1
|
Ma H, Hu B, Zhang Y, Li F, Liu Y, Zhan J, Liu Y, Yi X, Zhou H. Ca 2+-controlled Mn(II) removal process in Aurantimonas sp. HBX-1: Microbially-induced carbonate precipitation (MICP) versus Mn(II) oxidation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 951:175482. [PMID: 39147049 DOI: 10.1016/j.scitotenv.2024.175482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2024] [Revised: 08/09/2024] [Accepted: 08/11/2024] [Indexed: 08/17/2024]
Abstract
The application of manganese-oxidizing bacteria (MnOB) to produce manganese oxides (MnOx) has been widely studied, but often overlooking the concurrent formation of MnCO3. In this study, we found Ca2+ plays a crucial role in controlling Mn(II) removal in the bacterium Aurantimonas sp. HBX-1. Under conditions with 6.8 mM Ca2+ and without adding Ca2+, 100 μM Mn(II) was removed by 96.96 % and 38.28 % within 8 days, respectively. X-ray photoelectron spectroscopy (XPS) showed that adding Ca2+ increased the average oxidation state (AOS) of the solid products from 2.05 to 2.37. X-ray absorption fine structure (XAFS) analysis revealed the product proportions as follows: under Ca2+-supplemented condition, the ratio of MnOx (1 < x ≤ 2) to MnCO₃ was 52 % to 28.1 %, while under Ca2+-free condition, the ratio shifted to 4.6 % for MnOx (1 < x ≤ 2) and 55.2 % for MnCO₃. Urease activity assay and proteomic analysis confirmed the expression of urease and carbonic anhydrase, leading to the formation of MnCO3. Additionally, animal heme peroxidase (AHP) in strain HBX-1 was found to be responsible for Mn(II) oxidation through superoxide production, with Ca2+ addition promoting its expression level. Given the widespread presence of Ca2+ in wastewater, its potential impact on the biogeochemical Mn(II) cycle driven by bacteria should be reconsidered.
Collapse
Affiliation(s)
- Huiqing Ma
- Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education, School of Chemical Engineering, Ocean and Life Sciences, Panjin Campus, Dalian University of Technology, China; Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education, China, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Bingxin Hu
- College of Engineering, Peking University, Beijing 100871, China
| | - Yu Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education, China, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Fei Li
- Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education, School of Chemical Engineering, Ocean and Life Sciences, Panjin Campus, Dalian University of Technology, China
| | - Yu Liu
- Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education, School of Chemical Engineering, Ocean and Life Sciences, Panjin Campus, Dalian University of Technology, China
| | - Jingjing Zhan
- Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education, School of Chemical Engineering, Ocean and Life Sciences, Panjin Campus, Dalian University of Technology, China
| | - Yang Liu
- Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education, School of Chemical Engineering, Ocean and Life Sciences, Panjin Campus, Dalian University of Technology, China
| | - Xianliang Yi
- Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education, School of Chemical Engineering, Ocean and Life Sciences, Panjin Campus, Dalian University of Technology, China
| | - Hao Zhou
- Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education, School of Chemical Engineering, Ocean and Life Sciences, Panjin Campus, Dalian University of Technology, China.
| |
Collapse
|
2
|
Huang Y, Luo G, Peng K, Song Y, Wang Y, Zhang H, Li J, Qiu X, Pu M, Liu X, Peng C, Neculai D, Sun Q, Zhou T, Huang P, Liu W. Lactylation stabilizes TFEB to elevate autophagy and lysosomal activity. J Cell Biol 2024; 223:e202308099. [PMID: 39196068 PMCID: PMC11354204 DOI: 10.1083/jcb.202308099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 02/04/2024] [Accepted: 04/03/2024] [Indexed: 08/29/2024] Open
Abstract
The transcription factor TFEB is a major regulator of lysosomal biogenesis and autophagy. There is growing evidence that posttranslational modifications play a crucial role in regulating TFEB activity. Here, we show that lactate molecules can covalently modify TFEB, leading to its lactylation and stabilization. Mechanically, lactylation at K91 prevents TFEB from interacting with E3 ubiquitin ligase WWP2, thereby inhibiting TFEB ubiquitination and proteasome degradation, resulting in increased TFEB activity and autophagy flux. Using a specific antibody against lactylated K91, enhanced TFEB lactylation was observed in clinical human pancreatic cancer samples. Our results suggest that lactylation is a novel mode of TFEB regulation and that lactylation of TFEB may be associated with high levels of autophagy in rapidly proliferating cells, such as cancer cells.
Collapse
Affiliation(s)
- Yewei Huang
- Center for Metabolism Research, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University , Yiwu, China
| | - Gan Luo
- Center for Metabolism Research, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University , Yiwu, China
| | - Kesong Peng
- Center for Metabolism Research, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University , Yiwu, China
| | - Yue Song
- Department of Ultrasound Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Yusha Wang
- Center for Metabolism Research, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University , Yiwu, China
| | - Hongtao Zhang
- Center for Metabolism Research, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University , Yiwu, China
| | - Jin Li
- Center for Metabolism Research, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University , Yiwu, China
| | - Xiangmin Qiu
- Center for Metabolism Research, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University , Yiwu, China
| | - Maomao Pu
- Center for Metabolism Research, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University , Yiwu, China
| | - Xinchang Liu
- Center for Metabolism Research, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University , Yiwu, China
| | - Chao Peng
- National Center for Protein Science Shanghai, Institute of Biochemistry and Cell Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences , Shanghai, China
| | - Dante Neculai
- Center for Metabolism Research, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University , Yiwu, China
| | - Qiming Sun
- Center for Metabolism Research, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University , Yiwu, China
| | - Tianhua Zhou
- Center for Metabolism Research, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University , Yiwu, China
| | - Pintong Huang
- Department of Ultrasound Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Wei Liu
- Center for Metabolism Research, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University , Yiwu, China
- Department of Ultrasound Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| |
Collapse
|
3
|
Shen J, Qiao L. Proteomic and metabolic analysis of Moorella thermoacetica-g-C 3N 4 nanocomposite system for artificial photosynthesis. Talanta 2024; 278:126479. [PMID: 38941811 DOI: 10.1016/j.talanta.2024.126479] [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: 03/06/2024] [Revised: 06/18/2024] [Accepted: 06/24/2024] [Indexed: 06/30/2024]
Abstract
Artificial photosynthesis by microbe-semiconductor biohybrid systems has been demonstrated as a valuable strategy in providing sustainable energy and in carbon fixation. However, most of the developed biohybrid systems for light harvesting employ heavy metal materials, especially cadmium sulfide (CdS), which normally cause environmental pollution and restrict the widespread of the systems. Herein, we constructed an environmentally friendly biohybirid system based on a typical acetogenic bacteria, Moorella thermoacetica, coupling with a carbon-based semiconductor, graphitic carbon nitride (g-C3N4), to realize light-driven carbon fixation. The proposed biohybrid system displayed outstanding acetate productivity with a quantum yield of 2.66 ± 0.43 %. Non-targeted proteomic analysis indicated that the physiological activity of the bacteria was improved, coupling with the non-toxic material. We further proposed the mechanisms of energy generation, electron transfer and CO2 fixation of the irradiated biohybrid system by proteomic and metabolomic characterization. With the photoelectron generated in g-C3N4 under illumination, CO2 is finally converted to acetate via the Wood-Ljungdahl pathway (WLP). Other associated pathways were also proved to be activated, providing extra energy or substrates for acetate production. The study reveals that the future focus of the development of biohybrid systems for light harvesting can be on the metal-free biocompatible material, which can activate the expression of the key enzymes involved in the electron transfer and carbon metabolism under light irradiation.
