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Senavirathna L, Hasapes C, Chen R, Pan S. Accumulation of Intracellular Protein Advanced Glycation End Products Alters Cellular Homeostasis for Protein Clearance in Pancreatic Ductal Epithelial Cells. Biochemistry 2024; 63:1723-1729. [PMID: 38941592 DOI: 10.1021/acs.biochem.4c00250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Protein advanced glycation end products (AGEs) can be formed via nonenzymatic glycation and accumulated intracellularly to disrupt cellular homeostasis for protein clearance. Here, we investigated the formation particulars of intracellular protein AGEs and sought to elucidate the molecular events implicated in the impact of cellular clearance systems. The formation and accumulation of intracellular protein AGEs increased protein aggregation and protease resistance, potentially overwhelming the ubiquitin-proteasome system (UPS). At high levels of protein AGEs, the abundance of many E3 ligases decreased and the overall ubiquitination level was reduced, all of which indicated decreased UPS activity. On the other hand, autophagy activity was stimulated, as evidenced by the upregulation of autophagy marker LC3II and important proteins in autophagosome and autolysosome formation, as well as downregulation of mTOR. Understanding the functional impacts of intracellular protein AGEs on the UPS and autophagy could pave the way for the future development of pharmaceutical agents targeting AGE-related diseases.
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Affiliation(s)
| | | | - Ru Chen
- Department of Medicine, Baylor College of Medicine, Houston, Texas 77030, United States
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2
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Chin MY, Espinosa JA, Pohan G, Markossian S, Arkin MR. Reimagining dots and dashes: Visualizing structure and function of organelles for high-content imaging analysis. Cell Chem Biol 2021; 28:320-337. [PMID: 33600764 PMCID: PMC7995685 DOI: 10.1016/j.chembiol.2021.01.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/18/2020] [Accepted: 01/20/2021] [Indexed: 12/16/2022]
Abstract
Organelles are responsible for biochemical and cellular processes that sustain life and their dysfunction causes diseases from cancer to neurodegeneration. While researchers are continuing to appreciate new roles of organelles in disease, the rapid development of specifically targeted fluorescent probes that report on the structure and function of organelles will be critical to accelerate drug discovery. Here, we highlight four organelles that collectively exemplify the progression of phenotypic discovery, starting with mitochondria, where many functional probes have been described, then continuing with lysosomes and Golgi and concluding with nascently described membraneless organelles. We introduce emerging probe designs to explore organelle-specific morphology and dynamics and highlight recent case studies using high-content analysis to stimulate further development of probes and approaches for organellar high-throughput screening.
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Affiliation(s)
- Marcus Y Chin
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA
| | - Jether Amos Espinosa
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA
| | - Grace Pohan
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA
| | - Sarine Markossian
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA
| | - Michelle R Arkin
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA.
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3
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Liu PF, Farooqi AA, Peng SY, Yu TJ, Dahms HU, Lee CH, Tang JY, Wang SC, Shu CW, Chang HW. Regulatory effects of noncoding RNAs on the interplay of oxidative stress and autophagy in cancer malignancy and therapy. Semin Cancer Biol 2020; 83:269-282. [PMID: 33127466 DOI: 10.1016/j.semcancer.2020.10.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/15/2020] [Accepted: 10/18/2020] [Indexed: 12/15/2022]
Abstract
Noncoding RNAs (ncRNAs) regulation of various diseases including cancer has been extensively studied. Reactive oxidative species (ROS) elevated by oxidative stress are associated with cancer progression and drug resistance, while autophagy serves as an ROS scavenger in cancer cells. However, the regulatory effects of ncRNAs on autophagy and ROS in various cancer cells remains complex. Here, we explore how currently investigated ncRNAs, mainly miRNAs and lncRNAs, are involved in ROS production through modulating antioxidant genes. The regulatory effects of miRNAs and lncRNAs on autophagy-related (ATG) proteins to control autophagy activity in cancer cells are discussed. Moreover, differential expression of ncRNAs in tumor and normal tissues of cancer patients are further analyzed using The Cancer Genome Atlas (TCGA) database. This review hypothesizes links between ATG genes- or antioxidant genes-modulated ncRNAs and ROS production, which might result in tumorigenesis, malignancy, and cancer recurrence. A better understanding of the regulation of ROS and autophagy by ncRNAs might advance the use of ncRNAs as diagnostic and prognostic markers as well as therapeutic targets in cancer therapy.
