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Zhou Y, Tao L, Qiu J, Xu J, Yang X, Zhang Y, Tian X, Guan X, Cen X, Zhao Y. Tumor biomarkers for diagnosis, prognosis and targeted therapy. Signal Transduct Target Ther 2024; 9:132. [PMID: 38763973 PMCID: PMC11102923 DOI: 10.1038/s41392-024-01823-2] [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: 06/05/2023] [Revised: 03/07/2024] [Accepted: 04/02/2024] [Indexed: 05/21/2024] Open
Abstract
Tumor biomarkers, the substances which are produced by tumors or the body's responses to tumors during tumorigenesis and progression, have been demonstrated to possess critical and encouraging value in screening and early diagnosis, prognosis prediction, recurrence detection, and therapeutic efficacy monitoring of cancers. Over the past decades, continuous progress has been made in exploring and discovering novel, sensitive, specific, and accurate tumor biomarkers, which has significantly promoted personalized medicine and improved the outcomes of cancer patients, especially advances in molecular biology technologies developed for the detection of tumor biomarkers. Herein, we summarize the discovery and development of tumor biomarkers, including the history of tumor biomarkers, the conventional and innovative technologies used for biomarker discovery and detection, the classification of tumor biomarkers based on tissue origins, and the application of tumor biomarkers in clinical cancer management. In particular, we highlight the recent advancements in biomarker-based anticancer-targeted therapies which are emerging as breakthroughs and promising cancer therapeutic strategies. We also discuss limitations and challenges that need to be addressed and provide insights and perspectives to turn challenges into opportunities in this field. Collectively, the discovery and application of multiple tumor biomarkers emphasized in this review may provide guidance on improved precision medicine, broaden horizons in future research directions, and expedite the clinical classification of cancer patients according to their molecular biomarkers rather than organs of origin.
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Affiliation(s)
- Yue Zhou
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Lei Tao
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jiahao Qiu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jing Xu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xinyu Yang
- West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Yu Zhang
- West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
- School of Medicine, Tibet University, Lhasa, 850000, China
| | - Xinyu Tian
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xinqi Guan
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiaobo Cen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
- National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yinglan Zhao
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
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2
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Schreurs RRCE, Koulis A, Booiman T, Boeser-Nunnink B, Cloherty APM, Rader AG, Patel KS, Kootstra NA, Ribeiro CMS. Autophagy-enhancing ATG16L1 polymorphism is associated with improved clinical outcome and T-cell immunity in chronic HIV-1 infection. Nat Commun 2024; 15:2465. [PMID: 38548722 PMCID: PMC10979031 DOI: 10.1038/s41467-024-46606-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 03/04/2024] [Indexed: 04/01/2024] Open
Abstract
Chronic HIV-1 infection is characterized by T-cell dysregulation that is partly restored by antiretroviral therapy. Autophagy is a critical regulator of T-cell function. Here, we demonstrate a protective role for autophagy in HIV-1 disease pathogenesis. Targeted analysis of genetic variation in core autophagy gene ATG16L1 reveals the previously unidentified rs6861 polymorphism, which correlates functionally with enhanced autophagy and clinically with improved survival of untreated HIV-1-infected individuals. T-cells carrying ATG16L1 rs6861(TT) genotype display improved antiviral immunity, evidenced by increased proliferation, revamped immune responsiveness, and suppressed exhaustion/immunosenescence features. In-depth flow-cytometric and transcriptional profiling reveal T-helper-cell-signatures unique to rs6861(TT) individuals with enriched regulation of pro-inflammatory networks and skewing towards immunoregulatory phenotype. Therapeutic enhancement of autophagy recapitulates the rs6861(TT)-associated T-cell traits in non-carriers. These data underscore the in vivo relevance of autophagy for longer-lasting T-cell-mediated HIV-1 control, with implications towards development of host-directed antivirals targeting autophagy to restore immune function in chronic HIV-1 infection.
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Affiliation(s)
- Renée R C E Schreurs
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam institute for Immunology & Infectious Diseases, Amsterdam, The Netherlands
| | - Athanasios Koulis
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam institute for Immunology & Infectious Diseases, Amsterdam, The Netherlands
| | - Thijs Booiman
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam institute for Immunology & Infectious Diseases, Amsterdam, The Netherlands
| | - Brigitte Boeser-Nunnink
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam institute for Immunology & Infectious Diseases, Amsterdam, The Netherlands
| | - Alexandra P M Cloherty
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam institute for Immunology & Infectious Diseases, Amsterdam, The Netherlands
| | - Anusca G Rader
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam institute for Immunology & Infectious Diseases, Amsterdam, The Netherlands
| | - Kharishma S Patel
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam institute for Immunology & Infectious Diseases, Amsterdam, The Netherlands
| | - Neeltje A Kootstra
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam institute for Immunology & Infectious Diseases, Amsterdam, The Netherlands
| | - Carla M S Ribeiro
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9, Amsterdam, The Netherlands.
- Amsterdam institute for Immunology & Infectious Diseases, Amsterdam, The Netherlands.
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3
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Hudson L, Mason JW, Westphal MV, Richter MJR, Thielman JR, Hua BK, Gerry CJ, Xia G, Osswald HL, Knapp JM, Tan ZY, Kokkonda P, Tresco BIC, Liu S, Reidenbach AG, Lim KS, Poirier J, Capece J, Bonazzi S, Gampe CM, Smith NJ, Bradner JE, Coley CW, Clemons PA, Melillo B, Hon CSY, Ottl J, Dumelin CE, Schaefer JV, Faust AME, Berst F, Schreiber SL, Zécri FJ, Briner K. Diversity-oriented synthesis encoded by deoxyoligonucleotides. Nat Commun 2023; 14:4930. [PMID: 37582753 PMCID: PMC10427684 DOI: 10.1038/s41467-023-40575-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 07/31/2023] [Indexed: 08/17/2023] Open
Abstract
Diversity-oriented synthesis (DOS) is a powerful strategy to prepare molecules with underrepresented features in commercial screening collections, resulting in the elucidation of novel biological mechanisms. In parallel to the development of DOS, DNA-encoded libraries (DELs) have emerged as an effective, efficient screening strategy to identify protein binders. Despite recent advancements in this field, most DEL syntheses are limited by the presence of sensitive DNA-based constructs. Here, we describe the design, synthesis, and validation experiments performed for a 3.7 million-member DEL, generated using diverse skeleton architectures with varying exit vectors and derived from DOS, to achieve structural diversity beyond what is possible by varying appendages alone. We also show screening results for three diverse protein targets. We will make this DEL available to the academic scientific community to increase access to novel structural features and accelerate early-phase drug discovery.
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Affiliation(s)
- Liam Hudson
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Jeremy W Mason
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Matthias V Westphal
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Matthieu J R Richter
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Jonathan R Thielman
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Bruce K Hua
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Christopher J Gerry
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Guoqin Xia
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Heather L Osswald
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - John M Knapp
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Zher Yin Tan
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Praveen Kokkonda
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Ben I C Tresco
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Shuang Liu
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Andrew G Reidenbach
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Katherine S Lim
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Jennifer Poirier
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - John Capece
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Simone Bonazzi
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Christian M Gampe
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Nichola J Smith
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - James E Bradner
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Connor W Coley
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
- Department of Chemical Engineering, MIT, Cambridge, MA, 02139, USA
| | - Paul A Clemons
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Bruno Melillo
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - C Suk-Yee Hon
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
| | - Johannes Ottl
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, CH-4002, Basel, Switzerland
| | - Christoph E Dumelin
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, CH-4002, Basel, Switzerland
| | - Jonas V Schaefer
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, CH-4002, Basel, Switzerland
| | - Ann Marie E Faust
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Frédéric Berst
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, CH-4002, Basel, Switzerland
| | - Stuart L Schreiber
- Chemical Biology and Therapeutics Science Program, Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Frédéric J Zécri
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA.
| | - Karin Briner
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
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4
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Pandey P, Ghimire S, Wu B, Alexov E. On the linkage of thermodynamics and pathogenicity. Curr Opin Struct Biol 2023; 80:102572. [PMID: 36965249 PMCID: PMC10239362 DOI: 10.1016/j.sbi.2023.102572] [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: 01/25/2023] [Revised: 02/16/2023] [Accepted: 02/21/2023] [Indexed: 03/27/2023]
Abstract
This review outlines the effect of disease-causing mutations on proteins' thermodynamics. Two major thermodynamics quantities, which are essential for structural integrity, the folding and binding free energy changes caused by missense mutations, are considered. It is emphasized that disease effects in case of complex diseases may originate from several mutations over several genes, while monogenic diseases are caused by mutation is a single gene. Nevertheless, in both cases it is shown that pathogenic mutations cause larger perturbations of the above-mentioned thermodynamics quantities as compared with the benign mutations. Recent works demonstrating the effect of pathogenic mutations on the above-mentioned thermodynamics quantities, as well as on structural dynamics and allosteric pathways, are reviewed.
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Affiliation(s)
- Preeti Pandey
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Sanjeev Ghimire
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Bohua Wu
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Emil Alexov
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA.
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5
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Pfrieger FW. The Niemann-Pick type diseases – A synopsis of inborn errors in sphingolipid and cholesterol metabolism. Prog Lipid Res 2023; 90:101225. [PMID: 37003582 DOI: 10.1016/j.plipres.2023.101225] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/27/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023]
Abstract
Disturbances of lipid homeostasis in cells provoke human diseases. The elucidation of the underlying mechanisms and the development of efficient therapies represent formidable challenges for biomedical research. Exemplary cases are two rare, autosomal recessive, and ultimately fatal lysosomal diseases historically named "Niemann-Pick" honoring the physicians, whose pioneering observations led to their discovery. Acid sphingomyelinase deficiency (ASMD) and Niemann-Pick type C disease (NPCD) are caused by specific variants of the sphingomyelin phosphodiesterase 1 (SMPD1) and NPC intracellular cholesterol transporter 1 (NPC1) or NPC intracellular cholesterol transporter 2 (NPC2) genes that perturb homeostasis of two key membrane components, sphingomyelin and cholesterol, respectively. Patients with severe forms of these diseases present visceral and neurologic symptoms and succumb to premature death. This synopsis traces the tortuous discovery of the Niemann-Pick diseases, highlights important advances with respect to genetic culprits and cellular mechanisms, and exposes efforts to improve diagnosis and to explore new therapeutic approaches.
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6
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Lu G, Wang Y, Shi Y, Zhang Z, Huang C, He W, Wang C, Shen H. Autophagy in health and disease: From molecular mechanisms to therapeutic target. MedComm (Beijing) 2022; 3:e150. [PMID: 35845350 PMCID: PMC9271889 DOI: 10.1002/mco2.150] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 02/05/2023] Open
Abstract
Macroautophagy/autophagy is an evolutionally conserved catabolic process in which cytosolic contents, such as aggregated proteins, dysfunctional organelle, or invading pathogens, are sequestered by the double-membrane structure termed autophagosome and delivered to lysosome for degradation. Over the past two decades, autophagy has been extensively studied, from the molecular mechanisms, biological functions, implications in various human diseases, to development of autophagy-related therapeutics. This review will focus on the latest development of autophagy research, covering molecular mechanisms in control of autophagosome biogenesis and autophagosome-lysosome fusion, and the upstream regulatory pathways including the AMPK and MTORC1 pathways. We will also provide a systematic discussion on the implication of autophagy in various human diseases, including cancer, neurodegenerative disorders (Alzheimer disease, Parkinson disease, Huntington's disease, and Amyotrophic lateral sclerosis), metabolic diseases (obesity and diabetes), viral infection especially SARS-Cov-2 and COVID-19, cardiovascular diseases (cardiac ischemia/reperfusion and cardiomyopathy), and aging. Finally, we will also summarize the development of pharmacological agents that have therapeutic potential for clinical applications via targeting the autophagy pathway. It is believed that decades of hard work on autophagy research is eventually to bring real and tangible benefits for improvement of human health and control of human diseases.
