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Yi HB, Lee S, Seo K, Kim H, Kim M, Lee HS. Cellular and Biophysical Applications of Genetic Code Expansion. Chem Rev 2024; 124:7465-7530. [PMID: 38753805 DOI: 10.1021/acs.chemrev.4c00112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Despite their diverse functions, proteins are inherently constructed from a limited set of building blocks. These compositional constraints pose significant challenges to protein research and its practical applications. Strategically manipulating the cellular protein synthesis system to incorporate novel building blocks has emerged as a critical approach for overcoming these constraints in protein research and application. In the past two decades, the field of genetic code expansion (GCE) has achieved significant advancements, enabling the integration of numerous novel functionalities into proteins across a variety of organisms. This technological evolution has paved the way for the extensive application of genetic code expansion across multiple domains, including protein imaging, the introduction of probes for protein research, analysis of protein-protein interactions, spatiotemporal control of protein function, exploration of proteome changes induced by external stimuli, and the synthesis of proteins endowed with novel functions. In this comprehensive Review, we aim to provide an overview of cellular and biophysical applications that have employed GCE technology over the past two decades.
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Affiliation(s)
- Han Bin Yi
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Seungeun Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Kyungdeok Seo
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Hyeongjo Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Minah Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Hyun Soo Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
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2
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Gao P, Wang J, Tang H, Pang H, Liu J, Wang C, Xia F, Chen H, Xu L, Zhang J, Yuan L, Han G, Wang J, Liu G. Chemoproteomics-based profiling reveals potential antimalarial mechanism of Celastrol by disrupting spermidine and protein synthesis. Cell Commun Signal 2024; 22:139. [PMID: 38378659 PMCID: PMC10877925 DOI: 10.1186/s12964-023-01409-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 11/24/2023] [Indexed: 02/22/2024] Open
Abstract
BACKGROUND Malaria remains a global health burden, and the emergence and increasing spread of drug resistance to current antimalarials poses a major challenge to malaria control. There is an urgent need to find new drugs or strategies to alleviate this predicament. Celastrol (Cel) is an extensively studied natural bioactive compound that has shown potentially promising antimalarial activity, but its antimalarial mechanism remains largely elusive. METHODS We first established the Plasmodium berghei ANKA-infected C57BL/6 mouse model and systematically evaluated the antimalarial effects of Cel in conjunction with in vitro culture of Plasmodium falciparum. The potential antimalarial targets of Cel were then identified using a Cel activity probe based on the activity-based protein profiling (ABPP) technology. Subsequently, the antimalarial mechanism was analyzed by integrating with proteomics and transcriptomics. The binding of Cel to the identified key target proteins was verified by a series of biochemical experiments and functional assays. RESULTS The results of the pharmacodynamic assay showed that Cel has favorable antimalarial activity both in vivo and in vitro. The ABPP-based target profiling showed that Cel can bind to a number of proteins in the parasite. Among the 31 identified potential target proteins of Cel, PfSpdsyn and PfEGF1-α were verified to be two critical target proteins, suggesting the role of Cel in interfering with the de novo synthesis of spermidine and proteins of the parasite, thus exerting its antimalarial effects. CONCLUSIONS In conclusion, this study reports for the first time the potential antimalarial targets and mechanism of action of Cel using the ABPP strategy. Our work not only support the expansion of Cel as a potential antimalarial agent or adjuvant, but also establishes the necessary theoretical basis for the development of potential antimalarial drugs with pentacyclic triterpenoid structures, as represented by Cel. Video Abstract.
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Affiliation(s)
- Peng Gao
- Department of rehabilitation medicine, Shunde Hospital, Southern Medical University, Foshan, 528300, China
| | - Jianyou Wang
- State Key Laboratory of Antiviral Drugs, School of Pharmacy, Henan University, Kaifeng, 475004, China
| | - Huan Tang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Huanhuan Pang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Jiemei Liu
- Department of rehabilitation medicine, Shunde Hospital, Southern Medical University, Foshan, 528300, China
| | - Chen Wang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Fei Xia
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Honglin Chen
- State Key Laboratory of Antiviral Drugs, School of Pharmacy, Henan University, Kaifeng, 475004, China
| | - Liting Xu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Junzhe Zhang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Lixia Yuan
- School of Traditional Chinese Medicine and School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China.
- Guangdong Provincial Key Laboratory of Chinese Medicine Pharmaceutics, Southern Medical University, Guangzhou, 510515, China.
| | - Guang Han
- State Key Laboratory of Antiviral Drugs, School of Pharmacy, Henan University, Kaifeng, 475004, China.
| | - Jigang Wang
- State Key Laboratory of Antiviral Drugs, School of Pharmacy, Henan University, Kaifeng, 475004, China.
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
- Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Diseases, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital; First Affiliated Hospital of Southern University of Science and Technology; Second Clinical Medical College of Jinan University, Shenzhen, 518020, China.
| | - Gang Liu
- Department of rehabilitation medicine, Shunde Hospital, Southern Medical University, Foshan, 528300, China.
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Wang J, Su Q, Chen K, Wu Q, Ren J, Tang W, Hu Y, Zhu Z, Cheng C, Tu K, He H, Zhang Y. Pyrimethamine upregulates BNIP3 to interfere SNARE-mediated autophagosome-lysosomal fusion in hepatocellular carcinoma. J Pharm Anal 2024; 14:211-224. [PMID: 38464783 PMCID: PMC10921246 DOI: 10.1016/j.jpha.2023.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/13/2023] [Accepted: 05/29/2023] [Indexed: 03/12/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common tumor types and remains a major clinical challenge. Increasing evidence has revealed that mitophagy inhibitors can enhance the effect of chemotherapy on HCC. However, few mitophagy inhibitors have been approved for clinical use in humans. Pyrimethamine (Pyr) is used to treat infections caused by protozoan parasites. Recent studies have reported that Pyr may be beneficial in the treatment of various tumors. However, its mechanism of action is still not clearly defined. Here, we found that blocking mitophagy sensitized cells to Pyr-induced apoptosis. Mechanistically, Pyr potently induced the accumulation of autophagosomes by inhibiting autophagosome-lysosome fusion in human HCC cells. In vitro and in vivo studies revealed that Pyr blocked autophagosome-lysosome fusion by upregulating BNIP3 to inhibit synaptosomal-associated protein 29 (SNAP29)-vesicle-associated membrane protein 8 (VAMP8) interaction. Moreover, Pyr acted synergistically with sorafenib (Sora) to induce apoptosis and inhibit HCC proliferation in vitro and in vivo. Pyr enhances the sensitivity of HCC cells to Sora, a common chemotherapeutic, by inhibiting mitophagy. Thus, these results provide new insights into the mechanism of action of Pyr and imply that Pyr could potentially be further developed as a novel mitophagy inhibitor. Notably, Pyr and Sora combination therapy could be a promising treatment for malignant HCC.
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Affiliation(s)
- Jingjing Wang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Qi Su
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Kun Chen
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Qing Wu
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Jiayan Ren
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Wenjuan Tang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yu Hu
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Zeren Zhu
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Cheng Cheng
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Kaihui Tu
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Huaizhen He
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yanmin Zhang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
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Song F, Li J, Shi Q, Wong YK, Liu D, Lin Q, Wang J, Chen X. Quantitative Chemical Proteomics Reveals Triptolide Selectively Inhibits HCT116 Human Colon Cancer Cell Viability and Migration Through Binding to Peroxiredoxin 1 and Annexin A1. Adv Biol (Weinh) 2023:e2300452. [PMID: 37794608 DOI: 10.1002/adbi.202300452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 09/08/2023] [Indexed: 10/06/2023]
Abstract
Triptolide (TPL), a natural product extracted from Tripterygium wilfordii Hook F, exerts potential anti-cancer activity. Studies have shown that TPL is involved in multiple cellular processes and signal pathways; however, its pharmaceutical activity in human colorectal cancer (CRC) as well as the underlying molecular mechanism remain elusive. In this study, the effects of TPL on HCT116 human colon cancer cells and CCD841 human colon epithelial cells are first evaluated. Next, the protein targets of TPL in HCT116 cells are identified through an activity-based protein profiling approach. With subsequent in vitro experiments, the mode of action of TPL in HCT116 cells is elucidated. As a result, TPL is found to selectively inhibit HCT116 cell viability and migration. A total of 54 proteins are identified as the targets of TPL in HCT116 cells, among which, Annexin A1 (ANXA1) and Peroxiredoxin I/II (Prdx I/II) are picked out for further investigation due to their important role in CRC. The interaction between TPL and ANXA1 or Prdx I is confirmed, and it is discovered that TPL exerts inhibitory effect against HCT116 cells through binding to ANXA1 and Prdx I. The study reinforces the potential of TPL in the CRC therapy, and provides novel therapeutic targets for the treatment of CRC.