Collapse
Affiliation(s)
- Jiayuan Shen
- Department of Chemistry, and Minhang Hospital, Fudan University, Shanghai, 200000, China
| | - Liang Qiao
- Department of Chemistry, and Minhang Hospital, Fudan University, Shanghai, 200000, China.
| |
Collapse
|
4
|
Zhang H, Gao C, Yang D, Nie L, He K, Chen C, Li S, Huang G, Zhou L, Huang X, Wu D, Liu J, Huang Z, Wang J, Li W, Zhang Z, Yang X, Zou L. Urolithin a Improves Motor Dysfunction Induced by Copper Exposure in SOD1 G93A Transgenic Mice Via Activation of Mitophagy. Mol Neurobiol 2024:10.1007/s12035-024-04473-1. [PMID: 39292338 DOI: 10.1007/s12035-024-04473-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 08/30/2024] [Indexed: 09/19/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease pathologically characterized by selective degeneration of motor neurons resulting in a catastrophic loss of motor function. The present study aimed to investigate the effect of copper (Cu) exposure on progression of ALS and explore the therapeutic effect and mechanism of Urolithin A (UA) on ALS. 0.13 PPM copper chloride drinking water was administrated in SOD1G93A transgenic mice at 6 weeks, UA at a dosage of 50 mg/kg/day was given for 6 weeks after a 7-week Cu exposure. Motor ability was assessed before terminal anesthesia. Muscle atrophy and fibrosis, motor neurons, astrocytes and microglia in the spinal cord were evaluated by H&E, Masson, Sirius Red, Nissl and Immunohistochemistry Staining. Proteomics analysis, Western blotting and ELISA were conducted to detect protein expression. Mitochondrial adenosine triphosphate (ATP) and malondialdehyde (MDA) levels were measured using an assay kit. Cu-exposure worsened motor function, promoted muscle fibrosis, loss of motor neurons, and astrocyte and microglial activation. It also induced abnormal changes in mitochondria-related biological processes, leading to a significant reduction in ATP levels and an increase in MDA levels. Upregulation of P62 and downregulation of Parkin, PINK1, and LAMP1 were revealed in SOD1G93A mice with Cu exposure. Administration of UA activated mitophagy, modulated mitochondria dysfunction, reduced neuroinflammation, and improved gastrocnemius muscle atrophy and motor dysfunction in SOD1G93A mice with Cu exposure. Mitophagy plays critical role in ALS exacerbated by Cu exposure. UA administration may be a promising treatment strategy for ALS.
Collapse
Affiliation(s)
- Huan Zhang
- Shenzhen Key Laboratory of Modern Toxicology, Shenzhen Medical Key Discipline of Health Toxicology (2020-2024), Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Chuanyue Gao
- Shenzhen Key Laboratory of Modern Toxicology, Shenzhen Medical Key Discipline of Health Toxicology (2020-2024), Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
- Xi'an International Medical Center Hospital, Xi'an, 710100, China
| | - Deguang Yang
- Department of Cardiology, The Fifth Affiliated Hospital of Jinan University (Heyuan Shenhe People's Hospital), Heyuan, 517000, China
| | - Lulin Nie
- Shenzhen Key Laboratory of Modern Toxicology, Shenzhen Medical Key Discipline of Health Toxicology (2020-2024), Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
- College of Pharmacy, Jinan University, Guangzhou, 510632, China
| | - Kaiwu He
- Shenzhen Key Laboratory of Modern Toxicology, Shenzhen Medical Key Discipline of Health Toxicology (2020-2024), Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Chongyang Chen
- Shenzhen Key Laboratory of Modern Toxicology, Shenzhen Medical Key Discipline of Health Toxicology (2020-2024), Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Shangming Li
- Shenzhen Key Laboratory of Modern Toxicology, Shenzhen Medical Key Discipline of Health Toxicology (2020-2024), Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Guanqin Huang
- Shenzhen Key Laboratory of Modern Toxicology, Shenzhen Medical Key Discipline of Health Toxicology (2020-2024), Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Li Zhou
- Shenzhen Key Laboratory of Modern Toxicology, Shenzhen Medical Key Discipline of Health Toxicology (2020-2024), Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Xinfeng Huang
- Shenzhen Key Laboratory of Modern Toxicology, Shenzhen Medical Key Discipline of Health Toxicology (2020-2024), Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Desheng Wu
- Shenzhen Key Laboratory of Modern Toxicology, Shenzhen Medical Key Discipline of Health Toxicology (2020-2024), Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Jianjun Liu
- Shenzhen Key Laboratory of Modern Toxicology, Shenzhen Medical Key Discipline of Health Toxicology (2020-2024), Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Zhenlie Huang
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Jie Wang
- Department of Neurology, Shenzhen People's Hospital (First Affiliated Hospital of Southern University of Science and Technology), Second Clinical College, Jinan University, Shenzhen, China
| | - Weihua Li
- Department of Medical Imaging, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, 518035, China
| | - Zhaohui Zhang
- School of Public Health, University of South China, Hunan Hengyang, 421001, China.
| | - Xifei Yang
- Shenzhen Key Laboratory of Modern Toxicology, Shenzhen Medical Key Discipline of Health Toxicology (2020-2024), Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China.
| | - Liangyu Zou
- Department of Neurology, Shenzhen People's Hospital (First Affiliated Hospital of Southern University of Science and Technology), Second Clinical College, Jinan University, Shenzhen, China.
| |
Collapse
|
5
|
Gao X, Gao G, Zheng W, Liu H, Pan W, Xia X, Zhang D, Lin W, Wang Z, Feng B. PARylation of 14-3-3 proteins controls the virulence of Magnaporthe oryzae. Nat Commun 2024; 15:8047. [PMID: 39277621 PMCID: PMC11401899 DOI: 10.1038/s41467-024-51955-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 08/20/2024] [Indexed: 09/17/2024] Open
Abstract
Magnaporthe oryzae is a devastating fungal pathogen that causes the rice blast disease worldwide. The post-translational modification of ADP-ribosylation holds significant importance in various fundamental biological processes. However, the specific function of this modification in M. oryzae remains unknown. This study revealed that Poly(ADP-ribosyl)ation (PARylation) executes a critical function in M. oryzae. M. oryzae Poly(ADP-ribose) polymerase 1 (PARP1) exhibits robust PARylation activity. Disruption of PARylation by PARP1 knock-out or chemical inhibition reveals its involvement in M. oryzae virulence, particularly in appressorium formation. Furthermore, we identified two M. oryzae 14-3-3 proteins, GRF1 and GRF2, as substrates of PARP1. Deletion of GRF1 or GRF2 results in delayed and dysfunctional appressorium, diminished plant penetration, and reduced virulence of the fungus. Biochemical and genetic evidence suggest that PARylation of 14-3-3s is essential for its function in M. oryzae virulence. Moreover, PARylation regulates 14-3-3 dimerization and is required for the activation of the mitogen-activated protein kinases (MAPKs), Pmk1 and Mps1. GRF1 interacts with both Mst7 and Pmk1, and bridges their interaction in a PARylation-dependent manner. This study unveils a distinctive mechanism that PARylation of 14-3-3 proteins controls appressorium formation through MAPK activation, and could facilitate the development of new strategies of rice blast disease control.
