S, Schuschnig M, Klune L, Martens S. Faa1 membrane binding drives positive feedback in autophagosome biogenesis via fatty acid activation. J Cell Biol 2024; 223:e202309057. [PMID: 38573225 PMCID: PMC10993510 DOI: 10.1083/jcb.202309057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 02/14/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024] Open
Abstract
Autophagy serves as a stress response pathway by mediating the degradation of cellular material within lysosomes. In autophagy, this material is encapsulated in double-membrane vesicles termed autophagosomes, which form from precursors referred to as phagophores. Phagophores grow by lipid influx from the endoplasmic reticulum into Atg9-positive compartments and local lipid synthesis provides lipids for their expansion. How phagophore nucleation and expansion are coordinated with lipid synthesis is unclear. Here, we show that Faa1, an enzyme activating fatty acids, is recruited to Atg9 vesicles by directly binding to negatively charged membranes with a preference for phosphoinositides such as PI3P and PI4P. We define the membrane-binding surface of Faa1 and show that its direct interaction with the membrane is required for its recruitment to phagophores. Furthermore, the physiological localization of Faa1 is key for its efficient catalysis and promotes phagophore expansion. Our results suggest a positive feedback loop coupling phagophore nucleation and expansion to lipid synthesis.
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Affiliation(s)
- Verena Baumann
- Max Perutz Labs, Vienna BioCenter Campus (VBC), Vienna, Austria
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, Vienna, Austria
| | - Sonja Achleitner
- Max Perutz Labs, Vienna BioCenter Campus (VBC), Vienna, Austria
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, Vienna, Austria
- Vienna BioCenter PhD Program, A Doctoral School of the University of Vienna, Medical University of Vienna, Vienna, Austria
| | - Susanna Tulli
- Max Perutz Labs, Vienna BioCenter Campus (VBC), Vienna, Austria
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, Vienna, Austria
| | - Martina Schuschnig
- Max Perutz Labs, Vienna BioCenter Campus (VBC), Vienna, Austria
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, Vienna, Austria
| | - Lara Klune
- Max Perutz Labs, Vienna BioCenter Campus (VBC), Vienna, Austria
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, Vienna, Austria
| | - Sascha Martens
- Max Perutz Labs, Vienna BioCenter Campus (VBC), Vienna, Austria
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, Vienna, Austria
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3
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Gopaldass N, Mayer A. PROPPINs and membrane fission in the endo-lysosomal system. Biochem Soc Trans 2024; 52:1233-1241. [PMID: 38747700 DOI: 10.1042/bst20230897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/21/2024] [Accepted: 04/22/2024] [Indexed: 06/27/2024]
Abstract
PROPPINs constitute a conserved protein family with multiple members being expressed in many eukaryotes. PROPPINs have mainly been investigated for their role in autophagy, where they co-operate with several core factors for autophagosome formation. Recently, novel functions of these proteins on endo-lysosomal compartments have emerged. PROPPINs support the division of these organelles and the formation of tubulo-vesicular cargo carriers that mediate protein exit from them, such as those generated by the Retromer coat. In both cases, PROPPINs provide membrane fission activity. Integrating information from yeast and human cells this review summarizes the most important molecular features that allow these proteins to facilitate membrane fission and thus provide a critical element to endo-lysosomal protein traffic.
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Affiliation(s)
- Navin Gopaldass
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland
| | - Andreas Mayer
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland
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Bidisha B, Sowmya M, Shalini S, Mythri C, Gupta A, Vijayakumar G, Sudhagar S. Tamoxifen modulates nutrition deprivation-induced ER stress through AMPK-mediated ER-phagy in breast cancer cells. Breast Cancer Res Treat 2024:10.1007/s10549-024-07398-4. [PMID: 38874683 DOI: 10.1007/s10549-024-07398-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 06/05/2024] [Indexed: 06/15/2024]
Abstract
PURPOSE Rapid proliferation and nutrition starvation in the tumor microenvironment pose significant challenges to cellular protein homeostasis. The accumulation of misfolded proteins in the endoplasmic reticulum lumen induces stress on cells and causes irreversible damage to cells if unresolved. Emerging reports emphasize the influence of the tumor microenvironment on therapeutic molecule efficacy and treatment outcomes. Hence, we aimed to understand the influence of tamoxifen on the cellular adaptation to endoplasmic reticulum stress during metabolic stress in breast cancer cells. METHODS Nutrition deprivation induces endoplasmic reticulum stress (ER stress), and the unfolded protein response (UPR) in breast cancer cells was confirmed by a Thioflavin B assay and western blotting. Tamoxifen-indued ER-phagy was studied using an MCD assay, confocal microscopy, and western blotting. RESULTS Nutrition deprivation induces ER stress in breast cancer cells. Interestingly, tamoxifen modulates the nutrition deprivation-induced endoplasmic reticulum stress through enhancing the selective ER-phagy, a specialized autophagy. The tamoxifen-induced ER-phagy is mediated by AMPK activation. The pharmacological inhibition of AMPK blocks tamoxifen-induced ER-phagy and tamoxifen modulatory effect on ER stress during nutrition deprivation. CONCLUSION Tamoxifen modulates ER stress by inducing ER-phagy through AMPK, thereby, may support breast cancer cell survival during nutrition deprivation conditions.
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Affiliation(s)
- Biswas Bidisha
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research - Guwahati, Changsari, India
| | - Manickavasagan Sowmya
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research - Guwahati, Changsari, India
| | - Suchita Shalini
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research - Guwahati, Changsari, India
| | - Chandrasekaran Mythri
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research - Guwahati, Changsari, India
| | - Anshu Gupta
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research - Guwahati, Changsari, India
| | - Gangipangi Vijayakumar
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research - Guwahati, Changsari, India
- Center for Translational Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Jane and Leonard Korman Respiratory Institute, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Selvaraju Sudhagar
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research - Guwahati, Changsari, India.
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5
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Lee A, Davis JH. NCOA4 initiates ferritinophagy by binding GATE16 using two highly avid short linear interaction motifs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.09.597909. [PMID: 38895392 PMCID: PMC11185777 DOI: 10.1101/2024.06.09.597909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Cells carefully regulate cytosolic iron, which is a vital enzymatic cofactor, yet is toxic in excess. In mammalian cells, surplus iron is sequestered in ferritin cages that, in iron limiting conditions, are degraded through the selective autophagy pathway ferritinophagy to liberate free iron. Prior work identified the ferritinophagy receptor protein NCOA4, which links ferritin and LC3/GABARAP-family member GATE16, effectively tethering ferritin to the autophagic machinery. Here, we elucidate the molecular mechanism underlying this interaction, discovering two short linear motifs in NCOA4 that each bind GATE16 with weak affinity. These binding motifs are highly avid and, in concert, support high-affinity NCOA4•GATE16 complex formation. We further find the minimal NCOA4383-522 fragment bearing these motifs is sufficient for ferritinophagy and that both motifs are necessary for this activity. This work suggests a general mechanism wherein selective autophagy receptors can distinguish between the inactive soluble pools of LC3/GABARAPs and the active membrane-conjugated forms that drive autophagy. Finally, we find that iron decreases NCOA4383-522's affinity for GATE16, providing a plausible mechanism for iron-dependent regulation of ferritinophagy.
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Affiliation(s)
- April Lee
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Joseph H. Davis
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
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Cristian RE, Balta C, Herman H, Ciceu A, Trica B, Sbarcea BG, Miutescu E, Hermenean A, Dinischiotu A, Stan MS. Exploring In Vivo Pulmonary and Splenic Toxicity Profiles of Silicon Quantum Dots in Mice. MATERIALS (BASEL, SWITZERLAND) 2024; 17:2778. [PMID: 38894040 PMCID: PMC11173407 DOI: 10.3390/ma17112778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 05/26/2024] [Accepted: 06/05/2024] [Indexed: 06/21/2024]
Abstract
Silicon-based quantum dots (SiQDs) represent a special class of nanoparticles due to their low toxicity and easily modifiable surface properties. For this reason, they are used in applications such as bioimaging, fluorescent labeling, drug delivery, protein detection techniques, and tissue engineering despite a serious lack of information on possible in vivo effects. The present study aimed to characterize and evaluate the in vivo toxicity of SiQDs obtained by laser ablation in the lung and spleen of mice. The particles were administered in three different doses (1, 10, and 100 mg QDs/kg of body weight) by intravenous injection into the caudal vein of Swiss mice. After 1, 6, 24, and 72 h, the animals were euthanized, and the lung and spleen tissues were harvested for the evaluation of antioxidant enzyme activity, lipid peroxidation, protein expression, and epigenetic and morphological changes. The obtained results highlighted a low toxicity in pulmonary and splenic tissues for concentrations up to 10 mg SiQDs/kg body, demonstrated by biochemical and histopathological analysis. Therefore, our study brings new experimental evidence on the biocompatibility of this type of QD, suggesting the possibility of expanding research on the biomedical applications of SiQDs.
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Affiliation(s)
- Roxana-Elena Cristian
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, 91-95 Splaiul Independentei, 050095 Bucharest, Romania; (R.-E.C.); (A.H.); (M.S.S.)
- DANUBIUS Department, National Institute of Research and Development for Biological Sciences, Splaiul Independentei 296, 060031 Bucharest, Romania
| | - Cornel Balta
- “Aurel Ardelean” Institute of Life Sciences, Vasile Goldis Western University of Arad, 86 Rebreanu, 310414 Arad, Romania; (C.B.); (H.H.); (A.C.)
| | - Hildegard Herman
- “Aurel Ardelean” Institute of Life Sciences, Vasile Goldis Western University of Arad, 86 Rebreanu, 310414 Arad, Romania; (C.B.); (H.H.); (A.C.)
| | - Alina Ciceu
- “Aurel Ardelean” Institute of Life Sciences, Vasile Goldis Western University of Arad, 86 Rebreanu, 310414 Arad, Romania; (C.B.); (H.H.); (A.C.)
| | - Bogdan Trica
- National Institute for Research & Development in Chemistry and Petrochemistry (INCDCP-ICECHIM), 202 Spl. Independentei, 060021 Bucharest, Romania;
| | - Beatrice G. Sbarcea
- Materials Characterization Department, National Institute for Research & Development in Electrical Engineering (ICPE-CA), 313 Splaiul Unirii, 030138 Bucharest, Romania;
| | - Eftimie Miutescu
- Faculty of Medicine, Vasile Goldis Western University of Arad, 86 Rebreanu, 310414 Arad, Romania;
| | - Anca Hermenean
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, 91-95 Splaiul Independentei, 050095 Bucharest, Romania; (R.-E.C.); (A.H.); (M.S.S.)
- “Aurel Ardelean” Institute of Life Sciences, Vasile Goldis Western University of Arad, 86 Rebreanu, 310414 Arad, Romania; (C.B.); (H.H.); (A.C.)
| | - Anca Dinischiotu
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, 91-95 Splaiul Independentei, 050095 Bucharest, Romania; (R.-E.C.); (A.H.); (M.S.S.)
| | - Miruna S. Stan
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, 91-95 Splaiul Independentei, 050095 Bucharest, Romania; (R.-E.C.); (A.H.); (M.S.S.)
- Research Institute of the University of Bucharest (ICUB), University of Bucharest, 91-95 Spl. Independentei, 050095 Bucharest, Romania
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7
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Zhao G, Wang Y, Fan Z, Xiong J, Ertas YN, Ashammakhi N, Wang J, Ma T. Nanomaterials in crossroad of autophagy control in human cancers: Amplification of cell death mechanisms. Cancer Lett 2024; 591:216860. [PMID: 38583650 DOI: 10.1016/j.canlet.2024.216860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/24/2024] [Accepted: 04/02/2024] [Indexed: 04/09/2024]
Abstract
Cancer is the result of genetic abnormalities that cause normal cells to grow into neoplastic cells. Cancer is characterized by several distinct features, such as uncontrolled cell growth, extensive spreading to other parts of the body, and the ability to resist treatment. The scientists have stressed the development of nanostructures as novel therapeutic options in suppressing cancer, in response to the emergence of resistance to standard medicines. One of the specific mechanisms with dysregulation during cancer is autophagy. Nanomaterials have the ability to specifically carry medications and genes, and they can also enhance the responsiveness of tumor cells to standard therapy while promoting drug sensitivity. The primary mechanism in this process relies on autophagosomes and their fusion with lysosomes to break down the components of the cytoplasm. While autophagy was initially described as a form of cellular demise, it has been demonstrated to play a crucial role in controlling metastasis, proliferation, and treatment resistance in human malignancies. The pharmacokinetic profile of autophagy modulators is poor, despite their development for use in cancer therapy. Consequently, nanoparticles have been developed for the purpose of delivering medications and autophagy modulators selectively and specifically to the cancer process. Furthermore, several categories of nanoparticles have demonstrated the ability to regulate autophagy, which plays a crucial role in defining the biological characteristics and response to therapy of tumor cells.
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Affiliation(s)
- Gang Zhao
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yutao Wang
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Dongcheng, Beijing, 100000, China
| | - Zhongru Fan
- Department of Urology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | - Jian Xiong
- Department of Obstetrics and Gynaecology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Yavuz Nuri Ertas
- ERNAM-Nanotechnology Research and Application Center, Erciyes University, Kayseri, 38039, Türkiye; Department of Biomedical Engineering, Erciyes University, Kayseri, 39039, Türkiye.
| | - Nureddin Ashammakhi
- Institute for Quantitative Health Science and Engineering (IQ), Department of Biomedical Engineering, College of Engineering and Human Medicine, Michigan State University, East Lansing, MI, 48824, USA.
| | - Jianfeng Wang
- Department of Urology, First Hospital of China Medical University, Shenyang, Liaoning, 110001, China.
| | - Ting Ma
- Department of Hepatobiliary and Pancreatic Surgery, First Hospital of China Medical University, Shenyang, Liaoning, 110001, China.