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Affiliation(s)
- Fangli Song
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 10700, China
| | - Jinglin Li
- Department of biological Sciences, National University of Singapore, Singapore, 117600, Singapore
| | - Qiaoli Shi
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 10700, China
| | - Yin Kwan Wong
- Department of biological Sciences, National University of Singapore, Singapore, 117600, Singapore
| | - Dandan Liu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 10700, China
| | - Qingsong Lin
- Department of biological Sciences, National University of Singapore, Singapore, 117600, Singapore
| | - Jigang Wang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 10700, China
| | - Xiao Chen
- School of Biopharmacy, China Pharmaceutical University, Nanjing, 210009, China
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Wang H, Cheng Q, Bao L, Li M, Chang K, Yi X. Cytoprotective Role of Heme Oxygenase-1 in Cancer Chemoresistance: Focus on Antioxidant, Antiapoptotic, and Pro-Autophagy Properties. Antioxidants (Basel) 2023; 12:1217. [PMID: 37371947 DOI: 10.3390/antiox12061217] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
Chemoresistance remains the foremost challenge in cancer therapy. Targeting reactive oxygen species (ROS) manipulation is a promising strategy in cancer treatment since tumor cells present high levels of intracellular ROS, which makes them more vulnerable to further ROS elevation than normal cells. Nevertheless, dynamic redox evolution and adaptation of tumor cells are capable of counteracting therapy-induced oxidative stress, which leads to chemoresistance. Hence, exploring the cytoprotective mechanisms of tumor cells is urgently needed to overcome chemoresistance. Heme oxygenase-1 (HO-1), a rate-limiting enzyme of heme degradation, acts as a crucial antioxidant defense and cytoprotective molecule in response to cellular stress. Recently, emerging evidence indicated that ROS detoxification and oxidative stress tolerance owing to the antioxidant function of HO-1 contribute to chemoresistance in various cancers. Enhanced HO-1 expression or enzymatic activity was revealed to promote apoptosis resistance and activate protective autophagy, which also involved in the development of chemoresistance. Moreover, inhibition of HO-1 in multiple cancers was identified to reversing chemoresistance or improving chemosensitivity. Here, we summarize the most recent advances regarding the antioxidant, antiapoptotic, and pro-autophagy properties of HO-1 in mediating chemoresistance, highlighting HO-1 as a novel target for overcoming chemoresistance and improving the prognosis of cancer patients.
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Affiliation(s)
- Huan Wang
- Department of Gynecology, Hospital of Obstetrics and Gynecology, Fudan University, Shanghai 200011, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai 200011, China
| | - Qi Cheng
- Department of Gynecology, Hospital of Obstetrics and Gynecology, Fudan University, Shanghai 200011, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai 200011, China
| | - Lingjie Bao
- Department of Gynecology, Hospital of Obstetrics and Gynecology, Fudan University, Shanghai 200011, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai 200011, China
| | - Mingqing Li
- Department of Gynecology, Hospital of Obstetrics and Gynecology, Fudan University, Shanghai 200011, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai 200011, China
| | - Kaikai Chang
- Department of Gynecology, Hospital of Obstetrics and Gynecology, Fudan University, Shanghai 200011, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai 200011, China
| | - Xiaofang Yi
- Department of Gynecology, Hospital of Obstetrics and Gynecology, Fudan University, Shanghai 200011, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai 200011, China
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Romano PS, Akematsu T, Besteiro S, Bindschedler A, Carruthers VB, Chahine Z, Coppens I, Descoteaux A, Alberto Duque TL, He CY, Heussler V, Le Roch KG, Li FJ, de Menezes JPB, Menna-Barreto RFS, Mottram JC, Schmuckli-Maurer J, Turk B, Tavares Veras PS, Salassa BN, Vanrell MC. Autophagy in protists and their hosts: When, how and why? AUTOPHAGY REPORTS 2023; 2:2149211. [PMID: 37064813 PMCID: PMC10104450 DOI: 10.1080/27694127.2022.2149211] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 11/15/2022] [Indexed: 03/12/2023]
Abstract
Pathogenic protists are a group of organisms responsible for causing a variety of human diseases including malaria, sleeping sickness, Chagas disease, leishmaniasis, and toxoplasmosis, among others. These diseases, which affect more than one billion people globally, mainly the poorest populations, are characterized by severe chronic stages and the lack of effective antiparasitic treatment. Parasitic protists display complex life-cycles and go through different cellular transformations in order to adapt to the different hosts they live in. Autophagy, a highly conserved cellular degradation process, has emerged as a key mechanism required for these differentiation processes, as well as other functions that are crucial to parasite fitness. In contrast to yeasts and mammals, protist autophagy is characterized by a modest number of conserved autophagy-related proteins (ATGs) that, even though, can drive the autophagosome formation and degradation. In addition, during their intracellular cycle, the interaction of these pathogens with the host autophagy system plays a crucial role resulting in a beneficial or harmful effect that is important for the outcome of the infection. In this review, we summarize the current state of knowledge on autophagy and other related mechanisms in pathogenic protists and their hosts. We sought to emphasize when, how, and why this process takes place, and the effects it may have on the parasitic cycle. A better understanding of the significance of autophagy for the protist life-cycle will potentially be helpful to design novel anti-parasitic strategies.
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Affiliation(s)
- Patricia Silvia Romano
- Laboratorio de Biología de Trypanosoma cruzi y de la célula hospedadora. Instituto de Histología y Embriología de Mendoza. Universidad Nacional de Cuyo. (IHEM-CONICET-UNCUYO). Facultad de Ciencias Médicas. Universidad Nacional de Cuyo. Av. Libertador 80 (5500), Mendoza, Argentina
| | - Takahiko Akematsu
- Department of Biosciences, College of Humanities and Sciences, Nihon University, Tokyo, Japan
| | | | | | - Vern B Carruthers
- Department of Microbiology and Immunology, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Zeinab Chahine
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - Isabelle Coppens
- Department of Molecular Microbiology and Immunology. Department of Molecular Microbiology and Immunology. Johns Hopkins Malaria Research Institute. Johns Hopkins University Bloomberg School of Public Health. Baltimore 21205, MD, USA
| | - Albert Descoteaux
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, Laval, QC
| | - Thabata Lopes Alberto Duque
- Autophagy Inflammation and Metabolism Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA; Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Cynthia Y He
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Volker Heussler
- Institute of Cell Biology.University of Bern. Baltzerstr. 4 3012 Bern
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - Feng-Jun Li
- Department of Biological Sciences, National University of Singapore, Singapore
| | | | | | - Jeremy C Mottram
- York Biomedical Research Institute, Department of Biology, University of York, York, UK
| | | | - Boris Turk
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia
| | - Patricia Sampaio Tavares Veras
- Laboratory of Host-Parasite Interaction and Epidemiology, Gonçalo Moniz Institute, Fiocruz-Bahia
- National Institute of Science and Technology of Tropical Diseases - National Council for Scientific Research and Development (CNPq)
| | - Betiana Nebai Salassa
- Laboratorio de Biología de Trypanosoma cruzi y de la célula hospedadora. Instituto de Histología y Embriología de Mendoza. Universidad Nacional de Cuyo. (IHEM-CONICET-UNCUYO). Facultad de Ciencias Médicas. Universidad Nacional de Cuyo. Av. Libertador 80 (5500), Mendoza, Argentina
| | - María Cristina Vanrell
- Laboratorio de Biología de Trypanosoma cruzi y de la célula hospedadora. Instituto de Histología y Embriología de Mendoza. Universidad Nacional de Cuyo. (IHEM-CONICET-UNCUYO). Facultad de Ciencias Médicas. Universidad Nacional de Cuyo. Av. Libertador 80 (5500), Mendoza, Argentina
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Huang T, Jiang G, Zhang Y, Lei Y, Liu S, Li H, Lu K. The RNA polymerase II subunit Rpb9 activates ATG1 transcription and autophagy. EMBO Rep 2022; 23:e54993. [PMID: 36102592 PMCID: PMC9638876 DOI: 10.15252/embr.202254993] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 08/23/2022] [Accepted: 08/26/2022] [Indexed: 08/01/2023] Open
Abstract
Macroautophagy/autophagy is a conserved process in eukaryotic cells that mediates the degradation and recycling of intracellular substrates. Proteins encoded by autophagy-related (ATG) genes are essentially involved in the autophagy process and must be tightly regulated in response to various circumstances, such as nutrient-rich and starvation conditions. However, crucial transcriptional activators of ATG genes have remained obscure. Here, we identify the RNA polymerase II subunit Rpb9 as an essential regulator of autophagy by a high-throughput screen of a Saccharomyces cerevisiae gene knockout library. Rpb9 plays a crucial and specific role in upregulating ATG1 transcription, and its deficiency decreases autophagic activities. Rpb9 promotes ATG1 transcription by binding to its promoter region, which is mediated by Gcn4. Furthermore, the function of Rpb9 in autophagy and its regulation of ATG1/ULK1 transcription are conserved in mammalian cells. Together, our results indicate that Rpb9 specifically activates ATG1 transcription and thus positively regulates the autophagy process.