Collapse
Affiliation(s)
- Xiuqin Gao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Gaigai Gao
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Weifeng Zheng
- College of Jun Cao Science and Ecology (College of Carbon Neutrality), Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Haibing Liu
- Plant Immunity Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wenbo Pan
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xi Xia
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Dongmei Zhang
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wenwei Lin
- College of Jun Cao Science and Ecology (College of Carbon Neutrality), Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, 350108, China.
| | - Baomin Feng
- Plant Immunity Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| |
Collapse
|
6
|
Luo P, Zhao Z, Yang F, Zhang L, Li S, Qiao Y, Zhang L, Yang M, Zhou X, Zhao L, Yang Y, Tang X, Shi C. Stress-Induced Autophagy Is Essential for Microspore Cell Fate Transition to the Initial Cell of Androgenesis. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39267528 DOI: 10.1111/pce.15158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 08/23/2024] [Accepted: 09/02/2024] [Indexed: 09/17/2024]
Abstract
The isolated microspores can be reprogrammed towards embryogenesis via stress treatment during in vitro culture, and produce (doubled) haploid plants as a breeding source of new genetic variability. However, the mechanism underlying the cell fate transition from gametogenesis to embryogenesis remains largely unknown. Here, we report that autophagy plays a key role in cell fate transition for microspore embryogenesis (referred to as androgenesis) in Nicotiana tabacum. Immunofluorescence and transmission electronic microscopy detection unveiled that autophagy was triggered in microspores following exposure to inductive stress, and a transient wave of the numerous autophagy-related genes (ATGs) expression occurred before the initiation of microspore embryogenesis. Suppression or promotion of the original autophagy levels could inhibit microspore embryogenesis, indicating that stress-induced autophagic homeostasis is essential for cell fate transition. Furthermore, quantitative proteomics analysis revealed that autophagy might be involved in lignin biosynthesis and chromatin decondensation for promoting reprogramming for androgenesis initiation. Altogether, we reveal an essential role of autophagy in the microspore cell fate transition and androgenesis initiation, providing novel insight for understanding this critical developmental process.
Collapse
Affiliation(s)
- Pan Luo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Science, Hubei University, Wuhan, China
| | - Zifu Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Fan Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Science, Hubei University, Wuhan, China
| | - Lai Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Science, Hubei University, Wuhan, China
| | - Siyuan Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Science, Hubei University, Wuhan, China
| | - Ying Qiao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Science, Hubei University, Wuhan, China
| | - Liangxinyi Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Science, Hubei University, Wuhan, China
| | - Mingchun Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Science, Hubei University, Wuhan, China
| | - Xiaotong Zhou
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Science, Hubei University, Wuhan, China
| | - Linlin Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yong Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Science, Hubei University, Wuhan, China
| | - Xingchun Tang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Science, Hubei University, Wuhan, China
| | - Ce Shi
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| |
Collapse
|
7
|
He J, Ao C, Li M, Deng T, Zheng S, Zhang K, Tu C, Ouyang Y, Lang R, Jiang Y, Yang Y, Li C, Wu D. Clusterin-carrying extracellular vesicles derived from human umbilical cord mesenchymal stem cells restore the ovarian function of premature ovarian failure mice through activating the PI3K/AKT pathway. Stem Cell Res Ther 2024; 15:300. [PMID: 39272156 PMCID: PMC11401318 DOI: 10.1186/s13287-024-03926-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 09/05/2024] [Indexed: 09/15/2024] Open
Abstract
BACKGROUND Emerging evidence has highlighted the therapeutic potential of human umbilical cord mesenchymal stem cells (UC-MSCs) in chemotherapy-induced premature ovarian failure (POF). This study was designed to investigate the appropriate timing and molecular mechanism of UC-MSCs treatment for chemotherapy-induced POF. METHODS Ovarian structure and function of mice were assessed every 3 days after injections with cyclophosphamide (CTX) and busulfan (BUS). UC-MSCs and UC-MSCs-derived extracellular vesicles (EVs) were infused into mice via the tail vein, respectively. Ovarian function was analyzed by follicle counts, the serum levels of hormones and ovarian morphology. The apoptosis and proliferation of ovarian granulosa cells were analyzed in vitro and in vivo. Label-free quantitative proteomics was used to detect the differentially expressed proteins in UC-MSC-derived EVs. RESULTS After CTX/BUS injection, we observed that the ovarian function of POF mice was significantly deteriorated on day 9 after CTX/BUS infusion. TUNEL assay indicated that the number of apoptotic cells in the ovaries of POF mice was significantly higher than that in normal mice on day 3 after CTX/BUS injection. Transplantation of UC-MSCs on day 6 after CTX/BUS injection significantly improved ovarian function, enhanced proliferation and inhibited apoptosis of ovarian granulosa cells, whereas the therapeutic effect of UC-MSCs transplantation decreased on day 9, or day 12 after CTX/BUS injection. Moreover, EVs derived from UC-MSCs exerted similar therapeutic effects on POF. UC-MSCs-derived EVs could activate the PI3K/AKT signaling pathway and reduce ovarian granulosa cell apoptosis. Quantitative proteomics analysis revealed that clusterin (CLU) was highly expressed in the EVs of UC-MSCs. The supplementation of CLU proteins prevented ovarian granulosa cells from chemotherapy-induced apoptosis. Further mechanistic analysis showed that CLU-knockdown blocked the PI3K/AKT signaling and reversed the protective effects of UC-MSCs-derived EVs. CONCLUSIONS Administration of UC-MSCs and UC-MSCs-derived EVs on day 6 of CTX/BUS injection could effectively improve the ovarian function of POF mice. UC-MSCs-derived EVs carrying CLU promoted proliferation and inhibited apoptosis of ovarian granulosa cells through activating the PI3K/AKT pathway. This study identifies a previously unrecognized molecular mechanism of UC-MSCs-mediated protective effects on POF, which pave the way for the use of cell-free therapeutic approach for POF.
Collapse
Affiliation(s)
- Jing He
- Department of Biochemistry and Molecular Biology, Wuhan University School of Basic Medical Sciences, Wuhan, China
| | - Chunchun Ao
- Department of Biochemistry and Molecular Biology, Wuhan University School of Basic Medical Sciences, Wuhan, China
| | - Mao Li
- College of Life Sciences, Hubei University, Wuhan, China
| | - Taoran Deng
- Reproductive Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shuo Zheng
- R&D Center, Wuhan Hamilton Biotechnology Co., Ltd, Wuhan, China
| | - Ke Zhang
- Department of Biochemistry and Molecular Biology, Wuhan University School of Basic Medical Sciences, Wuhan, China
| | - Chengshu Tu
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yu Ouyang
- Department of Biochemistry and Molecular Biology, Wuhan University School of Basic Medical Sciences, Wuhan, China
| | - Ruibo Lang
- Department of Biochemistry and Molecular Biology, Wuhan University School of Basic Medical Sciences, Wuhan, China
| | - Yijia Jiang
- Department of Biochemistry and Molecular Biology, Wuhan University School of Basic Medical Sciences, Wuhan, China
| | - Yifan Yang
- Department of Biochemistry and Molecular Biology, Wuhan University School of Basic Medical Sciences, Wuhan, China
| | - Changyong Li
- Department of Physiology, Wuhan University School of Basic Medical Sciences, Wuhan, China.
- Xianning Medical College, Hubei University of Science and Technology, Xianning, China.
| | - Dongcheng Wu
- Department of Biochemistry and Molecular Biology, Wuhan University School of Basic Medical Sciences, Wuhan, China.
- R&D Center, Wuhan Hamilton Biotechnology Co., Ltd, Wuhan, China.