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Peng Y, Tao Y, Liu L, Zhang J, Wei B. Crosstalk among Reactive Oxygen Species, Autophagy and Metabolism in Myocardial Ischemia and Reperfusion Stages. Aging Dis 2024; 15:1075-1107. [PMID: 37728583 PMCID: PMC11081167 DOI: 10.14336/ad.2023.0823-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 08/23/2023] [Indexed: 09/21/2023] Open
Abstract
Myocardial ischemia is the most common cardiovascular disease. Reperfusion, an important myocardial ischemia tool, causes unexpected and irreversible damage to cardiomyocytes, resulting in myocardial ischemia/reperfusion (MI/R) injury. Upon stress, especially oxidative stress induced by reactive oxygen species (ROS), autophagy, which degrades the intracellular energy storage to produce metabolites that are recycled into metabolic pathways to buffer metabolic stress, is initiated during myocardial ischemia and MI/R injury. Excellent cardioprotective effects of autophagy regulators against MI and MI/R have been reported. Reversing disordered cardiac metabolism induced by ROS also exhibits cardioprotective action in patients with myocardial ischemia. Herein, we review current knowledge on the crosstalk between ROS, cardiac autophagy, and metabolism in myocardial ischemia and MI/R. Finally, we discuss the possible regulators of autophagy and metabolism that can be exploited to harness the therapeutic potential of cardiac metabolism and autophagy in the diagnosis and treatment of myocardial ischemia and MI/R.
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Affiliation(s)
- Yajie Peng
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China.
| | - Yachuan Tao
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China.
- Department of Pharmacology, School of Pharmaceutical Sciences, Fudan University, Shanghai, China
| | - Lingxu Liu
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China.
| | - Ji Zhang
- The First Affiliated Hospital of Zhengzhou University, Department of Pharmacy, Zhengzhou, Henan, China.
| | - Bo Wei
- Key Laboratory of Advanced Pharmaceutical Technology, Ministry of Education of China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China.
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Wang Z, Wang R, Niu L, Zhou X, Han J, Li K. EPB41L4A-AS1 is required to maintain basal autophagy to modulates Aβ clearance. NPJ AGING 2024; 10:24. [PMID: 38704365 PMCID: PMC11069514 DOI: 10.1038/s41514-024-00152-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 04/22/2024] [Indexed: 05/06/2024]
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disorder characterized by the deposition of β-amyloid (Aβ) plaques. Aβ is generated from the cleavage of the amyloid precursor protein by β and γ-secretases and cleared by neuroglial cells mediated autophagy. The imbalance of the intracellular Aβ generation and clearance is the causative factor for AD pathogenesis. However, the exact underlying molecular mechanisms remain unclear. Our previous study reported that EPB41L4A-AS1 is an aging-related long non-coding RNA (lncRNA) that is repressed in patients with AD. In this study, we found that downregulated EPB41L4A-AS1 in AD inhibited neuroglial cells mediated-Aβ clearance by decreasing the expression levels of multiple autophagy-related genes. We found that EPB41L4A-AS1 regulates the expression of general control of amino acid synthesis 5-like 2, an important histone acetyltransferase, thus affecting histone acetylation, crotonylation, and lactylation near the transcription start site of autophagy-related genes, ultimately influencing their transcription. Collectively, this study reveals EPB41L4A-AS1 as an AD-related lncRNA via mediating Aβ clearance and provides insights into the epigenetic regulatory mechanism of EPB41L4A-AS1 in gene expression and AD pathogenesis.
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Affiliation(s)
- Ziqiang Wang
- Department of Nuclear Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, 250014, China.
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250062, China.
| | - Ruomei Wang
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250062, China
| | - Lixin Niu
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250062, China
| | - Xiaoyan Zhou
- Department of Nuclear Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, 250014, China
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250062, China
| | - Jinxiang Han
- Department of Nuclear Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, 250014, China.
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250062, China.
| | - Kun Li
- Department of Nuclear Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, 250014, China.
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10
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Li Q, Wen W, Wang Y, Gong T, Wang X, Tan Q, Fan B, Xie H, Li Y, Li S, Yang C, Zhou Z, Duan X, Lin W, Chen L. Autophagy-related protein 5 (ATG5) interacts with bone marrow stromal cell antigen 2 (BST2) to stimulate HBV replication through antagonizing the antiviral activity of BST2. J Med Virol 2024; 96:e29659. [PMID: 38747016 DOI: 10.1002/jmv.29659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/15/2024] [Accepted: 04/30/2024] [Indexed: 06/05/2024]
Abstract
Hepatitis B virus (HBV) infection is a major global health burden with 820 000 deaths per year. In our previous study, we found that the knockdown of autophagy-related protein 5 (ATG5) significantly upregulated the interferon-stimulated genes (ISGs) expression to exert the anti-HCV effect. However, the regulation of ATG5 on HBV replication and its underlying mechanism remains unclear. In this study, we screened the altered expression of type I interferon (IFN-I) pathway genes using RT² Profiler™ PCR array following ATG5 knock-down and we found the bone marrow stromal cell antigen 2 (BST2) expression was significantly increased. We then verified the upregulation of BST2 by ATG5 knockdown using RT-qPCR and found that the knockdown of ATG5 activated the Janus kinase/signal transducer and activator of transcription (JAK-STAT) signaling pathway. ATG5 knockdown or BST2 overexpression decreased Hepatitis B core Antigen (HBcAg) protein, HBV DNA levels in cells and supernatants of HepAD38 and HBV-infected NTCP-HepG2. Knockdown of BST2 abrogated the anti-HBV effect of ATG5 knockdown. Furthermore, we found that ATG5 interacted with BST2, and further formed a ternary complex together with HBV-X (HBx). In conclusion, our finding indicates that ATG5 promotes HBV replication through decreasing BST2 expression and interacting with it directly to antagonize its antiviral function.
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Affiliation(s)
- Qingyuan Li
- Department of Clinical Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
- Research Platform for Transfusion-transmitted Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Key Laboratory for Transfusion-transmitted Infectious Diseases of the Health Commission of Sichuan Province, Chengdu, Sichuan, China
| | - Wenxian Wen
- Department of Clinical Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
- Research Platform for Transfusion-transmitted Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Key Laboratory for Transfusion-transmitted Infectious Diseases of the Health Commission of Sichuan Province, Chengdu, Sichuan, China
| | - Yijin Wang
- Department of Clinical Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Tao Gong
- Department of Clinical Medicine, North Sichuan Medical College, Nanchong, Sichuan, China
- Research Platform for Transfusion-transmitted Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Key Laboratory for Transfusion-transmitted Infectious Diseases of the Health Commission of Sichuan Province, Chengdu, Sichuan, China
| | - Xinwei Wang
- Joint Laboratory on Transfusion-transmitted Infectious Diseases between Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Nanning Blood Center, Nanning Blood Center, Key Laboratory for Transfusion-transmitted Infectious Diseases of the Health Commission of Nanning City, Nanning, Guangxi, China
| | - Qi Tan
- Research Platform for Transfusion-transmitted Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Key Laboratory for Transfusion-transmitted Infectious Diseases of the Health Commission of Sichuan Province, Chengdu, Sichuan, China
| | - Bin Fan
- Research Platform for Transfusion-transmitted Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Key Laboratory for Transfusion-transmitted Infectious Diseases of the Health Commission of Sichuan Province, Chengdu, Sichuan, China
| | - He Xie
- Department of Clinical Laboratory, The Hospital of Xidian Group, Xian, Shaanxi, China
| | - Yujia Li
- Research Platform for Transfusion-transmitted Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Key Laboratory for Transfusion-transmitted Infectious Diseases of the Health Commission of Sichuan Province, Chengdu, Sichuan, China
| | - Shilin Li
- Research Platform for Transfusion-transmitted Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Key Laboratory for Transfusion-transmitted Infectious Diseases of the Health Commission of Sichuan Province, Chengdu, Sichuan, China
| | - Chunhui Yang
- Research Platform for Transfusion-transmitted Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Key Laboratory for Transfusion-transmitted Infectious Diseases of the Health Commission of Sichuan Province, Chengdu, Sichuan, China
| | - Zhonghui Zhou
- Department of Infectious Diseases, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
| | - Xiaoqiong Duan
- Research Platform for Transfusion-transmitted Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Key Laboratory for Transfusion-transmitted Infectious Diseases of the Health Commission of Sichuan Province, Chengdu, Sichuan, China
| | - Wenyu Lin
- Department of Medicine, Liver Center and Gastrointestinal Division, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Limin Chen
- Research Platform for Transfusion-transmitted Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Key Laboratory for Transfusion-transmitted Infectious Diseases of the Health Commission of Sichuan Province, Chengdu, Sichuan, China
- Joint Laboratory on Transfusion-transmitted Infectious Diseases between Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Nanning Blood Center, Nanning Blood Center, Key Laboratory for Transfusion-transmitted Infectious Diseases of the Health Commission of Nanning City, Nanning, Guangxi, China
- Department of Clinical Laboratory, The Hospital of Xidian Group, Xian, Shaanxi, China
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11
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Xu Y, Liu W, Sun Z, Yu Y, Yang T, Lu X, Zhang G, Jiao J, Duan X. The two autophagy-related proteins 8a and 8b play distinct physiological roles in Drosophila. Genomics 2024; 116:110853. [PMID: 38701988 DOI: 10.1016/j.ygeno.2024.110853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/17/2024] [Accepted: 04/30/2024] [Indexed: 05/06/2024]
Abstract
Atg8 family proteins play crucial roles in autophagy to maintain cellular homeostasis. However, the physiological roles of Atg8 family proteins have not been systematically determined. In this study, we generated Atg8a and Atg8b (homologs of Atg8 in Drosophila melanogaster) knockout flies. We found that the loss of Atg8a affected autophagy and resulted in partial lethality, abnormal wings, decreased lifespan, and decreased climbing ability in flies. Furthermore, the loss of Atg8a resulted in reduced muscle integrity and the progressive degeneration of the neuron system. We also found that the phosphorylation at Ser88 of Atg8a is important for autophagy and neuronal integrity. The loss of Atg8b did not affect autophagy but induced male sterility in flies. Here, we take full advantage of the fly system to elucidate the physiological function of Atg8a and Atg8b in Drosophila.
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Affiliation(s)
- Yuchen Xu
- School of Life Sciences, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, China
| | - Wei Liu
- College of Basic Medicine, Xuzhou Medical University, Xuzhou 221004, China
| | - Zhaolin Sun
- School of Life Sciences, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, China
| | - Yurun Yu
- School of Life Sciences, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, China
| | - Tianhao Yang
- School of Life Sciences, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, China
| | - Xirui Lu
- School of Life Sciences, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, China
| | - Guiqiang Zhang
- School of Life Sciences, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, China
| | - Jianwei Jiao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Xiuying Duan
- School of Life Sciences, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, China.
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12
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Ortega MA, Fraile-Martinez O, de Leon-Oliva D, Boaru DL, Lopez-Gonzalez L, García-Montero C, Alvarez-Mon MA, Guijarro LG, Torres-Carranza D, Saez MA, Diaz-Pedrero R, Albillos A, Alvarez-Mon M. Autophagy in Its (Proper) Context: Molecular Basis, Biological Relevance, Pharmacological Modulation, and Lifestyle Medicine. Int J Biol Sci 2024; 20:2532-2554. [PMID: 38725847 PMCID: PMC11077378 DOI: 10.7150/ijbs.95122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 04/04/2024] [Indexed: 05/12/2024] Open
Abstract
Autophagy plays a critical role in maintaining cellular homeostasis and responding to various stress conditions by the degradation of intracellular components. In this narrative review, we provide a comprehensive overview of autophagy's cellular and molecular basis, biological significance, pharmacological modulation, and its relevance in lifestyle medicine. We delve into the intricate molecular mechanisms that govern autophagy, including macroautophagy, microautophagy and chaperone-mediated autophagy. Moreover, we highlight the biological significance of autophagy in aging, immunity, metabolism, apoptosis, tissue differentiation and systemic diseases, such as neurodegenerative or cardiovascular diseases and cancer. We also discuss the latest advancements in pharmacological modulation of autophagy and their potential implications in clinical settings. Finally, we explore the intimate connection between lifestyle factors and autophagy, emphasizing how nutrition, exercise, sleep patterns and environmental factors can significantly impact the autophagic process. The integration of lifestyle medicine into autophagy research opens new avenues for promoting health and longevity through personalized interventions.
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Affiliation(s)
- Miguel A Ortega
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
| | - Oscar Fraile-Martinez
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
| | - Diego de Leon-Oliva
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
| | - Diego Liviu Boaru
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
| | - Laura Lopez-Gonzalez
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
- Department of Surgery, Medical and Social Sciences, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain
| | - Cielo García-Montero
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
| | - Miguel Angel Alvarez-Mon
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
| | - Luis G Guijarro
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
- Unit of Biochemistry and Molecular Biology, Department of System Biology (CIBEREHD), University of Alcalá, 28801 Alcala de Henares, Spain
| | - Diego Torres-Carranza
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
| | - Miguel A Saez
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
- Pathological Anatomy Service, Central University Hospital of Defence-UAH Madrid, 28801 Alcala de Henares, Spain
| | - Raul Diaz-Pedrero
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
- Department of Surgery, Medical and Social Sciences, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain
- Department of General and Digestive Surgery, Príncipe de Asturias Universitary Hospital, 28805 Alcala de Henares, Spain
| | - Agustin Albillos
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
| | - Melchor Alvarez-Mon
- Department of Medicine and Medical Specialities, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Spain
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
- Immune System Diseases-Rheumatology, Oncology Service an Internal Medicine (CIBEREHD), Príncipe de Asturias University Hospital, 28806 Alcala de Henares, Spain
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13
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Chen T, Zheng L, Luo P, Zou J, Li W, Chen Q, Zou J, Qian B. Crosstalk between m6A modification and autophagy in cancer. Cell Biosci 2024; 14:44. [PMID: 38576024 PMCID: PMC10996158 DOI: 10.1186/s13578-024-01225-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 03/24/2024] [Indexed: 04/06/2024] Open
Abstract
Autophagy is a cellular self-degradation process that plays a crucial role in maintaining metabolic functions in cells and organisms. Dysfunctional autophagy has been linked to various diseases, including cancer. In cancer, dysregulated autophagy is closely associated with the development of cancer and drug resistance, and it can have both oncogenic and oncostatic effects. Research evidence supports the connection between m6A modification and human diseases, particularly cancer. Abnormalities in m6A modification are involved in the initiation and progression of cancer by regulating the expression of oncogenes and oncostatic genes. There is an interaction between m6A modification and autophagy, both of which play significant roles in cancer. However, the molecular mechanisms underlying this relationship are still unclear. m6A modification can either directly inhibit autophagy or promote its initiation, but the complex relationship between m6A modification, autophagy, and cancer remains poorly understood. Therefore, this paper aims to review the dual role of m6A and autophagy in cancer, explore the impact of m6A modification on autophagy regulation, and discuss the crucial role of the m6A modification-autophagy axis in cancer progression and treatment resistance.