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Affiliation(s)
- Pei-Feng Liu
- Department of Biomedical Science and Environmental Biology, PhD Program in Life Science, College of Life Science, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Center for Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan; Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan.
| | - Ammad Ahmad Farooqi
- Department of Molecular Oncology, Institute of Biomedical and Genetic Engineering (IBGE), Islamabad, Pakistan.
| | - Sheng-Yao Peng
- Department of Biomedical Science and Environmental Biology, PhD Program in Life Science, College of Life Science, Kaohsiung Medical University, Kaohsiung, Taiwan.
| | - Tzu-Jung Yu
- Graduate Institute of Natural Products, Kaohsiung Medical University, Kaohsiung, Taiwan.
| | - Hans-Uwe Dahms
- Department of Biomedical Science and Environmental Biology, PhD Program in Life Science, College of Life Science, Kaohsiung Medical University, Kaohsiung, Taiwan; Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung 80424, Taiwan.
| | - Cheng-Hsin Lee
- Department of Biomedical Science and Environmental Biology, PhD Program in Life Science, College of Life Science, Kaohsiung Medical University, Kaohsiung, Taiwan.
| | - Jen-Yang Tang
- Department of Radiation Oncology, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Radiation Oncology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.
| | - Sheng-Chieh Wang
- Department of Biomedical Science and Environmental Biology, PhD Program in Life Science, College of Life Science, Kaohsiung Medical University, Kaohsiung, Taiwan.
| | - Chih-Wen Shu
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan; Institute of Biopharmaceutical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan.
| | - Hsueh-Wei Chang
- Department of Biomedical Science and Environmental Biology, PhD Program in Life Science, College of Life Science, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Center for Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan; Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.
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Shi Y, Yang X, Xue X, Sun D, Cai P, Song Q, Zhang B, Qin L. HANR Enhances Autophagy-Associated Sorafenib Resistance Through miR-29b/ATG9A Axis in Hepatocellular Carcinoma. Onco Targets Ther 2020; 13:2127-2137. [PMID: 32210579 PMCID: PMC7069583 DOI: 10.2147/ott.s229913] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 12/12/2019] [Indexed: 12/15/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide and chemoresistance is the main obstacle for effective treatments of HCC. Accumulating studies indicated that long non-coding RNAs (lncRNAs) contribute to the chemoresistance of human carcinoma. However, the functional role of HANR in autophagy-mediated chemoresistance of HCC is unknown. Methods The expressions of HANR, miR-29b and ATG9A in tissues and cell lines were detected by real-time quantitative PCR (RT-qPCR). The expression of autophagy-related protein LC3-I and LC3-II was evaluated by Western blotting. The cell viability and apoptosis were examined by CCK-8 and flow cytometry, respectively. Bioinformatics analysis and luciferase activity assay were applied to determine the downstream target gene of HANR or miR-29b. Xenograft experiment was used to detect the effect of HANR on tumor growth. Results In the present study, we demonstrated that HANR was notably overexpressed in sorafenib-resistant HepG2 (HepG2/sora) and sorafenib-resistant Huh7 (Huh7/sora) cells, and HANR enhanced sorafenib resistance by facilitating autophagy in HepG2/sora and Huh7/sora cells. Furthermore, we demonstrated that miR‑29b could directly interact with HANR and abolished HANR-induced sorafenib resistance by suppressing autophagy in HepG2/sora and Huh7/sora cells. Moreover, ATG9A was validated as a target of miR-29b and its overexpression obviously reversed the inhibitory effect of miR-29b on sorafenib resistance and autophagy. In addition, HANR could act as a competing endogenous RNA (ceRNA) to upregulate ATG9A expression by sponging miR-29b. Hence, HANR increased autophagy-related sorafenib resistance via inhibiting the miR-29b/ATG9A axis in HepG2/sora and Huh7/sora cells, indicating that it may be a potential target to prevent chemoresistance of HCC. Conclusion Our study revealed HANR enhanced sorafenib resistance by acting as an autophagy promoter by regulating miR-29b/ATG9A axis in sorafenib‑resistant HCC cells and might provide potential therapeutic strategies for HCC treatment.