- R&D Center, Guangzhou Hamilton Biotechnology Co., Ltd, Guangzhou, China.
| |
Collapse
|
8
|
Li HY, Wang M, Jiang X, Jing Y, Wu Z, He Y, Yan K, Sun S, Ma S, Ji Z, Wang S, Belmonte JCI, Qu J, Zhang W, Wei T, Liu GH. CRISPR screening uncovers nucleolar RPL22 as a heterochromatin destabilizer and senescence driver. Nucleic Acids Res 2024:gkae740. [PMID: 39258545 DOI: 10.1093/nar/gkae740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 08/02/2024] [Accepted: 08/16/2024] [Indexed: 09/12/2024] Open
Abstract
Dysfunction of the ribosome manifests during cellular senescence and contributes to tissue aging, functional decline, and development of aging-related disorders in ways that have remained enigmatic. Here, we conducted a comprehensive CRISPR-based loss-of-function (LOF) screen of ribosome-associated genes (RAGs) in human mesenchymal progenitor cells (hMPCs). Through this approach, we identified ribosomal protein L22 (RPL22) as the foremost RAG whose deficiency mitigates the effects of cellular senescence. Consequently, absence of RPL22 delays hMPCs from becoming senescent, while an excess of RPL22 accelerates the senescence process. Mechanistically, we found in senescent hMPCs, RPL22 accumulates within the nucleolus. This accumulation triggers a cascade of events, including heterochromatin decompaction with concomitant degradation of key heterochromatin proteins, specifically heterochromatin protein 1γ (HP1γ) and heterochromatin protein KRAB-associated protein 1 (KAP1). Subsequently, RPL22-dependent breakdown of heterochromatin stimulates the transcription of ribosomal RNAs (rRNAs), triggering cellular senescence. In summary, our findings unveil a novel role for nucleolar RPL22 as a destabilizer of heterochromatin and a driver of cellular senescence, shedding new light on the intricate mechanisms underlying the aging process.
Collapse
Affiliation(s)
- Hong-Yu Li
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Xiaoyu Jiang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Yaobin Jing
- International center for Aging and Cancer, Hainan Academy of Medical Sciences, Hainan Medical University, Haikou 571199, China
| | - Zeming Wu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Yifang He
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Kaowen Yan
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuhui Sun
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuai Ma
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Aging Biomarker Consortium, Beijing 100101, China
| | - Zhejun Ji
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Si Wang
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, China
- Aging Translational Medicine Center, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing, China
- Aging Biomarker Consortium, Beijing 100101, China
| | | | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Aging Biomarker Consortium, Beijing 100101, China
| | - Weiqi Zhang
- CAS key laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Aging Biomarker Consortium, Beijing 100101, China
| | - Taotao Wei
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- International center for Aging and Cancer, Hainan Academy of Medical Sciences, Hainan Medical University, Haikou 571199, China
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, China
- Aging Translational Medicine Center, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing, China
- Aging Biomarker Consortium, Beijing 100101, China
| |
Collapse
|
9
|
Zhong L, Zheng J, Wang Z, Lin L, Cong Q, Qiao L. Metabolomics and proteomics reveal the inhibitory effect of Lactobacillus crispatus on cervical cancer. Talanta 2024; 281:126839. [PMID: 39265423 DOI: 10.1016/j.talanta.2024.126839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Revised: 09/04/2024] [Accepted: 09/07/2024] [Indexed: 09/14/2024]
Abstract
Cervical cancer remains a significant global health issue due to its high morbidity and mortality rates. Recently, Lactobacillus crispatus has been recognized for its crucial role in maintaining cervical health. While some studies have explored the use of L. crispatus to mitigate cervical cancer, the underlying mechanisms remain largely unknown. In this study, we employed non-targeted proteomics and metabolomics to investigate how L. crispatus affects the growth of cervical cancer cells (SiHa) and normal cervical cells (Ect1/E6E7). Our findings indicated that the inhibitory effect of L. crispatus on SiHa cells was associated with various biological processes, notably the ferroptosis pathway. Specifically, L. crispatus was found to regulate the expression of proteins such as HMOX1, SLC39A14, VDAC2, ACSL4, and LPCAT3 by SiHa cells, which are closely related to ferroptosis. Additionally, it activated the tricarboxylic acid (TCA) cycle in SiHa cells, leading to increased levels of reactive oxygen species (ROS) and lipid peroxides (LPO). These results revealed the therapeutic potential of L. crispatus in targeting the ferroptosis pathway for cervical cancer treatment, opening new avenues for research and therapy in cervical cancer.
Collapse
Affiliation(s)
- Lingyan Zhong
- Department of Chemistry, Zhongshan Hospital, and Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200000, China
| | - Jianxujie Zheng
- Department of Chemistry, Zhongshan Hospital, and Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200000, China
| | - Zengyu Wang
- Department of Chemistry, Zhongshan Hospital, and Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200000, China
| | - Ling Lin
- Department of Chemistry, Zhongshan Hospital, and Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200000, China.
| | - Qing Cong
- Department of Chemistry, Zhongshan Hospital, and Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200000, China.
| | - Liang Qiao
- Department of Chemistry, Zhongshan Hospital, and Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200000, China.
| |
Collapse
|
10
|
Lu C, Cai Y, Wu S, Wang Y, Li JB, Xu G, Ma J. Deubiquitinating enzyme USP39 promotes the growth and metastasis of gastric cancer cells by modulating the degradation of RNA-binding protein RBM39. J Biol Chem 2024:107751. [PMID: 39260689 DOI: 10.1016/j.jbc.2024.107751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 08/05/2024] [Accepted: 08/26/2024] [Indexed: 09/13/2024] Open
Abstract
It has been revealed recently that the RNA-binding motif protein RBM39 is highly expressed in several cancers, which results in poor patient survival. However, how RBM39 is regulated in gastric cancer cells is unknown. Here, affinity purification-mass spectrometry and a biochemical screening are employed to identify the RBM39-interacting proteins and the deubiquitinating enzymes (DUBs) that regulate the RBM39 protein level. Integration of the data obtained from these two approaches uncovers USP39 as the potential DUB that regulates RBM39 stability. Bioinformatic analysis discloses that USP39 is increased in gastric cancer tissues and its elevation shortens the duration of overall survival for gastric cancer patients. Biochemical experiments verify that USP39 and RBM39 interact with each other and highly colocalize in the nucleus. Expression of USP39 elevates while USP39 knockdown attenuates the RBM39 protein level and their interaction regulates this modulation and their colocalization. Mechanistic studies reveal that USP39 reduces the K48-linked polyubiquitin chains on RBM39, thus enhancing its stability and increasing the protein level by preventing its proteasomal degradation. USP39 overexpression promotes while its knockdown attenuates the growth, colony formation, migration, and invasion of gastric cancer cells. Interestingly, overexpression of RBM39 partially restores the impact of USP39 depletion while RBM39 knockdown partially abolishes the effect of USP39 overexpression on the growth, colony formation, migration, and invasion of gastric cancer cells. Collectively, this work identifies the first DUB for RBM39 and elucidates the regulatory functions and the underlying mechanism, providing a possible alternative approach to suppressing RBM39 by inhibiting USP39 in cancer therapy.