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Affiliation(s)
- Guang Lu
- Department of Physiology, Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
| | - Yu Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic MedicineSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Yin Shi
- Department of BiochemistryZhejiang University School of MedicineHangzhouChina
| | - Zhe Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic MedicineSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic MedicineSichuan University and Collaborative Innovation Center for BiotherapyChengduChina
| | - Weifeng He
- State Key Laboratory of Trauma, Burn and Combined Injury, Institute of Burn ResearchSouthwest HospitalArmy Medical UniversityChongqingChina
| | - Chuang Wang
- Department of Pharmacology, Provincial Key Laboratory of PathophysiologyNingbo University School of MedicineNingboZhejiangChina
| | - Han‐Ming Shen
- Department of Biomedical Sciences, Faculty of Health Sciences, Ministry of Education Frontiers Science Center for Precision OncologyUniversity of MacauMacauChina
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7
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Sabitha KR, Chandran D, Shetty AK, Upadhya D. Delineating the neuropathology of lysosomal storage diseases using patient-derived induced pluripotent stem cells. Stem Cells Dev 2022; 31:221-238. [PMID: 35316126 DOI: 10.1089/scd.2021.0304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Lysosomal storage diseases (LSD) are inherited metabolic diseases caused due to deficiency of lysosomal enzymes, essential for the normal development of the brain and other organs. Approximately two-thirds of the patients suffering from LSD exhibit neurological deficits and impose an escalating challenge to the medical and scientific field. The advent of iPSC technology has aided researchers in efficiently generating functional neuronal and non-neuronal cells through directed differentiation protocols, as well as in decoding the cellular, subcellular and molecular defects associated with LSDs using two-dimensional cultures and cerebral organoid models. This review highlights the information assembled from patient-derived iPSCs on neurodevelopmental and neuropathological defects identified in LSDs. Multiple studies have identified neural progenitor cell migration and differentiation defects, substrate accumulation, axon growth and myelination defects, impaired calcium homeostasis and altered electrophysiological properties, using patient-derived iPSCs. In addition, these studies have also uncovered defective lysosomes, mitochondria, endoplasmic reticulum, Golgi complex, autophagy and vesicle trafficking and signaling pathways, oxidative stress, neuroinflammation, blood brain barrier dysfunction, neurodegeneration, gliosis, altered transcriptomes in LSDs. The review also discusses the therapeutic applications such as drug discovery, repurposing of drugs, synergistic effects of drugs, targeted molecular therapies, gene therapy, and transplantation applications of mutation corrected lines identified using patient-derived iPSCs for different LSDs.
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Affiliation(s)
- K R Sabitha
- Kasturba Medical College Manipal, 29224, Centre for Molecular Neurosciences, Manipal, Karnataka, India;
| | - Divya Chandran
- Kasturba Medical College Manipal, 29224, Centre for Molecular Neurosciences, Manipal, Karnataka, India;
| | - Ashok K Shetty
- Texas A&M University College Station, 14736, College of Medicine, Institute for Regenerative Medicine, College Station, Texas, United States;
| | - Dinesh Upadhya
- Kasturba Medical College Manipal, 29224, Centre for Molecular Neurosciences, Manipal, Karnataka, India;
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8
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Vessey KA, Jobling AI, Tran MX, Wang AY, Greferath U, Fletcher EL. Treatments targeting autophagy ameliorate the age-related macular degeneration phenotype in mice lacking APOE (apolipoprotein E). Autophagy 2022; 18:2368-2384. [PMID: 35196199 PMCID: PMC9542759 DOI: 10.1080/15548627.2022.2034131] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Age-related macular degeneration (AMD) is a leading cause of vision loss with recent evidence indicating an important role for macroautophagy/autophagy in disease progression. In this study we investigate the efficacy of targeting autophagy for slowing dysfunction in a mouse model with features of early AMD. Mice lacking APOE (apolipoprotein E; B6.129P2-Apoetm1UncJ/Arc) and C57BL/6 J- (wild-type, WT) mice were treated with metformin or trehalose in the drinking water from 5 months of age and the ocular phenotype investigated at 13 months. Control mice received normal drinking water. APOE-control mice had reduced retinal function and thickening of Bruch’s membrane consistent with an early AMD phenotype. Immunohistochemical labeling showed reductions in MAP1LC3B/LC3 (microtubule-associated protein 1 light chain 3 beta) and LAMP1 (lysosomal-associated membrane protein 1) labeling in the photoreceptors and retinal pigment epithelium (RPE). This correlated with increased LC3-II:LC3-I ratio and alterations in protein expression in multiple autophagy pathways measured by reverse phase protein array, suggesting autophagy was slowed. Treatment of APOE-mice with metformin or trehalose ameliorated the loss of retinal function and reduced Bruch’s membrane thickening, enhancing LC3 and LAMP1 labeling in the ocular tissues and restoring LC3-II:LC3-I ratio to WT levels. Protein analysis indicated that both treatments boost ATM-AMPK driven autophagy. Additionally, trehalose increased p-MAPK14/p38 to enhance autophagy. Our study shows that treatments targeting pathways to enhance autophagy have the potential for treating early AMD and provide support for the use of metformin, which has been found to reduce the risk of AMD development in human patients.Abbreviations:AMD: age-related macular degeneration; AMPK: 5’ adenosine monophosphate-activated protein kinase APOE: apolipoprotein E; ATM: ataxia telangiectasia mutated; BCL2L1/Bcl-xL: BCL2-like 1; DAPI: 4ʹ-6-diamidino-2-phenylindole; ERG: electroretinogram; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GCL: ganglion cell layer; INL: inner nuclear layer; IPL: inner plexiform layer; IS/OS: inner and outer photoreceptor segments; LAMP1: lysosomal-associated membrane protein 1; MAP1LC3B/LC3: microtubule-associated protein 1 light chain 3 beta; MTOR: mechanistic target of rapamycin kinase; OCT: optical coherence tomography; ONL: outer nuclear layer; OPs: oscillatory potentials; p-EIF4EBP1: phosphorylated eukaryotic translation initiation factor 4E binding protein 1; p-MAPK14/p38: phosphorylated mitogen-activated protein kinase 14; RPE: retinal pigment epithelium; RPS6KB/p70 S6 kinase: ribosomal protein S6 kinase; SQSTM1/p62: sequestosome 1; TP53/TRP53/p53: tumor related protein 53; TSC2: TSC complex subunit 2; WT: wild type
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Affiliation(s)
- Kirstan A Vessey
- Department of Anatomy and Physiology, The University of Melbourne, Level 5, Medical Building, Grattan St, Parkville, Victoria, Australia, 3010
| | - Andrew I Jobling
- Department of Anatomy and Physiology, The University of Melbourne, Level 5, Medical Building, Grattan St, Parkville, Victoria, Australia, 3010
| | - Mai X Tran
- Department of Anatomy and Physiology, The University of Melbourne, Level 5, Medical Building, Grattan St, Parkville, Victoria, Australia, 3010
| | - Anna Y Wang
- Department of Anatomy and Physiology, The University of Melbourne, Level 5, Medical Building, Grattan St, Parkville, Victoria, Australia, 3010
| | - Ursula Greferath
- Department of Anatomy and Physiology, The University of Melbourne, Level 5, Medical Building, Grattan St, Parkville, Victoria, Australia, 3010
| | - Erica L Fletcher
- Department of Anatomy and Physiology, The University of Melbourne, Level 5, Medical Building, Grattan St, Parkville, Victoria, Australia, 3010
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9
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Safren N, Tank EM, Malik AM, Chua JP, Santoro N, Barmada SJ. Development of a specific live-cell assay for native autophagic flux. J Biol Chem 2021; 297:101003. [PMID: 34303705 PMCID: PMC8368035 DOI: 10.1016/j.jbc.2021.101003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 05/27/2021] [Accepted: 07/21/2021] [Indexed: 01/09/2023] Open
Abstract
Autophagy is an evolutionarily conserved pathway mediating the breakdown of cellular proteins and organelles. Emphasizing its pivotal nature, autophagy dysfunction contributes to many diseases; nevertheless, development of effective autophagy modulating drugs is hampered by fundamental deficiencies in available methods for measuring autophagic activity or flux. To overcome these limitations, we introduced the photoconvertible protein Dendra2 into the MAP1LC3B locus of human cells via CRISPR/Cas9 genome editing, enabling accurate and sensitive assessments of autophagy in living cells by optical pulse labeling. We used this assay to perform high-throughput drug screens of four chemical libraries comprising over 30,000 diverse compounds, identifying several clinically relevant drugs and novel autophagy modulators. A select series of candidate compounds also modulated autophagy flux in human motor neurons modified by CRISPR/Cas9 to express GFP-labeled LC3. Using automated microscopy, we tested the therapeutic potential of autophagy induction in several distinct neuronal models of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). In doing so, we found that autophagy induction exhibited discordant effects, improving survival in disease models involving the RNA binding protein TDP-43, while exacerbating toxicity in neurons expressing mutant forms of UBQLN2 and C9ORF72 associated with familial ALS/FTD. These studies confirm the utility of the Dendra2-LC3 assay, while illustrating the contradictory effects of autophagy induction in different ALS/FTD subtypes.
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Affiliation(s)
- Nathaniel Safren
- Department of Neurology, University of Michigan, Ann Arbor Michigan, USA
| | - Elizabeth M Tank
- Department of Neurology, University of Michigan, Ann Arbor Michigan, USA
| | - Ahmed M Malik
- Department of Neurology, University of Michigan, Ann Arbor Michigan, USA
| | - Jason P Chua
- Department of Neurology, University of Michigan, Ann Arbor Michigan, USA
| | - Nicholas Santoro
- Center for Chemical Genomics, Life Sciences Institute, University of Michigan, Ann Arbor Michigan, USA
| | - Sami J Barmada
- Department of Neurology, University of Michigan, Ann Arbor Michigan, USA.
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10
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Small molecule probes for targeting autophagy. Nat Chem Biol 2021; 17:653-664. [PMID: 34035513 DOI: 10.1038/s41589-021-00768-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 02/08/2021] [Indexed: 02/02/2023]
Abstract
Autophagy is implicated in a wide range of (patho)physiological processes including maintenance of cellular homeostasis, neurodegenerative disorders, aging and cancer. As such, small molecule autophagy modulators are in great demand, both for their ability to act as tools to better understand this essential process and as potential therapeutics. Despite substantial advances in the field, major challenges remain in the development and comprehensive characterization of probes that are specific to autophagy. In this Review, we discuss recent developments in autophagy-modulating small molecules, including the specific challenges faced in the development of activators and inhibitors, and recommend guidelines for their use. Finally, we discuss the potential to hijack the process for targeted protein degradation, an area of great importance in chemical biology and drug discovery.
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11
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Bittencourt TL, da Silva Prata RB, de Andrade Silva BJ, de Mattos Barbosa MG, Dalcolmo MP, Pinheiro RO. Autophagy as a Target for Drug Development Of Skin Infection Caused by Mycobacteria. Front Immunol 2021; 12:674241. [PMID: 34113346 PMCID: PMC8185338 DOI: 10.3389/fimmu.2021.674241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/28/2021] [Indexed: 12/11/2022] Open
Abstract
Pathogenic mycobacteria species may subvert the innate immune mechanisms and can modulate the activation of cells that cause disease in the skin. Cutaneous mycobacterial infection may present different clinical presentations and it is associated with stigma, deformity, and disability. The understanding of the immunopathogenic mechanisms related to mycobacterial infection in human skin is of pivotal importance to identify targets for new therapeutic strategies. The occurrence of reactional episodes and relapse in leprosy patients, the emergence of resistant mycobacteria strains, and the absence of effective drugs to treat mycobacterial cutaneous infection increased the interest in the development of therapies based on repurposed drugs against mycobacteria. The mechanism of action of many of these therapies evaluated is linked to the activation of autophagy. Autophagy is an evolutionary conserved lysosomal degradation pathway that has been associated with the control of the mycobacterial bacillary load. Here, we review the role of autophagy in the pathogenesis of cutaneous mycobacterial infection and discuss the perspectives of autophagy as a target for drug development and repurposing against cutaneous mycobacterial infection.
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Affiliation(s)
| | | | | | | | - Margareth Pretti Dalcolmo
- Helio Fraga Reference Center, Sergio Arouca National School of Public Health, Fiocruz, Rio de Janeiro, Brazil
| | - Roberta Olmo Pinheiro
- Leprosy Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil
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12
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Zhang Q, Presswalla F, Ali RR, Zacks DN, Thompson DA, Miller JML. Pharmacologic activation of autophagy without direct mTOR inhibition as a therapeutic strategy for treating dry macular degeneration. Aging (Albany NY) 2021; 13:10866-10890. [PMID: 33872219 PMCID: PMC8109132 DOI: 10.18632/aging.202974] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 03/13/2021] [Indexed: 12/15/2022]
Abstract
Dry age-related macular degeneration (AMD) is marked by the accumulation of extracellular and intracellular lipid-rich deposits within and around the retinal pigment epithelium (RPE). Inducing autophagy, a conserved, intracellular degradative pathway, is a potential treatment strategy to prevent disease by clearing these deposits. However, mTOR inhibition, the major mechanism for inducing autophagy, disrupts core RPE functions. Here, we screened autophagy inducers that do not directly inhibit mTOR for their potential as an AMD therapeutic in primary human RPE culture. Only two out of more than thirty autophagy inducers tested reliably increased autophagy flux in RPE, emphasizing that autophagy induction mechanistically differs across distinct tissues. In contrast to mTOR inhibitors, these compounds preserved RPE health, and one inducer, the FDA-approved compound flubendazole (FLBZ), reduced the secretion of apolipoprotein that contributes to extracellular deposits termed drusen. Simultaneously, FLBZ increased production of the lipid-degradation product β-hydroxybutyrate, which is used by photoreceptor cells as an energy source. FLBZ also reduced the accumulation of intracellular deposits, termed lipofuscin, and alleviated lipofuscin-induced cellular senescence and tight-junction disruption. FLBZ triggered compaction of lipofuscin-like granules into a potentially less toxic form. Thus, induction of RPE autophagy without direct mTOR inhibition is a promising therapeutic approach for dry AMD.