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Affiliation(s)
- Ting Huang
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengduChina
| | - Gaoyue Jiang
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengduChina
| | - Yabin Zhang
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengduChina
| | - Yuqing Lei
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengduChina
| | - Shiyan Liu
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengduChina
| | - Huihui Li
- West China Second University HospitalSichuan UniversityChengduChina
| | - Kefeng Lu
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengduChina
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8
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Li L, Lee CP, Ding X, Qin Y, Wijerathna-Yapa A, Broda M, Otegui MS, Millar AH. Defects in autophagy lead to selective in vivo changes in turnover of cytosolic and organelle proteins in Arabidopsis. THE PLANT CELL 2022; 34:3936-3960. [PMID: 35766863 PMCID: PMC9516138 DOI: 10.1093/plcell/koac185] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/21/2022] [Indexed: 05/26/2023]
Abstract
Identification of autophagic protein cargo in plants in autophagy-related genes (ATG) mutants is complicated by changes in protein synthesis and protein degradation. To detect autophagic cargo, we measured protein degradation rate in shoots and roots of Arabidopsis (Arabidopsis thaliana) atg5 and atg11 mutants. These data show that less than a quarter of proteins changing in abundance are probable cargo and revealed roles of ATG11 and ATG5 in degradation of specific glycolytic enzymes and of other cytosol, chloroplast, and ER-resident proteins, and a specialized role for ATG11 in degradation of proteins from mitochondria and chloroplasts. Protein localization in transformed protoplasts and degradation assays in the presence of inhibitors confirm a role for autophagy in degrading glycolytic enzymes. Autophagy induction by phosphate (Pi) limitation changed metabolic profiles and the protein synthesis and degradation rates of atg5 and atg11 plants. A general decrease in the abundance of amino acids and increase in secondary metabolites in autophagy mutants was consistent with altered catabolism and changes in energy conversion caused by reduced degradation rate of specific proteins. Combining measures of changes in protein abundance and degradation rates, we also identify ATG11 and ATG5-associated protein cargo of low Pi-induced autophagy in chloroplasts and ER-resident proteins involved in secondary metabolism.
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Affiliation(s)
- Lei Li
- Authors for correspondence (L.L.) and (A.H.M)
| | - Chun Pong Lee
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, Crawley, WA 6009, Australia
| | - Xinxin Ding
- Department of Botany and Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Yu Qin
- Frontiers Science Center for Cell Responses, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Akila Wijerathna-Yapa
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, Crawley, WA 6009, Australia
| | - Martyna Broda
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, Crawley, WA 6009, Australia
| | - Marisa S Otegui
- Department of Botany and Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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Cao X, Meng P, Shao Y, Yan G, Yao J, Zhou X, Liu C, Zhang L, Shu H, Lu H. Nascent Glycoproteome Reveals That N-Linked Glycosylation Inhibitor-1 Suppresses Expression of Glycosylated Lysosome-Associated Membrane Protein-2. Front Mol Biosci 2022; 9:899192. [PMID: 35573732 PMCID: PMC9092021 DOI: 10.3389/fmolb.2022.899192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 04/12/2022] [Indexed: 11/15/2022] Open
Abstract
Glycosylation inhibition has great potential in cancer treatment. However, the corresponding cellular response, protein expression and glycosylation changes remain unclear. As a cell-permeable small-molecule inhibitor with reduced cellular toxicity, N-linked glycosylation inhibitor-1 (NGI-1) has become a great approach to regulate glycosylation in mammalian cells. Here for the first time, we applied a nascent proteomic method to investigate the effect of NGI-1 in hepatocellular carcinoma (HCC) cell line. Besides, hydrophilic interaction liquid chromatography (HILIC) was adopted for the enrichment of glycosylated peptides. Glycoproteomic analysis revealed the abundance of glycopeptides from LAMP2, NICA, and CEIP2 was significantly changed during NGI-1 treatment. Moreover, the alterations of LAMP2 site-specific intact N-glycopeptides were comprehensively assessed. NGI-1 treatment also led to the inhibition of Cathepsin D maturation and the induction of autophagy. In summary, we provided evidence that NGI-1 repressed the expression of glycosylated LAMP2 accompanied with the occurrence of lysosomal defects and autophagy.
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Affiliation(s)
- Xinyi Cao
- Institutes of Biomedical Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Peiyi Meng
- Department of Chemistry, Fudan University, Shanghai, China
| | - Yuyin Shao
- Institutes of Biomedical Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Guoquan Yan
- Institutes of Biomedical Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jun Yao
- Institutes of Biomedical Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Xinwen Zhou
- Institutes of Biomedical Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Chao Liu
- Beijing Advanced Innovation Center for Precision Medicine, Beihang University, Beijing, China
| | - Lei Zhang
- Institutes of Biomedical Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Hong Shu
- Department of Clinical Laboratory, Guangxi Medical University Cancer Hospital, Nanning, China
- *Correspondence: Hong Shu, ; Haojie Lu,
| | - Haojie Lu
- Institutes of Biomedical Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
- Department of Chemistry, Fudan University, Shanghai, China
- NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China
- *Correspondence: Hong Shu, ; Haojie Lu,
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10
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Hubbard EE, Heil LR, Merrihew GE, Chhatwal JP, Farlow MR, McLean CA, Ghetti B, Newell KL, Frosch MP, Bateman RJ, Larson EB, Keene CD, Perrin RJ, Montine TJ, MacCoss MJ, Julian RR. Does Data-Independent Acquisition Data Contain Hidden Gems? A Case Study Related to Alzheimer's Disease. J Proteome Res 2022; 21:118-131. [PMID: 34818016 PMCID: PMC8741752 DOI: 10.1021/acs.jproteome.1c00558] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
One of the potential benefits of using data-independent acquisition (DIA) proteomics protocols is that information not originally targeted by the study may be present and discovered by subsequent analysis. Herein, we reanalyzed DIA data originally recorded for global proteomic analysis to look for isomerized peptides, which occur as a result of spontaneous chemical modifications to long-lived proteins. Examination of a large set of human brain samples revealed a striking relationship between Alzheimer's disease (AD) status and isomerization of aspartic acid in a peptide from tau. Relative to controls, a surprising increase in isomer abundance was found in both autosomal dominant and sporadic AD samples. To explore potential mechanisms that might account for these observations, quantitative analysis of proteins related to isomerization repair and autophagy was performed. Differences consistent with reduced autophagic flux in AD-related samples relative to controls were found for numerous proteins, including most notably p62, a recognized indicator of autophagic inhibition. These results suggest, but do not conclusively demonstrate, that lower autophagic flux may be strongly associated with loss of function in AD brains. This study illustrates that DIA data may contain unforeseen results of interest and may be particularly useful for pilot studies investigating new research directions. In this case, a promising target for future investigations into the therapy and prevention of AD has been identified.