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Affiliation(s)
- Yang Shi
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China
| | - Xiaohua Yang
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China
| | - Xiaofeng Xue
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China
| | - Ding Sun
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China
| | - Peng Cai
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, People's Republic of China
| | - Qingwei Song
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, People's Republic of China
| | - Bin Zhang
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, People's Republic of China
| | - Lei Qin
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China
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Targeting ATG4 in Cancer Therapy. Cancers (Basel) 2019; 11:cancers11050649. [PMID: 31083460 PMCID: PMC6562779 DOI: 10.3390/cancers11050649] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/06/2019] [Accepted: 05/08/2019] [Indexed: 12/30/2022] Open
Abstract
Autophagy is a lysosome-mediated degradation pathway that enables the degradation and recycling of cytoplasmic components to sustain metabolic homoeostasis. Recently, autophagy has been reported to have an astonishing number of connections to cancer, as tumor cells require proficient autophagy in response to metabolic and therapeutic stresses to sustain cell proliferation. Autophagy-related gene 4 (ATG4) is essential for autophagy by affecting autophagosome formation through processing full-length microtubule-associated protein 1A/1B-light chain 3 (pro-LC3) and lipidated LC3. An increasing amount of evidence suggests that ATG4B expression is elevated in certain types of cancer, implying that ATG4B is a potential anticancer target. In this review, we address the central roles of ATG4B in the autophagy machinery and in targeted cancer therapy. Specifically, we discuss how pharmacologically inhibiting ATG4B can benefit cancer therapies.
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6
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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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Wehbe M, Leung AWY, Abrams MJ, Orvig C, Bally MB. A Perspective - can copper complexes be developed as a novel class of therapeutics? Dalton Trans 2018; 46:10758-10773. [PMID: 28702645 DOI: 10.1039/c7dt01955f] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Although copper-ligand complexes appear to be promising as a new class of therapeutics, other than the family of copper(ii) coordination compounds referred to as casiopeínas these compounds have yet to reach the clinic for human use. The pharmaceutical challenges associated with developing copper-based therapeutics will be presented in this article along with a discussion of the potential for high-throughput chemistry, computer-aided drug design, and nanotechnology to address the development of this important class of drug candidates.
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Affiliation(s)
- Mohamed Wehbe
- Experimental Therapeutics, British Columbia Cancer Agency, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada.
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Zhang XM, An DQ, Guo LL, Yang NH, Zhang H. Identification and screening of active components from Ziziphora clinopodioides Lam. in regulating autophagy. Nat Prod Res 2018; 33:2549-2553. [PMID: 29614870 DOI: 10.1080/14786419.2018.1452002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This study investigated the flavonoid constituents of a traditional Chinese medical plant Ziziphora clinopodioides Lam. by using ultra-performance liquid chromatography coupled with quadruple time-of-flight mass spectrometry and screened the active components in regulating autophagy.Normal rat kidney (NRK) cells transfected with green fluorescent protein- microtubule-associated protein 1 light Chain 3(GFP-LC3) were treated with Z. clinopodioides flavonoids and its chemical compositions. After 4 h of treatment, the auto-phagy spot aggregation in NRK cells was photographed and observed by laser scanning confocal microscopy. The following 10 flavonoid components of Z. clinopodioides were identified: baicalein(1), quercetin(2), hyperoside(3), quercetin3-O-β-d-glucopyranoside(4), apigenin(5), kaempferol(6), chrysin(7), diosimin(8), linarin(9) and rutin(10). Among these flavonoids, chrysin, apigenin and quercetin were identified as the active principles in activating autophagy. This research may provide a reference for further developing and utilizing Z. clinopodioides.