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Affiliation(s)
- Qitao Zhang
- Kellogg Eye Center, University of Michigan, Ann Arbor, MI 48105, USA
| | - Feriel Presswalla
- Kellogg Eye Center, University of Michigan, Ann Arbor, MI 48105, USA
| | - Robin R. Ali
- Kellogg Eye Center, University of Michigan, Ann Arbor, MI 48105, USA
- KCL Centre for Cell and Gene Therapy, London, England WC2R 2LS, United Kingdom
| | - David N. Zacks
- Kellogg Eye Center, University of Michigan, Ann Arbor, MI 48105, USA
| | - Debra A. Thompson
- Kellogg Eye Center, University of Michigan, Ann Arbor, MI 48105, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48105, USA
| | - Jason ML. Miller
- Kellogg Eye Center, University of Michigan, Ann Arbor, MI 48105, USA
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13
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Nayak A, Saxena H, Bathula C, Kumar T, Bhattacharjee S, Sen S, Gupta A. Diversity-oriented synthesis derived indole based spiro and fused small molecules kills artemisinin-resistant Plasmodium falciparum. Malar J 2021; 20:100. [PMID: 33596950 PMCID: PMC7891021 DOI: 10.1186/s12936-021-03632-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 02/06/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Despite numerous efforts to eradicate the disease, malaria continues to remain one of the most dangerous infectious diseases plaguing the world. In the absence of any effective vaccines and with emerging drug resistance in the parasite against the majority of anti-malarial drugs, the search for new drugs is urgently needed for effective malaria treatment. METHODS The goal of the present study was to examine the compound library, based on indoles generated through diversity-oriented synthesis belonging to four different architecture, i.e., 1-aryltetrahydro/dihydro-β-carbolines and piperidine/pyrrolidine-fused indole derivatives, for their in vitro anti-plasmodial activity. Trifluoroacetic acid catalyzed transformation involving tryptamine and various aldehydes/ketones provided the library. RESULTS Among all the compounds screened, 1-aryltetrahydro-β-carbolines 2 and 3 displayed significant anti-plasmodial activity against both the artemisinin-sensitive and artemisinin-resistant strain of Plasmodium falciparum. It was observed that these compounds inhibited the overall parasite growth in intra-erythrocytic developmental cycle (IDC) via reactive oxygen species-mediated parasitic death and thus could be potential anti-malarial compounds. CONCLUSION Overall the compounds 2 and 3 identified in this study shows promising anti-plasmodial activity that can kill both artemisinin-sensitive and artemisinin-resistant strains of P. falciparum.
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Affiliation(s)
- Akshaykumar Nayak
- Epigenetics & Human Disease Laboratory, Department of Life Sciences, Shiv Nadar University, Uttar Pradesh, NH-91, Tehsil-Dadri, Greater Noida, 201314, India
| | - Himani Saxena
- Epigenetics & Human Disease Laboratory, Department of Life Sciences, Shiv Nadar University, Uttar Pradesh, NH-91, Tehsil-Dadri, Greater Noida, 201314, India
| | - Chandramohan Bathula
- Department of Chemistry, Shiv Nadar University, Uttar Pradesh, Tehsil-Dadri, Greater Noida, 201314, India
| | - Tarkeshwar Kumar
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Souvik Bhattacharjee
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Subhabrata Sen
- Department of Chemistry, Shiv Nadar University, Uttar Pradesh, Tehsil-Dadri, Greater Noida, 201314, India.
| | - Ashish Gupta
- Epigenetics & Human Disease Laboratory, Department of Life Sciences, Shiv Nadar University, Uttar Pradesh, NH-91, Tehsil-Dadri, Greater Noida, 201314, India.
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14
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Understanding and Treating Niemann-Pick Type C Disease: Models Matter. Int J Mol Sci 2020; 21:ijms21238979. [PMID: 33256121 PMCID: PMC7730076 DOI: 10.3390/ijms21238979] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 02/06/2023] Open
Abstract
Biomedical research aims to understand the molecular mechanisms causing human diseases and to develop curative therapies. So far, these goals have been achieved for a small fraction of diseases, limiting factors being the availability, validity, and use of experimental models. Niemann–Pick type C (NPC) is a prime example for a disease that lacks a curative therapy despite substantial breakthroughs. This rare, fatal, and autosomal-recessive disorder is caused by defects in NPC1 or NPC2. These ubiquitously expressed proteins help cholesterol exit from the endosomal–lysosomal system. The dysfunction of either causes an aberrant accumulation of lipids with patients presenting a large range of disease onset, neurovisceral symptoms, and life span. Here, we note general aspects of experimental models, we describe the line-up used for NPC-related research and therapy development, and we provide an outlook on future topics.
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15
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Lualdi M, Alberio T, Fasano M. Proteostasis and Proteotoxicity in the Network Medicine Era. Int J Mol Sci 2020; 21:E6405. [PMID: 32899160 PMCID: PMC7503343 DOI: 10.3390/ijms21176405] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 08/28/2020] [Accepted: 09/02/2020] [Indexed: 02/06/2023] Open
Abstract
Neurodegenerative proteinopathies are complex diseases that share some pathogenetic processes. One of these is the failure of the proteostasis network (PN), which includes all components involved in the synthesis, folding, and degradation of proteins, thus leading to the aberrant accumulation of toxic protein aggregates in neurons. The single components that belong to the three main modules of the PN are highly interconnected and can be considered as part of a single giant network. Several pharmacological strategies have been proposed to ameliorate neurodegeneration by targeting PN components. Nevertheless, effective disease-modifying therapies are still lacking. In this review article, after a general description of the PN and its failure in proteinopathies, we will focus on the available pharmacological tools to target proteostasis. In this context, we will discuss the main advantages of systems-based pharmacology in contrast to the classical targeted approach, by focusing on network pharmacology as a strategy to innovate rational drug design.
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Affiliation(s)
| | | | - Mauro Fasano
- Department of Science and High Technology and Center of Bioinformatics, University of Insubria, I-21052 Busto Arsizio, Italy; (M.L.); (T.A.)
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16
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Kinarivala N, Morsy A, Patel R, Carmona AV, Sajib MS, Raut S, Mikelis CM, Al-Ahmad A, Trippier PC. An iPSC-Derived Neuron Model of CLN3 Disease Facilitates Small Molecule Phenotypic Screening. ACS Pharmacol Transl Sci 2020; 3:931-947. [PMID: 33073192 DOI: 10.1021/acsptsci.0c00077] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Indexed: 02/06/2023]
Abstract
The neuronal ceroid lipofuscinoses (NCLs) are a family of rare lysosomal storage disorders. The most common form of NCL occurs in children harboring a mutation in the CLN3 gene. This form is lethal with no existing cure or treatment beyond symptomatic relief. The pathophysiology of CLN3 disease is complex and poorly understood, with current in vivo and in vitro models failing to identify pharmacological targets for therapeutic intervention. This study reports the characterization of the first CLN3 patient-specific induced pluripotent stem cell (iPSC)-derived model of the blood-brain barrier and establishes the suitability of an iPSC-derived neuron model of the disease to facilitate compound screening. Upon differentiation, hallmarks of CLN3 disease are apparent, including lipofuscin and subunit c of mitochondrial ATP synthase accumulation, mitochondrial dysfunction, and attenuated Bcl-2 expression. The model led to the identification of small molecules that cleared subunit c accumulation by mTOR-independent modulation of autophagy, conferred protective effects through induction of Bcl-2 and rescued mitochondrial dysfunction.
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Affiliation(s)
- Nihar Kinarivala
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas 79106, United States
| | - Ahmed Morsy
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Ronak Patel
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas 79106, United States
| | - Angelica V Carmona
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Md Sanaullah Sajib
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas 79106, United States
| | - Snehal Raut
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas 79106, United States
| | - Constantinos M Mikelis
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas 79106, United States
| | - Abraham Al-Ahmad
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas 79106, United States
| | - Paul C Trippier
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States.,Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas 79106, United States.,UNMC Center for Drug Discovery, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
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17
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Varma M, Kadoki M, Lefkovith A, Conway KL, Gao K, Mohanan V, Tusi BK, Graham DB, Latorre IJ, Tolonen AC, Khor B, Ng A, Xavier RJ. Cell Type- and Stimulation-Dependent Transcriptional Programs Regulated by Atg16L1 and Its Crohn's Disease Risk Variant T300A. THE JOURNAL OF IMMUNOLOGY 2020; 205:414-424. [PMID: 32522834 DOI: 10.4049/jimmunol.1900750] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 05/06/2020] [Indexed: 12/15/2022]
Abstract
Genome-wide association studies have identified common genetic variants impacting human diseases; however, there are indications that the functional consequences of genetic polymorphisms can be distinct depending on cell type-specific contexts, which produce divergent phenotypic outcomes. Thus, the functional impact of genetic variation and the underlying mechanisms of disease risk are modified by cell type-specific effects of genotype on pathological phenotypes. In this study, we extend these concepts to interrogate the interdependence of cell type- and stimulation-specific programs influenced by the core autophagy gene Atg16L1 and its T300A coding polymorphism identified by genome-wide association studies as linked with increased risk of Crohn's disease. We applied a stimulation-based perturbational profiling approach to define Atg16L1 T300A phenotypes in dendritic cells and T lymphocytes. Accordingly, we identified stimulus-specific transcriptional signatures revealing T300A-dependent functional phenotypes that mechanistically link inflammatory cytokines, IFN response genes, steroid biosynthesis, and lipid metabolism in dendritic cells and iron homeostasis and lysosomal biogenesis in T lymphocytes. Collectively, these studies highlight the combined effects of Atg16L1 genetic variation and stimulatory context on immune function.
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Affiliation(s)
- Mukund Varma
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Motohiko Kadoki
- Broad Institute of MIT and Harvard, Cambridge, MA 02142.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114.,Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114; and
| | | | - Kara L Conway
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
| | - Kevin Gao
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
| | - Vishnu Mohanan
- Broad Institute of MIT and Harvard, Cambridge, MA 02142.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114.,Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114; and
| | - Betsabeh Khoramian Tusi
- Broad Institute of MIT and Harvard, Cambridge, MA 02142.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114.,Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114; and
| | - Daniel B Graham
- Broad Institute of MIT and Harvard, Cambridge, MA 02142.,Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114; and.,Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
| | - Isabel J Latorre
- Broad Institute of MIT and Harvard, Cambridge, MA 02142.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114.,Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114; and
| | | | - Bernard Khor
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
| | - Aylwin Ng
- Broad Institute of MIT and Harvard, Cambridge, MA 02142; .,Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142; .,Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114.,Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114; and.,Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
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18
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Loos B, Klionsky DJ, Du Toit A, Hofmeyr JHS. On the relevance of precision autophagy flux control in vivo - Points of departure for clinical translation. Autophagy 2020; 16:750-762. [PMID: 31679454 PMCID: PMC7138200 DOI: 10.1080/15548627.2019.1687211] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 10/11/2019] [Accepted: 10/28/2019] [Indexed: 12/14/2022] Open
Abstract
Macroautophagy (which we will call autophagy hereafter) is a critical intracellular bulk degradation system that is active at basal rates in eukaryotic cells. This process is embedded in the homeostasis of nutrient availability and cellular metabolic demands, degrading primarily long-lived proteins and specific organelles.. Autophagy is perturbed in many pathologies, and its manipulation to enhance or inhibit this pathway therapeutically has received considerable attention. Although better probes are being developed for a more precise readout of autophagic activity in vitro and increasingly in vivo, many questions remain. These center in particular around the accurate measurement of autophagic flux and its translation from the in vitro to the in vivo environment as well as its clinical application. In this review, we highlight key aspects that appear to contribute to stumbling blocks on the road toward clinical translation and discuss points of departure for reaching some of the desired goals. We discuss techniques that are well aligned with achieving desirable spatiotemporal resolution to gather data on autophagic flux in a multi-scale fashion, to better apply the existing tools that are based on single-cell analysis and to use them in the living organism. We assess how current techniques may be used for the establishment of autophagic flux standards or reference points and consider strategies for a conceptual approach on titrating autophagy inducers based on their effect on autophagic flux . Finally, we discuss potential solutions for inherent controls for autophagy analysis, so as to better discern systemic and tissue-specific autophagic flux in future clinical applications.Abbreviations: GFP: Green fluorescent protein; J: Flux; MAP1LC3/LC3: Microtubule-associated protein 1 light chain 3; nA: Number of autophagosomes; TEM: Transmission electron microscopy; τ: Transition time.