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Affiliation(s)
- Evan E. Hubbard
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Lilian R. Heil
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98195, United States
| | - Gennifer E. Merrihew
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98195, United States
| | - Jasmeer P. Chhatwal
- Harvard Medical School, Massachusetts General Hospital, Department of Neurology, 15 Parkman St, Suite 835, Boston MA 02114
| | - Martin R. Farlow
- Department of Neurology, Indiana University School of Medicine, Indianapolis, Indiana, 46202
| | | | - Bernardino Ghetti
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202
| | - Kathy L. Newell
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202
| | - Matthew P. Frosch
- C.S. Kubik Laboratory for Neuropathology, and Massachusetts Alzheimer Disease Research Center, Massachusetts General Hospital, Boston, MA 02114
| | - Randall J. Bateman
- Department of Neurology, Washington University School of Medicine, 660 South Euclid Avenue, Box 8111, St. Louis, 63110, Missouri, USA
| | - Eric B. Larson
- Kaiser Permanente Washington Health Research Institute and Department of Medicine, University of Washington, Seattle WA
| | - C. Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, 98195, United States
| | - Richard J. Perrin
- Department of Pathology and Immunology, Department of Neurology, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
| | - Thomas J. Montine
- Department of Pathology, Stanford University, Stanford, CA, 94305, United States
| | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98195, United States
| | - Ryan R. Julian
- Department of Chemistry, University of California, Riverside, California 92521, United States,corresponding author:
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11
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Homogentisic acid induces autophagy alterations leading to chondroptosis in human chondrocytes: Implications in Alkaptonuria. Arch Biochem Biophys 2022; 717:109137. [DOI: 10.1016/j.abb.2022.109137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 01/20/2022] [Accepted: 01/22/2022] [Indexed: 11/17/2022]
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12
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Dabbah M, Lishner M, Jarchowsky-Dolberg O, Tartakover-Matalon S, Brin YS, Pasmanik-Chor M, Neumann A, Drucker L. Ribosomal proteins as distinct "passengers" of microvesicles: new semantics in myeloma and mesenchymal stem cells' communication. Transl Res 2021; 236:117-132. [PMID: 33887527 DOI: 10.1016/j.trsl.2021.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/23/2021] [Accepted: 04/12/2021] [Indexed: 01/10/2023]
Abstract
Aberrant mesenchymal stem cells (MSCs) in multiple myeloma (MM) bone marrows (BM) promote disease progression and drug resistance. Here, we assayed the protein cargo transported from MM-MSCs to MM cells via microvesicles (MVs) with focus on ribosomal proteins (RPs) and assessment of their influence on translation initiation and design of MM phenotype. Proteomics analysis (mass spectrometry) demonstrated increased levels and repertoire of RPs in MM-MSCs MVs compared to normal donors (ND) counterparts (n = 3-8; P = 9.96E - 08). We limited the RPs load in MM-MSCs MVs (starvation, RSK and XPO1 inhibitions), reapplied the modified MVs to MM cell lines (U266, MM1S), and demonstrated that the RPs are essential to the proliferative effect of MM-MSCs MVs on MM cells (n = 3; P < 0.05). We also observed that inhibition with KPT-185 (XPO1 inhibitor) displayed the most extensive effect on RPs delivery into the MVs (↓80%; P = 3.12E - 05). Using flow cytometry we assessed the expression of select RPs (n = 10) in BM-MSCs cell populations (ND and MM; n ≥ 6 each). This demonstrated a heterogeneous expression of RPs in MM-MSCs with distinct subgroups, a phenomenon absent from ND-MSCs samples. These findings bring to light a new mechanism in which the tumor microenvironment participates in cancer promotion. MVs-mediated horizontal transfer of RPs between niche MSCs and myeloma cells is a systemic way to bestow pro-cancer advantages. This capacity also differentiates normal MSCs from the MM-modified MSCs and may mark their reprogramming. Future studies will be aimed at assessing the clinical and therapeutic potential of the increased RPs levels in MM-MSCs MVs.
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Affiliation(s)
- Mahmoud Dabbah
- Oncogenetic Laboratory, Meir Medical Center, Kfar Saba, Israel; Sackler faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Michael Lishner
- Oncogenetic Laboratory, Meir Medical Center, Kfar Saba, Israel; Resaerch Institute, Meir Medical Center, Kfar saba, Israel; Sackler faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Osnat Jarchowsky-Dolberg
- Hematology Unit, Meir Medical Center, Kfar saba, Israel; Sackler faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shelly Tartakover-Matalon
- Autoimmunity laboratory, Meir Medical Center, Kfar saba, Israel; Sackler faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yaron S Brin
- Orthopedics Department, Meir Medical Center, Kfar Saba, Israel
| | - Metsada Pasmanik-Chor
- Bioinformatics Unit, G.S.W. Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Avivit Neumann
- Oncology Department, Rambam Medical Center, Haifa, Israel
| | - Liat Drucker
- Oncogenetic Laboratory, Meir Medical Center, Kfar Saba, Israel; Sackler faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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13
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Shao Y, Bao H, Ma L, Yuan W, Zhang L, Yao J, Meng P, Peng Y, Zhang S, Cao T, Lu H. Enhancing Comprehensive Analysis of Newly Synthesized Proteins Based on Cleavable Bioorthogonal Tagging. Anal Chem 2021; 93:9408-9417. [PMID: 34197092 DOI: 10.1021/acs.analchem.1c00965] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Protein synthesis and degradation responding to environmental cues is critical for understanding the mechanisms involved. Chemical proteomics introducing bioorthogonal tagging into proteins and isolation by biotin affinity purification is applicable for enrichment of newly synthesized proteins (NSPs). Current enrichment methods based on biotin-streptavidin interaction lack efficiency to release enriched NSPs under mild conditions. Here we designed a novel method for enriching newly synthesized peptides by click chemistry followed by release of enriched peptides via tryptic digestion based on cleavable bioorthogonal tagging (CBOT). CBOT-modified peptides can further enhance identification in mass spectrometry analysis and provide a confirmation by small mass shift. Our method achieved an improvement in specificity (97.1%) and sensitivity for NSPs in cell lysate, corresponding to profiling at a depth of 4335 NSPs from 2 mg of starting materials in a single LC-MS/MS run. In addition, the CBOT strategy can quantify NSPs when coupling a pair of isotope-labeled azidohomoalanine (AHA/hAHA) with decent reproducibility. Furthermore, we applied it to analyze newly synthesized proteomes in the autophagy process after 6 h rapamycin stimulation in cells, 2910 NSPs were quantified, and 337 NSPs among them were significantly up- and down-regulated. We envision CBOT as an effective and alternative approach for bioorthogonal chemical proteomics to study stimuli-sensitive subsets.
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Affiliation(s)
- Yuyin Shao
- Shanghai Cancer Center and Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai 200032, P. R. China
| | - Huimin Bao
- Shanghai Cancer Center and Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai 200032, P. R. China
| | - Lixiang Ma
- Department of Anatomy, Histology & Embryology, School of Medical Sciences, Fudan University, Shanghai 200032, P. R. China
| | - Wenjuan Yuan
- Shanghai Cancer Center and Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai 200032, P. R. China
| | - Lei Zhang
- Shanghai Cancer Center and Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai 200032, P. R. China
| | - Jun Yao
- Shanghai Cancer Center and Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai 200032, P. R. China
| | - Peiyi Meng
- Shanghai Cancer Center and Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai 200032, P. R. China
| | - Ye Peng
- Shanghai Cancer Center and Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai 200032, P. R. China
| | - Siwen Zhang
- Shanghai Cancer Center and Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai 200032, P. R. China
| | - Ting Cao
- Shanghai Cancer Center and Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai 200032, P. R. China
| | - Haojie Lu
- Shanghai Cancer Center and Institutes of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai 200032, P. R. China
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14
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Hou Z, Han X, Wang Z, Ghazanfar S, Yang J, Liu H. A terminal alkyne and disulfide functionalized agarose resin specifically enriches azidohomoalanine labeled nascent proteins. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1165:122527. [PMID: 33486215 DOI: 10.1016/j.jchromb.2021.122527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 12/27/2020] [Accepted: 01/02/2021] [Indexed: 10/22/2022]
Abstract
Nascent proteome presents dynamic changes in response to a certain stimulus. Thus, monitoring nascent proteome is critical to uncovering the involved biological mechanism. But the low-abundance of nascent proteome against an overwhelming pre-existing proteome limits its identification and quantification. Herein, we present a novel strategy to enrich nascent proteome from whole cell lysate for further analysis by mass spectrometry. We employed a terminal alkyne and disulfide functionalized agarose resin to capture nascent proteome which had been labeled by L-azidohomoalanine. Results from the western blot, silver staining and pulse metabolic labeling suggested that the nascent proteome could be enriched efficiently. Applied to Hela cells, the method identified about 700 nascent proteins with good correlation with previous reports. The above indicates that our strategy can be used to reveal the proteome dynamics of biological processes.
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Affiliation(s)
- Zhanwu Hou
- Center for Mitochondrial Biology and Medicine & Douglas C. Wallace Institute for Mitochondrial and Epigenetic Information Sciences, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Xiao Han
- Center for Mitochondrial Biology and Medicine & Douglas C. Wallace Institute for Mitochondrial and Epigenetic Information Sciences, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Zhen Wang
- Center for Mitochondrial Biology and Medicine & Douglas C. Wallace Institute for Mitochondrial and Epigenetic Information Sciences, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Sana Ghazanfar
- Center for Mitochondrial Biology and Medicine & Douglas C. Wallace Institute for Mitochondrial and Epigenetic Information Sciences, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Jeffy Yang
- Schulich Medicine and Dentistry, Western University, London N6A3K7, Canada
| | - Huadong Liu
- Center for Mitochondrial Biology and Medicine & Douglas C. Wallace Institute for Mitochondrial and Epigenetic Information Sciences, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China.
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15
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Liu DD, Zou C, Zhang J, Gao P, Zhu Y, Meng Y, Ma N, Lv M, Xu C, Lin Q, Wang J. Target Profiling of an Anticancer Drug Curcumin by an In Situ Chemical Proteomics Approach. Methods Mol Biol 2021; 2213:147-161. [PMID: 33270200 DOI: 10.1007/978-1-0716-0954-5_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Interdisciplinary chemical proteomics approaches have been widely applied to the identification of specific targets of bioactive small molecules or drugs. In this chapter, we describe the application of a cell-permeable activity-based curcumin probe (Cur-P) with an alkyne moiety to detect and identify specific binding targets of curcumin in HCT116 colon cancer cells. Through click chemistry, a fluorescent tag or a biotin tag is attached to the probe-modified curcumin targets for visualization or affinity purification followed by mass spectrometric identification. A quantitative proteomics approach of isobaric tags for relative and absolute quantification (iTRAQ)™ is applied to distinguish specific curcumin targets from nonspecific binding proteins.