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Affiliation(s)
- Xuan-Ming Zhang
- a College of TCM , Xinjiang Medical University , Urumqi , China.,b Department of TCM , The First Affiliated Hospital of the Medical College, Shihezi University , Shihezi , China
| | - Dong-Qing An
- a College of TCM , Xinjiang Medical University , Urumqi , China.,c Xinjiang Key Laboratory of Famous Prescription and Science of Formulas , Xinjiang , China
| | - Long-Long Guo
- a College of TCM , Xinjiang Medical University , Urumqi , China
| | - Ning-Hui Yang
- a College of TCM , Xinjiang Medical University , Urumqi , China
| | - Hua Zhang
- a College of TCM , Xinjiang Medical University , Urumqi , China
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9
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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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Chinchwadkar S, Padmanabhan S, Mishra P, Singh S, Suresh SN, Vats S, Barve G, Ammanathan V, Manjithaya R. Multifaceted Housekeeping Functions of Autophagy. J Indian Inst Sci 2017. [DOI: 10.1007/s41745-016-0015-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Abstract
While only one Atg4 is present in yeast, there are four Atg4 homologues in human and in mouse with different substrate specificities and catalytic efficiencies. The molecule Atg4 is a type of cysteine protease, and is known for its crucial roles in cleavage of the Atg8 family proteins before they can be conjugated to phospholipids, and also in cleavage of the conjugated Atg8 molecules from the membrane, a process known as deconjugation. Both processes are required for the maximal efficiency in autophagosome biogenesis. Atg4 could thus be a target for intervention of the autophagy process. It is thus important to measure Atg4 activity to determine and to modulate the autophagy function. Here, we review the catalytic functions and regulatory mechanisms of human Atg4 proteases and discuss the methodology for analyzing Atg4 activity in details.
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Affiliation(s)
- M Li
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China.
| | - Y Fu
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Z Yang
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - X-M Yin
- Indiana University School of Medicine, Indianapolis, IN, United States.
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12
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Brown AS, Kong SW, Kohane IS, Patel CJ. ksRepo: a generalized platform for computational drug repositioning. BMC Bioinformatics 2016; 17:78. [PMID: 26860211 PMCID: PMC4746802 DOI: 10.1186/s12859-016-0931-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 01/29/2016] [Indexed: 01/22/2023] Open
Abstract
Background Repositioning approved drug and small molecules in novel therapeutic areas is of key interest to the pharmaceutical industry. A number of promising computational techniques have been developed to aid in repositioning, however, the majority of available methodologies require highly specific data inputs that preclude the use of many datasets and databases. There is a clear unmet need for a generalized methodology that enables the integration of multiple types of both gene expression data and database schema. Results ksRepo eliminates the need for a single microarray platform as input and allows for the use of a variety of drug and chemical exposure databases. We tested ksRepo’s performance on a set of five prostate cancer datasets using the Comparative Toxicogenomics Database (CTD) as our database of gene-compound interactions. ksRepo successfully predicted significance for five frontline prostate cancer therapies, representing a significant enrichment from over 7000 CTD compounds, and achieved specificity similar to other repositioning methods. Conclusions We present ksRepo, which enables investigators to use any data inputs for computational drug repositioning. ksRepo is implemented in a series of four functions in the R statistical environment under a BSD3 license. Source code is freely available at http://github.com/adam-sam-brown/ksRepo. A vignette is provided to aid users in performing ksRepo analysis.
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Affiliation(s)
- Adam S Brown
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA.
| | - Sek Won Kong
- Boston Children's Hospital, Boston, MA, 02115, USA.
| | - Isaac S Kohane
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA.
| | - Chirag J Patel
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA.