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Affiliation(s)
- Ben Loos
- Department of Physiological Sciences, Faculty of Natural Sciences, University of Stellenbosch, Stellenbosch, South Africa
| | - Daniel J. Klionsky
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, USA
| | - Andre Du Toit
- Department of Biochemistry, Faculty of Natural Sciences, University of Stellenbosch, Stellenbosch, South Africa
| | - Jan-Hendrik S. Hofmeyr
- Department of Biochemistry, Faculty of Natural Sciences, University of Stellenbosch, Stellenbosch, South Africa
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19
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Ammanathan V, Vats S, Abraham IM, Manjithaya R. Xenophagy in cancer. Semin Cancer Biol 2020; 66:163-170. [PMID: 32126260 DOI: 10.1016/j.semcancer.2020.02.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 02/17/2020] [Indexed: 12/24/2022]
Abstract
Macroautophagy (herein autophagy) is an intracellular pathway in which cytoplasmic components are captured by double-membrane vesicles (autophagosomes) that eventually fuse with lysosomes to degrade the cargo. Basal levels of autophagy in all eukaryotic cells maintain cellular homeostasis and under conditions of stress, organelles and proteins not essential for survival are degraded. Apart from these functions, cargoes like aggregated proteins, damaged organelles and intracellular pathogens, which are otherwise harmful to cells, are also selectively captured by autophagy and are destined for degradation. In terms of infectious diseases, pathogens are cleared by a specific form of autophagy known as xenophagy. This lysosomal mediated degradation of pathogens also increases the antigen presentation of cells thereby inducing a further immune response. The process of xenophagy provides a broad spectrum of defense mechanism to capture bacterial, viral and protozoan pathogens. However, pathogens have developed ingenious mechanisms to modulate xenophagy to enhance their intracellular survival. Meanwhile, certain pathogens also induce deleterious effects such as chronic inflammation and overexpression of oncogenes in the host system. This over time can increase the susceptibility of the host for tumorigenesis. Hence targeting tumor through anti-microbial mechanisms like xenophagy could be a novel strategy for combinatorial anti-cancer therapy. The recent developments in understanding the role of xenophagy in combating cancer causing pathogens will be discussed in this review.
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Affiliation(s)
- Veena Ammanathan
- Jawaharlal Nehru Centre for Advanced Scientific Research, 560064, Bangalore, India
| | - Somya Vats
- Jawaharlal Nehru Centre for Advanced Scientific Research, 560064, Bangalore, India
| | - Irine Maria Abraham
- Jawaharlal Nehru Centre for Advanced Scientific Research, 560064, Bangalore, India
| | - Ravi Manjithaya
- Jawaharlal Nehru Centre for Advanced Scientific Research, 560064, Bangalore, India
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20
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Andrianova NV, Zorova LD, Babenko VA, Pevzner IB, Popkov VA, Silachev DN, Plotnikov EY, Zorov DB. Rapamycin Is Not Protective against Ischemic and Cisplatin-Induced Kidney Injury. BIOCHEMISTRY (MOSCOW) 2020; 84:1502-1512. [PMID: 31870254 DOI: 10.1134/s0006297919120095] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Autophagy plays an important role in the pathogenesis of acute kidney injury (AKI). Although autophagy activation was shown to be associated with an increased lifespan and beneficial effects in various pathologies, the impact of autophagy activators, particularly, rapamycin and its analogues on AKI remains obscure. In our study, we explored the effects of rapamycin treatment in in vivo and in vitro models of ischemic and cisplatin-induced AKI. The impact of rapamycin on the kidney function after renal ischemia/reperfusion (I/R) or exposure to the nephrotoxic agent cisplatin was assessed by quantifying blood urea nitrogen and serum creatinine and evaluating the content of neutrophil gelatinase-associated lipocalin, a novel biomarker of AKI. In vitro experiments were performed on the primary culture of renal tubular cells (RTCs) that were subjected to oxygen-glucose deprivation (OGD) or incubated with cisplatin under various rapamycin treatment protocols. Cell viability and proliferation were estimated by the MTT assay and real-time cell analysis using an RTCA iCELLigence system. Although rapamycin inhibited mTOR (mammalian target of rapamycin) signaling, it failed to enhance the autophagy and to ameliorate the severity of AKI caused by ischemia or cisplatin-induced nephrotoxicity. Experiments with RTCs demonstrated that rapamycin exhibited the anti-proliferative effect in primary RTCs cultures but did not protect renal cells exposed to OGD or cisplatin. Our study revealed for the first time that the mTOR inhibitor rapamycin did not prevent AKI caused by renal I/R or cisplatin-induced nephrotoxicity and, therefore, cannot be considered as an ideal mimetic of the autophagy-associated nephroprotective mechanisms (e.g., those induced by caloric restriction), as it had been suggested earlier. The protective action of such approaches like caloric restriction might not be limited to mTOR inhibition and can proceed through more complex mechanisms involving alternative autophagy-related targets. Thus, the use of rapamycin and its analogues for the treatment of various AKI forms requires further studies in order to understand potential protective or adverse effects of these compounds in different contexts.
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Affiliation(s)
- N V Andrianova
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119992, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - L D Zorova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.,Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, Moscow, 117997, Russia
| | - V A Babenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.,Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, Moscow, 117997, Russia
| | - I B Pevzner
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.,Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, Moscow, 117997, Russia
| | - V A Popkov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.,Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, Moscow, 117997, Russia
| | - D N Silachev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.,Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, Moscow, 117997, Russia
| | - E Y Plotnikov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia. .,Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, Moscow, 117997, Russia.,Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Moscow, 119991, Russia
| | - D B Zorov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia. .,Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, Moscow, 117997, Russia
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21
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Joshi V, Upadhyay A, Prajapati VK, Mishra A. How autophagy can restore proteostasis defects in multiple diseases? Med Res Rev 2020; 40:1385-1439. [PMID: 32043639 DOI: 10.1002/med.21662] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 01/03/2020] [Accepted: 01/28/2020] [Indexed: 12/12/2022]
Abstract
Cellular evolution develops several conserved mechanisms by which cells can tolerate various difficult conditions and overall maintain homeostasis. Autophagy is a well-developed and evolutionarily conserved mechanism of catabolism, which endorses the degradation of foreign and endogenous materials via autolysosome. To decrease the burden of the ubiquitin-proteasome system (UPS), autophagy also promotes the selective degradation of proteins in a tightly regulated way to improve the physiological balance of cellular proteostasis that may get perturbed due to the accumulation of misfolded proteins. However, the diverse as well as selective clearance of unwanted materials and regulations of several cellular mechanisms via autophagy is still a critical mystery. Also, the failure of autophagy causes an increase in the accumulation of harmful protein aggregates that may lead to neurodegeneration. Therefore, it is necessary to address this multifactorial threat for in-depth research and develop more effective therapeutic strategies against lethal autophagy alterations. In this paper, we discuss the most relevant and recent reports on autophagy modulations and their impact on neurodegeneration and other complex disorders. We have summarized various pharmacological findings linked with the induction and suppression of autophagy mechanism and their promising preclinical and clinical applications to provide therapeutic solutions against neurodegeneration. The conclusion, key questions, and future prospectives sections summarize fundamental challenges and their possible feasible solutions linked with autophagy mechanism to potentially design an impactful therapeutic niche to treat neurodegenerative diseases and imperfect aging.
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Affiliation(s)
- Vibhuti Joshi
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Karwar, India
| | - Arun Upadhyay
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Karwar, India
| | - Vijay K Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Karwar, India
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22
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Seranova E, Palhegyi AM, Verma S, Dimova S, Lasry R, Naama M, Sun C, Barrett T, Rosenstock TR, Kumar D, Cohen MA, Buganim Y, Sarkar S. Human Induced Pluripotent Stem Cell Models of Neurodegenerative Disorders for Studying the Biomedical Implications of Autophagy. J Mol Biol 2020; 432:2754-2798. [PMID: 32044344 DOI: 10.1016/j.jmb.2020.01.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/22/2020] [Accepted: 01/23/2020] [Indexed: 12/12/2022]
Abstract
Autophagy is an intracellular degradation process that is essential for cellular survival, tissue homeostasis, and human health. The housekeeping functions of autophagy in mediating the clearance of aggregation-prone proteins and damaged organelles are vital for post-mitotic neurons. Improper functioning of this process contributes to the pathology of myriad human diseases, including neurodegeneration. Impairment in autophagy has been reported in several neurodegenerative diseases where pharmacological induction of autophagy has therapeutic benefits in cellular and transgenic animal models. However, emerging studies suggest that the efficacy of autophagy inducers, as well as the nature of the autophagy defects, may be context-dependent, and therefore, studies in disease-relevant experimental systems may provide more insights for clinical translation to patients. With the advancements in human stem cell technology, it is now possible to establish disease-affected cellular platforms from patients for investigating disease mechanisms and identifying candidate drugs in the appropriate cell types, such as neurons that are otherwise not accessible. Towards this, patient-derived human induced pluripotent stem cells (hiPSCs) have demonstrated considerable promise in constituting a platform for effective disease modeling and drug discovery. Multiple studies have utilized hiPSC models of neurodegenerative diseases to study autophagy and evaluate the therapeutic efficacy of autophagy inducers in neuronal cells. This review provides an overview of the regulation of autophagy, generation of hiPSCs via cellular reprogramming, and neuronal differentiation. It outlines the findings in various neurodegenerative disorders where autophagy has been studied using hiPSC models.
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Affiliation(s)
- Elena Seranova
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Adina Maria Palhegyi
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Surbhi Verma
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom; Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Simona Dimova
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Rachel Lasry
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University Hadassah Medical School, Jerusalem, 91120, Israel
| | - Moriyah Naama
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University Hadassah Medical School, Jerusalem, 91120, Israel
| | - Congxin Sun
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Timothy Barrett
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Tatiana Rosado Rosenstock
- Department of Physiological Science, Santa Casa de São Paulo School of Medical Sciences, São Paulo, SP, 01221-020, Brazil
| | - Dhiraj Kumar
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Malkiel A Cohen
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
| | - Yosef Buganim
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University Hadassah Medical School, Jerusalem, 91120, Israel
| | - Sovan Sarkar
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom.
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23
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Jayaraj GG, Hipp MS, Hartl FU. Functional Modules of the Proteostasis Network. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a033951. [PMID: 30833457 DOI: 10.1101/cshperspect.a033951] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cells invest in an extensive network of factors to maintain protein homeostasis (proteostasis) and prevent the accumulation of potentially toxic protein aggregates. This proteostasis network (PN) comprises the machineries for the biogenesis, folding, conformational maintenance, and degradation of proteins with molecular chaperones as central coordinators. Here, we review recent progress in understanding the modular architecture of the PN in mammalian cells and how it is modified during cell differentiation. We discuss the capacity and limitations of the PN in maintaining proteome integrity in the face of proteotoxic stresses, such as aggregate formation in neurodegenerative diseases. Finally, we outline various pharmacological interventions to ameliorate proteostasis imbalance.