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Affiliation(s)
- Dan-Dan Liu
- Institute of Chinese Materia Medica, and Artemisinin Research Center, China Academy of Chinese Medical Sciences, Beijing, China
| | - Chang Zou
- Clinical Medical Research Center, The First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen Public Service Platform on Tumor Precision Medicine and Molecular Diagnosis, Shenzhen People's Hospital, Shenzhen, China
| | - Jianbin Zhang
- Department of Oncology, Clinical Research Institute, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Peng Gao
- Institute of Chinese Materia Medica, and Artemisinin Research Center, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yongping Zhu
- Institute of Chinese Materia Medica, and Artemisinin Research Center, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yuqing Meng
- Institute of Chinese Materia Medica, and Artemisinin Research Center, China Academy of Chinese Medical Sciences, Beijing, China
| | - Nan Ma
- Institute of Chinese Materia Medica, and Artemisinin Research Center, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ming Lv
- Institute of Chinese Materia Medica, and Artemisinin Research Center, China Academy of Chinese Medical Sciences, Beijing, China
| | - Chengchao Xu
- Institute of Chinese Materia Medica, and Artemisinin Research Center, China Academy of Chinese Medical Sciences, Beijing, China.,Clinical Medical Research Center, The First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen Public Service Platform on Tumor Precision Medicine and Molecular Diagnosis, Shenzhen People's Hospital, Shenzhen, China
| | - Qingsong Lin
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Jigang Wang
- Institute of Chinese Materia Medica, and Artemisinin Research Center, China Academy of Chinese Medical Sciences, Beijing, China. .,Clinical Medical Research Center, The First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen Public Service Platform on Tumor Precision Medicine and Molecular Diagnosis, Shenzhen People's Hospital, Shenzhen, China.
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16
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Wijerathna-Yapa A, Stroeher E, Fenske R, Li L, Duncan O, Millar AH. Proteomics for Autophagy Receptor and Cargo Identification in Plants. J Proteome Res 2020; 20:129-138. [PMID: 33241938 DOI: 10.1021/acs.jproteome.0c00609] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Autophagy is a catabolic process facilitating the degradation of cytoplasmic proteins and organelles in a lysosome- or vacuole-dependent manner in plants, animals, and fungi. Proteomic studies have demonstrated that autophagy controls and shapes the proteome and has identified both receptor and cargo proteins inside autophagosomes. In a smaller selection of studies, proteomics has been used for the analysis of post-translational modifications that target proteins for elimination and protein-protein interactions between receptors and cargo, providing a better understanding of the complex regulatory processes controlling autophagy. In this perspective, we highlight how proteomic studies have contributed to our understanding of autophagy in plants against the backdrop of yeast and animal studies. We then provide a framework for how the future application of proteomics in plant autophagy can uncover the mechanisms and outcomes of sculpting organelles during plant development, particularly through the identification of autophagy receptors and cargo in plants.
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Affiliation(s)
- Akila Wijerathna-Yapa
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009 Crawley, Western Australia, Australia
| | - Elke Stroeher
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009 Crawley, Western Australia, Australia
| | - Ricarda Fenske
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009 Crawley, Western Australia, Australia
| | - Lei Li
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009 Crawley, Western Australia, Australia.,Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, 300071 Tianjin, China
| | - Owen Duncan
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009 Crawley, Western Australia, Australia
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009 Crawley, Western Australia, Australia
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17
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Sun X, Shu Y, Xu M, Jiang J, Wang L, Wang J, Huang D, Zhang J. ANXA6 suppresses the tumorigenesis of cervical cancer through autophagy induction. Clin Transl Med 2020; 10:e208. [PMID: 33135350 PMCID: PMC7571625 DOI: 10.1002/ctm2.208] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 09/18/2020] [Accepted: 10/03/2020] [Indexed: 12/17/2022] Open
Abstract
Background Autophagy is an intracellular degradation pathway conserved in eukaryotes. ANXA6 (annexin A6) belongs to a family of calcium‐dependent membrane and phospholipid‐binding proteins. Here, we identify ANXA6 as a newly synthesized protein in starvation‐induced autophagy and validate it as a novel autophagy modulator that regulates autophagosome formation. Results ANXA6 knockdown attenuates starvation‐induced autophagy, while restoration of its expression enhances autophagy. GO (gene ontology) analysis of ANXA6 targets showed that ANXA6 interacts with many RAB GTPases and targets endocytosis and phagocytosis pathways, indicating that ANXA6 exerts its function through protein trafficking. ATG9A (autophagy‐related 9A) is the sole multispanning transmembrane protein and its trafficking through recycling endosomes is an essential step for autophagosome formation. Our results showed that ANXA6 enables appropriate ATG9A+ vesicle trafficking from endosomes to autophagosomes through RAB proteins or F‐actin. In addition, restoration of ANXA6 expression suppresses mTOR (mammalian target of rapamycin) activity through the inhibition of the PI3K (phosphoinositide 3‐kinase)‐AKT and ERK (extracellular signal‐regulated kinase) signaling pathways, which is a negative regulator of autophagy. Functionally, ANXA6 expression is correlated with LC3 (microtubule‐associated protein 1 light chain 3) expression in cervical cancer, and ANXA6 inhibits tumorigenesis through autophagy induction. Conclusions Our results reveal an important mechanism for ANXA6 in tumor suppression and autophagy regulation.
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Affiliation(s)
- Xin Sun
- Department of Oncology, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Yuhan Shu
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, China
| | - Mengting Xu
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, China
| | - Jiukun Jiang
- Department of Emergency Medicine, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Liming Wang
- Department of Physiology, National University of Singapore, Singapore, Singapore
| | - Jigang Wang
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.,The First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, China.,Department of Toxicology, School of Public Health, Guangxi Medical University, Nanning, China
| | - Dongsheng Huang
- Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, People's Hospital of Hangzhou Medical College, Clinical Research Institute, Hangzhou, China
| | - Jianbin Zhang
- Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, People's Hospital of Hangzhou Medical College, Clinical Research Institute, Hangzhou, China
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18
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Wu X, Luo L, Kong R, Song Y, Li Q, Nice EC, Wang K. Recent advances in autophagic machinery: a proteomic perspective. Expert Rev Proteomics 2020; 17:561-579. [PMID: 32772586 DOI: 10.1080/14789450.2020.1808464] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Autophagy is an evolutionarily conserved cellular clearance process, by which cytosolic components are delivered to autolysosomes for breakdown and recycling to maintain cellular homeostasis. During the past decades, autophagy has been found to be tightly implicated in various physiological and pathological progresses. Unraveling the regulatory mechanisms of the autophagy process will contribute to the development of emerging autophagy-targeting strategies for the treatment of various diseases. Recently, the rapid development of proteomics approaches has enabled the use of large-scale unbiased strategies to unravel autophagy machinery. AREAS COVERED In this review, we will highlight the recent contributions of proteomics strategies in clarifying the autophagy machinery, with an emphasis on the three different types of autophagy (namely macroautophagy, microautophagy, and chaperone-mediated autophagy). We will also discuss the emerging role of proteomics approaches in investigating the mechanism of the autophagy-based unconventional secretory pathway (secretory autophagy). EXPERT OPINION Proteomics has provided an effective strategy for the comprehensive analysis of the autophagy process, which will broaden our understanding of autophagy machinery, and holds great promise for developing clinical therapies targeting autophagy.