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Pan B, Chen Y, Song H, Xu Y, Wang R, Chen L. Mir-24-3p downregulation contributes to VP16-DDP resistance in small-cell lung cancer by targeting ATG4A. Oncotarget 2016; 6:317-31. [PMID: 25426560 PMCID: PMC4381597 DOI: 10.18632/oncotarget.2787] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 11/15/2014] [Indexed: 01/22/2023] Open
Abstract
Although the combination of etoposide (VP16) and cisplatin (DDP) is widely used as a first-line treatment for advanced-stage small-cell lung cancer (SCLC), chemoresistance limits its clinical use. Abnormalities of autophagy are associated with tumor chemoresistance. The present study found that miR-24-3p, a recently discovered microRNA, is significantly downregulated in VP16-DDP-resistant SCLC cells (H446/EP) compared with VP16-DDP-sensitive parent cells (H446). Forced expression of miR-24-3p sensitized H446/EP cells to VP16-DDP treatment because of a blockade of autophagic activity. We further found that downregulated miR-24-3p enhanced autophagy activation as it directly targets and inhibits autophagy-associated gene 4A (ATG4A). Overexpression of miR-24-3p into H446/EP cells led to reduction of the ATG4A protein level, allowing SCLC cells to resensitize to VP16-DDP. We conclude that miR-24-3p regulates autophagy by targeting ATG4A. Inhibition of autophagy by increasing miR-24-3p could be the basis of a strategy to prevent and treat SCLC with combination chemotherapy, particularly in chemoresistant disease.
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Affiliation(s)
- Banzhou Pan
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, China
| | - Yitian Chen
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, China
| | - Haizhu Song
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, China
| | - Yichen Xu
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, China
| | - Rui Wang
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, China
| | - Longbang Chen
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, China
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HAN KYUNGREEM, KIM JINWOONG, CHOI MOOYOUNG. COMPUTER SIMULATIONS UNVEIL THE DYNAMICS OF AUTOPHAGY AND ITS IMPLICATIONS FOR THE CELLULAR QUALITY CONTROL. J BIOL SYST 2014. [DOI: 10.1142/s0218339014500260] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Since the discovery of autophagy half a century ago, a number of physiological and molecular-level studies of autophagy have been carried out, revealing the basic mechanism and role of autophagy in the protein and organelle quality control. However, a reliable assessment method for the autophagy-mediated protein/organelle quality control with the help of an adequate mathematical model has not yet been reported. Based on the previous mathematical modeling of autophagy, we have carried out simulations to prove whether and how basal autophagy achieves substrate specificity and contributes to the cellular protein/organelle quality control. By means of numerical simulations, we probe the selective autophagic mode and observe that autophagic fluxes from abnormal protein/organelle are much greater than those from resident protein/organelle. Such a selective autophagic mode is found to correlate with the fractional abnormal protein/organelle concentration. Finally, it is shown that the fractional abnormal protein/organelle concentration against cellular damaging is efficiently controlled and regulated by suppression or promotion of the autophagosome formation rate. Mathematical modeling and numerical simulations allow one to analyze the autophagic protein/organelle quality control in a specific and quantitative manner and disclose that autophagy serves as a critical cellular quality control mechanism.
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Affiliation(s)
- KYUNGREEM HAN
- Department of Physics and Astronomy and Center for Theoretical Physics, Seoul National University, Seoul, 151-747, Korea
| | - JINWOONG KIM
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 151-742, Korea
| | - MOOYOUNG CHOI
- Department of Physics and Astronomy and Center for Theoretical Physics, Seoul National University, Seoul, 151-747, Korea
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15
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Liu PF, Leung CM, Chang YH, Cheng JS, Chen JJ, Weng CJ, Tsai KW, Hsu CJ, Liu YC, Hsu PC, Pan HW, Shu CW. ATG4B promotes colorectal cancer growth independent of autophagic flux. Autophagy 2014; 10:1454-65. [PMID: 24991826 DOI: 10.4161/auto.29556] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Autophagy is reported to suppress tumor proliferation, whereas deficiency of autophagy is associated with tumorigenesis. ATG4B is a deubiquitin-like protease that plays dual roles in the core machinery of autophagy; however, little is known about the role of ATG4B on autophagy and proliferation in tumor cells. In this study, we found that ATG4B knockdown induced autophagic flux and reduced CCND1 expression to inhibit G 1/S phase transition of cell cycle in colorectal cancer cell lines, indicating functional dominance of ATG4B on autophagy inhibition and tumor proliferation in cancer cells. Interestingly, based on the genetic and pharmacological ablation of autophagy, the growth arrest induced by silencing ATG4B was independent of autophagic flux. Moreover, dephosphorylation of MTOR was involved in reduced CCND1 expression and G 1/S phase transition in both cells and xenograft tumors with depletion of ATG4B. Furthermore, ATG4B expression was significantly increased in tumor cells of colorectal cancer patients compared with adjacent normal cells. The elevated expression of ATG4B was highly correlated with CCND1 expression, consistently supporting the notion that ATG4B might contribute to MTOR-CCND1 signaling for G 1/S phase transition in colorectal cancer cells. Thus, we report that ATG4B independently plays a role as a positive regulator on tumor proliferation and a negative regulator on autophagy in colorectal cancer cells. These results suggest that ATG4B is a potential biomarker and drug target for cancer therapy.