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Affiliation(s)
- Tao Chen
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Liying Zheng
- Department of Graduate, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
| | - Peiyue Luo
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Jun Zou
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Wei Li
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Qi Chen
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Junrong Zou
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Biao Qian
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China.
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China.
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14
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Sala-Gaston J, Pérez-Villegas EM, Armengol JA, Rawlins LE, Baple EL, Crosby AH, Ventura F, Rosa JL. Autophagy dysregulation via the USP20-ULK1 axis in the HERC2-related neurodevelopmental disorder. Cell Death Discov 2024; 10:163. [PMID: 38570483 PMCID: PMC10991529 DOI: 10.1038/s41420-024-01931-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/18/2024] [Accepted: 03/25/2024] [Indexed: 04/05/2024] Open
Abstract
Sequence variants in the HERC2 gene are associated with a significant reduction in HERC2 protein levels and cause a neurodevelopmental disorder known as the HERC2-related disorder, which shares clinical features with Angelman syndrome, including global developmental delay, intellectual disability, autism, and movement disorders. Remarkably, the HERC2 gene is commonly deleted in individuals with Angelman syndrome, suggesting a potential contribution of HERC2 to the pathophysiology of this disease. Given the known critical role of autophagy in brain development and its implication in neurodevelopmental diseases, we undertook different experimental approaches to monitor autophagy in fibroblasts derived from individuals affected by the HERC2-related disorder. Our findings reveal alterations in the levels of the autophagy-related protein LC3. Furthermore, experiments with lysosomal inhibitors provide confirmation of an upregulation of the autophagy pathway in these patient-derived cells. Mechanistically, we corroborate an interaction between HERC2 and the deubiquitylating enzyme USP20; and demonstrate that HERC2 deficiency leads to increased USP20 protein levels. Notably, USP20 upregulation correlates with enhanced stability of the autophagy initiating kinase ULK1, highlighting the role of HERC2 as an autophagy regulator factor through the USP20-ULK1 axis. Moreover, we show that p38 acts as a modulator of this pathway, since p38 activation disrupts HERC2-USP20 interaction, leading to increased USP20 and LC3-II protein levels. Together, these findings uncover a previously unknown role for HERC2 in autophagy regulation and provide insights into the pathomolecular mechanisms underlying the HERC2-related disorder and Angelman syndrome.
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Affiliation(s)
- Joan Sala-Gaston
- Department of Physiological Sciences, University of Barcelona (UB), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Spain
| | - Eva M Pérez-Villegas
- Department of Physiology, Anatomy and Cell Biology, University Pablo de Olavide, 41013, Seville, Spain
| | - José A Armengol
- Department of Physiology, Anatomy and Cell Biology, University Pablo de Olavide, 41013, Seville, Spain
| | - Lettie E Rawlins
- RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Exeter, UK
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital (Heavitree), Exeter, UK
| | - Emma L Baple
- RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Exeter, UK
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital (Heavitree), Exeter, UK
| | - Andrew H Crosby
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital (Heavitree), Exeter, UK
| | - Francesc Ventura
- Department of Physiological Sciences, University of Barcelona (UB), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Spain
| | - Jose Luis Rosa
- Department of Physiological Sciences, University of Barcelona (UB), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Spain.
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15
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Binotti B, Ninov M, Cepeda AP, Ganzella M, Matti U, Riedel D, Urlaub H, Sambandan S, Jahn R. ATG9 resides on a unique population of small vesicles in presynaptic nerve terminals. Autophagy 2024; 20:883-901. [PMID: 37881948 PMCID: PMC11062364 DOI: 10.1080/15548627.2023.2274204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 10/17/2023] [Indexed: 10/27/2023] Open
Abstract
In neurons, autophagosome biogenesis occurs mainly in distal axons, followed by maturation during retrograde transport. Autophagosomal growth depends on the supply of membrane lipids which requires small vesicles containing ATG9, a lipid scramblase essential for macroautophagy/autophagy. Here, we show that ATG9-containing vesicles are enriched in synapses and resemble synaptic vesicles in size and density. The proteome of ATG9-containing vesicles immuno-isolated from nerve terminals showed conspicuously low levels of trafficking proteins except of the AP2-complex and some enzymes involved in endosomal phosphatidylinositol metabolism. Super resolution microscopy of nerve terminals and isolated vesicles revealed that ATG9-containing vesicles represent a distinct vesicle population with limited overlap not only with synaptic vesicles but also other membranes of the secretory pathway, uncovering a surprising heterogeneity in their membrane composition. Our results are compatible with the view that ATG9-containing vesicles function as lipid shuttles that scavenge membrane lipids from various intracellular membranes to support autophagosome biogenesis.Abbreviations: AP: adaptor related protein complex: ATG2: autophagy related 2; ATG9: autophagy related 9; DNA PAINT: DNA-based point accumulation for imaging in nanoscale topography; DyMIN STED: dynamic minimum stimulated emission depletion; EL: endosome and lysosome; ER: endoplasmic reticulum; GA: Golgi apparatus; iBAQ: intensity based absolute quantification; LAMP: lysosomal-associated membrane protein; M6PR: mannose-6-phosphate receptor, cation dependent; Minflux: minimal photon fluxes; Mito: mitochondria; MS: mass spectrometry; PAS: phagophore assembly site; PM: plasma membrane; Px: peroxisome; RAB26: RAB26, member RAS oncogene family; RAB3A: RAB3A, member RAS oncogene family; RAB5A: RAB5A, member RAS oncogene family; SNARE: soluble N-ethylmaleimide-sensitive-factor attachment receptor; SVs: synaptic vesicles; SYP: synaptophysin; TGN: trans-Golgi network; TRAPP: transport protein particle; VTI1: vesicle transport through interaction with t-SNAREs.
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Affiliation(s)
- Beyenech Binotti
- Laboratory of Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Department of Biochemistry, Biocenter, University of Würzburg, Würzburg, Germany
| | - Momchil Ninov
- Laboratory of Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Bioanalytics, Institute of Clinical Chemistry, University Medical Center Göttingen, Germany
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Andreia P. Cepeda
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Marcelo Ganzella
- Laboratory of Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Ulf Matti
- Abberior Instruments GmbH, Göttingen, Germany
| | - Dietmar Riedel
- Facility for Transmission Electron Microscopy, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytics, Institute of Clinical Chemistry, University Medical Center Göttingen, Germany
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging : from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, Göttingen, Germany
| | - Sivakumar Sambandan
- Laboratory of Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Synaptic Metal Ion Dynamics and Signalin, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Reinhard Jahn
- Laboratory of Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
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16
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Li X, Wu T, Chen W, Zhang J, Jiang Y, Deng J, Long W, Qin X, Zhou Y. Andrographolide acts with dexamethasone to inhibit the growth of acute lymphoblastic leukemia CEM‑C1 cells via the regulation of the autophagy‑dependent PI3K/AKT/mTOR signaling pathway. Biomed Rep 2024; 20:43. [PMID: 38357243 PMCID: PMC10865295 DOI: 10.3892/br.2024.1731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 08/29/2023] [Indexed: 02/16/2024] Open
Abstract
Acute lymphoblastic leukemia (ALL) is one of the most common malignant tumor types of the circulatory system. Dexamethasone (DEX) acts on the glucocorticoid (GC) receptor (GR) and is a first-line chemotherapy drug for ALL. However, long-term or high-dose applications of the drug can not only cause adverse reactions, such as osteoporosis and high blood pressure, but can also cause downregulation of GR and lead to drug resistance. In the present study, reverse transcription-quantitative PCR, western blotting and LysoTracker Red staining were used to observe the effects of DEX and andrographolide (AND; a botanical with antitumorigenic properties) combined treatment. It was found that AND enhanced the sensitivity of CEM-C1 cells, a GC-resistant cell line, to DEX, and synergistically upregulated GR both at the transcriptional and post-transcriptional level with DEX. The combination of AND with DEX synergistically alkalized lysosomal lumen and downregulated the expression of autophagy-related genes Beclin1 and microtubule-associated 1 protein light chain 3 (LC3), thereby inhibiting autophagy. Knocking down LC3 expression enhanced GR expression, suggesting that GR was regulated by autophagy. Furthermore, compared with the monotherapy group (AND or DEX in isolation), AND interacted with DEX to activate the autophagy-dependent PI3K/AKT/mTOR signaling pathway by enhancing the phosphorylation of PI3K, AKT and mTOR, thereby decreasing GR degradation and increasing the sensitivity of cells to GCs. In conclusion, the present study demonstrated that AND exhibited a synergistic anti-ALL effect with DEX via upregulation of GR, which was orchestrated by the autophagy-related PI3K/AKT/mTOR signaling pathway. The results of the present study therefore provided novel research avenues and strategies for the treatment of ALL.
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Affiliation(s)
- Xiaowen Li
- Department of Clinical Pharmacy, College of Pharmacy, Guilin Medical University, Guilin, Guangxi Zhuang Autonomous Region 541199, P.R. China
| | - Tong Wu
- Department of Clinical Pharmacy, College of Pharmacy, Guilin Medical University, Guilin, Guangxi Zhuang Autonomous Region 541199, P.R. China
| | - Weihong Chen
- Department of Clinical Pharmacy, College of Pharmacy, Guilin Medical University, Guilin, Guangxi Zhuang Autonomous Region 541199, P.R. China
| | - Jiannan Zhang
- Department of Clinical Pharmacy, College of Pharmacy, Guilin Medical University, Guilin, Guangxi Zhuang Autonomous Region 541199, P.R. China
| | - Yanping Jiang
- Department of Clinical Medicine, College of Lingui Clinical Medicine, Guilin Medical University, Guilin, Guangxi Zhuang Autonomous Region 541199, P.R. China
| | - Jianzhi Deng
- Guangxi Key Laboratory of Embedded Technology and Intelligent System, Guilin University of Technology, Guilin, Guangxi Zhuang Autonomous Region 541004, P.R. China
| | - Wenqing Long
- Department of Clinical Medicine, College of Lingui Clinical Medicine, Guilin Medical University, Guilin, Guangxi Zhuang Autonomous Region 541199, P.R. China
| | - Xi Qin
- Department of Medical Oncology, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi Zhuang Autonomous Region 541001, P.R. China
| | - Yuehan Zhou
- Department of Clinical Pharmacy, College of Pharmacy, Guilin Medical University, Guilin, Guangxi Zhuang Autonomous Region 541199, P.R. China
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17
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Zhou J, Li C, Lu M, Jiang G, Chen S, Li H, Lu K. Pharmacological induction of autophagy reduces inflammation in macrophages by degrading immunoproteasome subunits. PLoS Biol 2024; 22:e3002537. [PMID: 38447109 PMCID: PMC10917451 DOI: 10.1371/journal.pbio.3002537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 02/05/2024] [Indexed: 03/08/2024] Open
Abstract
Defective autophagy is linked to proinflammatory diseases. However, the mechanisms by which autophagy limits inflammation remain elusive. Here, we found that the pan-FGFR inhibitor LY2874455 efficiently activated autophagy and suppressed expression of proinflammatory factors in macrophages stimulated by lipopolysaccharide (LPS). Multiplex proteomic profiling identified the immunoproteasome, which is a specific isoform of the 20s constitutive proteasome, as a substrate that is degraded by selective autophagy. SQSTM1/p62 was found to be a selective autophagy-related receptor that mediated this degradation. Autophagy deficiency or p62 knockdown blocked the effects of LY2874455, leading to the accumulation of immunoproteasomes and increases in inflammatory reactions. Expression of proinflammatory factors in autophagy-deficient macrophages could be reversed by immunoproteasome inhibitors, confirming the pivotal role of immunoproteasome turnover in the autophagy-mediated suppression on the expression of proinflammatory factors. In mice, LY2874455 protected against LPS-induced acute lung injury and dextran sulfate sodium (DSS)-induced colitis and caused low levels of proinflammatory cytokines and immunoproteasomes. These findings suggested that selective autophagy of the immunoproteasome was a key regulator of signaling via the innate immune system.
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Affiliation(s)
- Jiao Zhou
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and the Research Units of West China, Chinese Academy of Medical Sciences, Chengdu, China
- National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Chunxia Li
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and the Research Units of West China, Chinese Academy of Medical Sciences, Chengdu, China
| | - Meng Lu
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and the Research Units of West China, Chinese Academy of Medical Sciences, Chengdu, China
| | - Gaoyue Jiang
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and the Research Units of West China, Chinese Academy of Medical Sciences, Chengdu, China
| | - Shanze Chen
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, Shenzhen Institute of Respiratory Diseases, Shenzhen, China
| | - Huihui Li
- West China Second University Hospital, Sichuan University, Chengdu, China
| | - Kefeng Lu
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and the Research Units of West China, Chinese Academy of Medical Sciences, Chengdu, China
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18
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Varela YR, Iriondo MN, Goñi FM, Alonso A, Montes LR. Ceramide regulation of autophagy: A biophysical approach. Biochim Biophys Acta Mol Cell Biol Lipids 2024; 1869:159444. [PMID: 38056762 DOI: 10.1016/j.bbalip.2023.159444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 12/08/2023]
Abstract
Specific membrane lipids play unique roles in (macro)autophagy. Those include phosphatidylethanolamine, to which LC3/GABARAP autophagy proteins become covalently bound in the process, or cardiolipin, an important effector in mitochondrial autophagy (or mitophagy). Ceramide (Cer), or N-acyl sphingosine, is one of the simplest sphingolipids, known as a stress signal in the apoptotic pathway. Moreover, Cer is increasingly being recognized as an autophagy activator, although its mechanism of action is unclear. In the present review, the proposed Cer roles in autophagy are summarized, together with some biophysical properties of Cer in membranes. Possible pathways for Cer activation of autophagy are discussed, including specific protein binding of the lipid, and Cer-dependent perturbation of bilayer properties. Cer generation of lateral inhomogeneities (domain formation) is given special attention. Recent biophysical results, including fluorescence and atomic force microscopy data, show Cer-promoted enhanced binding of LC3/GABARAP to lipid bilayers. These observations could be interpreted in terms of the putative formation of Cer-rich nanodomains.