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Affiliation(s)
- Xingyun Wu
- West China School of Basic Medical Sciences & Forensic Medicine, Center of Reproductive Medicine, West China Second University Hospital, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu, P.R. China
| | - Li Luo
- West China School of Basic Medical Sciences & Forensic Medicine, Center of Reproductive Medicine, West China Second University Hospital, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu, P.R. China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education , Chengdu, P.R. China
| | - Ruxin Kong
- West China School of Basic Medical Sciences & Forensic Medicine, Center of Reproductive Medicine, West China Second University Hospital, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu, P.R. China
| | - Yabing Song
- West China School of Basic Medical Sciences & Forensic Medicine, Center of Reproductive Medicine, West China Second University Hospital, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu, P.R. China
| | - Qifu Li
- Department of Neurology, the First Affiliated Hospital of Hainan Medical University, and Key Laboratory of Brain Science Research & Transformation in Tropical Environment of Hainan Province, Hainan Medical University , Haikou, P.R. China
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Monash University , Clayton, Australia
| | - Kui Wang
- West China School of Basic Medical Sciences & Forensic Medicine, Center of Reproductive Medicine, West China Second University Hospital, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu, P.R. China
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19
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Sun N, Wang Y, Wang J, Sun W, Yang J, Liu N. Highly Efficient Peptide-Based Click Chemistry for Proteomic Profiling of Nascent Proteins. Anal Chem 2020; 92:8292-8297. [PMID: 32434323 DOI: 10.1021/acs.analchem.0c00594] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Ningning Sun
- Central Laboratory, The Second Hospital of Jilin University, Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun, China
| | - Yong Wang
- College of Life Science, Shenzhen University, Shenzhen, China
| | - Jun Wang
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Wanchun Sun
- Central Laboratory, The Second Hospital of Jilin University, Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun, China
| | - Jingbo Yang
- Central Laboratory, The Second Hospital of Jilin University, Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun, China
| | - Ning Liu
- Central Laboratory, The Second Hospital of Jilin University, Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun, China
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20
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Chen H, Huang Y, Yang P, Shi Y, Ahmed N, Liu T, Bai X, Haseeb A, Chen Q. Autophagy enhances lipid droplet development during spermiogenesis in Chinese soft-shelled turtle, Pelodiscus sinensis. Theriogenology 2019; 147:154-165. [PMID: 31787469 DOI: 10.1016/j.theriogenology.2019.11.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 11/11/2019] [Accepted: 11/17/2019] [Indexed: 12/22/2022]
Abstract
Spermiogenesis is a highly organized process of the metamorphosis of round spermatids into spermatozoa in the testes. Autophagy is involved in the physiological process of spermiogenesis and its crucial role in germ-plasm clearance conserved across kingdoms. However, the fate of by-products generated through autophagy during spermiogenesis is still largely unknown. In the present study, we showed that the autophagy enhanced lipid droplets (LDs) formation during spermiogenesis in Chinese soft-shelled turtle, Pelodiscus sinensis. TEM and Oil Red O staining results found that the number and size of LDs within spermatid increased considerably during the process of spermiogenesis. RNA-Seq analysis revealed that autophagy was highly activated via the PI3K pathway during spermatogenesis. Inhibiting autophagy with 3-methyladenine (3-MA) significantly decreased testicular triglycerides (TGs) and fatty acid (FAs) content. In comparison with the control group, the number and size of LD within elongating spermatids was reduced significantly in the 3-MA group. Moreover, DGAT1, a diacylglycerol acyltransferase, which normally localize to the endoplasmic reticulum, was found to co-localize with LDs. Taken together, our results showed that FAs released through the autophagic degradation of germ-plasm was replenished LDs of spermatid, increasing LD number and size, during the process of spermiogenesis. These LDs facilitate long-term sperm storage in the epididymis of Chinese soft-shelled turtle.
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Affiliation(s)
- Hong Chen
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Yufei Huang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Ping Yang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Yonghong Shi
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Nisar Ahmed
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Tengfei Liu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Xuebing Bai
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Abdul Haseeb
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Qiusheng Chen
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China.
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21
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Activity-based proteomic profiling: The application of photoaffinity probes in the target identification of bioactive molecules. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.03.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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22
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Abstract
Measuring proteome response to perturbations is critical for understanding the underlying mechanisms involved. Traditional quantitative proteomic methods are limited by the large numbers of proteins in the proteome and the mass spectrometer's dynamic range. A previous method uses the biorthogonal reagent azidohomoalanine (AHA), a methionine analog, for labeling, enrichment and detection of newly synthesized proteins (NSPs). Newly synthesized AHA proteins can be coupled to biotin via CuAAC-mediated click chemistry and enriched using avidin-based affinity purification. The combination of AHA-mediated NSP labeling with metabolic stable isotope labeling allows quantitation of low-abundant, newly secreted proteins by mass spectrometry (MS). However, the resulting multiplicity of labeling complicates NSP analysis. We developed a new NSP quantification strategy, called HILAQ (heavy isotope-labeled azidohomoalanine quantification), that uses a heavy isotope-labeled AHA molecule to enable NSP labeling, enrichment, identification and quantification. In addition, the AHA-peptide enrichment used in HILAQ improves both the identification and quantification of NSPs over AHA-protein enrichment. Here, we provide a description of the HILAQ method that includes procedures for (i) pulse-labeling and harvesting NSPs; (ii) addition of biotin by click reaction; (iii) protein precipitation; (iv) protein digestion; (v) enrichment of AHA-biotin peptides by NeutrAvidin beads and four-step elution; (vi) MS analysis; and (vii) data analysis for the identification and quantification of NSPs by ProLuCID and pQuant. We demonstrate our HILAQ approach by identifying NSPs from cell cultures, but we anticipate that it can be adapted for applications in animal models. The whole protocol takes ~6 d to complete.
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23
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Jacomin AC, Gul L, Sudhakar P, Korcsmaros T, Nezis IP. What We Learned From Big Data for Autophagy Research. Front Cell Dev Biol 2018; 6:92. [PMID: 30175097 PMCID: PMC6107789 DOI: 10.3389/fcell.2018.00092] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 07/27/2018] [Indexed: 12/13/2022] Open
Abstract
Autophagy is the process by which cytoplasmic components are engulfed in double-membraned vesicles before being delivered to the lysosome to be degraded. Defective autophagy has been linked to a vast array of human pathologies. The molecular mechanism of the autophagic machinery is well-described and has been extensively investigated. However, understanding the global organization of the autophagy system and its integration with other cellular processes remains a challenge. To this end, various bioinformatics and network biology approaches have been developed by researchers in the last few years. Recently, large-scale multi-omics approaches (like genomics, transcriptomics, proteomics, lipidomics, and metabolomics) have been developed and carried out specifically focusing on autophagy, and generating multi-scale data on the related components. In this review, we outline recent applications of in silico investigations and big data analyses of the autophagy process in various biological systems.
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Affiliation(s)
| | - Lejla Gul
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Padhmanand Sudhakar
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
- Gut Microbes and Health Programme, Quadram Institute, Norwich Research Park, Norwich, United Kingdom
| | - Tamas Korcsmaros
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
- Gut Microbes and Health Programme, Quadram Institute, Norwich Research Park, Norwich, United Kingdom
| | - Ioannis P. Nezis
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
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24
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Ma Y, Yates JR. Proteomics and pulse azidohomoalanine labeling of newly synthesized proteins: what are the potential applications? Expert Rev Proteomics 2018; 15:545-554. [PMID: 30005169 PMCID: PMC6329588 DOI: 10.1080/14789450.2018.1500902] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Measuring the immediate changes in cells that arise from changing environmental conditions is crucial to understanding the underlying mechanisms involved. These changes can be measured with metabolic stable isotope fully labeled proteomes, but requires looking for changes in the midst of a large background. In addition, labeling efficiency can be an issue in primary and fully differentiated cells. Area covered: Azidohomoalanine (AHA), an analog of methionine, can be accepted by cellular translational machinery and incorporated into newly synthesized proteins (NSPs). AHA-NSPs can be coupled to biotin via CuAAC-mediated click-chemistry and enriched using avidin-based affinity purification. Thus, AHA-containing proteins or peptides can be enriched and efficiently separated from the whole proteome. In this review, we describe the development of mass spectrometry (MS) based AHA strategies and discuss their potential to measure proteins involved in immune response, secretome, gut microbiome, and proteostasis as well as their potential for clinical uses. Expert commentary: AHA strategies have been used to identify synthesis activity and to compare two biological conditions in various biological model organisms. In combination with instrument development, improved sample preparation and fractionation strategies, MS-based AHA strategies have the potential for broad application, and the methods should translate into clinical use.
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Affiliation(s)
- Yuanhui Ma
- a Departments of Molecular Medicine and Neurobiology , The Scripps Research Institute , La Jolla , CA , USA
| | - John R Yates
- a Departments of Molecular Medicine and Neurobiology , The Scripps Research Institute , La Jolla , CA , USA
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25
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Cudjoe EK, Saleh T, Hawkridge AM, Gewirtz DA. Proteomics Insights into Autophagy. Proteomics 2017; 17. [DOI: 10.1002/pmic.201700022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 08/25/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Emmanuel K. Cudjoe
- Department of Pharmacotherapy & Outcomes Science; Virginia Commonwealth University; Richmond VA
| | - Tareq Saleh
- Department of Pharmacology & Toxicology; Virginia Commonwealth University; Richmond VA
| | - Adam M. Hawkridge
- Department of Pharmacotherapy & Outcomes Science; Virginia Commonwealth University; Richmond VA
- Department of Pharmaceutics; Virginia Commonwealth University; Richmond VA
| | - David A. Gewirtz
- Department of Pharmacology & Toxicology; Virginia Commonwealth University; Richmond VA
- Massey Cancer Center; Virginia Commonwealth University; Richmond VA
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26
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Chen X, Zhang J, Yuan L, Lay Y, Wong YK, Lim TK, Ong CS, Lin Q, Wang J, Hua Z. Andrographolide Suppresses MV4-11 Cell Proliferation through the Inhibition of FLT3 Signaling, Fatty Acid Synthesis and Cellular Iron Uptake. Molecules 2017; 22:molecules22091444. [PMID: 28858244 PMCID: PMC6151431 DOI: 10.3390/molecules22091444] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 08/28/2017] [Accepted: 08/29/2017] [Indexed: 12/28/2022] Open
Abstract
Background: Andrographolide (ADR), the main active component of Andrographis paniculata, displays anticancer activity in various cancer cell lines, among which leukemia cell lines exhibit the highest sensitivity to ADR. In particular, ADR was also reported to have reduced drug resistance in multidrug resistant cell lines. However, the mechanism of action (MOA) of ADR’s anticancer and anti-drug-resistance activities remain elusive. Methods: In this study, we used the MV4-11 cell line, a FLT3 positive acute myeloid leukemia (AML) cell line that displays multidrug resistance, as our experimental system. We first evaluated the effect of ADR on MV4-11 cell proliferation. Then, a quantitative proteomics approach was applied to identify differentially expressed proteins in ADR-treated MV4-11 cells. Finally, cellular processes and signal pathways affected by ADR in MV4-11 cell were predicted with proteomic analysis and validated with in vitro assays. Results: ADR inhibits MV4-11 cell proliferation in a dose- and time-dependent manner. With a proteomic approach, we discovered that ADR inhibited fatty acid synthesis, cellular iron uptake and FLT3 signaling pathway in MV4-11 cells. Conclusions: ADR inhibits MV4-11 cell proliferation through inhibition of fatty acid synthesis, iron uptake and protein synthesis. Furthermore, ADR reduces drug resistance by blocking FLT3 signaling.