Collapse
Affiliation(s)
- Chengpiao Lu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu 215123, China
| | - Yunxin Cai
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu 215123, China
| | - Shenglong Wu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu 215123, China
| | - Yuhong Wang
- Department of Pathology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, China
| | - Jia-Bin Li
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu 215123, China.
| | - Guoqiang Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu 215123, China; Suzhou International Joint Laboratory for Diagnosis and Treatment of Brain Diseases, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China; MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, Jiangsu Province 215123, China.
| | - Jingjing Ma
- Department of Pharmacy, The Fourth Affiliated Hospital of Soochow University, Suzhou Dushu Lake Hospital, Medical Center of Soochow University, Suzhou, Jiangsu 215123, China.
| |
Collapse
|
11
|
Zhang K, Wang P, Huang W, Tang SH, Xue H, Wu H, Zhang Y, Rong Y, Dong SS, Chen JB, Zou Y, Tian D, Yang N, Liang Y, Liu C, Li D, Zhang K, Yang TL, Guo Y. Integrated landscape of plasma metabolism and proteome of patients with post-traumatic deep vein thrombosis. Nat Commun 2024; 15:7831. [PMID: 39244606 PMCID: PMC11380666 DOI: 10.1038/s41467-024-52262-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/02/2024] [Indexed: 09/09/2024] Open
Abstract
Deep vein thrombosis (DVT) is a leading cause of morbidity and mortality after trauma. Here, we integrate plasma metabolomics and proteomics to evaluate the metabolic alterations and their function in up to 680 individuals with and without DVT after trauma (pt-DVT). We identify 28 metabolites and 2 clinical parameter clusters associated with pt-DVT. Then, we develop a panel of 9 metabolites (hexadecanedioic acid, pyruvic acid, L-Carnitine, serotonin, PE(P-18:1(11Z)/18:2(9Z,12Z)), 3-Hydroxycapric acid, 5,6-DHET, 3-Methoxybenzenepropanoic acid and pentanenitrile) that can predict pt-DVT with high performance, which can be verified in an independent cohort. Furthermore, the integration analysis of metabolomics and proteomics data indicates that the upregulation of glycolysis/gluconeogenesis-TCA cycle may promote thrombosis by regulating ROS levels in red blood cells, suggesting that interfering with this process might be potential therapeutic strategies for pt-DVT. Together, our study comprehensively delineates the metabolic and hematological dysregulations for pt-DVT, and provides potential biomarkers for early detection.
Collapse
Affiliation(s)
- Kun Zhang
- Department of Trauma Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
- Key Laboratory of Biology Multiomics and Diseases in Shaanxi Province Higher Education Institutions, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Pengfei Wang
- Department of Trauma Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Wei Huang
- Department of Trauma Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
- Key Laboratory of Biology Multiomics and Diseases in Shaanxi Province Higher Education Institutions, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Shi-Hao Tang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
- Key Laboratory of Biology Multiomics and Diseases in Shaanxi Province Higher Education Institutions, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Hanzhong Xue
- Department of Trauma Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Hao Wu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
- Key Laboratory of Biology Multiomics and Diseases in Shaanxi Province Higher Education Institutions, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Ying Zhang
- Instrument Analysis Center, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Yu Rong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
- Key Laboratory of Biology Multiomics and Diseases in Shaanxi Province Higher Education Institutions, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
- Key Laboratory of Biology Multiomics and Diseases in Shaanxi Province Higher Education Institutions, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Jia-Bin Chen
- Department of Trauma Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Yan Zou
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
- Key Laboratory of Biology Multiomics and Diseases in Shaanxi Province Higher Education Institutions, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Ding Tian
- Department of Trauma Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Na Yang
- Department of Trauma Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Yifan Liang
- Department of Trauma Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Chungui Liu
- Department of Trauma Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Dongyang Li
- Department of Trauma Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Kun Zhang
- Department of Trauma Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China.
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China.
- Key Laboratory of Biology Multiomics and Diseases in Shaanxi Province Higher Education Institutions, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China.
| | - Yan Guo
- Department of Trauma Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China.
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China.
- Key Laboratory of Biology Multiomics and Diseases in Shaanxi Province Higher Education Institutions, Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China.
| |
Collapse
|
12
|
Shen J, Zhao X, Bai X, Zhu W, Li Z, Yang Z, Wang Q, Ji J. Phosphoproteomic analysis reveals CDK5-Mediated phosphorylation of MTDH inhibits protein synthesis in microglia. Biochem Biophys Res Commun 2024; 735:150669. [PMID: 39260336 DOI: 10.1016/j.bbrc.2024.150669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 09/02/2024] [Accepted: 09/05/2024] [Indexed: 09/13/2024]
Abstract
CDK5 plays a crucial role in maintaining normal central nervous system (CNS) development and synaptic function, while microglia are the primary immune cells present in the CNS and play vital physiological roles in CNS development, immune surveillance, and regulation of synaptic plasticity. Despite this, our understanding of both the substrate proteins and functional mechanisms of CDK5 in microglia remains limited. To address this, we utilized CRISPR-Cas9 knockout of Cdk5 in BV2 cells and conducted quantitative phosphoproteomics analysis to systematically screen potential CDK5 substrates in microglia. Our findings identified 335 phosphorylation sites on 234 proteins as potential CDK5 substrates in microglia based on the reported sequence motif. Through in vitro kinase assay and intracellular inhibition and knockout of CDK5 experiments, we confirmed that ER proteins MTDH (protein LYRIC) and Calnexin are novel substrate proteins of CDK5. Moreover, we demonstrated for the first time a critical mechanism for regulating protein synthesis in microglia, that the phosphorylation of S565 site on MTDH, a key protein mediating cell growth, by CDK5 inhibits protein synthesis. Our data provide valuable insights for the discovery of new substrate proteins of CDK5 and the in-depth investigation of the function and mechanism of CDK5 in microglia.
Collapse
Affiliation(s)
- Jian Shen
- Department of General Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
| | - Xuyang Zhao
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Xue Bai
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Wenyuan Zhu
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Zeyang Li
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Zihao Yang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Qingsong Wang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China.
| | - Jianguo Ji
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China.
| |
Collapse
|
13
|
Yao WD, Zhou JN, Tang C, Zhang JL, Chen ZY, Li Y, Gong XJ, Qu MY, Zeng Q, Jia YL, Wang HY, Fan T, Ren J, Guo LL, Xi JF, Pei XT, Han Y, Yue W. Hydrogel Microneedle Patches Loaded with Stem Cell Mitochondria-Enriched Microvesicles Boost the Chronic Wound Healing. ACS NANO 2024. [PMID: 39238258 DOI: 10.1021/acsnano.4c06921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/07/2024]
Abstract
Rescuing or compensating mitochondrial function represents a promising therapeutic avenue for radiation-induced chronic wounds. Adult stem cell efficacies are primarily dependent on the paracrine secretion of mitochondria-containing extracellular vesicles (EVs). However, effective therapeutic strategies addressing the quantity of mitochondria and mitochondria-delivery system are lacking. Thus, in this study, we aimed to design an effective hydrogel microneedle patch (MNP) loaded with stem cell-derived mitochondria-rich EVs to gradually release and deliver mitochondria into the wound tissues and boost wound healing. We, first, used metformin to enhance mitochondrial biogenesis and thereby increasing the secretion of mitochondria-containing EVs (termed "Met-EVs") in adipose-derived stem cells. To verify the therapeutic effects of Met-EVs, we established an in vitro and an in vivo model of X-ray-induced mitochondrial dysfunction. The Met-EVs ameliorated the mitochondrial dysfunction by rescuing mitochondrial membrane potential, increasing adenosine 5'-triphosphate levels, and decreasing reactive oxygen species production by transferring active mitochondria. To sustain the release of EVs into damaged tissues, we constructed a Met-EVs@Decellularized Adipose Matrix (DAM)/Hyaluronic Acid Methacrylic Acid (HAMA)-MNP. Met-EVs@DAM/HAMA-MNP can load and gradually release Met-EVs and their contained mitochondria into wound tissues to alleviate mitochondrial dysfunction. Moreover, we found Met-EVs@DAM/HAMA-MNP can markedly promote macrophage polarization toward the M2 subtype with anti-inflammatory and regenerative functions, which can, in turn, enhance the healing process in mice with skin wounds combined radiation injuries. Collectively, we successfully fabricated a delivery system for EVs, Met-EVs@DAM/HAMA-MNP, to effectively deliver stem cell-derived mitochondria-rich EVs. The effectiveness of this system has been demonstrated, holding great potential for chronic wound treatments in clinic.