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Affiliation(s)
- Yaiza R Varela
- Instituto Biofisika (UPV/EHU, CSIC) and Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa, Spain
| | - Marina N Iriondo
- Instituto Biofisika (UPV/EHU, CSIC) and Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa, Spain
| | - Félix M Goñi
- Instituto Biofisika (UPV/EHU, CSIC) and Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa, Spain
| | - Alicia Alonso
- Instituto Biofisika (UPV/EHU, CSIC) and Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa, Spain.
| | - L Ruth Montes
- Instituto Biofisika (UPV/EHU, CSIC) and Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa, Spain
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19
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Chiduza GN, Garza-Garcia A, Almacellas E, De Tito S, Pye VE, van Vliet AR, Cherepanov P, Tooze SA. ATG9B is a tissue-specific homotrimeric lipid scramblase that can compensate for ATG9A. Autophagy 2024; 20:557-576. [PMID: 37938170 PMCID: PMC10936676 DOI: 10.1080/15548627.2023.2275905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 10/20/2023] [Indexed: 11/09/2023] Open
Abstract
Macroautophagy/autophagy is a fundamental aspect of eukaryotic biology, and the autophagy-related protein ATG9A is part of the core machinery facilitating this process. In addition to ATG9A vertebrates encode ATG9B, a poorly characterized paralog expressed in a subset of tissues. Herein, we characterize the structure of human ATG9B revealing the conserved homotrimeric quaternary structure and explore the conformational dynamics of the protein. Consistent with the experimental structure and computational chemistry, we establish that ATG9B is a functional lipid scramblase. We show that ATG9B can compensate for the absence of ATG9A in starvation-induced autophagy displaying similar subcellular trafficking and steady-state localization. Finally, we demonstrate that ATG9B can form a heteromeric complex with ATG2A. By establishing the molecular structure and function of ATG9B, our results inform the exploration of niche roles for autophagy machinery in more complex eukaryotes and reveal insights relevant across species.Abbreviation: ATG: autophagy related; CHS: cholesteryl hemisuccinate; cryo-EM: single-particle cryogenic electron microscopy; CTF: contrast transfer function: CTH: C- terminal α helix; FSC: fourier shell correlation; HDIR: HORMA domain interacting region; LMNG: lauryl maltose neopentyl glycol; MD: molecular dynamics simulations; MSA: multiple sequence alignment; NBD-PE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-(7-nitro-2-1,3-benzoxadiazol-4-yl ammonium salt); POPC: palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine; RBG: repeating beta groove domain; RMSD: root mean square deviation; SEC: size-exclusion chromatography; TMH: transmembrane helix.
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Affiliation(s)
- George N. Chiduza
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, London, UK
| | - Acely Garza-Garcia
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, London, UK
| | - Eugenia Almacellas
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, London, UK
| | - Stefano De Tito
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, London, UK
| | - Valerie E Pye
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | | | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
- Department of Infectious Disease, Imperial College London, London, UK
| | - Sharon A. Tooze
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, London, UK
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20
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Umargamwala R, Manning J, Dorstyn L, Denton D, Kumar S. Understanding Developmental Cell Death Using Drosophila as a Model System. Cells 2024; 13:347. [PMID: 38391960 PMCID: PMC10886741 DOI: 10.3390/cells13040347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 02/24/2024] Open
Abstract
Cell death plays an essential function in organismal development, wellbeing, and ageing. Many types of cell deaths have been described in the past 30 years. Among these, apoptosis remains the most conserved type of cell death in metazoans and the most common mechanism for deleting unwanted cells. Other types of cell deaths that often play roles in specific contexts or upon pathological insults can be classed under variant forms of cell death and programmed necrosis. Studies in Drosophila have contributed significantly to the understanding and regulation of apoptosis pathways. In addition to this, Drosophila has also served as an essential model to study the genetic basis of autophagy-dependent cell death (ADCD) and other relatively rare types of context-dependent cell deaths. Here, we summarise what is known about apoptosis, ADCD, and other context-specific variant cell death pathways in Drosophila, with a focus on developmental cell death.
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Affiliation(s)
- Ruchi Umargamwala
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA 5001, Australia; (J.M.); (L.D.)
| | - Jantina Manning
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA 5001, Australia; (J.M.); (L.D.)
| | - Loretta Dorstyn
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA 5001, Australia; (J.M.); (L.D.)
| | - Donna Denton
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA 5001, Australia; (J.M.); (L.D.)
| | - Sharad Kumar
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA 5001, Australia; (J.M.); (L.D.)
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
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21
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van Vliet AR, Jefferies HBJ, Faull PA, Chadwick J, Ibrahim F, Skehel MJ, Tooze SA. Exploring the ATG9A interactome uncovers interaction with VPS13A. J Cell Sci 2024; 137:jcs261081. [PMID: 38294121 PMCID: PMC10911177 DOI: 10.1242/jcs.261081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 01/17/2024] [Indexed: 02/01/2024] Open
Abstract
ATG9A, a transmembrane protein of the core autophagy pathway, cycles between the Golgi, endosomes and a vesicular compartment. ATG9A was recently shown to act as a lipid scramblase, and this function is thought to require its interaction with another core autophagy protein, ATG2A, which acts as a lipid transfer protein. Together, ATG9A and ATG2A are proposed to function to expand the growing autophagosome. However, ATG9A is implicated in other pathways including membrane repair and lipid droplet homeostasis. To elucidate other ATG9A interactors within the autophagy pathway, or interactors beyond autophagy, we performed an interactome analysis through mass spectrometry. This analysis revealed a host of proteins involved in lipid synthesis and trafficking, including ACSL3, VPS13A and VPS13C. Furthermore, we show that ATG9A directly interacts with VPS13A and forms a complex that is distinct from the ATG9A-ATG2A complex.
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Affiliation(s)
| | | | - Peter A. Faull
- Proteomics Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | | | - Fairouz Ibrahim
- Proteomics Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Mark J. Skehel
- Proteomics Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Sharon A. Tooze
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, London NW1 1AT, UK
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22
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Uribe-Carretero E, Rey V, Fuentes JM, Tamargo-Gómez I. Lysosomal Dysfunction: Connecting the Dots in the Landscape of Human Diseases. BIOLOGY 2024; 13:34. [PMID: 38248465 PMCID: PMC10813815 DOI: 10.3390/biology13010034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/22/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024]
Abstract
Lysosomes are the main organelles responsible for the degradation of macromolecules in eukaryotic cells. Beyond their fundamental role in degradation, lysosomes are involved in different physiological processes such as autophagy, nutrient sensing, and intracellular signaling. In some circumstances, lysosomal abnormalities underlie several human pathologies with different etiologies known as known as lysosomal storage disorders (LSDs). These disorders can result from deficiencies in primary lysosomal enzymes, dysfunction of lysosomal enzyme activators, alterations in modifiers that impact lysosomal function, or changes in membrane-associated proteins, among other factors. The clinical phenotype observed in affected patients hinges on the type and location of the accumulating substrate, influenced by genetic mutations and residual enzyme activity. In this context, the scientific community is dedicated to exploring potential therapeutic approaches, striving not only to extend lifespan but also to enhance the overall quality of life for individuals afflicted with LSDs. This review provides insights into lysosomal dysfunction from a molecular perspective, particularly in the context of human diseases, and highlights recent advancements and breakthroughs in this field.
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Affiliation(s)
- Elisabet Uribe-Carretero
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Enfermería y Terapia Ocupacional, Universidad de Extremadura, 10003 Caceres, Spain; (E.U.-C.)
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativa, Instituto de Salud Carlos III (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
- Instituto Universitario de Investigación Biosanitaria de Extremadura (INUBE), 10003 Caceres, Spain
| | - Verónica Rey
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Jose Manuel Fuentes
- Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Enfermería y Terapia Ocupacional, Universidad de Extremadura, 10003 Caceres, Spain; (E.U.-C.)
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativa, Instituto de Salud Carlos III (CIBER-CIBERNED-ISCIII), 28029 Madrid, Spain
- Instituto Universitario de Investigación Biosanitaria de Extremadura (INUBE), 10003 Caceres, Spain
| | - Isaac Tamargo-Gómez
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
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23
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Zhang W, Nishimura T, Tooze SA. Real-Time Monitoring of ATG8 Lipidation in vitro Using Fluorescence Spectroscopy. Bio Protoc 2024; 14:e4917. [PMID: 38213320 PMCID: PMC10777053 DOI: 10.21769/bioprotoc.4917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/27/2023] [Accepted: 12/11/2023] [Indexed: 01/13/2024] Open
Abstract
Autophagy is an essential catabolic pathway used to sequester and engulf cytosolic substrates via a unique double-membrane structure, called an autophagosome. The ubiquitin-like ATG8 proteins play an important role in mediating autophagosome membrane expansion. They are covalently conjugated to phosphatidylethanolamine (PE) on the autophagosomes via a ubiquitin-like conjugation system called ATG8 lipidation. In vitro reconstitution of ATG8 lipidation with synthetic liposomes has been previously established and used widely to characterise the function of the E1 ATG7, the E2 ATG3, and the E3 complex ATG12-ATG5-ATG16L1. However, there is still a lack of a tool to provide kinetic measurements of this enzymatic reaction. In this protocol, we describe a real-time lipidation assay using NBD-labelled ATG8. This real-time assay can distinguish the formation of ATG8 intermediates (ATG7~ATG8 and/or ATG3~ATG8) and, finally, ATG8-PE conjugation. It allows kinetic characterisation of the activity of ATG7, ATG3, and the E3 complex during ATG8 lipidation. Furthermore, this protocol can be adapted to characterise the upstream regulators that may affect protein activity in ATG8 lipidation reaction with a kinetic readout. Key features • Preparation of ATG7 E1 from insect cells (Sf9 cells). • Preparation of ATG3 E2 from bacteria (E. coli). • Preparation of LC3B S3C from bacteria (E. coli). • Preparation of liposomes to monitor the kinetics of ATG8 lipidation in a real-time manner.
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Affiliation(s)
- Wenxin Zhang
- Molecular Cell Biology of Autophagy Laboratory, The Francis Crick Institute, London, UK
| | - Taki Nishimura
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
- PRESTO, Japan Science and Technology Agency, Tokyo, Japan
| | - Sharon A. Tooze
- Molecular Cell Biology of Autophagy Laboratory, The Francis Crick Institute, London, UK
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24
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Tooze SA, Zhang W, Lazzeri G, Gahlot D, Thukral L, Covino R, Nishimura T. Membrane association of the ATG8 conjugation machinery emerges as a key regulatory feature for autophagosome biogenesis. FEBS Lett 2024; 598:107-113. [PMID: 37259601 PMCID: PMC10952647 DOI: 10.1002/1873-3468.14676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 05/10/2023] [Accepted: 05/10/2023] [Indexed: 06/02/2023]
Abstract
Autophagy is a highly conserved intracellular pathway that is essential for survival in all eukaryotes. In healthy cells, autophagy is used to remove damaged intracellular components, which can be as simple as unfolded proteins or as complex as whole mitochondria. Once the damaged component is captured, the autophagosome engulfs it and closes, isolating the content from the cytoplasm. The autophagosome then fuses with the late endosome and/or lysosome to deliver its content to the lysosome for degradation. Formation of the autophagosome, sequestration or capture of content, and closure all require the ATG proteins, which constitute the essential core autophagy protein machinery. This brief 'nutshell' will highlight recent data revealing the importance of small membrane-associated domains in the ATG proteins. In particular, recent findings from two parallel studies reveal the unexpected key role of α-helical structures in the ATG8 conjugation machinery and ATG8s. These studies illustrate how unique membrane association modules can control the formation of autophagosomes.
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Affiliation(s)
- Sharon A. Tooze
- Molecular Cell Biology of Autophagy LaboratoryThe Francis Crick InstituteLondonUK
| | - Wenxin Zhang
- Molecular Cell Biology of Autophagy LaboratoryThe Francis Crick InstituteLondonUK
| | | | - Deepanshi Gahlot
- CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
- Academy of Scientific and Innovative Research (AcSIR)GhaziabadIndia
| | - Lipi Thukral
- CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
- Academy of Scientific and Innovative Research (AcSIR)GhaziabadIndia
| | | | - Taki Nishimura
- PRESTO, Japan Science and Technology AgencyTokyoJapan
- Department of Biochemistry and Molecular Biology, Graduate School of MedicineThe University of TokyoJapan
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25
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Wu M, Ying J, Lin X, Xu C, Zheng X, Zheng Y, Fang Z, Yan B, Zhang N, Mou Y, Tan F. Toxoplasma gondii autophagy-related protein ATG7 maintains apicoplast inheritance by stabilizing and lipidating ATG8. Biochim Biophys Acta Mol Basis Dis 2024; 1870:166891. [PMID: 37739091 DOI: 10.1016/j.bbadis.2023.166891] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/12/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023]
Abstract
ATG8/LC3-mediated autophagosome formation is a key rate-limiting step in the process of autophagy. The parasitic protist Toxoplasma gondii possesses a single ATG8 homolog (TgATG8), which can localize to either cytosolic autophagosome involved in delivery of autophagic material in bradyzoites, or the outermost membrane of apicoplast, a nonphotosynthetic plastid-like organelle, responsible for maintaining homeostasis in tachyzoites. However, mechanisms that regulate TgATG8 remain insufficiently understood. Here, a TgATG7 conditional knockdown line that we have generated is severely impaired in parasite's growth and exhibits significant defects in the organelle level, strikingly with a fragmentation of the mitochondrial network and a loss of the apicoplast. Specific TgATG7C1133S point mutant complemented line showed that these defects were associated with its E1-type enzyme activity. Both depletion of TgATG7 and mutation of its catalytic cysteine 1133 hindered TgATG8 lipidation and apicoplast localization. Unexpectedly, we also found that depletion of TgATG7 reduced the unlipidated TgATG8 protein level. Subsequently, we determined that TgATG7 was able to interact with TgATG8 directly via its C-terminal domain and multi-monoubiquitination stimulated proteasome-dependent degradation of TgATG8, while TgATG7 could inhibit the degradation through stabilization of TgATG8. Additionally, we identified a putative TgATG8 interacting fragment of TgATG7, 1281-1290aa. Depletion of the fragment impaired the parasite growth and apicoplast inheritance. To our knowledge, our study is the first to elucidate the role of TgATG7 and the ubiquitin-proteasome system in synergistically regulating the non-lipidated pool of TgATG8, suggesting a potential homeostatic mechanism responsible for balancing autophagic activity in T. gondii.