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Affiliation(s)
- Xiao Chen
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China.
| | - Jianbin Zhang
- Department of Oncology, Clinical Research Institute, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou 310014, China.
| | - Lixia Yuan
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China.
| | - Yifei Lay
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.
| | - Yin Kwan Wong
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.
| | - Teck Kwang Lim
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.
| | - Chye Sun Ong
- Institute of Mental Health, Education Office, Singapore 539747, Singapore.
| | - Qingsong Lin
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.
| | - Jigang Wang
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.
- Changzhou High-Tech Research Institute of Nanjing University, Institute of Biotechnology, Jiangsu Industrial Technology Research Institute and Jiangsu Target Pharma Laboratories Inc., Changzhou 213164, China.
| | - Zichun Hua
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China.
- Changzhou High-Tech Research Institute of Nanjing University, Institute of Biotechnology, Jiangsu Industrial Technology Research Institute and Jiangsu Target Pharma Laboratories Inc., Changzhou 213164, China.
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27
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Wong YK, Zhang J, Hua ZC, Lin Q, Shen HM, Wang J. Recent advances in quantitative and chemical proteomics for autophagy studies. Autophagy 2017; 13:1472-1486. [PMID: 28820289 DOI: 10.1080/15548627.2017.1313944] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Macroautophagy/autophagy is an evolutionarily well-conserved cellular degradative process with important biological functions that is closely implicated in health and disease. In recent years, quantitative mass spectrometry-based proteomics and chemical proteomics have emerged as important tools for the study of autophagy, through large-scale unbiased analysis of the proteome or through highly specific and accurate analysis of individual proteins of interest. At present, a variety of approaches have been successfully applied, including (i) expression and interaction proteomics for the study of protein post-translational modifications, (ii) investigating spatio-temporal dynamics of protein synthesis and degradation, and (iii) direct determination of protein activity and profiling molecular targets in the autophagic process. In this review, we attempted to provide an overview of principles and techniques relevant to the application of quantitative and chemical proteomics methods to autophagy, and outline the current landscape as well as future outlook of these methods in autophagy research.
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Affiliation(s)
- Yin-Kwan Wong
- a Department of Physiology, Yong Loo Lin School of Medicine , National University of Singapore , Singapore
| | - Jianbin Zhang
- b Department of Oncology, Clinical Research Institute , Zhejiang Provincial People's Hospital , Hangzhou , China
| | - Zi-Chun Hua
- c Changzhou High-Tech Research Institute of Nanjing University and the State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences , Nanjing University , Nanjing , China
| | - Qingsong Lin
- d Department of Biological Sciences , National University of Singapore , Singapore
| | - Han-Ming Shen
- a Department of Physiology, Yong Loo Lin School of Medicine , National University of Singapore , Singapore.,e NUS Graduate School for Integrative Sciences and Engineering , National University of Singapore , Singapore
| | - Jigang Wang
- a Department of Physiology, Yong Loo Lin School of Medicine , National University of Singapore , Singapore.,c Changzhou High-Tech Research Institute of Nanjing University and the State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences , Nanjing University , Nanjing , China
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28
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Wang J, Zhang J, Shi Y, Xu C, Zhang C, Wong YK, Lee YM, Krishna S, He Y, Lim TK, Sim W, Hua ZC, Shen HM, Lin Q. Mechanistic Investigation of the Specific Anticancer Property of Artemisinin and Its Combination with Aminolevulinic Acid for Enhanced Anticolorectal Cancer Activity. ACS CENTRAL SCIENCE 2017; 3:743-750. [PMID: 28776016 PMCID: PMC5532725 DOI: 10.1021/acscentsci.7b00156] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Indexed: 05/11/2023]
Abstract
The antimalarial artemisinin (ART) possesses anticancer activity, but its underlying mechanism remains largely unclear. Using a chemical proteomics approach with artemisinin-based activity probes, we identified over 300 specific ART targets. This reveals an anticancer mechanism whereby ART promiscuously targets multiple critical biological pathways and leads to cancer cell death. The specific cytotoxicity of ART against colorectal cancer (CRC) cells rather than normal colon epithelial cells is due to the elevated capacity of heme synthesis in the cancer cells. Guided by this mechanism, the specific cytotoxicity of ART toward CRC cells can be dramatically enhanced with the addition of aminolevulinic acid (ALA), a clinically used heme synthesis precursor, to increase heme levels. Importantly, this novel ART/ALA combination therapy proves to be more effective than an ART monotherapy in a mouse xenograft CRC model. Thus, ART can be repurposed and potentiated by exploitation of its mechanism of action and the metabolic features of the CRC cells.
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Affiliation(s)
- Jigang Wang
- Department
of Physiology, National University of Singapore, 117597, Singapore
- Changzhou
High-Tech Research Institute of Nanjing University and the State Key
Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, 210023, China
- Department
of Biological Sciences, National University
of Singapore, 117543, Singapore
- E-mail:
| | - Jianbin Zhang
- Department
of Physiology, National University of Singapore, 117597, Singapore
| | - Yin Shi
- Department
of Physiology, National University of Singapore, 117597, Singapore
| | - Chengchao Xu
- Department
of Biological Sciences, National University
of Singapore, 117543, Singapore
| | - Chongjing Zhang
- Department
of Biological Sciences, National University
of Singapore, 117543, Singapore
- Department
of Chemical and Biomolecular Engineering, National University of Singapore, 117585, Singapore
| | - Yin Kwan Wong
- Department
of Physiology, National University of Singapore, 117597, Singapore
| | - Yew Mun Lee
- Department
of Biological Sciences, National University
of Singapore, 117543, Singapore
| | - Sanjeev Krishna
- Institute
for Infection and Immunity, St. George’s,
University of London, London, SW17 0RE, United Kingdom
| | - Yingke He
- Department
of Anaesthesiology, Singapore General Hospital, 169608, Singapore
| | - Teck Kwang Lim
- Department
of Biological Sciences, National University
of Singapore, 117543, Singapore
| | - Weiying Sim
- Department
of Biological Sciences, National University
of Singapore, 117543, Singapore
| | - Zi-Chun Hua
- Changzhou
High-Tech Research Institute of Nanjing University and the State Key
Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Han-Ming Shen
- Department
of Physiology, National University of Singapore, 117597, Singapore
- E-mail:
| | - Qingsong Lin
- Department
of Biological Sciences, National University
of Singapore, 117543, Singapore
- E-mail:
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29
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Stastna M, Gottlieb RA, Van Eyk JE. Exploring ribosome composition and newly synthesized proteins through proteomics and potential biomedical applications. Expert Rev Proteomics 2017; 14:529-543. [PMID: 28532181 DOI: 10.1080/14789450.2017.1333424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
INTRODUCTION Protein synthesis is the outcome of tightly regulated gene expression which is responsive to a variety of conditions. Efforts are ongoing to monitor individual stages of protein synthesis to ensure maximum efficiency and accuracy. Due to post-transcriptional regulation mechanisms, the correlation between translatome and proteome is higher than between transcriptome and proteome. However, the most accurate approach to assess the key modulators and final protein expression is directly by using proteomics. Areas covered: This review covers various proteomic strategies that were used to better understand post-transcriptional regulation, specifically during and early after translation. The methods that identify both regulatory proteins associated with translational components and newly synthesized proteins are discussed. Expert commentary: Emerging proteomic approaches make it possible to monitor protein dynamics in cells, tissues and whole animals. The ability to detect alteration in protein abundance soon after their synthesis enables earlier recognition of disease causing factors and candidates to prevent/rectify disease phenotype.