Collapse
Affiliation(s)
- Wen-De Yao
- School of Medicine, Nankai University, 94 Weijin Road, Tianjin 300071, China
- Department of Plastic and Reconstructive Surgery, The First Medical Centre, Chinese PLA General Hospital, 28 Fuxing Street, Beijing 100853, China
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Jun-Nian Zhou
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Chao Tang
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Ju-Lei Zhang
- Department of Plastic and Reconstructive Surgery, The First Medical Centre, Chinese PLA General Hospital, 28 Fuxing Street, Beijing 100853, China
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Zhao-Yang Chen
- Department of Plastic and Reconstructive Surgery, The First Medical Centre, Chinese PLA General Hospital, 28 Fuxing Street, Beijing 100853, China
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Yan Li
- Department of Plastic and Reconstructive Surgery, The First Medical Centre, Chinese PLA General Hospital, 28 Fuxing Street, Beijing 100853, China
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Xiao-Jing Gong
- Department of Plastic and Reconstructive Surgery, The First Medical Centre, Chinese PLA General Hospital, 28 Fuxing Street, Beijing 100853, China
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Ming-Yi Qu
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Quan Zeng
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Ya-Li Jia
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Hai-Yang Wang
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Tao Fan
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Jing Ren
- Department of Plastic and Reconstructive Surgery, The First Medical Centre, Chinese PLA General Hospital, 28 Fuxing Street, Beijing 100853, China
| | - Ling-Li Guo
- Department of Plastic and Reconstructive Surgery, The First Medical Centre, Chinese PLA General Hospital, 28 Fuxing Street, Beijing 100853, China
| | - Jia-Fei Xi
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Xue-Tao Pei
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Yan Han
- School of Medicine, Nankai University, 94 Weijin Road, Tianjin 300071, China
- Department of Plastic and Reconstructive Surgery, The First Medical Centre, Chinese PLA General Hospital, 28 Fuxing Street, Beijing 100853, China
| | - Wen Yue
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| |
Collapse
|
14
|
Yang XY, Wang SL, Xue WC, Zhang YP, Li LL, Luo ZH, Zhang FJ. Nattokinase's Neuroprotective Mechanisms in Ischemic Stroke: Targeting Inflammation, Oxidative Stress, and Coagulation. Antioxid Redox Signal 2024. [PMID: 39135387 DOI: 10.1089/ars.2023.0527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/06/2024]
Abstract
Aims: Nattokinase (NK), a potent serine endopeptidase, has exhibited a variety of pharmacological effects, including thrombolysis, anti-inflammation, and antioxidative stress. Building on previous research highlighting NK's promise in nerve regeneration, our study investigated whether NK exerted protective effects in transient middle cerebral artery occlusion (tMCAO)-induced cerebral ischemia-reperfusion injury and the underlying mechanisms. Results: The rats were administered NK (5000, 10000, 20000 FU/kg, i.g., 7 days before surgery, once daily). We showed that NK treatment dose dependently reduced the infarction volume and improved neurological symptoms, decreased the proinflammatory and coagulation cytokines levels, and attenuated reactive oxygen species (ROS) in the infarcted area of tMCAO rats. We also found that NK could exert neuroprotective effects in a variety of vitro models, including the microglia inflammation model and neuronal oxygen-glucose deprivation/reperfusion (OGD/R) model. Notably, NK effectively countered OGD/R-induced neuron death, modulating diverse pathways, including autophagy, apoptosis, PARP-dependent death, and endoplasmic reticulum stress. Furthermore, the neuroprotection of NK was blocked by phenylmethylsulfonyl fluoride (PMSF), a serine endopeptidase inhibitor. We revealed that heat-inactive NK was unable to protect against tMCAO injury and other vitro models, suggesting NK attenuated ischemic injury by its enzymatic activity. We conducted a proteomic analysis and found inflammation and coagulation were involved in the occurrence of tMCAO model and in the therapeutic effect of NK. Innovation and Conclusion: In conclusion, these data demonstrated that NK had multifaceted neuroprotection in ischemic brain injury, and the therapeutic effect of NK was related with serine endopeptidase activity.
Collapse
Affiliation(s)
- Xin-Ying Yang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, China
| | - Sheng-Lin Wang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, China
| | - Wen-Chi Xue
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, China
| | - Yu-Peng Zhang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, China
| | - Liang-Liang Li
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, China
| | - Zhao-Hu Luo
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, China
| | - Feng-Jiao Zhang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, China
| |
Collapse
|
15
|
Shao X, Huang Y, Xu R, He Q, Zhang M, He F, Wang D. ZASP: A highly compatible and sensitive ZnCl 2-precipitation assisted sample preparation method for proteomic analysis. Mol Cell Proteomics 2024:100837. [PMID: 39243857 DOI: 10.1016/j.mcpro.2024.100837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 08/30/2024] [Accepted: 09/03/2024] [Indexed: 09/09/2024] Open
Abstract
Universal sample preparation for proteomic analysis that enables unbiased protein manipulation, flexible reagent use, and low protein loss is required to ensure the highest sensitivity of downstream liquid chromatography-mass spectrometry (LC-MS) analysis. To address these needs, we developed a ZnCl2 precipitation-assisted sample preparation method (ZASP) that depletes harsh detergents and impurities in protein solutions prior to trypsin digestion via 10 min of ZnCl2 and methanol-induced protein precipitation at room temperature (RT). ZASP can remove trypsin digestion and LC-MS incompatible detergents such as SDS, Triton X-100, and urea at high concentrations in solution and unbiasedly recover proteins independent of the amount of protein input. We demonstrated the sensitivity and reproducibility of ZASP in an analysis of samples with 1 μg to 1000 μg of proteins. Compared to commonly used sample preparation methods such as SDC-based in-solution digestion, acetone precipitation, FASP, and SP3, ZASP has proven to be an efficient approach. Here, we present ZASP, a practical, robust, and cost-effective proteomic sample preparation method that can be applied to profile different types of samples.