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Affiliation(s)
- Mimi Wu
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, Zhejiang, China; Department of Parasitology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jiaqi Ying
- School of the Second Clinical Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xuejing Lin
- Department of Parasitology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Chao Xu
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiaozi Zheng
- Teaching Center of Morphological Experiment, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yi Zheng
- Laser Confocal Microscope Lab, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zhouxi Fang
- Zhejiang Provincial Key Laboratory for Technology and Application of Model Organisms, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Baolong Yan
- Department of Parasitology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Nu Zhang
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Yani Mou
- Department of Parasitology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Feng Tan
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, Zhejiang, China; Department of Parasitology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China.
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26
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Dupont N, Claude-Taupin A, Codogno P. A historical perspective of macroautophagy regulation by biochemical and biomechanical stimuli. FEBS Lett 2024; 598:17-31. [PMID: 37777819 DOI: 10.1002/1873-3468.14744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 10/02/2023]
Abstract
Macroautophagy is a lysosomal degradative pathway for intracellular macromolecules, protein aggregates, and organelles. The formation of the autophagosome, a double membrane-bound structure that sequesters cargoes before their delivery to the lysosome, is regulated by several stimuli in multicellular organisms. Pioneering studies in rat liver showed the importance of amino acids, insulin, and glucagon in controlling macroautophagy. Thereafter, many studies have deciphered the signaling pathways downstream of these biochemical stimuli to control autophagosome formation. Two signaling hubs have emerged: the kinase mTOR, in a complex at the surface of lysosomes which is sensitive to nutrients and hormones; and AMPK, which is sensitive to the cellular energetic status. Besides nutritional, hormonal, and energetic fluctuations, many organs have to respond to mechanical forces (compression, stretching, and shear stress). Recent studies have shown the importance of mechanotransduction in controlling macroautophagy. This regulation engages cell surface sensors, such as the primary cilium, in order to translate mechanical stimuli into biological responses.
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Affiliation(s)
- Nicolas Dupont
- INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker-Enfants Malades, Université Paris Cité, France
| | - Aurore Claude-Taupin
- INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker-Enfants Malades, Université Paris Cité, France
| | - Patrice Codogno
- INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker-Enfants Malades, Université Paris Cité, France
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27
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Wu MY, Li ZW, Lu JH. Molecular Modulators and Receptors of Selective Autophagy: Disease Implication and Identification Strategies. Int J Biol Sci 2024; 20:751-764. [PMID: 38169614 PMCID: PMC10758101 DOI: 10.7150/ijbs.83205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 08/31/2023] [Indexed: 01/05/2024] Open
Abstract
Autophagy is a highly conserved physiological process that maintains cellular homeostasis by recycling cellular contents. Selective autophagy is based on the specificity of cargo recognition and has been implicated in various human diseases, including neurodegenerative diseases and cancer. Selective autophagy receptors and modulators play key roles in this process. Identifying these receptors and modulators and their roles is critical for understanding the machinery and physiological function of selective autophagy and providing therapeutic value for diseases. Using modern researching tools and novel screening technologies, an increasing number of selective autophagy receptors and modulators have been identified. A variety of Strategies and approaches, including protein-protein interactions (PPIs)-based identification and genome-wide screening, have been used to identify selective autophagy receptors and modulators. Understanding the strengths and challenges of these approaches not only promotes the discovery of even more such receptors and modulators but also provides a useful reference for the identification of regulatory proteins or genes involved in other cellular mechanisms. In this review, we summarize the functions, disease association, and identification strategies of selective autophagy receptors and modulators.
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Affiliation(s)
| | | | - Jia-Hong Lu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China
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28
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Lecordier L, Heo P, Graversen JH, Hennig D, Skytthe MK, Cornet d'Elzius A, Pincet F, Pérez-Morga D, Pays E. Apolipoproteins L1 and L3 control mitochondrial membrane dynamics. Cell Rep 2023; 42:113528. [PMID: 38041817 PMCID: PMC10765320 DOI: 10.1016/j.celrep.2023.113528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 11/08/2023] [Accepted: 11/17/2023] [Indexed: 12/04/2023] Open
Abstract
Apolipoproteins L1 and L3 (APOLs) are associated at the Golgi with the membrane fission factors phosphatidylinositol 4-kinase-IIIB (PI4KB) and non-muscular myosin 2A. Either APOL1 C-terminal truncation (APOL1Δ) or APOL3 deletion (APOL3-KO [knockout]) reduces PI4KB activity and triggers actomyosin reorganization. We report that APOL3, but not APOL1, controls PI4KB activity through interaction with PI4KB and neuronal calcium sensor-1 or calneuron-1. Both APOLs are present in Golgi-derived autophagy-related protein 9A vesicles, which are involved in PI4KB trafficking. Like APOL3-KO, APOL1Δ induces PI4KB dissociation from APOL3, linked to reduction of mitophagy flux and production of mitochondrial reactive oxygen species. APOL1 and APOL3, respectively, can interact with the mitophagy receptor prohibitin-2 and the mitophagosome membrane fusion factor vesicle-associated membrane protein-8 (VAMP8). While APOL1 conditions PI4KB and APOL3 involvement in mitochondrion fission and mitophagy, APOL3-VAMP8 interaction promotes fusion between mitophagosomal and endolysosomal membranes. We propose that APOL3 controls mitochondrial membrane dynamics through interactions with the fission factor PI4KB and the fusion factor VAMP8.
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Affiliation(s)
- Laurence Lecordier
- Laboratory of Molecular Parasitology, IBMM, Université Libre de Bruxelles, 6041 Gosselies, Belgium
| | - Paul Heo
- Laboratoire de Physique de l'Ecole Normale Supérieure, Ecole Normale Supérieure (ENS), Université Paris Sciences et Lettres (PSL), CNRS, Sorbonne Université, Université Paris-Cité, 75005 Paris, France; Institute of Psychiatry and Neuroscience of Paris, INSERM U1266, 75014 Paris, France
| | - Jonas H Graversen
- Department of Molecular Medicine, Cancer and Inflammation Research, University of Southern Denmark, 5000 Odense C, Denmark
| | - Dorle Hennig
- Department of Molecular Medicine, Cancer and Inflammation Research, University of Southern Denmark, 5000 Odense C, Denmark
| | - Maria Kløjgaard Skytthe
- Department of Molecular Medicine, Cancer and Inflammation Research, University of Southern Denmark, 5000 Odense C, Denmark
| | | | - Frédéric Pincet
- Laboratoire de Physique de l'Ecole Normale Supérieure, Ecole Normale Supérieure (ENS), Université Paris Sciences et Lettres (PSL), CNRS, Sorbonne Université, Université Paris-Cité, 75005 Paris, France
| | - David Pérez-Morga
- Laboratory of Molecular Parasitology, IBMM, Université Libre de Bruxelles, 6041 Gosselies, Belgium; Center for Microscopy and Molecular Imaging (CMMI), Université Libre de Bruxelles, 6041 Gosselies, Belgium
| | - Etienne Pays
- Laboratory of Molecular Parasitology, IBMM, Université Libre de Bruxelles, 6041 Gosselies, Belgium.
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29
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Verhoeven J, Jacobs KA, Rizzollo F, Lodi F, Hua Y, Poźniak J, Narayanan Srinivasan A, Houbaert D, Shankar G, More S, Schaaf MB, Dubroja Lakic N, Ganne M, Lamote J, Van Weyenbergh J, Boon L, Bechter O, Bosisio F, Uchiyama Y, Bertrand MJ, Marine JC, Lambrechts D, Bergers G, Agrawal M, Agostinis P. Tumor endothelial cell autophagy is a key vascular-immune checkpoint in melanoma. EMBO Mol Med 2023; 15:e18028. [PMID: 38009521 DOI: 10.15252/emmm.202318028] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/29/2023] Open
Abstract
Tumor endothelial cells (TECs) actively repress inflammatory responses and maintain an immune-excluded tumor phenotype. However, the molecular mechanisms that sustain TEC-mediated immunosuppression remain largely elusive. Here, we show that autophagy ablation in TECs boosts antitumor immunity by supporting infiltration and effector function of T-cells, thereby restricting melanoma growth. In melanoma-bearing mice, loss of TEC autophagy leads to the transcriptional expression of an immunostimulatory/inflammatory TEC phenotype driven by heightened NF-kB and STING signaling. In line, single-cell transcriptomic datasets from melanoma patients disclose an enriched InflammatoryHigh /AutophagyLow TEC phenotype in correlation with clinical responses to immunotherapy, and responders exhibit an increased presence of inflamed vessels interfacing with infiltrating CD8+ T-cells. Mechanistically, STING-dependent immunity in TECs is not critical for the immunomodulatory effects of autophagy ablation, since NF-kB-driven inflammation remains functional in STING/ATG5 double knockout TECs. Hence, our study identifies autophagy as a principal tumor vascular anti-inflammatory mechanism dampening melanoma antitumor immunity.
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Affiliation(s)
- Jelle Verhoeven
- Cell Death Research and Therapy Laboratory, Center for Cancer Biology, VIB, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Kathryn A Jacobs
- Cell Death Research and Therapy Laboratory, Center for Cancer Biology, VIB, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Francesca Rizzollo
- Cell Death Research and Therapy Laboratory, Center for Cancer Biology, VIB, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Francesca Lodi
- Laboratory of Translational Genetics, Center for Cancer Biology, VIB, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Yichao Hua
- Laboratory of Tumor Microenvironment and Therapeutic Resistance Center for Cancer Biology, VIB, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Joanna Poźniak
- Department of Oncology, KU Leuven, Leuven, Belgium
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium
| | - Adhithya Narayanan Srinivasan
- Cell Death Research and Therapy Laboratory, Center for Cancer Biology, VIB, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Diede Houbaert
- Cell Death Research and Therapy Laboratory, Center for Cancer Biology, VIB, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Gautam Shankar
- Laboratory of Translational Cell and Tissue Research, Department of Pathology, KULeuven and UZ Leuven, Leuven, Belgium
- Department of Pathology, UZLeuven, Leuven, Belgium
| | - Sanket More
- Cell Death Research and Therapy Laboratory, Center for Cancer Biology, VIB, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Marco B Schaaf
- Cell Death Research and Therapy Laboratory, Center for Cancer Biology, VIB, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Nikolina Dubroja Lakic
- Laboratory of Translational Cell and Tissue Research, Department of Pathology, KULeuven and UZ Leuven, Leuven, Belgium
- Department of Pathology, UZLeuven, Leuven, Belgium
| | - Maarten Ganne
- Cell Death Research and Therapy Laboratory, Center for Cancer Biology, VIB, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Jochen Lamote
- Department of Oncology, KU Leuven, Leuven, Belgium
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium
| | - Johan Van Weyenbergh
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Louis Boon
- Polpharma Biologics, Utrecht, The Netherlands
| | - Oliver Bechter
- Department of General Medical Oncology, UZ Leuven, Leuven, Belgium
| | - Francesca Bosisio
- Laboratory of Translational Cell and Tissue Research, Department of Pathology, KULeuven and UZ Leuven, Leuven, Belgium
- Department of Pathology, UZLeuven, Leuven, Belgium
| | - Yasuo Uchiyama
- Department of Cellular and Molecular Neuropathology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Mathieu Jm Bertrand
- VIB Center for Inflammation Research, Ghent University, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Jean Christophe Marine
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium
| | - Diether Lambrechts
- Laboratory of Translational Genetics, Center for Cancer Biology, VIB, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Gabriele Bergers
- Laboratory of Tumor Microenvironment and Therapeutic Resistance Center for Cancer Biology, VIB, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Madhur Agrawal
- Cell Death Research and Therapy Laboratory, Center for Cancer Biology, VIB, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Patrizia Agostinis
- Cell Death Research and Therapy Laboratory, Center for Cancer Biology, VIB, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
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30
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Vaughan RM, Dickson BM, Martin KR, MacKeigan JP. Molecular dynamics simulations provide insights into ULK-101 potency and selectivity toward autophagic kinases ULK1/2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.01.569261. [PMID: 38077086 PMCID: PMC10705459 DOI: 10.1101/2023.12.01.569261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Kinase domains are highly conserved within protein kinases in both sequence and structure. Many factors, including phosphorylation, amino acid substitutions or mutations, and small molecule inhibitor binding, influence conformations of the kinase domain and enzymatic activity. The serine/threonine kinases ULK1 and ULK2 are highly conserved with N- and C-terminal domains, phosphate-binding P-loops, αC-helix, regulatory and catalytic spines, and activation loop DFG and APE motifs. Here, we performed molecular dynamics (MD) simulations to understand better the potency and selectivity of the ULK1/2 small molecule inhibitor, ULK-101. We observed stable bound states for ULK-101 to the adenosine triphosphate (ATP)-binding site of ULK2, coordinated by hydrogen bonding with the hinge backbone and the catalytic lysine sidechain. Notably, ULK-101 occupies a hydrophobic pocket associated with the N-terminus of the αC-helix. Large movements in the P-loop are also associated with ULK-101 inhibitor binding and exit from ULK2. Our data further suggests that ULK-101 could induce a folded P-loop conformation and hydrophobic pocket reflected in its nanomolar potency and kinome selectivity.