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Affiliation(s)
- Gopal G Jayaraj
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Mark S Hipp
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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24
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Ammanathan V, Mishra P, Chavalmane AK, Muthusamy S, Jadhav V, Siddamadappa C, Manjithaya R. Restriction of intracellular Salmonella replication by restoring TFEB-mediated xenophagy. Autophagy 2019; 16:1584-1597. [PMID: 31744366 DOI: 10.1080/15548627.2019.1689770] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Macroautophagy/autophagy functions as a part of the innate immune system in clearing intracellular pathogens. Although this process is well known, the mechanisms that control antibacterial autophagy are not clear. In this study we show that during intracellular Salmonella typhimurium infection, the activity of TFEB (transcription factor EB), a master regulator of autophagy and lysosome biogenesis, is suppressed by maintaining it in a phosphorylated state on the lysosomes. Furthermore, we have identified a novel, antibacterial small molecule autophagy (xenophagy) modulator, acacetin. The xenophagy effect exerted by acacetin occurs in an MTOR (mechanistic target of rapamycin kinase)-independent, TFEB-dependent manner. Acacetin treatment results in persistently maintaining active TFEB in the nucleus and also in TFEB mediated induction of functional lysosomes that target Salmonella-containing vacuoles (SCVs). The enhanced proteolytic activity due to deployment of lysosomes results in clamping down Salmonella replication in SCVs. Acacetin is effective as a xenophagy compound in an in vivo mouse model of infection and reduces intracellular Salmonella burden. ABBREVIATIONS 3-MA: 3-methyladenine; BafA1: bafilomycin A1; CFU: colony-forming units; DQ-BSA: dye quenched-bovine serum albumin; EEA1: early endosome antigen 1; FITC: fluorescein isothiocyanate; FM 4-64: pyridinium,4-(6-[4-{diethylamino}phenyl]-1,3,5-hexatrienyl)-1-(3[triethylammonio] propyl)-dibromide; GFP: green fluorescent protein; LAMP1: lysosomal associated membrane protein 1; MAPILC3/LC3: microtubule associated protein 1 light chain 3; MOI: multiplicity of infection; MTOR: mechanistic target of rapamycin kinase; RFP: red fluorescent protein; SCVs: Salmonella-containing vacuoles; SD: standard deviation; SDS: sodium dodecyl sulfate; SEM: standard mean error; SQSTM1: sequestosome 1; TBK1: TANK binding kinase 1; TFEB: transcription factor EB.
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Affiliation(s)
- Veena Ammanathan
- Autophagy Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore, India
| | - Piyush Mishra
- Autophagy Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore, India.,Mitocare Center, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University , Philadelphia, PA, USA
| | - Aravinda K Chavalmane
- Autophagy Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore, India.,School of Biological Sciences, Nanyang Technological University , Singapore, Singapore
| | | | - Vidya Jadhav
- Autophagy Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore, India.,Department of Neurosciences, University of Montreal , Quebec, Canada
| | | | - Ravi Manjithaya
- Autophagy Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore, India
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25
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Palhegyi AM, Seranova E, Dimova S, Hoque S, Sarkar S. Biomedical Implications of Autophagy in Macromolecule Storage Disorders. Front Cell Dev Biol 2019; 7:179. [PMID: 31555645 PMCID: PMC6742707 DOI: 10.3389/fcell.2019.00179] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 08/19/2019] [Indexed: 12/20/2022] Open
Abstract
An imbalance between the production and clearance of macromolecules such as proteins, lipids and carbohydrates can lead to a category of diseases broadly known as macromolecule storage disorders. These include, but not limited to, neurodegenerative diseases such as Alzheimer’s, Parkinson’s and Huntington’s disease associated with accumulation of aggregation-prone proteins, Lafora and Pompe disease associated with glycogen accumulation, whilst lipid accumulation is characteristic to Niemann-Pick disease and Gaucher disease. One of the underlying factors contributing to the build-up of macromolecules in these storage disorders is the intracellular degradation pathway called autophagy. This process is the primary clearance route for unwanted macromolecules, either via bulk non-selective degradation, or selectively via aggrephagy, glycophagy and lipophagy. Since autophagy plays a vital role in maintaining cellular homeostasis, cell viability and human health, malfunction of this process could be detrimental. Indeed, defective autophagy has been reported in a number of macromolecule storage disorders where autophagy is impaired at distinct stages, such as at the level of autophagosome formation, autophagosome maturation or improper lysosomal degradation of the autophagic cargo. Of biomedical relevance, autophagy is regulated by multiple signaling pathways that are amenable to chemical perturbations by small molecules. Induction of autophagy has been shown to improve cell viability and exert beneficial effects in experimental models of various macromolecule storage disorders where the lysosomal functionality is not overtly compromised. In this review, we will discuss the role of autophagy in certain macromolecule storage disorders and highlight the potential therapeutic benefits of autophagy enhancers in these pathological conditions.
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Affiliation(s)
- Adina Maria Palhegyi
- College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, United Kingdom
| | - Elena Seranova
- College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, United Kingdom
| | - Simona Dimova
- College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, United Kingdom
| | - Sheabul Hoque
- College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, United Kingdom
| | - Sovan Sarkar
- College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, United Kingdom
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26
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Panda PK, Fahrner A, Vats S, Seranova E, Sharma V, Chipara M, Desai P, Torresi J, Rosenstock T, Kumar D, Sarkar S. Chemical Screening Approaches Enabling Drug Discovery of Autophagy Modulators for Biomedical Applications in Human Diseases. Front Cell Dev Biol 2019; 7:38. [PMID: 30949479 PMCID: PMC6436197 DOI: 10.3389/fcell.2019.00038] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 03/01/2019] [Indexed: 12/12/2022] Open
Abstract
Autophagy is an intracellular degradation pathway for malfunctioning aggregation-prone proteins, damaged organelles, unwanted macromolecules and invading pathogens. This process is essential for maintaining cellular and tissue homeostasis that contribute to organismal survival. Autophagy dysfunction has been implicated in the pathogenesis of diverse human diseases, and therefore, therapeutic exploitation of autophagy is of potential biomedical relevance. A number of chemical screening approaches have been established for the drug discovery of autophagy modulators based on the perturbations of autophagy reporters or the clearance of autophagy substrates. These readouts can be detected by fluorescence and high-content microscopy, flow cytometry, microplate reader and immunoblotting, and the assays have evolved to enable high-throughput screening and measurement of autophagic flux. Several pharmacological modulators of autophagy have been identified that act either via the classical mechanistic target of rapamycin (mTOR) pathway or independently of mTOR. Many of these autophagy modulators have been demonstrated to exert beneficial effects in transgenic models of neurodegenerative disorders, cancer, infectious diseases, liver diseases, myopathies as well as in lifespan extension. This review describes the commonly used chemical screening approaches in mammalian cells and the key autophagy modulators identified through these methods, and highlights the therapeutic benefits of these compounds in specific disease contexts.
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Affiliation(s)
- Prashanta Kumar Panda
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Alexandra Fahrner
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Somya Vats
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Elena Seranova
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Vartika Sharma
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Miruna Chipara
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Priyal Desai
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Jorge Torresi
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
- Department of Physiological Science, Santa Casa de São Paulo School of Medical Sciences, São Paulo, Brazil
| | - Tatiana Rosenstock
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
- Department of Physiological Science, Santa Casa de São Paulo School of Medical Sciences, São Paulo, Brazil
| | - Dhiraj Kumar
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Sovan Sarkar
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
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27
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Zhang L, Liu B. Targeting Autophagy with Small-Molecule Modulators in Immune-Related Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1209:181-203. [PMID: 31728871 DOI: 10.1007/978-981-15-0606-2_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Autophagy, a highly conserved and multistep lysosomal degradation process, plays a pivotal role in maintaining cellular and physiological homeostasis. Of note, autophagy controls intracellular homeostasis and cell responses to stresses by regulating the self-renewal, maturation, and survival of immune cells. And dysregulation of autophagy in immune cells may contribute to the inflammatory disorders and defect in immune responses against invasive pathogens. Accumulating evidence have indicated that dysregulated autophagy participates in the pathology of immune-related diseases. Therefore, targeting autophagy might represent a promising therapeutic strategy for treatment of immune-related diseases. In this chapter, we focus on discussing the link between autophagy and pathogenesis of immune-related diseases, as well as the dysregulation of autophagy-related signaling pathways, in different diseases. Moreover, we highlight the therapeutic potential of currently used small-molecule modulators of autophagy for treatment of immune-related diseases and illustrate the mechanisms of these small-molecule modulators.
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Affiliation(s)
- Lan Zhang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Bo Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China.
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28
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Seranova E, Ward C, Chipara M, Rosenstock TR, Sarkar S. In Vitro Screening Platforms for Identifying Autophagy Modulators in Mammalian Cells. Methods Mol Biol 2019; 1880:389-428. [PMID: 30610712 DOI: 10.1007/978-1-4939-8873-0_26] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Autophagy is a vital homeostatic pathway essential for cellular survival and human health. It primarily functions as an intracellular degradation process for the turnover of aggregation-prone proteins and unwanted organelles. Dysregulation of autophagy underlying diverse human diseases reduces cell viability, whereas stimulation of autophagy is cytoprotective in a number of transgenic disease models including neurodegenerative disorders. Thus, therapeutic exploitation of autophagy is considered a potential treatment strategy in certain human diseases, and therefore, chemical inducers of autophagy have tremendous biomedical relevance. In this review, we describe the in vitro screening platforms to identify autophagy modulators in mammalian cells using various methodologies including fluorescence and high-content imaging, flow cytometry, fluorescence and luminescence detection by microplate reader, immunoblotting, and immunofluorescence. The commonly used autophagy reporters in these screening platforms are either based on autophagy marker like LC3 or autophagy substrate such as aggregation-prone proteins or p62/SQSTM1. The reporters and assays for monitoring autophagy are evolving over time to become more sensitive in measuring autophagic flux with the capability of high-throughput applications for drug discovery. Here we highlight these developments and also describe the stringent secondary autophagy assays for characterizing the autophagy modulators arising from the primary screen. Since autophagy is implicated in myriad human physiological and pathological conditions, these technologies will enable identifying novel chemical modulators or genetic regulators of autophagy that will be of biomedical and fundamental importance to human health.
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Affiliation(s)
- Elena Seranova
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Carl Ward
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Miruna Chipara
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Tatiana R Rosenstock
- Department of Physiological Science, Santa Casa de São Paulo School of Medical Science, São Paulo, Brazil
| | - Sovan Sarkar
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
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29
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Lee YM, Kim MK, Choo H, Chong Y. Conjugation with Phenylalanine Enhances Autophagy-Inducing Activity of (-)-Epigallocatechin Gallate in Hepatic Cells. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:12741-12747. [PMID: 30418776 DOI: 10.1021/acs.jafc.8b05361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Given the importance of (-)-epigallocatechin gallate (EGCG) as an autophagy-enhancing and thereby lipid-lowering agent, optimization of its activity warrants its therapeutic potential in the treatment of hepatic diseases as well as metabolic disorders. On the basis of our previous observations that structural modifications provided substantial improvements in the bioactivity of EGCG, we investigated the autophagy-enhancing activity of EGCG derivatives. Among 14 EGCG derivatives, E10 with a phenylalanine attached to the D ring of EGCG exhibited the most promising effects in stimulating autophagy in Huh7 cells, which was supported by several lines of evidence: (1) stimulation of autophagy revealed by an increased amount of LC3B-II (4.1 ± 0.8-fold compared to the control) as well as the 2.0 ± 0.1-fold activation of adenosine monophosphate-activated protein kinase in the presence of E10 and (2) E10-stimulated autophagic flux demonstrated by a 1.6 ± 0.4-fold increase in LC3B-II upon co-treatment with chloroquine, 38.1 ± 5.6% reduction of p62/SQSTM1, and an increase in the formation of autophagic compartments visualized by both CYTO-ID staining (3.0 ± 0.1-fold) and tandem RFP-GFP-LC3 fluorescence (2.7 ± 0.4- and 3.2 ± 0.3-fold for green and red fluorescence, respectively). Finally, the autophagy-inducing activity of E10 culminated in a 5.3-fold reduction of hepatic lipid accumulation caused by fatty acids. In all of the assay settings, E10 was consistently 1.3-3.5-fold more potent than EGCG. Taken together, we demonstrated a significant increase in autophagy-stimulating activity of EGCG through structural modifications.