Collapse
Affiliation(s)
- Xianfeng Shao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; Beijing Proteome Research Center, Beijing 102206, China; International Academy of Phronesis Medicine, Guangzhou 510005, Guangdong, China; The π-Hub Infrastructure, Guangzhou 510535, Guangdong, China
| | - Yuanxuan Huang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; Beijing Proteome Research Center, Beijing 102206, China; International Academy of Phronesis Medicine, Guangzhou 510005, Guangdong, China; The π-Hub Infrastructure, Guangzhou 510535, Guangdong, China
| | - Rong Xu
- Guangzhou Laboratory, Guangzhou 510005, Guangdong, China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Qiqing He
- International Academy of Phronesis Medicine, Guangzhou 510005, Guangdong, China; The π-Hub Infrastructure, Guangzhou 510535, Guangdong, China
| | - Min Zhang
- Department of Dermatology, Xiangya Hospital of Central South University, Changsha, 410008, Hunan, China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; Beijing Proteome Research Center, Beijing 102206, China; International Academy of Phronesis Medicine, Guangzhou 510005, Guangdong, China; The π-Hub Infrastructure, Guangzhou 510535, Guangdong, China; Guangzhou Laboratory, Guangzhou 510005, Guangdong, China.
| | - Dongxue Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; Beijing Proteome Research Center, Beijing 102206, China; International Academy of Phronesis Medicine, Guangzhou 510005, Guangdong, China; The π-Hub Infrastructure, Guangzhou 510535, Guangdong, China.
| |
Collapse
|
16
|
Dang T, Yu J, Cao Z, Zhang B, Li S, Xin Y, Yang L, Lou R, Zhuang M, Shui W. Endogenous cell membrane interactome mapping for the GLP-1 receptor in different cell types. Nat Chem Biol 2024:10.1038/s41589-024-01714-1. [PMID: 39227725 DOI: 10.1038/s41589-024-01714-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 07/29/2024] [Indexed: 09/05/2024]
Abstract
The GLP-1 receptor, one of the most successful drug targets for the treatment of type 2 diabetes and obesity, is known to engage multiple intracellular signaling proteins. However, it remains less explored how the receptor interacts with proteins on the cell membrane. Here, we present a ligand-based proximity labeling approach to interrogate the native cell membrane interactome for the GLP-1 receptor after agonist simulation. Our study identified several unreported putative cell membrane interactors for the endogenous receptor in either a pancreatic β cell line or a neuronal cell line. We further uncovered new regulators of GLP-1 receptor-mediated signaling and insulinotropic responses in β cells. Additionally, we obtained a time-resolved cell membrane interactome map for the receptor in β cells. Therefore, our study provides a new approach that is generalizable to map endogenous cell membrane interactomes for G-protein-coupled receptors to decipher the molecular basis of their cell-type-specific functional regulation.
Collapse
Affiliation(s)
- Ting Dang
- iHuman Institute, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jie Yu
- iHuman Institute, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- Lingang Laboratory, Shanghai, China
| | - Zhihe Cao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bingjie Zhang
- iHuman Institute, ShanghaiTech University, Shanghai, China
| | - Shanshan Li
- iHuman Institute, ShanghaiTech University, Shanghai, China
| | - Ye Xin
- iHuman Institute, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lingyun Yang
- iHuman Institute, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ronghui Lou
- iHuman Institute, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Min Zhuang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
| | - Wenqing Shui
- iHuman Institute, ShanghaiTech University, Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
| |
Collapse
|
17
|
Li P, Hu X, Fan Z, Sun S, Ran Q, Wei T, Wei P, Jiang Q, Yan J, Yang N, Jia C, Yang T, Mao Y, Cai X, Xu T, Zhao Z, Qian X, Qin W, Zhuang X, Fan F, Xiao J, Zheng Z, Li S. Novel potent molecular glue degraders against broad range of hematological cancer cell lines via multiple neosubstrates degradation. J Hematol Oncol 2024; 17:77. [PMID: 39218923 PMCID: PMC11367868 DOI: 10.1186/s13045-024-01592-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND Targeted protein degradation of neosubstrates plays a crucial role in hematological cancer treatment involving immunomodulatory imide drugs (IMiDs) therapy. Nevertheless, the persistence of inevitable drug resistance and hematological toxicities represents a significant obstacle to their clinical effectiveness. METHODS Phenotypic profiling of a small molecule compounds library in multiple hematological cancer cell lines was conducted to screen for hit degraders. Molecular dynamic-based rational design and cell-based functional assays were conducted to develop more potent degraders. Multiple myeloma (MM) tumor xenograft models were employed to investigate the antitumor efficacy of the degraders as single or combined agents with standard of care agents. Unbiased proteomics was employed to identify multiple therapeutically relevant neosubstrates targeted by the degraders. MM patient-derived cell lines (PDCs) and a panel of solid cancer cell lines were utilized to investigate the effects of candidate degrader on different stage of MM cells and solid malignancies. Unbiased proteomics of IMiDs-resistant MM cells, cell-based functional assays and RT-PCR analysis of clinical MM specimens were utilized to explore the role of BRD9 associated with IMiDs resistance and MM progression. RESULTS We identified a novel cereblon (CRBN)-dependent lead degrader with phthalazinone scaffold, MGD-4, which induced the degradation of Ikaros proteins. We further developed a novel potent candidate, MGD-28, significantly inhibited the growth of hematological cancer cells and induced the degradation of IKZF1/2/3 and CK1α with nanomolar potency via a Cullin-CRBN dependent pathway. Oral administration of MGD-4 and MGD-28 effectively inhibited MM tumor growth and exhibited significant synergistic effects with standard of care agents. MGD-28 exhibited preferentially profound cytotoxicity towards MM PDCs at different disease stages and broad antiproliferative activity in multiple solid malignancies. BRD9 modulated IMiDs resistance, and the expression of BRD9 was significant positively correlated with IKZF1/2/3 and CK1α in MM specimens at different stages. We also observed pronounced synergetic efficacy between the BRD9 inhibitor and MGD-28 for MM treatment. CONCLUSIONS Our findings present a strategy for the multi-targeted degradation of Ikaros proteins and CK1α against hematological cancers, which may be expanded to additional targets and indications. This strategy may enhance efficacy treatment against multiple hematological cancers and solid tumors.
Collapse
Affiliation(s)
- Pengyun Li
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Xiaotong Hu
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Zhiya Fan
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Shiyang Sun
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Qijie Ran
- Department of Clinical Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100039, China
- Department of Hematology, General Hospital of Central Theater Command, Wuhan, 430012, China
| | - Ting Wei
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Pengli Wei
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Qiyu Jiang
- Department of Clinical Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100039, China
| | - Jian Yan
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Ning Yang
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Changkai Jia
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Tingting Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Yaqiu Mao
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Xu Cai
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Tingting Xu
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Zhiyuan Zhao
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Xiaohong Qian
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Weijie Qin
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Xiaomei Zhuang
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China.
| | - Feng Fan
- Department of Clinical Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100039, China.
| | - Junhai Xiao
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China.
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China.
| | - Zhibing Zheng
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China.