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Affiliation(s)
- Robert M. Vaughan
- Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Bradley M. Dickson
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Katie R. Martin
- Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Jeffrey P. MacKeigan
- Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
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31
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Khalil MI, Ali MM, Holail J, Houssein M. Growth or death? Control of cell destiny by mTOR and autophagy pathways. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023; 185:39-55. [PMID: 37944568 DOI: 10.1016/j.pbiomolbio.2023.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/08/2023] [Accepted: 10/23/2023] [Indexed: 11/12/2023]
Abstract
One of the central regulators of cell growth, proliferation, and metabolism is the mammalian target of rapamycin, mTOR, which exists in two structurally and functionally different complexes: mTORC1 and mTORC2; unlike m TORC2, mTORC1 is activated in response to the sufficiency of nutrients and is inhibited by rapamycin. mTOR complexes have critical roles not only in protein synthesis, gene transcription regulation, proliferation, tumor metabolism, but also in the regulation of the programmed cell death mechanisms such as autophagy and apoptosis. Autophagy is a conserved catabolic mechanism in which damaged molecules are recycled in response to nutrient starvation. Emerging evidence indicates that the mTOR signaling pathway is frequently activated in tumors. In addition, dysregulation of autophagy was associated with the development of a variety of human diseases, such as cancer and aging. Since mTOR can inhibit the induction of the autophagic process from the early stages of autophagosome formation to the late stage of lysosome degradation, the use of mTOR inhibitors to regulate autophagy could be considered a potential therapeutic option. The present review sheds light on the mTOR and autophagy signaling pathways and the mechanisms of regulation of mTOR-autophagy.
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Affiliation(s)
- Mahmoud I Khalil
- Department of Biological Sciences, Faculty of Science, Beirut Arab University, Beirut, 11072809, Lebanon; Molecular Biology Unit, Department of Zoology, Faculty of Science, Alexandria University, Alexandria, 21511, Egypt.
| | - Mohamad M Ali
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, SE-751 23, Uppsala, Sweden.
| | - Jasmine Holail
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia; Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom.
| | - Marwa Houssein
- Department of Biological Sciences, Faculty of Science, Beirut Arab University, Beirut, 11072809, Lebanon.
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32
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Malhotra N, Khatri S, Kumar A, Arun A, Daripa P, Fatihi S, Venkadesan S, Jain N, Thukral L. AI-based AlphaFold2 significantly expands the structural space of the autophagy pathway. Autophagy 2023; 19:3201-3220. [PMID: 37516933 PMCID: PMC10621275 DOI: 10.1080/15548627.2023.2238578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/08/2023] [Accepted: 07/14/2023] [Indexed: 07/31/2023] Open
Abstract
ABBREVIATIONS AF2: AlphaFold2; AF2-Mult: AlphaFold2 multimer; ATG: autophagy-related; CTD: C-terminal domain; ECTD: extreme C-terminal domain; FR: flexible region; MD: molecular dynamics; NTD: N-terminal domain; pLDDT: predicted local distance difference test; UBL: ubiquitin-like.
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Affiliation(s)
- Nidhi Malhotra
- Computational Structural Biology Lab, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Shantanu Khatri
- Computational Structural Biology Lab, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSir), Ghaziabad, India
| | - Ajit Kumar
- Computational Structural Biology Lab, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSir), Ghaziabad, India
| | - Akanksha Arun
- Computational Structural Biology Lab, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSir), Ghaziabad, India
| | - Purba Daripa
- Computational Structural Biology Lab, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Saman Fatihi
- Computational Structural Biology Lab, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSir), Ghaziabad, India
| | | | - Niyati Jain
- Computational Structural Biology Lab, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Lipi Thukral
- Computational Structural Biology Lab, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSir), Ghaziabad, India
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Ye J, Zhang J, Zhu Y, Wang L, Jiang X, Liu B, He G. Targeting autophagy and beyond: Deconvoluting the complexity of Beclin-1 from biological function to cancer therapy. Acta Pharm Sin B 2023; 13:4688-4714. [PMID: 38045051 PMCID: PMC10692397 DOI: 10.1016/j.apsb.2023.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 07/05/2023] [Accepted: 08/02/2023] [Indexed: 12/05/2023] Open
Abstract
Beclin-1 is the firstly-identified mammalian protein of the autophagy machinery, which functions as a molecular scaffold for the assembly of PI3KC3 (class III phosphatidylinositol 3 kinase) complex, thus controlling autophagy induction and other cellular trafficking events. Notably, there is mounting evidence establishing the implications of Beclin-1 in diverse tumorigenesis processes, including tumor suppression and progression as well as resistance to cancer therapeutics and CSC (cancer stem-like cell) maintenance. More importantly, Beclin-1 has been confirmed as a potential target for the treatment of multiple cancers. In this review, we provide a comprehensive survey of the structure, functions, and regulations of Beclin-1, and we discuss recent advances in understanding the controversial roles of Beclin-1 in oncology. Moreover, we focus on summarizing the targeted Beclin-1-regulating strategies in cancer therapy, providing novel insights into a promising strategy for regulating Beclin-1 to improve cancer therapeutics in the future.
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Affiliation(s)
- Jing Ye
- Department of Dermatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jin Zhang
- Department of Dermatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yanghui Zhu
- Department of Dermatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Lian Wang
- Department of Dermatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology (CIII), Frontiers Science Center for Disease Related Molecular Network, Chengdu 610041, China
| | - Xian Jiang
- Department of Dermatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Bo Liu
- Department of Dermatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Gu He
- Department of Dermatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology (CIII), Frontiers Science Center for Disease Related Molecular Network, Chengdu 610041, China
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Liu W, Wei T, Wang X. Plant reoviruses hijack autophagy in insect vectors. Trends Microbiol 2023; 31:1251-1261. [PMID: 37453843 DOI: 10.1016/j.tim.2023.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/18/2023]
Abstract
Plant reoviruses, transmitted only by insect vectors, seriously threaten global cereal production. Understanding how insect vectors efficiently transmit the viruses is key to controlling the viral diseases. Autophagy commonly plays important roles in plant host defense against virus infection, but recent studies have shown that plant reoviruses can hijack the autophagy pathway in insect cells to enable their persistence in the insect and continued transmission to plants. Here, we summarize and discuss new insights on viral activation, evasion, regulation, and manipulation of autophagy within the insect vectors and the role of autophagy in virus survival in insect vectors. Deeper knowledge of the functions of autophagy in vectors may lead to novel strategies for blocking transmission of insect-borne plant viruses.
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Affiliation(s)
- Wenwen Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Taiyun Wei
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China.
| | - Xifeng Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
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Ballesteros U, González-Ramirez EJ, de la Arada I, Sot J, Etxaniz A, Goñi FM, Alonso A, Montes LR. Effects of a N-Maleimide-derivatized Phosphatidylethanolamine on the Architecture and Properties of Lipid Bilayers. Int J Mol Sci 2023; 24:16570. [PMID: 38068893 PMCID: PMC10706405 DOI: 10.3390/ijms242316570] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 11/15/2023] [Accepted: 11/19/2023] [Indexed: 12/18/2023] Open
Abstract
N-maleimide-derivatized phospholipids are often used to facilitate protein anchoring to membranes. In autophagy studies, this is applied to the covalent binding of Atg8, an autophagy protein, to a phosphatidylethanolamine (PE) in the nascent autophagosome. However, the question remains on how closely the N-maleimide PE derivative (PE-mal) mimicks the native PE in the bilayer. In the present paper, spectroscopic and calorimetric techniques have been applied to vesicles containing either PE or PE-mal (together with other phospholipids) to compare the properties of the native and derivatized forms of PE. According to differential scanning calorimetry, and to infrared spectroscopy, the presence of PE-mal did not perturb the fatty acyl chains in the bilayer. Fluorescence spectroscopy and microscopy showed that PE-mal did not alter the bilayer permeability either. However, fluorescence emission polarization of the Laurdan and DPH probes indicated an increased order, or decreased fluidity, in the bilayers containing PE-mal. In addition, the infrared spectral data from the phospholipid phosphate region revealed a PE-mal-induced conformational change in the polar heads, accompanied by increased hydration. Globally considered, the results suggest that PE-mal would be a reasonable substitute for PE in model membranes containing reconstituted proteins.
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Affiliation(s)
| | | | | | | | | | - Félix M. Goñi
- Department of Biochemistry, Instituto Biofisika (CSIC, UPV/EHU), University of the Basque Country, 48940 Leioa, Spain; (U.B.); (E.J.G.-R.); (I.d.l.A.); (J.S.); (A.E.); (A.A.); (L.R.M.)
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36
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Feng X, Sun D, Li Y, Zhang J, Liu S, Zhang D, Zheng J, Xi Q, Liang H, Zhao W, Li Y, Xu M, He J, Liu T, Hasim A, Ma M, Xu P, Mi N. Local membrane source gathering by p62 body drives autophagosome formation. Nat Commun 2023; 14:7338. [PMID: 37957156 PMCID: PMC10643672 DOI: 10.1038/s41467-023-42829-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Autophagosomes are double-membrane vesicles generated intracellularly to encapsulate substrates for lysosomal degradation during autophagy. Phase separated p62 body plays pivotal roles during autophagosome formation, however, the underlying mechanisms are still not fully understood. Here we describe a spatial membrane gathering mode by which p62 body functions in autophagosome formation. Mass spectrometry-based proteomics reveals significant enrichment of vesicle trafficking components within p62 body. Combining cellular experiments and biochemical reconstitution assays, we confirm the gathering of ATG9 and ATG16L1-positive vesicles around p62 body, especially in Atg2ab DKO cells with blocked lipid transfer and vesicle fusion. Interestingly, p62 body also regulates ATG9 and ATG16L vesicle trafficking flux intracellularly. We further determine the lipid contents associated with p62 body via lipidomic profiling. Moreover, with in vitro kinase assay, we uncover the functions of p62 body as a platform to assemble ULK1 complex and invigorate PI3KC3-C1 kinase cascade for PI3P generation. Collectively, our study raises a membrane-based working model for multifaceted p62 body in controlling autophagosome biogenesis, and highlights the interplay between membraneless condensates and membrane vesicles in regulating cellular functions.
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Affiliation(s)
- Xuezhao Feng
- State Key Laboratory of Pathogenesis, Prevention and Treatment of Central Asian High Incidence Diseases, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
- Basic Medical College, Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
| | - Daxiao Sun
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany.
| | - Yanchang Li
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, 102206, Beijing, China
| | - Jinpei Zhang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of Central Asian High Incidence Diseases, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
- Basic Medical College, Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
| | - Shiyu Liu
- State Key Laboratory of Pathogenesis, Prevention and Treatment of Central Asian High Incidence Diseases, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
- Basic Medical College, Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
| | - Dachuan Zhang
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Jingxiang Zheng
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Qing Xi
- State Key Laboratory of Pathogenesis, Prevention and Treatment of Central Asian High Incidence Diseases, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
- Basic Medical College, Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
| | - Haisha Liang
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Wenkang Zhao
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Ying Li
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Mengbo Xu
- State Key Laboratory of Pathogenesis, Prevention and Treatment of Central Asian High Incidence Diseases, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
- Basic Medical College, Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
| | - Jiayu He
- State Key Laboratory of Pathogenesis, Prevention and Treatment of Central Asian High Incidence Diseases, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
- Basic Medical College, Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
| | - Tong Liu
- State Key Laboratory of Pathogenesis, Prevention and Treatment of Central Asian High Incidence Diseases, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
- Basic Medical College, Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
| | - Ayshamgul Hasim
- Basic Medical College, Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
- Department of Pathology, School of Basic Medicine, Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
| | - Meisheng Ma
- Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ping Xu
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, 102206, Beijing, China.
| | - Na Mi
- State Key Laboratory of Pathogenesis, Prevention and Treatment of Central Asian High Incidence Diseases, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, Xinjiang, China.
- Basic Medical College, Xinjiang Medical University, Urumqi, 830011, Xinjiang, China.
- Key Laboratory of High Incidence Disease Research in Xinjiang (Xinjiang Medical University), Ministry of Education, Urumqi, 830011, Xinjiang, China.
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37
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Xiang H, Zhou M, Li Y, Zhou L, Wang R. Drug discovery by targeting the protein-protein interactions involved in autophagy. Acta Pharm Sin B 2023; 13:4373-4390. [PMID: 37969735 PMCID: PMC10638514 DOI: 10.1016/j.apsb.2023.07.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 05/31/2023] [Accepted: 07/10/2023] [Indexed: 11/17/2023] Open
Abstract
Autophagy is a cellular process in which proteins and organelles are engulfed in autophagosomal vesicles and transported to the lysosome/vacuole for degradation. Protein-protein interactions (PPIs) play a crucial role at many stages of autophagy, which present formidable but attainable targets for autophagy regulation. Moreover, selective regulation of PPIs tends to have a lower risk in causing undesired off-target effects in the context of a complicated biological network. Thus, small-molecule regulators, including peptides and peptidomimetics, targeting the critical PPIs involved in autophagy provide a new opportunity for innovative drug discovery. This article provides general background knowledge of the critical PPIs involved in autophagy and reviews a range of successful attempts on discovering regulators targeting those PPIs. Successful strategies and existing limitations in this field are also discussed.
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Affiliation(s)
- Honggang Xiang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Mi Zhou
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Yan Li
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Lu Zhou
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Renxiao Wang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
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38
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McAllaster MR, Bhushan J, Balce DR, Orvedahl A, Park A, Hwang S, Sullender ME, Sibley LD, Virgin HW. Autophagy gene-dependent intracellular immunity triggered by interferon-γ. mBio 2023; 14:e0233223. [PMID: 37905813 PMCID: PMC10746157 DOI: 10.1128/mbio.02332-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 09/19/2023] [Indexed: 11/02/2023] Open
Abstract
Genes required for the lysosomal degradation pathway of autophagy play key roles in topologically distinct and physiologically important cellular processes. Some functions of ATG genes are independent of their role in degradative autophagy. One of the first described of these ATG gene-dependent, but degradative autophagy independent, processes is the requirement for a subset of ATG genes in interferon-γ (IFNγ)-induced inhibition of norovirus and Toxoplasma gondii replication. Herein, we identified additional genes that are required for, or that negatively regulate, this innate immune effector pathway. Enzymes in the UFMylation pathway negatively regulated IFNγ-induced inhibition of norovirus replication via effects of Ern1. IFNγ-induced inhibition of norovirus replication required Gate-16 (also termed GabarapL2), Wipi2b, Atg9a, Cul3, and Klhl9 but not Becn1 (encoding Beclin 1), Atg14, Uvrag, or Sqstm1. The phosphatidylinositol-3-phosphate and ATG16L1-binding domains of WIPI2B, as well as the ATG5-binding domain of ATG16L1, were required for IFNγ-induced inhibition of norovirus replication. Other members of the Cul3, Atg8, and Wipi2 gene families were not required, demonstrating exquisite specificity within these gene families for participation in IFNγ action. The generality of some aspects of this mechanism was demonstrated by a role for GATE-16 and WIPI2 in IFNγ-induced control of Toxoplasma gondii infection in human cells. These studies further delineate the genes and mechanisms of an ATG gene-dependent programmable form of cytokine-induced innate intracellular immunity. IMPORTANCE Interferon-γ (IFNγ) is a critical mediator of cell-intrinsic immunity to intracellular pathogens. Understanding the complex cellular mechanisms supporting robust interferon-γ-induced host defenses could aid in developing new therapeutics to treat infections. Here, we examined the impact of autophagy genes in the interferon-γ-induced host response. We demonstrate that genes within the autophagy pathway including Wipi2, Atg9, and Gate-16, as well as ubiquitin ligase complex genes Cul3 and Klhl9 are required for IFNγ-induced inhibition of murine norovirus (norovirus hereinafter) replication in mouse cells. WIPI2 and GATE-16 were also required for IFNγ-mediated restriction of parasite growth within the Toxoplasma gondii parasitophorous vacuole in human cells. Furthermore, we found that perturbation of UFMylation pathway components led to more robust IFNγ-induced inhibition of norovirus via regulation of endoplasmic reticulum (ER) stress. Enhancing or inhibiting these dynamic cellular components could serve as a strategy to control intracellular pathogens and maintain an effective immune response.