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Affiliation(s)
- Miroslava Stastna
- a Heart Institute , Cedars-Sinai Medical Center , Los Angeles , CA , USA.,b Advanced Clinical BioSystems Research Institute , Cedars-Sinai Medical Center , Los Angeles , CA , USA.,c Institute of Analytical Chemistry of the Czech Academy of Sciences, v. v. i ., Brno , Czech Republic
| | - Roberta A Gottlieb
- a Heart Institute , Cedars-Sinai Medical Center , Los Angeles , CA , USA
| | - Jennifer E Van Eyk
- a Heart Institute , Cedars-Sinai Medical Center , Los Angeles , CA , USA.,b Advanced Clinical BioSystems Research Institute , Cedars-Sinai Medical Center , Los Angeles , CA , USA
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30
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Tang HM, Talbot CC, Fung MC, Tang HL. Molecular signature of anastasis for reversal of apoptosis. F1000Res 2017; 6:43. [PMID: 28299189 DOI: 10.12688/f1000research.10568.1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/10/2017] [Indexed: 12/22/2022] Open
Abstract
Anastasis (Greek for "rising to life") is a cell recovery phenomenon that rescues dying cells from the brink of cell death. We recently discovered anastasis to occur after the execution-stage of apoptosis in vitro and in vivo. Promoting anastasis could in principle preserve injured cells that are difficult to replace, such as cardiomyocytes and neurons. Conversely, arresting anastasis in dying cancer cells after cancer therapies could improve treatment efficacy. To develop new therapies that promote or inhibit anastasis, it is essential to identify the key regulators and mediators of anastasis - the therapeutic targets. Therefore, we performed time-course microarray analysis to explore the molecular mechanisms of anastasis during reversal of ethanol-induced apoptosis in mouse primary liver cells. We found striking changes in transcription of genes involved in multiple pathways, including early activation of pro-cell survival, anti-oxidation, cell cycle arrest, histone modification, DNA-damage and stress-inducible responses, and at delayed times, angiogenesis and cell migration. Validation with RT-PCR confirmed similar changes in the human liver cancer cell line, HepG2, during anastasis. Here, we present the time-course whole-genome gene expression dataset revealing gene expression profiles during the reversal of apoptosis. This dataset provides important insights into the physiological, pathological, and therapeutic implications of anastasis.
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Affiliation(s)
- Ho Man Tang
- Institute for Basic Biomedical Sciences, Johns Hopkins University School of Medicine, Baltimore, USA
| | - C Conover Talbot
- Institute for Basic Biomedical Sciences, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Ming Chiu Fung
- School of Life Sciences, Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ho Lam Tang
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, USA
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31
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Abstract
Anastasis (Greek for "rising to life") is a cell recovery phenomenon that rescues dying cells from the brink of cell death. We recently discovered anastasis to occur after the execution-stage of apoptosis
in vitro and
in vivo. Promoting anastasis could in principle preserve injured cells that are difficult to replace, such as cardiomyocytes and neurons. Conversely, arresting anastasis in dying cancer cells after cancer therapies could improve treatment efficacy. To develop new therapies that promote or inhibit anastasis, it is essential to identify the key regulators and mediators of anastasis – the therapeutic targets. Therefore, we performed time-course microarray analysis to explore the molecular mechanisms of anastasis during reversal of ethanol-induced apoptosis in mouse primary liver cells. We found striking changes in transcription of genes involved in multiple pathways, including early activation of pro-cell survival, anti-oxidation, cell cycle arrest, histone modification, DNA-damage and stress-inducible responses, and at delayed times, angiogenesis and cell migration. Validation with RT-PCR confirmed similar changes in the human liver cancer cell line, HepG2, during anastasis. Here, we present the time-course whole-genome gene expression dataset revealing gene expression profiles during the reversal of apoptosis. This dataset provides important insights into the physiological, pathological, and therapeutic implications of anastasis.
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Affiliation(s)
- Ho Man Tang
- Institute for Basic Biomedical Sciences, Johns Hopkins University School of Medicine, Baltimore, USA
| | - C Conover Talbot
- Institute for Basic Biomedical Sciences, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Ming Chiu Fung
- School of Life Sciences, Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ho Lam Tang
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, USA
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32
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Drug Target Identification Using an iTRAQ-Based Quantitative Chemical Proteomics Approach—Based on a Target Profiling Study of Andrographolide. Methods Enzymol 2017; 586:291-309. [DOI: 10.1016/bs.mie.2016.09.049] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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33
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Chen X, Wong YK, Wang J, Zhang J, Lee YM, Shen HM, Lin Q, Hua ZC. Target identification with quantitative activity based protein profiling (ABPP). Proteomics 2016; 17. [PMID: 27723264 DOI: 10.1002/pmic.201600212] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/14/2016] [Accepted: 10/06/2016] [Indexed: 12/20/2022]
Abstract
As many small bioactive molecules fulfill their functions through interacting with protein targets, the identification of such targets is crucial in understanding their mechanisms of action (MOA) and side effects. With technological advancements in target identification, it has become possible to accurately and comprehensively study the MOA and side effects of small molecules. While small molecules with therapeutic potential were derived solely from nature in the past, the remodeling and synthesis of such molecules have now been made possible. Presently, while some small molecules have seen successful application as drugs, the majority remain undeveloped, requiring further understanding of their MOA and side effects to fully tap into their potential. Given the typical promiscuity of many small molecules and the complexity of the cellular proteome, a high-flux and high-accuracy method is necessary. While affinity chromatography approaches combined with MS have had successes in target identification, limitations associated with nonspecific results remain. To overcome these complications, quantitative chemical proteomics approaches have been developed including metabolic labeling, chemical labeling, and label-free methods. These new approaches are adopted in conjunction with activity-based protein profiling (ABPP), allowing for a rapid process and accurate results. This review will briefly introduce the principles involved in ABPP, then summarize current advances in quantitative chemical proteomics approaches as well as illustrate with examples how ABPP coupled with quantitative chemical proteomics has been used to detect the targets of drugs and other bioactive small molecules including natural products.
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Affiliation(s)
- Xiao Chen
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, P. R., China
| | - Yin Kwan Wong
- Department of Biological Sciences, National University of Singapore, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jigang Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, P. R., China.,Department of Biological Sciences, National University of Singapore, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Interdisciplinary Research Group in Infectious Diseases, Singapore-MIT Alliance for Research & Technology (SMART), Singapore
| | - Jianbin Zhang
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Clinical Research Institute, Zhejiang Provincial People's Hospital, Hangzhou, P. R., China
| | - Yew-Mun Lee
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Han-Ming Shen
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
| | - Qingsong Lin
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Zi-Chun Hua
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, P. R., China
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34
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Zhang J, Wang J, Lee YM, Lim TK, Lin Q, Shen HM. Proteomic Profiling of De Novo Protein Synthesis in Starvation-Induced Autophagy Using Bioorthogonal Noncanonical Amino Acid Tagging. Methods Enzymol 2016; 588:41-59. [PMID: 28237112 DOI: 10.1016/bs.mie.2016.09.075] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Autophagy is an intracellular degradation process activated by stress factors such as nutrient starvation to maintain cellular homeostasis. There is emerging evidence demonstrating that de novo protein synthesis is involved in the autophagic process. However, up-to-date characterizing of these de novo proteins is technically difficult. In this chapter, we describe a novel method to identify newly synthesized proteins during starvation-mediated autophagy by bioorthogonal noncanonical amino acid tagging (BONCAT), in conjunction with isobaric tagging for relative and absolute quantification (iTRAQ)-based quantitative proteomics. l-azidohomoalanine (AHA) is an analog of methionine, and it can be readily incorporated into the newly synthesized proteins. The AHA-containing proteins can be enriched with avidin beads after a "click" reaction between alkyne-bearing biotin and the azide moiety of AHA. The enriched proteins are then subjected to iTRAQ™ labeling for protein identification and quantification using liquid chromatography-tandem mass spectrometry (LC-MS/MS). By using this technique, we have successfully profiled more than 700 proteins that are synthesized during starvation-induced autophagy. We believe that this approach is effective in identification of newly synthesized proteins in the process of autophagy and provides useful insights to the molecular mechanisms and biological functions of autophagy.
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Affiliation(s)
- J Zhang
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - J Wang
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore; National University of Singapore, Singapore, Singapore; Interdisciplinary Research Group in Infectious Diseases, Singapore-MIT Alliance for Research & Technology (SMART), Singapore
| | - Y-M Lee
- National University of Singapore, Singapore, Singapore
| | - T-K Lim
- National University of Singapore, Singapore, Singapore
| | - Q Lin
- National University of Singapore, Singapore, Singapore.
| | - H-M Shen
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore; NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore.
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