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Affiliation(s)
- Yong Min Lee
- Department of Bioscience and Biotechnology, Reverse Metabolomics Research Center , Konkuk University , 1 Hwayang-dong , Gwangjin-gu, Seoul 143-701 , Korea
| | - Mi Kyoung Kim
- Department of Bioscience and Biotechnology, Reverse Metabolomics Research Center , Konkuk University , 1 Hwayang-dong , Gwangjin-gu, Seoul 143-701 , Korea
| | - Hyunah Choo
- Neuro-Medicine Center, Life/Health Division , Korea Institute of Science and Technology , 39-1 Hawolgok-dong , Seongbuk-gu, Seoul 136-791 , Korea
| | - Youhoon Chong
- Department of Bioscience and Biotechnology, Reverse Metabolomics Research Center , Konkuk University , 1 Hwayang-dong , Gwangjin-gu, Seoul 143-701 , Korea
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30
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Shetty AK, Kodali M, Upadhya R, Madhu LN. Emerging Anti-Aging Strategies - Scientific Basis and Efficacy. Aging Dis 2018; 9:1165-1184. [PMID: 30574426 PMCID: PMC6284760 DOI: 10.14336/ad.2018.1026] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 11/30/2018] [Indexed: 12/11/2022] Open
Abstract
The prevalence of age-related diseases is in an upward trend due to increased life expectancy in humans. Age-related conditions are among the leading causes of morbidity and death worldwide currently. Therefore, there is an urgent need to find apt interventions that slow down aging and reduce or postpone the incidence of debilitating age-related diseases. This review discusses the efficacy of emerging anti-aging approaches for maintaining better health in old age. There are many anti-aging strategies in development, which include procedures such as augmentation of autophagy, elimination of senescent cells, transfusion of plasma from young blood, intermittent fasting, enhancement of adult neurogenesis, physical exercise, antioxidant intake, and stem cell therapy. Multiple pre-clinical studies suggest that administration of autophagy enhancers, senolytic drugs, plasma from young blood, drugs that enhance neurogenesis and BDNF are promising approaches to sustain normal health during aging and also to postpone age-related neurodegenerative diseases such as Alzheimer's disease. Stem cell therapy has also shown promise for improving regeneration and function of the aged or Alzheimer's disease brain. Several of these approaches are awaiting critical appraisal in clinical trials to determine their long-term efficacy and possible adverse effects. On the other hand, procedures such as intermittent fasting, physical exercise, intake of antioxidants such as resveratrol and curcumin have shown considerable promise for improving function in aging, some of which are ready for large-scale clinical trials, as they are non-invasive, and seem to have minimal side effects. In summary, several approaches are at the forefront of becoming mainstream therapies for combating aging and postponing age-related diseases in the coming years.
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Affiliation(s)
- Ashok K. Shetty
- Institute for Regenerative Medicine, Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center College of Medicine, College Station, Texas 77843, USA
- Olin E. Teague Veterans’ Medical Center, Central Texas Veterans Health Care System, Temple, Texas 76504, USA
| | - Maheedhar Kodali
- Institute for Regenerative Medicine, Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center College of Medicine, College Station, Texas 77843, USA
- Olin E. Teague Veterans’ Medical Center, Central Texas Veterans Health Care System, Temple, Texas 76504, USA
| | - Raghavendra Upadhya
- Institute for Regenerative Medicine, Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center College of Medicine, College Station, Texas 77843, USA
- Olin E. Teague Veterans’ Medical Center, Central Texas Veterans Health Care System, Temple, Texas 76504, USA
| | - Leelavathi N. Madhu
- Institute for Regenerative Medicine, Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center College of Medicine, College Station, Texas 77843, USA
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31
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Mishra P, Ammanathan V, Manjithaya R. Chemical Biology Strategies to Study Autophagy. Front Cell Dev Biol 2018; 6:160. [PMID: 30538986 PMCID: PMC6277461 DOI: 10.3389/fcell.2018.00160] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 11/06/2018] [Indexed: 11/13/2022] Open
Abstract
Growing amount of evidence in the last two decades highlight that macroautophagy (generally referred to as autophagy) is not only indispensable for survival in yeast but also equally important to maintain cellular quality control in higher eukaryotes as well. Importantly, dysfunctional autophagy has been explicitly shown to be involved in various physiological and pathological conditions such as cell death, cancer, neurodegenerative, and other diseases. Therefore, modulation and regulation of the autophagy pathway has emerged as an alternative strategy for the treatment of various disease conditions in the recent years. Several studies have shown genetic or pharmacological modulation of autophagy to be effective in treating cancer, clearing intracellular aggregates and pathogens. Understanding and controlling the autophagic flux, either through a genetic or pharmacological approach is therefore a highly promising approach and of great scientific interest as spatiotemporal and cell-tissue-organ level autophagy regulation is not clearly understood. Indeed, chemical biology approaches that identify small molecule effectors of autophagy have thus a dual benefit: the modulators act as tools to study and understand the process of autophagy, and may also have therapeutic potential. In this review, we discuss different strategies that have appeared to screen and identify potent small molecule modulators of autophagy.
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Affiliation(s)
- Piyush Mishra
- Autophagy Lab, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Veena Ammanathan
- Autophagy Lab, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Ravi Manjithaya
- Autophagy Lab, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
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32
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Yi S, Varun BV, Choi Y, Park SB. A Brief Overview of Two Major Strategies in Diversity-Oriented Synthesis: Build/Couple/Pair and Ring-Distortion. Front Chem 2018; 6:507. [PMID: 30406085 PMCID: PMC6204370 DOI: 10.3389/fchem.2018.00507] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 10/03/2018] [Indexed: 12/13/2022] Open
Abstract
In the interdisciplinary research field of chemical biology and drug discovery, diversity-oriented synthesis (DOS) has become indispensable in the construction of novel small-molecule libraries rich in skeletal and stereochemical diversity. DOS aims to populate the unexplored chemical space with new potential bioactive molecules via forward synthetic analysis. Since the introduction of this concept by Schreiber, DOS has evolved along with many significant breakthroughs. It is therefore important to understand the key DOS strategies to build molecular diversity with maximized biological relevancy. Due to the length limitations of this mini review, we briefly discuss the recent DOS plans using build/couple/pair (B/C/P) and ring-distortion strategies for the synthesis of major biologically relevant target molecules like natural products and their related compounds, macrocycles, and privileged structures.
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Affiliation(s)
- Sihyeong Yi
- Department of Chemistry, CRI Center for Chemical Proteomics, Seoul National University, Seoul, South Korea
| | - Begur Vasanthkumar Varun
- Department of Chemistry, CRI Center for Chemical Proteomics, Seoul National University, Seoul, South Korea
| | - Yoona Choi
- Department of Chemistry, CRI Center for Chemical Proteomics, Seoul National University, Seoul, South Korea
| | - Seung Bum Park
- Department of Chemistry, CRI Center for Chemical Proteomics, Seoul National University, Seoul, South Korea
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Kidd SL, Osberger TJ, Mateu N, Sore HF, Spring DR. Recent Applications of Diversity-Oriented Synthesis Toward Novel, 3-Dimensional Fragment Collections. Front Chem 2018; 6:460. [PMID: 30386766 PMCID: PMC6198038 DOI: 10.3389/fchem.2018.00460] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 09/14/2018] [Indexed: 12/23/2022] Open
Abstract
Fragment-based drug discovery (FBDD) is a well-established approach for the discovery of novel medicines, illustrated by the approval of two FBBD-derived drugs. This methodology is based on the utilization of small "fragment" molecules (<300 Da) as starting points for drug discovery and optimization. Organic synthesis has been identified as a significant obstacle in FBDD, however, in particular owing to the lack of novel 3-dimensional (3D) fragment collections that feature useful synthetic vectors for modification of hit compounds. Diversity-oriented synthesis (DOS) is a synthetic strategy that aims to efficiently produce compound collections with high levels of structural diversity and three-dimensionality and is therefore well-suited for the construction of novel fragment collections. This Mini-Review highlights recent studies at the intersection of DOS and FBDD aiming to produce novel libraries of diverse, polycyclic, fragment-like compounds, and their application in fragment-based screening projects.
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Affiliation(s)
| | | | | | | | - David R. Spring
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
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34
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Chung KM, Hernández N, Sproul AA, Yu WH. Alzheimer's disease and the autophagic-lysosomal system. Neurosci Lett 2018; 697:49-58. [PMID: 29758300 DOI: 10.1016/j.neulet.2018.05.017] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 05/08/2018] [Accepted: 05/10/2018] [Indexed: 02/06/2023]
Abstract
Age-related neurodegenerative diseases are of critical concern to the general population and research/medical community due to their health impact and socioeconomic consequences. A feature of most, if not all, neurodegenerative disorders is the presence of proteinopathies, in which misfolded or conformationally altered proteins drive disease progression and are often used as a primary neuropathological marker of disease. In particular, Alzheimer's disease (AD) is characterized by abnormal accumulation of protein aggregates, primarily extracellular plaques composed of the Aβ peptide and intracellular tangles comprised of the tau protein, both of which may indicate a primary defect in protein clearance. Protein degradation is a key cellular mechanism for protein homeostasis and is essential for cell survival but is disrupted in neurodegenerative diseases. Dysregulation in proteolytic pathways - mainly the autophagic-lysosomal system (A-LS) and the ubiquitin-proteasome system (UPS) - has been increasingly associated with proteinopathies in neurodegenerative diseases. Here we review the role of dysfunctional autophagy underlying AD-related proteinopathy and discuss how to model this aspect of disease, as well as summarize recent advances in translational strategies for targeted A-LS dysfunction in AD.
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Affiliation(s)
- Kyung Min Chung
- Taub Institute and the Department of Pathology & Cell Biology, Columbia University, New York, NY, 10032, United States
| | - Nancy Hernández
- Taub Institute and the Department of Pathology & Cell Biology, Columbia University, New York, NY, 10032, United States
| | - Andrew A Sproul
- Taub Institute and the Department of Pathology & Cell Biology, Columbia University, New York, NY, 10032, United States
| | - Wai Haung Yu
- Taub Institute and the Department of Pathology & Cell Biology, Columbia University, New York, NY, 10032, United States.
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35
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Gerry CJ, Schreiber SL. Chemical probes and drug leads from advances in synthetic planning and methodology. Nat Rev Drug Discov 2018; 17:333-352. [PMID: 29651105 PMCID: PMC6707071 DOI: 10.1038/nrd.2018.53] [Citation(s) in RCA: 150] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Screening of small-molecule libraries is a productive method for identifying both chemical probes of disease-related targets and potential starting points for drug discovery. In this article, we focus on strategies such as diversity-oriented synthesis that aim to explore novel areas of chemical space efficiently by populating small-molecule libraries with compounds containing structural features that are typically under-represented in commercially available screening collections. Drawing from more than a decade's worth of examples, we highlight how the design and synthesis of such libraries have been enabled by modern synthetic chemistry, and we illustrate the impact of the resultant chemical probes and drug leads in a wide range of diseases.
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Affiliation(s)
- Christopher J Gerry
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- The Broad Institute of Harvard & MIT, Cambridge, MA, USA
| | - Stuart L Schreiber
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- The Broad Institute of Harvard & MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
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36
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Iron(III)-Tannic Molecular Nanoparticles Enhance Autophagy effect and T 1 MRI Contrast in Liver Cell Lines. Sci Rep 2018; 8:6647. [PMID: 29703912 PMCID: PMC5923259 DOI: 10.1038/s41598-018-25108-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 04/16/2018] [Indexed: 02/06/2023] Open
Abstract
Herein, a new molecular nanoparticle based on iron(III)-tannic complexes (Fe–TA NPs) is presented. The Fe–TA NPs were simply obtained by mixing the precursors in a buffered solution at room temperature, and they exhibited good physicochemical properties with capability of inducing autophagy in both hepatocellular carcinoma cells (HepG2.2.15) and normal rat hepatocytes (AML12). The Fe–TA NPs were found to induce HepG2.2.15 cell death via autophagic cell death but have no effect on cell viability in AML12 cells. This is possibly due to the much higher uptake of the Fe–TA NPs by the HepG2.2.15 cells via the receptor-mediated endocytosis pathway. As a consequence, enhancement of the T1 MRI contrast was clearly observed in the HepG2.2.15 cells. The results demonstrate that the Fe–TA NPs could provide a new strategy combining diagnostic and therapeutic functions for hepatocellular carcinoma. Additionally, because of their autophagy-inducing properties, they can be applied as autophagy enhancers for prevention and treatment of other diseases.