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Affiliation(s)
- Michael R. McAllaster
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Vir Biotechnology, San Francisco, California, USA
| | - Jaya Bhushan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Dale R. Balce
- Vir Biotechnology, San Francisco, California, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Anthony Orvedahl
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Arnold Park
- Vir Biotechnology, San Francisco, California, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | | | - Meagan E. Sullender
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - L. David Sibley
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Herbert W. Virgin
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas, USA
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39
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Lin YW, Lin TT, Chen CH, Wang RH, Lin YH, Tseng TY, Zhuang YJ, Tang SY, Lin YC, Pang JY, Chakravarthy RD, Lin HC, Tzou SC, Chao JI. Enhancing Efficacy of Albumin-Bound Paclitaxel for Human Lung and Colorectal Cancers through Autophagy Receptor Sequestosome 1 (SQSTM1)/p62-Mediated Nanodrug Delivery and Cancer therapy. ACS NANO 2023; 17:19033-19051. [PMID: 37737568 DOI: 10.1021/acsnano.3c04739] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
Selective autophagy is a defense mechanism by which foreign pathogens and abnormal substances are processed to maintain cellular homeostasis. Sequestosome 1 (SQSTM1)/p62, a vital selective autophagy receptor, recruits ubiquitinated cargo to form autophagosomes for lysosomal degradation. Nab-PTX is an albumin-bound paclitaxel nanoparticle used in clinical cancer therapy. However, the role of SQSTM1 in regulating the delivery and efficacy of nanodrugs remains unclear. Here we showed that SQSTM1 plays a crucial role in Nab-PTX drug delivery and efficacy in human lung and colorectal cancers. Nab-PTX induces SQSTM1 phosphorylation at Ser403, which facilitates its incorporation into the selective autophagy of nanoparticles, known as nanoparticulophagy. Nab-PTX increased LC3-II protein expression, which triggered autophagosome formation. SQSTM1 enhanced Nab-PTX recognition to form autophagosomes, which were delivered to lysosomes for albumin degradation, thereby releasing PTX to induce mitotic catastrophe and apoptosis. Knockout of SQSTM1 downregulated Nab-PTX-induced mitotic catastrophe, apoptosis, and tumor inhibition in vitro and in vivo and inhibited Nab-PTX-induced caspase 3 activation via a p53-independent pathway. Ectopic expression of SQSTM1 by transfection of an SQSTM1-GFP vector restored the drug efficacy of Nab-PTX. Importantly, SQSTM1 is highly expressed in advanced lung and colorectal tumors and is associated with poor overall survival in clinical patients. Targeting SQSTM1 may provide an important strategy to improve nanodrug efficacy in clinical cancer therapy. This study demonstrates the enhanced efficacy of Nab-PTX for human lung and colorectal cancers via SQSTM1-mediated nanodrug delivery.
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Affiliation(s)
- Yu-Wei Lin
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Tzu-Ting Lin
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Chien-Hung Chen
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Rou-Hsin Wang
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Ya-Hui Lin
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Tzu-Yen Tseng
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Yan-Jun Zhuang
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Sheng-Yueh Tang
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Yen-Cheng Lin
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Jiun-Yu Pang
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Rajan Deepan Chakravarthy
- Department of Materials Science and Engineering, National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
| | - Hsin-Chieh Lin
- Department of Materials Science and Engineering, National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
| | - Shey-Cherng Tzou
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Jui-I Chao
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Center For Intelligent Drug Systems and Smart Bio-devices, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
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40
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Titus AS, Sung EA, Zablocki D, Sadoshima J. Mitophagy for cardioprotection. Basic Res Cardiol 2023; 118:42. [PMID: 37798455 PMCID: PMC10556134 DOI: 10.1007/s00395-023-01009-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 10/07/2023]
Abstract
Mitochondrial function is maintained by several strictly coordinated mechanisms, collectively termed mitochondrial quality control mechanisms, including fusion and fission, degradation, and biogenesis. As the primary source of energy in cardiomyocytes, mitochondria are the central organelle for maintaining cardiac function. Since adult cardiomyocytes in humans rarely divide, the number of dysfunctional mitochondria cannot easily be diluted through cell division. Thus, efficient degradation of dysfunctional mitochondria is crucial to maintaining cellular function. Mitophagy, a mitochondria specific form of autophagy, is a major mechanism by which damaged or unnecessary mitochondria are targeted and eliminated. Mitophagy is active in cardiomyocytes at baseline and in response to stress, and plays an essential role in maintaining the quality of mitochondria in cardiomyocytes. Mitophagy is mediated through multiple mechanisms in the heart, and each of these mechanisms can partially compensate for the loss of another mechanism. However, insufficient levels of mitophagy eventually lead to mitochondrial dysfunction and the development of heart failure. In this review, we discuss the molecular mechanisms of mitophagy in the heart and the role of mitophagy in cardiac pathophysiology, with the focus on recent findings in the field.
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Affiliation(s)
- Allen Sam Titus
- Department of Cell Biology and Molecular Medicine, Cardiovascular Research Institute, Rutgers New Jersey Medical School, 185 South Orange Ave, MSB G-609, Newark, NJ, 07103, USA
| | - Eun-Ah Sung
- Department of Cell Biology and Molecular Medicine, Cardiovascular Research Institute, Rutgers New Jersey Medical School, 185 South Orange Ave, MSB G-609, Newark, NJ, 07103, USA
| | - Daniela Zablocki
- Department of Cell Biology and Molecular Medicine, Cardiovascular Research Institute, Rutgers New Jersey Medical School, 185 South Orange Ave, MSB G-609, Newark, NJ, 07103, USA
| | - Junichi Sadoshima
- Department of Cell Biology and Molecular Medicine, Cardiovascular Research Institute, Rutgers New Jersey Medical School, 185 South Orange Ave, MSB G-609, Newark, NJ, 07103, USA.
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41
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Soni N, Nandi G, Chaudhary M, Bissa B. The role of ncRNA in the co-regulation of autophagy and exosome pathways during cancer progression. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119523. [PMID: 37348764 DOI: 10.1016/j.bbamcr.2023.119523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 06/24/2023]
Abstract
Since its discovery a few decades ago, autophagy has been recognized as a crucial signaling pathway, linked to the recycling of cellular components in nutrient stress. Autophagy is a two-way sword, playing a dual role in tumorigenesis. In this catabolic process, dysfunctional organelles, biomolecules, and misfolded proteins are sequestered in the autophagosome and sent to the lysosome for degradation. Alongside, there are cellular messengers called exosomes, which are released from cells and are known to communicate and regulate metabolism in recipient cells. Multivesicular bodies (MVB) act as the intricate link between autophagy and exosome pathways. The continuous crosstalk between the two pathways is coordinated and regulated by multiple players among which ncRNA is the emerging candidates. The exosomes carry varied cargo of which non-coding RNA exerts an immediate regulatory effect on recipient cells. ncRNA is known to exhibit dual behavior in both promoting and inhibiting tumor growth. There is increasing evidence for the involvement of ncRNAs' in the regulation of different hallmarks of cancer. Different ncRNAs are involved in the co-regulation of autophagy and exosome pathways and therefore represent a superior therapeutic approach to target cancer chemoresistance. Here, we will discuss the ncRNA involved in regulating autophagy, and exosomes pathways and its relevance in cancer therapeutics.
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Affiliation(s)
- Naveen Soni
- Dept. of Biochemistry, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Gargi Nandi
- Dept. of Biochemistry, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Megha Chaudhary
- Dept. of Biochemistry, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Bhawana Bissa
- Dept. of Biochemistry, Central University of Rajasthan, Ajmer, Rajasthan, India.
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42
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Ulutas S, Mutaf M, Koc MN, Oztuzcu T, Ulasli M, Oztuzcu S. High-throughput screening and clinical importance of autophagy-associated genes in basal cell carcinoma. Pathol Res Pract 2023; 250:154786. [PMID: 37690223 DOI: 10.1016/j.prp.2023.154786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/01/2023] [Accepted: 08/28/2023] [Indexed: 09/12/2023]
Abstract
Autophagy is a type II programmed cell death mechanism that plays a critical role in preserving cellular homeostasis through the regulation of protein, lipid, and organelle quality control. It has become gradually evident that autophagy plays a fundamental role in the initiation and progression of various types of human cancers. Nevertheless, its significance in non-melanoma skin cancers, particularly in basal cell carcinoma, has not been well documented and remains largely elusive. In this study, we aimed to illuminate the role of autophagy-associated signaling signatures during development and progression of basal cell carcinoma. For the study, a total of 72 autophagy-related genes were screened using a high-throughput qPCR approach integrating Fluidigm 96.96 Dynamic Array™ integrated fluidic circuits (IFC) and BioMark™ HD Real-Time PCR system, which enabled efficient and precise analysis of gene expression patterns. Results were analyzed using Fluidigm's Real-Time PCR Analysis software and 2-ΔΔCt formula was used for the calculation of expression changes. Notably, expression levels of INS, TMEM74 and IFNA2 genes were identified to be prominently altered in BCC comparted to adjacent healthy tissues. However, only IFNA2 expression showed statistically significant change in BCC. Consequently, these findings suggest that IFNA2 might play significant role in the regulation of autophagy in BCC development and progression and can be therapeutically targeted.
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Affiliation(s)
- Saffet Ulutas
- Department of Plastic and Reconstructive Surgery, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey.
| | - Mehmet Mutaf
- Department of Plastic and Reconstructive Surgery, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey
| | - Mustafa Nihat Koc
- Department of Plastic and Reconstructive Surgery, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey
| | - Tarik Oztuzcu
- Department of Medical Biology, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey
| | - Mustafa Ulasli
- Department of Medical Biology, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey
| | - Serdar Oztuzcu
- Department of Medical Biology, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey
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43
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Suzuki M, Funakoshi T, Kumagai K, Komatsu M, Waguri S. ATG9A supports Chlamydia trachomatis infection via autophagy-independent mechanisms. Microbiol Spectr 2023; 11:e0277423. [PMID: 37707289 PMCID: PMC10580829 DOI: 10.1128/spectrum.02774-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 07/18/2023] [Indexed: 09/15/2023] Open
Abstract
Chlamydia trachomatis infection can be regulated by autophagy-related (ATG) genes. Here, we found that the depletion of ATG9A, one of the core ATG genes, in HeLa cells suppressed C. trachomatis growth in the inclusion. The growth was restored by re-expressing ATG9A or an ATG9A mutant impairing lipid scramblase activity in ATG9A-knockout (KO) cells. Moreover, the depletion of lipid transfer proteins ATG2A/B, responsible for isolation membrane expansion together with ATG9A, did not significantly alter the growth, suggesting that the non-autophagic function of ATG9A supports C. trachomatis infection. ATG9A-KO cells showed no infection-induced redistribution of the Golgi from the perinuclear region to inclusion, which was restored by re-expressing the mutant but not the ATG9A mutant lacking an N-terminal adapter protein-binding domain. Re-expression of the N-terminal deletion mutant in ATG9A-KO cells did not rescue C. trachomatis growth, suggesting the importance of this domain for its growth. Although ATG9A-KO cells showed enhanced TBK1 activation, interferon (IFN)-β was not significantly increased, excluding the possibility that upregulation of stimulator of IFN genes (STING) signaling suppressed bacterial growth. Taken together, these findings suggest that the proper trafficking, rather than the isolation membrane expansion function, of ATG9A assists C. trachomatis growth in the inclusion. IMPORTANCE ATG9A is an autophagy-related gene that functions during the isolation membrane expansion process to form autophagosomes, but it also has other functions independent of autophagy. In this study, we employed ATG9A-deficient HeLa cells and found that the absence of ATG9A negatively impacted proliferation of Chlamydia trachomatis in inclusions. Furthermore, rescue experiments using ATG9A mutants revealed that this action was mediated not by its autophagic function but by its binding ability to clathrin adapter proteins. These findings suggest that the proper trafficking of ATG9A assists C. trachomatis growth in the inclusion.
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Affiliation(s)
- Michitaka Suzuki
- Department of Anatomy and Histology, Fukushima Medical University School of Medicine, Hikarigaoka, Fukushima, Japan
| | - Tomoko Funakoshi
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Keigo Kumagai
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, Toyama, Shinjuku-ku, Tokyo, Japan
| | - Masaaki Komatsu
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Satoshi Waguri
- Department of Anatomy and Histology, Fukushima Medical University School of Medicine, Hikarigaoka, Fukushima, Japan
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44
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Hela F, Aguayo-Mazzucato C. Interaction between Autophagy and Senescence in Pancreatic Beta Cells. BIOLOGY 2023; 12:1205. [PMID: 37759604 PMCID: PMC10525299 DOI: 10.3390/biology12091205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/01/2023] [Accepted: 09/02/2023] [Indexed: 09/29/2023]
Abstract
Aging leads to an increase in cellular stress due to the fragility of the organism and the inability to cope with it. In this setting, there is a higher chance of developing different cardiometabolic diseases like diabetes. Cellular senescence and autophagy, both hallmarks of aging and stress-coping mechanisms, have gained increased attention for their role in the pathophysiology of diabetes. Studies show that impairing senescence dampens and even prevents diabetes while the role of autophagy is more contradictory, implying a context- and disease-stage-dependent effect. Reports show conflicting data about the effect of autophagy on senescence while the knowledge about this interaction in beta cells remains scarce. Elucidating this interaction between autophagy and senescence in pancreatic beta cells will lead to an identification of their respective roles and the extent of the effect each mechanism has on beta cells and open new horizons for developing novel therapeutic agents. To help illuminate this relationship we will review the latest findings of cellular senescence and autophagy with a special emphasis on pancreatic beta cells and diabetes.