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Affiliation(s)
- Pei-Feng Liu
- Department of Medical Education and Research; Kaohsiung Veterans General Hospital; Kaohsiung, Taiwan; Department of Biotechnology; Fooyin University; Kaohsiung, Taiwan
| | - Chung-Man Leung
- Department of Radiation Oncology; Kaohsiung Veterans General Hospital; Kaohsiung, Taiwan; Department of Safety, Health and Environmental Engineering; National Kaohsiung First University of Science and Technology; Kaohsiung, Taiwan
| | - Yu-Hsiang Chang
- Department of Pediatrics; Kaohsiung Veterans General Hospital; Kaohsiung, Taiwan; School of Medicine; National Yang-Ming University; Taipei, Taiwan; Department of Nursing; Tajen University; Pingtung, Taiwan
| | - Jin-Shiung Cheng
- Department of Internal Medicine; Kaohsiung Veterans General Hospital; Kaohsiung, Taiwan
| | - Jih-Jung Chen
- Department of Pharmacy and Graduate Institute of Pharmaceutical Technology; Tajen University; Pingtung, Taiwan
| | - Chung-Jeu Weng
- Department of Obstetrics Gynecology; Zuoying Branch of Kaohsiung Armed Forces General Hospital; Kaohsiung, Taiwan
| | - Kuo-Wang Tsai
- Department of Medical Education and Research; Kaohsiung Veterans General Hospital; Kaohsiung, Taiwan
| | - Chien-Jen Hsu
- Department of Medical Education and Research; Kaohsiung Veterans General Hospital; Kaohsiung, Taiwan
| | - Yen-Chen Liu
- Department of Medical Education and Research; Kaohsiung Veterans General Hospital; Kaohsiung, Taiwan
| | - Ping-Chi Hsu
- Department of Safety, Health and Environmental Engineering; National Kaohsiung First University of Science and Technology; Kaohsiung, Taiwan
| | - Hung-Wei Pan
- Department of Medical Education and Research; Kaohsiung Veterans General Hospital; Kaohsiung, Taiwan
| | - Chih-Wen Shu
- Department of Medical Education and Research; Kaohsiung Veterans General Hospital; Kaohsiung, Taiwan
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16
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Li X, Xu HL, Liu YX, An N, Zhao S, Bao JK. Autophagy modulation as a target for anticancer drug discovery. Acta Pharmacol Sin 2013; 34:612-24. [PMID: 23564085 DOI: 10.1038/aps.2013.23] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Autophagy, an evolutionarily conserved catabolic process involving the engulfment and degradation of non-essential or abnormal cellular organelles and proteins, is crucial for homeostatic maintenance in living cells. This highly regulated, multi-step process has been implicated in diverse diseases including cancer. Autophagy can function as either a promoter or a suppressor of cancer, which makes it a promising and challenging therapeutic target. Herein, we overview the regulatory mechanisms and dual roles of autophagy in cancer. We also describe some of the representative agents that exert their anticancer effects by regulating autophagy. Additionally, some emerging strategies aimed at modulating autophagy are discussed as having the potential for future anticancer drug discovery. In summary, these findings will provide valuable information to better utilize autophagy in the future development of anticancer therapeutics that meet clinical requirements.
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