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37
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Lopes F, Keita ÅV, Saxena A, Reyes JL, Mancini NL, Al Rajabi A, Wang A, Baggio CH, Dicay M, van Dalen R, Ahn Y, Carneiro MBH, Peters NC, Rho JM, MacNaughton WK, Girardin SE, Jijon H, Philpott DJ, Söderholm JD, McKay DM. ER-stress mobilization of death-associated protein kinase-1-dependent xenophagy counteracts mitochondria stress-induced epithelial barrier dysfunction. J Biol Chem 2018; 293:3073-3087. [PMID: 29317503 DOI: 10.1074/jbc.ra117.000809] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 12/21/2017] [Indexed: 12/14/2022] Open
Abstract
The gut microbiome contributes to inflammatory bowel disease (IBD), in which bacteria can be present within the epithelium. Epithelial barrier function is decreased in IBD, and dysfunctional epithelial mitochondria and endoplasmic reticulum (ER) stress have been individually associated with IBD. We therefore hypothesized that the combination of ER and mitochondrial stresses significantly disrupt epithelial barrier function. Here, we treated human colonic biopsies, epithelial colonoids, and epithelial cells with an uncoupler of oxidative phosphorylation, dinitrophenol (DNP), with or without the ER stressor tunicamycin and assessed epithelial barrier function by monitoring internalization and translocation of commensal bacteria. We also examined barrier function and colitis in mice exposed to dextran sodium sulfate (DSS) or DNP and co-treated with DAPK6, an inhibitor of death-associated protein kinase 1 (DAPK1). Contrary to our hypothesis, induction of ER stress (i.e. the unfolded protein response) protected against decreased barrier function caused by the disruption of mitochondrial function. ER stress did not prevent DNP-driven uptake of bacteria; rather, specific mobilization of the ATF6 arm of ER stress and recruitment of DAPK1 resulted in enhanced autophagic killing (xenophagy) of bacteria. Of note, epithelia with a Crohn's disease-susceptibility mutation in the autophagy gene ATG16L1 exhibited less xenophagy. Systemic delivery of the DAPK1 inhibitor DAPK6 increased bacterial translocation in DSS- or DNP-treated mice. We conclude that promoting ER stress-ATF6-DAPK1 signaling in transporting enterocytes counters the transcellular passage of bacteria evoked by dysfunctional mitochondria, thereby reducing the potential for metabolic stress to reactivate or perpetuate inflammation.
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Affiliation(s)
- Fernando Lopes
- From the Gastrointestinal Research Group, Departments of Physiology and Pharmacology and
| | - Åsa V Keita
- the Department of Clinical and Experimental Medicine, Division of Surgery, Linköping University, Linköping 581 83, Sweden, and
| | - Alpana Saxena
- From the Gastrointestinal Research Group, Departments of Physiology and Pharmacology and
| | - Jose Luis Reyes
- From the Gastrointestinal Research Group, Departments of Physiology and Pharmacology and
| | - Nicole L Mancini
- From the Gastrointestinal Research Group, Departments of Physiology and Pharmacology and
| | - Ala Al Rajabi
- From the Gastrointestinal Research Group, Departments of Physiology and Pharmacology and
| | - Arthur Wang
- From the Gastrointestinal Research Group, Departments of Physiology and Pharmacology and
| | - Cristiane H Baggio
- From the Gastrointestinal Research Group, Departments of Physiology and Pharmacology and
| | - Michael Dicay
- From the Gastrointestinal Research Group, Departments of Physiology and Pharmacology and
| | - Rob van Dalen
- the Departments of Laboratory Medicine and Pathobiology and
| | - Younghee Ahn
- the Departments of Pediatrics, Clinical Neurosciences, and Physiology and Pharmacology and
| | - Matheus B H Carneiro
- the Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N4N1, Canada
| | - Nathan C Peters
- the Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N4N1, Canada
| | - Jong M Rho
- the Departments of Pediatrics, Clinical Neurosciences, and Physiology and Pharmacology and
| | - Wallace K MacNaughton
- From the Gastrointestinal Research Group, Departments of Physiology and Pharmacology and
| | | | - Humberto Jijon
- Medicine, Calvin, Joan, and Phoebe Snyder Institute for Chronic Diseases, and
| | - Dana J Philpott
- Immunology, University of Toronto, Toronto, Ontario M5S1A1, Canada
| | - Johan D Söderholm
- the Department of Clinical and Experimental Medicine, Division of Surgery, Linköping University, Linköping 581 83, Sweden, and
| | - Derek M McKay
- From the Gastrointestinal Research Group, Departments of Physiology and Pharmacology and
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38
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Crosstalk of Autophagy and the Secretory Pathway and Its Role in Diseases. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2018; 337:153-184. [DOI: 10.1016/bs.ircmb.2017.12.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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39
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Dysregulation of autophagy as a common mechanism in lysosomal storage diseases. Essays Biochem 2017; 61:733-749. [PMID: 29233882 PMCID: PMC5869865 DOI: 10.1042/ebc20170055] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 10/08/2017] [Accepted: 10/12/2017] [Indexed: 12/19/2022]
Abstract
The lysosome plays a pivotal role between catabolic and anabolic processes as the nexus for signalling pathways responsive to a variety of factors, such as growth, nutrient availability, energetic status and cellular stressors. Lysosomes are also the terminal degradative organelles for autophagy through which macromolecules and damaged cellular components and organelles are degraded. Autophagy acts as a cellular homeostatic pathway that is essential for organismal physiology. Decline in autophagy during ageing or in many diseases, including late-onset forms of neurodegeneration is considered a major contributing factor to the pathology. Multiple lines of evidence indicate that impairment in autophagy is also a central mechanism underlying several lysosomal storage disorders (LSDs). LSDs are a class of rare, inherited disorders whose histopathological hallmark is the accumulation of undegraded materials in the lysosomes due to abnormal lysosomal function. Inefficient degradative capability of the lysosomes has negative impact on the flux through the autophagic pathway, and therefore dysregulated autophagy in LSDs is emerging as a relevant disease mechanism. Pathology in the LSDs is generally early-onset, severe and life-limiting but current therapies are limited or absent; recognizing common autophagy defects in the LSDs raises new possibilities for therapy. In this review, we describe the mechanisms by which LSDs occur, focusing on perturbations in the autophagy pathway and present the latest data supporting the development of novel therapeutic approaches related to the modulation of autophagy.
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40
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Johnson BG, Dang LT, Marsh G, Roach AM, Levine ZG, Monti A, Reyon D, Feigenbaum L, Duffield JS. Uromodulin p.Cys147Trp mutation drives kidney disease by activating ER stress and apoptosis. J Clin Invest 2017; 127:3954-3969. [PMID: 28990932 DOI: 10.1172/jci93817] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 08/24/2017] [Indexed: 12/13/2022] Open
Abstract
Uromodulin-associated kidney disease (UAKD) is caused by mutations in the uromodulin (UMOD) gene that result in a misfolded form of UMOD protein, which is normally secreted by nephrons. In UAKD patients, mutant UMOD is poorly secreted and accumulates in the ER of distal kidney epithelium, but its role in disease progression is largely unknown. Here, we modeled UMOD accumulation in mice by expressing the murine equivalent of the human UMOD p.Cys148Trp point mutation (UmodC147W/+ mice). Like affected humans, these UmodC147W/+ mice developed spontaneous and progressive kidney disease with organ failure over 24 weeks. Analysis of diseased kidneys and purified UMOD-producing cells revealed early activation of the PKR-like ER kinase/activating transcription factor 4 (PERK/ATF4) ER stress pathway, innate immune mediators, and increased apoptotic signaling, including caspase-3 activation. Unexpectedly, we also detected autophagy deficiency. Human cells expressing UMOD p.Cys147Trp recapitulated the findings in UmodC147W/+ mice, and autophagy activation with mTOR inhibitors stimulated the intracellular removal of aggregated mutant UMOD. Human cells producing mutant UMOD were susceptible to TNF-α- and TRAIL-mediated apoptosis due to increased expression of the ER stress mediator tribbles-3. Blocking TNF-α in vivo with the soluble recombinant fusion protein TNFR:Fc slowed disease progression in UmodC147W/+ mice by reducing active caspase-3, thereby preventing tubule cell death and loss of epithelial function. These findings reveal a targetable mechanism for disease processes involved in UAKD.
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Affiliation(s)
- Bryce G Johnson
- Research and Development, Biogen, Cambridge, Massachusetts, USA.,Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Lan T Dang
- Research and Development, Biogen, Cambridge, Massachusetts, USA
| | - Graham Marsh
- Research and Development, Biogen, Cambridge, Massachusetts, USA
| | - Allie M Roach
- Research and Development, Biogen, Cambridge, Massachusetts, USA.,Department of Medicine, University of Washington, Seattle, Washington, USA
| | | | - Anthony Monti
- Research and Development, Biogen, Cambridge, Massachusetts, USA
| | - Deepak Reyon
- Research and Development, Biogen, Cambridge, Massachusetts, USA
| | | | - Jeremy S Duffield
- Research and Development, Biogen, Cambridge, Massachusetts, USA.,Department of Medicine, University of Washington, Seattle, Washington, USA.,Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
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41
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Byun S, Lee E, Lee KW. Therapeutic Implications of Autophagy Inducers in Immunological Disorders, Infection, and Cancer. Int J Mol Sci 2017; 18:ijms18091959. [PMID: 28895911 PMCID: PMC5618608 DOI: 10.3390/ijms18091959] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/10/2017] [Accepted: 09/11/2017] [Indexed: 12/19/2022] Open
Abstract
Autophagy is an essential catabolic program that forms part of the stress response and enables cells to break down their own intracellular components within lysosomes for recycling. Accumulating evidence suggests that autophagy plays vital roles in determining pathological outcomes of immune responses and tumorigenesis. Autophagy regulates innate and adaptive immunity affecting the pathologies of infectious, inflammatory, and autoimmune diseases. In cancer, autophagy appears to play distinct roles depending on the context of the malignancy by either promoting or suppressing key determinants of cancer cell survival. This review covers recent developments in the understanding of autophagy and discusses potential therapeutic interventions that may alter the outcomes of certain diseases.
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Affiliation(s)
- Sanguine Byun
- Division of Bioengineering, Incheon National University, Incheon 22012, Korea.
| | - Eunjung Lee
- Traditional Alcoholic Beverage Research Team, Korea Food Research Institute, Seongnam 13539, Korea.
| | - Ki Won Lee
- Advanced Institutes of Convergence Technology, Seoul National University, Suwon 16495, Korea.
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.
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42
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Ramesh N, Pandey UB. Autophagy Dysregulation in ALS: When Protein Aggregates Get Out of Hand. Front Mol Neurosci 2017; 10:263. [PMID: 28878620 PMCID: PMC5572252 DOI: 10.3389/fnmol.2017.00263] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 08/03/2017] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder that results from the loss of upper and lower motor neurons. One of the key pathological hallmarks in diseased neurons is the mislocalization of disease-associated proteins and the formation of cytoplasmic aggregates of these proteins and their interactors due to defective protein quality control. This apparent imbalance in the cellular protein homeostasis could be a crucial factor in causing motor neuron death in the later stages of the disease in patients. Autophagy is a major protein degradation pathway that is involved in the clearance of protein aggregates and damaged organelles. Abnormalities in autophagy have been observed in numerous neurodegenerative disorders, including ALS. In this review, we discuss the contribution of autophagy dysfunction in various in vitro and in vivo models of ALS. Furthermore, we examine the crosstalk between autophagy and other cellular stresses implicated in ALS pathogenesis and the therapeutic implications of regulating autophagy in ALS.
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Affiliation(s)
- Nandini Ramesh
- Department of Human Genetics, University of Pittsburgh Graduate School of Public HealthPittsburgh, PA, United States.,Division of Child Neurology, Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical CenterPittsburgh, PA, United States
| | - Udai Bhan Pandey
- Department of Human Genetics, University of Pittsburgh Graduate School of Public HealthPittsburgh, PA, United States.,Division of Child Neurology, Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical CenterPittsburgh, PA, United States.,Department of Neurology, University of Pittsburgh School of MedicinePittsburgh, PA, United States
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43
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Mishra P, Dauphinee AN, Ward C, Sarkar S, Gunawardena AHLAN, Manjithaya R. Discovery of pan autophagy inhibitors through a high-throughput screen highlights macroautophagy as an evolutionarily conserved process across 3 eukaryotic kingdoms. Autophagy 2017; 13:1556-1572. [PMID: 28792845 PMCID: PMC5612355 DOI: 10.1080/15548627.2017.1339002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Due to the involvement of macroautophagy/autophagy in different pathophysiological conditions such as infections, neurodegeneration and cancer, identification of novel small molecules that modulate the process is of current research and clinical interest. In this work, we developed a luciferase-based sensitive and robust kinetic high-throughput screen (HTS) of small molecules that modulate autophagic degradation of peroxisomes in the budding yeast Saccharomyces cerevisiae. Being a pathway-specific rather than a target-driven assay, we identified small molecule modulators that acted at key steps of autophagic flux. Two of the inhibitors, Bay11 and ZPCK, obtained from the screen were further characterized using secondary assays in yeast. Bay11 inhibited autophagy at a step before fusion with the vacuole whereas ZPCK inhibited the cargo degradation inside the vacuole. Furthermore, we demonstrated that these molecules altered the process of autophagy in mammalian cells as well. Strikingly, these molecules also modulated autophagic flux in a novel model plant, Aponogeton madagascariensis. Thus, using small molecule modulators identified by using a newly developed HTS autophagy assay, our results support that macroautophagy is a conserved process across fungal, animal and plant kingdoms.