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Affiliation(s)
| | - Cristina Aguayo-Mazzucato
- Section on Islet Cell Biology and Regenerative Medicine, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA
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45
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Luo M, Law KC, He Y, Chung KK, Po MK, Feng L, Chung KP, Gao C, Zhuang X, Jiang L. Arabidopsis AUTOPHAGY-RELATED2 is essential for ATG18a and ATG9 trafficking during autophagosome closure. PLANT PHYSIOLOGY 2023; 193:304-321. [PMID: 37195145 DOI: 10.1093/plphys/kiad287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 05/18/2023]
Abstract
As a fundamental metabolic pathway, autophagy plays important roles in plant growth and development, particularly under stress conditions. A set of autophagy-related (ATG) proteins is recruited for the formation of a double-membrane autophagosome. Among them, the essential roles of ATG2, ATG18, and ATG9 have been well established in plant autophagy via genetic analysis; however, the underlying molecular mechanism for ATG2 in plant autophagosome formation remains poorly understood. In this study, we focused on the specific role of ATG2 in the trafficking of ATG18a and ATG9 during autophagy in Arabidopsis (Arabidopsis thaliana). Under normal conditions, YFP-ATG18a proteins are partially localized on late endosomes and translocated to ATG8e-labeled autophagosomes upon autophagic induction. Real-time imaging analysis revealed sequential recruitment of ATG18a on the phagophore membrane, showing that ATG18a specifically decorated the closing edges and finally disassociated from the completed autophagosome. However, in the absence of ATG2, most of the YFP-ATG18a proteins are arrested on autophagosomal membranes. Ultrastructural and 3D tomography analysis showed that unclosed autophagosome structures are accumulated in the atg2 mutant, displaying direct connections with the endoplasmic reticulum membrane and vesicular structures. Dynamic analysis of ATG9 vesicles suggested that ATG2 depletion also affects the association between ATG9 vesicles and the autophagosomal membrane. Furthermore, using interaction and recruitment analysis, we mapped the interaction relationship between ATG2 and ATG18a, implying a possible role of ATG18a in recruiting ATG2 and ATG9 to the membrane. Our findings unveil a specific role of ATG2 in coordinating ATG18a and ATG9 trafficking to mediate autophagosome closure in Arabidopsis.
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Affiliation(s)
- Mengqian Luo
- Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kai Ching Law
- Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yilin He
- Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Ka Kit Chung
- Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Muk Kuen Po
- Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Lanlan Feng
- Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kin Pan Chung
- Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Caiji Gao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Xiaohong Zhuang
- Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Liwen Jiang
- Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
- CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China
- Institute of Plant Molecular Biology and Agricultural Biotechnology, The Chinese University of Hong Kong, Hong Kong, China
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46
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Wang N, Shibata Y, Paulo JA, Gygi SP, Rapoport TA. A conserved membrane curvature-generating protein is crucial for autophagosome formation in fission yeast. Nat Commun 2023; 14:4765. [PMID: 37553386 PMCID: PMC10409813 DOI: 10.1038/s41467-023-40530-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 07/26/2023] [Indexed: 08/10/2023] Open
Abstract
Organelles are shaped by curvature-generating proteins, which include the reticulons and REEPs that are involved in forming the endoplasmic reticulum (ER). A conserved REEP subfamily differs from the ER-shaping REEPs in abundance and membrane topology and has unidentified functions. Here, we show that Rop1, the single member of this family in the fission yeast Schizosacharomyces pombe, is crucial for the macroautophagy of organelles and cytosolic proteins. Rop1 is needed for the formation of phagophores, cup-like structures consisting of two closely apposed membrane sheets that encapsulate cargo. It is recruited at early stages to phagophores and is required for their maturation into autophagosomes. Rop1 function relies on its ability to generate high membrane curvature and on its colocalization with the autophagy component Atg2 that is thought to reside at the phagophore rim. We propose that Rop1 facilitates the formation and growth of the double-membrane structure of the autophagosome.
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Affiliation(s)
- Ning Wang
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Yoko Shibata
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Tom A Rapoport
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA.
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47
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Abstract
Maintenance of protein homeostasis and organelle integrity and function is critical for cellular homeostasis and cell viability. Autophagy is the principal mechanism that mediates the delivery of various cellular cargoes to lysosomes for degradation and recycling. A myriad of studies demonstrate important protective roles for autophagy against disease. However, in cancer, seemingly opposing roles of autophagy are observed in the prevention of early tumour development versus the maintenance and metabolic adaptation of established and metastasizing tumours. Recent studies have addressed not only the tumour cell intrinsic functions of autophagy, but also the roles of autophagy in the tumour microenvironment and associated immune cells. In addition, various autophagy-related pathways have been described, which are distinct from classical autophagy, that utilize parts of the autophagic machinery and can potentially contribute to malignant disease. Growing evidence on how autophagy and related processes affect cancer development and progression has helped guide efforts to design anticancer treatments based on inhibition or promotion of autophagy. In this Review, we discuss and dissect these different functions of autophagy and autophagy-related processes during tumour development, maintenance and progression. We outline recent findings regarding the role of these processes in both the tumour cells and the tumour microenvironment and describe advances in therapy aimed at autophagy processes in cancer.
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Affiliation(s)
- Jayanta Debnath
- Department of Pathology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.
| | - Noor Gammoh
- MRC Institute of Genetics & Cancer, The University of Edinburgh, Edinburgh, UK.
| | - Kevin M Ryan
- Cancer Research UK Beatson Institute, Glasgow, UK.
- School of Cancer Sciences, University of Glasgow, Glasgow, UK.
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48
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Gan T, Qu S, Zhang H, Zhou X. Modulation of the immunity and inflammation by autophagy. MedComm (Beijing) 2023; 4:e311. [PMID: 37405276 PMCID: PMC10315166 DOI: 10.1002/mco2.311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 05/12/2023] [Accepted: 05/26/2023] [Indexed: 07/06/2023] Open
Abstract
Autophagy, a highly conserved cellular self-degradation pathway, has emerged with novel roles in the realms of immunity and inflammation. Genome-wide association studies have unveiled a correlation between genetic variations in autophagy-related genes and heightened susceptibility to autoimmune and inflammatory diseases. Subsequently, substantial progress has been made in unraveling the intricate involvement of autophagy in immunity and inflammation through functional studies. The autophagy pathway plays a crucial role in both innate and adaptive immunity, encompassing various key functions such as pathogen clearance, antigen processing and presentation, cytokine production, and lymphocyte differentiation and survival. Recent research has identified novel approaches in which the autophagy pathway and its associated proteins modulate the immune response, including noncanonical autophagy. This review provides an overview of the latest advancements in understanding the regulation of immunity and inflammation through autophagy. It summarizes the genetic associations between variants in autophagy-related genes and a range of autoimmune and inflammatory diseases, while also examining studies utilizing transgenic animal models to uncover the in vivo functions of autophagy. Furthermore, the review delves into the mechanisms by which autophagy dysregulation contributes to the development of three common autoimmune and inflammatory diseases and highlights the potential for autophagy-targeted therapies.
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Affiliation(s)
- Ting Gan
- Renal DivisionPeking University First HospitalBeijingChina
- Peking University Institute of NephrologyBeijingChina
- Key Laboratory of Renal DiseaseMinistry of Health of ChinaBeijingChina
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University)Ministry of EducationBeijingChina
| | - Shu Qu
- Renal DivisionPeking University First HospitalBeijingChina
- Peking University Institute of NephrologyBeijingChina
- Key Laboratory of Renal DiseaseMinistry of Health of ChinaBeijingChina
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University)Ministry of EducationBeijingChina
| | - Hong Zhang
- Renal DivisionPeking University First HospitalBeijingChina
- Peking University Institute of NephrologyBeijingChina
- Key Laboratory of Renal DiseaseMinistry of Health of ChinaBeijingChina
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University)Ministry of EducationBeijingChina
| | - Xu‐jie Zhou
- Renal DivisionPeking University First HospitalBeijingChina
- Peking University Institute of NephrologyBeijingChina
- Key Laboratory of Renal DiseaseMinistry of Health of ChinaBeijingChina
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University)Ministry of EducationBeijingChina
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49
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Park W, Wei S, Kim BS, Kim B, Bae SJ, Chae YC, Ryu D, Ha KT. Diversity and complexity of cell death: a historical review. Exp Mol Med 2023; 55:1573-1594. [PMID: 37612413 PMCID: PMC10474147 DOI: 10.1038/s12276-023-01078-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/22/2023] [Accepted: 07/11/2023] [Indexed: 08/25/2023] Open
Abstract
Death is the inevitable fate of all living organisms, whether at the individual or cellular level. For a long time, cell death was believed to be an undesirable but unavoidable final outcome of nonfunctioning cells, as inflammation was inevitably triggered in response to damage. However, experimental evidence accumulated over the past few decades has revealed different types of cell death that are genetically programmed to eliminate unnecessary or severely damaged cells that may damage surrounding tissues. Several types of cell death, including apoptosis, necrosis, autophagic cell death, and lysosomal cell death, which are classified as programmed cell death, and pyroptosis, necroptosis, and NETosis, which are classified as inflammatory cell death, have been described over the years. Recently, several novel forms of cell death, namely, mitoptosis, paraptosis, immunogenic cell death, entosis, methuosis, parthanatos, ferroptosis, autosis, alkaliptosis, oxeiptosis, cuproptosis, and erebosis, have been discovered and advanced our understanding of cell death and its complexity. In this review, we provide a historical overview of the discovery and characterization of different forms of cell death and highlight their diversity and complexity. We also briefly discuss the regulatory mechanisms underlying each type of cell death and the implications of cell death in various physiological and pathological contexts. This review provides a comprehensive understanding of different mechanisms of cell death that can be leveraged to develop novel therapeutic strategies for various diseases.
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Affiliation(s)
- Wonyoung Park
- Department of Korean Medical Science, School of Korean Medicine, Pusan National University, Yangsan, Gyeongsangnam-do, 50612, Republic of Korea
- Korean Medical Research Center for Healthy Aging, Pusan National University, Yangsan, Gyeongsangnam-do, 50612, Republic of Korea
| | - Shibo Wei
- Department of Precision Medicine, School of Medicine, Sungkyunkwan University School of Medicine, Suwon, Gyeonggi-do, 16419, Republic of Korea
| | - Bo-Sung Kim
- Department of Korean Medical Science, School of Korean Medicine, Pusan National University, Yangsan, Gyeongsangnam-do, 50612, Republic of Korea
- Korean Medical Research Center for Healthy Aging, Pusan National University, Yangsan, Gyeongsangnam-do, 50612, Republic of Korea
| | - Bosung Kim
- Department of Korean Medical Science, School of Korean Medicine, Pusan National University, Yangsan, Gyeongsangnam-do, 50612, Republic of Korea
- Korean Medical Research Center for Healthy Aging, Pusan National University, Yangsan, Gyeongsangnam-do, 50612, Republic of Korea
| | - Sung-Jin Bae
- Department of Molecular Biology and Immunology, Kosin University College of Medicine, Busan, 49267, Republic of Korea
| | - Young Chan Chae
- Department of Biological Sciences, UNIST, Ulsan, 44919, Republic of Korea
| | - Dongryeol Ryu
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea
| | - Ki-Tae Ha
- Department of Korean Medical Science, School of Korean Medicine, Pusan National University, Yangsan, Gyeongsangnam-do, 50612, Republic of Korea.
- Korean Medical Research Center for Healthy Aging, Pusan National University, Yangsan, Gyeongsangnam-do, 50612, Republic of Korea.
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Nishimura T, Lazzeri G, Mizushima N, Covino R, Tooze SA. Unique amphipathic α helix drives membrane insertion and enzymatic activity of ATG3. SCIENCE ADVANCES 2023; 9:eadh1281. [PMID: 37352354 PMCID: PMC10289646 DOI: 10.1126/sciadv.adh1281] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/22/2023] [Indexed: 06/25/2023]
Abstract
Autophagosome biogenesis requires a localized perturbation of lipid membrane dynamics and a unique protein-lipid conjugate. Autophagy-related (ATG) proteins catalyze this biogenesis on cellular membranes, but the underlying molecular mechanism remains unclear. Focusing on the final step of the protein-lipid conjugation reaction, the ATG8/LC3 lipidation, we show how the membrane association of the conjugation machinery is organized and fine-tuned at the atomistic level. Amphipathic α helices in ATG3 proteins (AHATG3) have low hydrophobicity and contain less bulky residues. Molecular dynamics simulations reveal that AHATG3 regulates the dynamics and accessibility of the thioester bond of the ATG3~LC3 conjugate to lipids, enabling the covalent lipidation of LC3. Live-cell imaging shows that the transient membrane association of ATG3 with autophagic membranes is governed by the less bulky-hydrophobic feature of AHATG3. The unique properties of AHATG3 facilitate protein-lipid bilayer association, leading to the remodeling of the lipid bilayer required for the formation of autophagosomes.
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Affiliation(s)
- Taki Nishimura
- PRESTO, Japan Science and Technology Agency, Chiyoda-ku, Tokyo 102-0076, Japan
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
- Molecular Cell Biology of Autophagy Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Gianmarco Lazzeri
- Frankfurt Institute for Advanced Studies, Ruth-Moufang-Straße 1, Frankfurt am Main 60438, Germany
- Goethe University, Frankfurt am Main 60438, Germany
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Roberto Covino
- Frankfurt Institute for Advanced Studies, Ruth-Moufang-Straße 1, Frankfurt am Main 60438, Germany
- Goethe University, Frankfurt am Main 60438, Germany
| | - Sharon A. Tooze
- Molecular Cell Biology of Autophagy Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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