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Affiliation(s)
- Piyush Mishra
- a Molecular Biology and Genetics Unit , Jawaharlal Nehru Centre for Advanced Scientific Research , Jakkur, Bangalore , India
| | - Adrian N Dauphinee
- b Biology Department, Life Sciences Centre , Dalhousie University , Halifax , NS , Canada
| | - Carl Ward
- c Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences , University of Birmingham , Edgbaston, Birmingham , UK
| | - Sovan Sarkar
- c Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences , University of Birmingham , Edgbaston, Birmingham , UK
| | | | - Ravi Manjithaya
- a Molecular Biology and Genetics Unit , Jawaharlal Nehru Centre for Advanced Scientific Research , Jakkur, Bangalore , India
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44
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Hwang HY, Cho SM, Kwon HJ. Approaches for discovering novel bioactive small molecules targeting autophagy. Expert Opin Drug Discov 2017; 12:909-923. [PMID: 28758515 DOI: 10.1080/17460441.2017.1349751] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION In recent years, development of novel bioactive small molecules targeting autophagy has been implicated for autophagy-related disease treatment. Screening new small molecules regulating autophagy allows for the discovery of novel autophagy machinery and therapeutic agents. Areas covered: Two major screening methods for novel autophagy modulators are introduced in this review, namely target based screening and phenotype based screening. With increasing attention focused on chemical compound libraries, coupled with the development of new assay systems, this review attempts to provide an efficient strategy to explore autophagy biology and discover small molecules for the treatment of autophagy-related diseases. Expert opinion: Adopting an appropriate autophagy screening strategy is important for developing small molecules capable of treating neurodegenerative diseases and cancers. Phenotype based screening and target based screening were both used for developing effective small molecules. However, each of these methods has many pros and cons. An efficient approach is suggested to screen for novel lead compounds targeting autophagy, which could provide new hits with better efficiency and rapidity.
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Affiliation(s)
- Hui-Yun Hwang
- a Chemical Genomics Global Research Laboratory, Department of Biotechnology, College of Life Science and Biotechnology , Yonsei University , Seoul , Republic of Korea
| | - Sung Min Cho
- a Chemical Genomics Global Research Laboratory, Department of Biotechnology, College of Life Science and Biotechnology , Yonsei University , Seoul , Republic of Korea
| | - Ho Jeong Kwon
- a Chemical Genomics Global Research Laboratory, Department of Biotechnology, College of Life Science and Biotechnology , Yonsei University , Seoul , Republic of Korea
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45
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Rabenstein M, Peter F, Joost S, Trilck M, Rolfs A, Frech MJ. Decreased calcium flux in Niemann-Pick type C1 patient-specific iPSC-derived neurons due to higher amount of calcium-impermeable AMPA receptors. Mol Cell Neurosci 2017; 83:27-36. [PMID: 28666962 DOI: 10.1016/j.mcn.2017.06.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 06/08/2017] [Accepted: 06/25/2017] [Indexed: 01/31/2023] Open
Abstract
Niemann-Pick disease type C1 (NPC1) is a rare progressive neurodegenerative disorder caused by mutations in the NPC1 gene, resulting mainly in the accumulation of cholesterol and the ganglioside GM2. Recently, we described accumulations of these lipids in neuronal differentiated cells derived from NPC1 patient-specific induced pluripotent stem cells (iPSCs). As these lipids are essential for proper cell membrane composition, we were interested in the expression and function of voltage-gated ion channels and excitatory AMPA receptors (AMPARs) in neurons derived from three patient-specific iPSC lines. By means of patch clamp recordings and microfluorimetric measurements of calcium (Ca2+), we examined the expression of voltage-gated ion channels and AMPARs. Cells of the three used cell lines carrying the c.1836A>C/c.1628delC, the c.1180T>C or the c.3182T>C mutation demonstrated a significantly reduced AMPA-induced Ca2+-influx, suggesting an altered expression profile of these receptors. RT-qPCR revealed a significant upregulation of mRNA for the AMPA receptor subunits GluA1 and GluA2 and western blot analysis showed increased protein level of GluA2. Thus, we conclude that the observed reduced Ca2+-influx is based on an increase of GluA2 containing Ca2+-impermeable AMPARs. An attenuated function of GluRs in neurons potentially contributes to the progressive neurodegeneration observed in NPC1 and might represent an objective in regard of the development of new therapeutic approaches in NPC1.
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Affiliation(s)
- Michael Rabenstein
- Albrecht-Kossel-Institute for Neuroregeneration (AKos), University Medicine Rostock, Gehlsheimer Straße 20, D-18147 Rostock, Germany.
| | - Franziska Peter
- Albrecht-Kossel-Institute for Neuroregeneration (AKos), University Medicine Rostock, Gehlsheimer Straße 20, D-18147 Rostock, Germany.
| | - Sarah Joost
- Albrecht-Kossel-Institute for Neuroregeneration (AKos), University Medicine Rostock, Gehlsheimer Straße 20, D-18147 Rostock, Germany.
| | - Michaela Trilck
- Albrecht-Kossel-Institute for Neuroregeneration (AKos), University Medicine Rostock, Gehlsheimer Straße 20, D-18147 Rostock, Germany.
| | - Arndt Rolfs
- Albrecht-Kossel-Institute for Neuroregeneration (AKos), University Medicine Rostock, Gehlsheimer Straße 20, D-18147 Rostock, Germany.
| | - Moritz J Frech
- Albrecht-Kossel-Institute for Neuroregeneration (AKos), University Medicine Rostock, Gehlsheimer Straße 20, D-18147 Rostock, Germany.
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46
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Pharmacological modulation of autophagy: therapeutic potential and persisting obstacles. Nat Rev Drug Discov 2017; 16:487-511. [PMID: 28529316 DOI: 10.1038/nrd.2017.22] [Citation(s) in RCA: 600] [Impact Index Per Article: 85.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Autophagy is central to the maintenance of organismal homeostasis in both physiological and pathological situations. Accordingly, alterations in autophagy have been linked to clinically relevant conditions as diverse as cancer, neurodegeneration and cardiac disorders. Throughout the past decade, autophagy has attracted considerable attention as a target for the development of novel therapeutics. However, such efforts have not yet generated clinically viable interventions. In this Review, we discuss the therapeutic potential of autophagy modulators, analyse the obstacles that have limited their development and propose strategies that may unlock the full therapeutic potential of autophagy modulation in the clinic.
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47
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Matalonga L, Gort L, Ribes A. Small molecules as therapeutic agents for inborn errors of metabolism. J Inherit Metab Dis 2017; 40:177-193. [PMID: 27966099 DOI: 10.1007/s10545-016-0005-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 11/22/2016] [Accepted: 11/23/2016] [Indexed: 01/03/2023]
Abstract
Most inborn errors of metabolism (IEM) remain without effective treatment mainly due to the incapacity of conventional therapeutic approaches to target the neurological symptomatology and to ameliorate the multisystemic involvement frequently observed in these patients. However, in recent years, the therapeutic use of small molecules has emerged as a promising approach for treating this heterogeneous group of disorders. In this review, we focus on the use of therapeutically active small molecules to treat IEM, including readthrough agents, pharmacological chaperones, proteostasis regulators, substrate inhibitors, and autophagy inducers. The small molecules reviewed herein act at different cellular levels, and this knowledge provides new tools to set up innovative treatment approaches for particular IEM. We review the molecular mechanism underlying therapeutic properties of small molecules, methodologies used to screen for these compounds, and their applicability in preclinical and clinical practice.
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Affiliation(s)
- Leslie Matalonga
- Secció Errors Congènits del Metabolisme-IBC. Servei de Bioquímica i Genètica Molecular, Hospital Clínic, CIBERER-U737; IDIBAPS, C/ Mejía Lequerica s/n, 08028, Barcelona, Spain.
| | - Laura Gort
- Secció Errors Congènits del Metabolisme-IBC. Servei de Bioquímica i Genètica Molecular, Hospital Clínic, CIBERER-U737; IDIBAPS, C/ Mejía Lequerica s/n, 08028, Barcelona, Spain
| | - Antonia Ribes
- Secció Errors Congènits del Metabolisme-IBC. Servei de Bioquímica i Genètica Molecular, Hospital Clínic, CIBERER-U737; IDIBAPS, C/ Mejía Lequerica s/n, 08028, Barcelona, Spain
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Cuív PÓ, Begun J, Keely S, Lewindon PJ, Morrison M. Towards an integrated understanding of the therapeutic utility of exclusive enteral nutrition in the treatment of Crohn's disease. Food Funct 2017; 7:1741-51. [PMID: 26948398 DOI: 10.1039/c5fo01196e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Crohn's disease (CD) is a chronic disease characterized by episodic and disabling inflammation of the gastrointestinal tract in genetically susceptible individuals. The incidence and prevalence of CD is rising rapidly across the world emphasising that disease risk is also influenced by environmental and lifestyle factors, as well as the microbial community resident in the gut. Childhood-onset CD is associated with an aggressive disease course that can adversely impact patient growth and development. There is no cure for CD however new onset and recurrent cases of paediatric CD are often responsive to exclusive enteral nutrition (EEN) treatment. EEN treatment involves the exclusive consumption of an elemental or polymeric formula for several weeks and it is well established as a primary intervention strategy. EEN treatments typically achieve remission rates of over 80% and importantly they are associated with a high rate of mucosal healing, far superior to steroids, which is prognostic of improved long-term health outcomes. Furthermore, they are safe, have few side effects, and improve nutritional status and linear growth. Surprisingly, despite the utility of EEN our understanding of the host-microbe-diet interactions that underpin clinical remission and mucosal healing are limited. Here, we review the current state of knowledge and propose that the induction of autophagy, in addition to modulation of the microbiota and coordinated effects on inflammation and epithelial cell biology, may be critical for the therapeutic effects associated with EEN. A better understanding of EEN treatment will provide new opportunities to restore gut homeostasis and prolong periods of remission, as well as provide new insights into the factors that trigger and perhaps prevent CD.
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Affiliation(s)
- Páraic Ó Cuív
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia.
| | - Jakob Begun
- Mater Research Institute, The University of Queensland, Brisbane, QLD 4102, Australia and School of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia and Department of Gastroenterology, Mater Health Services, Brisbane, Australia
| | - Simon Keely
- School of Biomedical Science and Pharmacy, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia and Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia
| | - Peter J Lewindon
- The University of Queensland, Department of Paediatrics and Child Health, Lady Cilento Children's Hospital, QLD 4101, Australia
| | - Mark Morrison
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD 4102, Australia.
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Anti-infective Activity of 2-Cyano-3-Acrylamide Inhibitors with Improved Drug-Like Properties against Two Intracellular Pathogens. Antimicrob Agents Chemother 2016; 60:4183-96. [PMID: 27139470 DOI: 10.1128/aac.03021-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 04/24/2016] [Indexed: 12/17/2022] Open
Abstract
Due to the rise of antibiotic resistance and the small number of effective antiviral drugs, new approaches for treating infectious diseases are urgently needed. Identifying targets for host-based therapies represents an emerging strategy for drug discovery. The ubiquitin-proteasome system is a central mode of signaling in the eukaryotic cell and may be a promising target for therapies that bolster the host's ability to control infection. Deubiquitinase (DUB) enzymes are key regulators of the host inflammatory response, and we previously demonstrated that a selective DUB inhibitor and its derivative promote anti-infective activities in host cells. To find compounds with anti-infective efficacy but improved toxicity profiles, we tested a library of predominantly 2-cyano-3-acrylamide small-molecule DUB inhibitors for anti-infective activity in macrophages against two intracellular pathogens: murine norovirus (MNV) and Listeria monocytogenes We identified compound C6, which inhibited DUB activity in human and murine cells and reduced intracellular replication of both pathogens with minimal toxicity in cell culture. Treatment with C6 did not significantly affect the ability of macrophages to internalize virus, suggesting that the anti-infective activity interferes with postentry stages of the MNV life cycle. Metabolic stability and pharmacokinetic assays showed that C6 has a half-life in mouse liver microsomes of ∼20 min and has a half-life of approximately 4 h in mice when administered intravenously. Our results provide a framework for targeting the host ubiquitin system in the development of host-based therapies for infectious disease. Compound C6 represents a promising tool with which to elucidate the role of DUBs in the macrophage response to infection.
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Ward C, Martinez-Lopez N, Otten EG, Carroll B, Maetzel D, Singh R, Sarkar S, Korolchuk VI. Autophagy, lipophagy and lysosomal lipid storage disorders. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1861:269-84. [DOI: 10.1016/j.bbalip.2016.01.006] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 01/07/2016] [Accepted: 01/12/2016] [Indexed: 12/30/2022]
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