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China.
| | - Song Li
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| |
Collapse
|
18
|
Duan CY, Li Y, Zhi HY, Tian Y, Huang ZY, Chen SP, Zhang Y, Liu Q, Zhou L, Jiang XG, Ullah K, Guo Q, Liu ZH, Xu Y, Han JH, Hou J, O'Connor DP, Xu G. E3 ubiquitin ligase UBR5 modulates circadian rhythm by facilitating the ubiquitination and degradation of the key clock transcription factor BMAL1. Acta Pharmacol Sin 2024; 45:1793-1808. [PMID: 38740904 PMCID: PMC11336169 DOI: 10.1038/s41401-024-01290-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 04/10/2024] [Indexed: 05/16/2024] Open
Abstract
The circadian clock is the inner rhythm of life activities and is controlled by a self-sustained and endogenous molecular clock, which maintains a ~ 24 h internal oscillation. As the core element of the circadian clock, BMAL1 is susceptible to degradation through the ubiquitin-proteasome system (UPS). Nevertheless, scant information is available regarding the UPS enzymes that intricately modulate both the stability and transcriptional activity of BMAL1, affecting the cellular circadian rhythm. In this work, we identify and validate UBR5 as a new E3 ubiquitin ligase that interacts with BMAL1 by using affinity purification, mass spectrometry, and biochemical experiments. UBR5 overexpression induced BMAL1 ubiquitination, leading to diminished stability and reduced protein level of BMAL1, thereby attenuating its transcriptional activity. Consistent with this, UBR5 knockdown increases the BMAL1 protein. Domain mapping discloses that the C-terminus of BMAL1 interacts with the N-terminal domains of UBR5. Similarly, cell-line-based experiments discover that HYD, the UBR5 homolog in Drosophila, could interact with and downregulate CYCLE, the BMAL1 homolog in Drosophila. PER2-luciferase bioluminescence real-time reporting assay in a mammalian cell line and behavioral experiments in Drosophila reveal that UBR5 or hyd knockdown significantly reduces the period of the circadian clock. Therefore, our work discovers a new ubiquitin ligase UBR5 that regulates BMAL1 stability and circadian rhythm and elucidates the underlying molecular mechanism. This work provides an additional layer of complexity to the regulatory network of the circadian clock at the post-translational modification level, offering potential insights into the modulation of the dysregulated circadian rhythm.
Collapse
Affiliation(s)
- Chun-Yan Duan
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, China
- School of Pharmacy and Biomolecular Sciences, RCSI University of Medicine and Health Sciences, 123 St Stephen's Green, Dublin 2, D02 YN77, Dublin, Ireland
| | - Yue Li
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, China
| | - Hao-Yu Zhi
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, China
| | - Yao Tian
- School of Life Science and Technology, The Key Laboratory of Developmental Genes and Human Disease, Southeast University, 2 Sipailou Road, Nanjing, 210096, China
| | - Zheng-Yun Huang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Cambridge-Suda Genomic Resource Center, Soochow University, Suzhou, 215123, China
| | - Su-Ping Chen
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, China
| | - Yang Zhang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, China
| | - Qing Liu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, China
| | - Liang Zhou
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, China
| | - Xiao-Gang Jiang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, China
| | - Kifayat Ullah
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, China
| | - Qing Guo
- Department of Human Anatomy and Cytoneurobiology, Medical School of Soochow University, Suzhou, 215123, China
| | - Zhao-Hui Liu
- Department of Human Anatomy and Cytoneurobiology, Medical School of Soochow University, Suzhou, 215123, China
| | - Ying Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Cambridge-Suda Genomic Resource Center, Soochow University, Suzhou, 215123, China
| | - Jun-Hai Han
- School of Life Science and Technology, The Key Laboratory of Developmental Genes and Human Disease, Southeast University, 2 Sipailou Road, Nanjing, 210096, China
| | - Jiajie Hou
- Cancer Centre, Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Darran P O'Connor
- School of Pharmacy and Biomolecular Sciences, RCSI University of Medicine and Health Sciences, 123 St Stephen's Green, Dublin 2, D02 YN77, Dublin, Ireland
| | - Guoqiang Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, China.
- Suzhou International Joint Laboratory for Diagnosis and Treatment of Brain Diseases, College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China.
- MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, 215123, China.
| |
Collapse
|
19
|
Xi Q, Yang G, He X, Zhuang H, Li L, Lin B, Wang L, Wang X, Fang C, Chen Q, Yang Y, Yu Z, Zhang H, Cai W, Li Y, Shen H, Liu L, Zhang R. M 6A-mediated upregulation of lncRNA TUG1 in liver cancer cells regulates the antitumor response of CD8 + T cells and phagocytosis of macrophages. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400695. [PMID: 38981064 DOI: 10.1002/advs.202400695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 06/11/2024] [Indexed: 07/11/2024]
Abstract
Tumor immune evasion relies on the crosstalk between tumor cells and adaptive/innate immune cells. Immune checkpoints play critical roles in the crosstalk, and immune checkpoint inhibitors have achieved promising clinical effects. The long non-coding RNA taurine-upregulated gene 1 (TUG1) is upregulated in hepatocellular carcinoma (HCC). However, how TUG1 is upregulated and the effects on tumor immune evasion are incompletely understood. Here, METTL3-mediated m6A modification led to TUG1 upregulation is demonstrated. Knockdown of TUG1 inhibited tumor growth and metastasis, increased the infiltration of CD8+ T cells and M1-like macrophages in tumors, promoted the activation of CD8+ T cells through PD-L1, and improved the phagocytosis of macrophages through CD47. Mechanistically, TUG1 regulated PD-L1 and CD47 expressions by acting as a sponge of miR-141 and miR-340, respectively. Meanwhile, TUG1 interacted with YBX1 to facilitate the upregulation of PD-L1 and CD47 transcriptionally, which ultimately regulated tumor immune evasion. Clinically, TUG1 positively correlated with PD-L1 and CD47 in HCC tissues. Moreover, the combination of Tug1-siRNA therapy with a Pdl1 antibody effectively suppressed tumor growth. Therefore, the mechanism of TUG1 in regulating tumor immune evasion is revealed and can inform existing strategies targeting TUG1 for enhancing HCC immune therapy and drug development.
Collapse
Affiliation(s)
- Qing Xi
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510080, China
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou, 511442, China
| | - Guangze Yang
- Laboratory of Immunology and Inflammation, Department of Immunology, Key Laboratory of Immune Microenvironment and Diseases of Educational Ministry of China, Tianjin Medical University, Tianjin, 300070, China
| | - Xue He
- Laboratory of Immunology and Inflammation, Department of Biotechnology, School of Life Sciences and Biopharmaceutics, Guangdong Provincial Key Laboratory of Advanced Drug Delivery, Guangdong Provincial Engineering Center of Topical Precise Drug Delivery System, Guangdong Pharmaceutical University, Guangzhou, 51006, China
| | - Hao Zhuang
- Department of Hepatobiliopancreatic Surgery, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, 450008, China
| | - Li Li
- Laboratory of Immunology and Inflammation, Department of Biotechnology, School of Life Sciences and Biopharmaceutics, Guangdong Provincial Key Laboratory of Advanced Drug Delivery, Guangdong Provincial Engineering Center of Topical Precise Drug Delivery System, Guangdong Pharmaceutical University, Guangzhou, 51006, China
| | - Bing Lin
- Laboratory of Immunology and Inflammation, Department of Biotechnology, School of Life Sciences and Biopharmaceutics, Guangdong Provincial Key Laboratory of Advanced Drug Delivery, Guangdong Provincial Engineering Center of Topical Precise Drug Delivery System, Guangdong Pharmaceutical University, Guangzhou, 51006, China
| | - Lingling Wang
- Laboratory of Immunology and Inflammation, Department of Biotechnology, School of Life Sciences and Biopharmaceutics, Guangdong Provincial Key Laboratory of Advanced Drug Delivery, Guangdong Provincial Engineering Center of Topical Precise Drug Delivery System, Guangdong Pharmaceutical University, Guangzhou, 51006, China
| | - Xianyang Wang
- Laboratory of Immunology and Inflammation, Department of Biotechnology, School of Life Sciences and Biopharmaceutics, Guangdong Provincial Key Laboratory of Advanced Drug Delivery, Guangdong Provincial Engineering Center of Topical Precise Drug Delivery System, Guangdong Pharmaceutical University, Guangzhou, 51006, China
| | - Chunqiang Fang
- Laboratory of Immunology and Inflammation, Department of Biotechnology, School of Life Sciences and Biopharmaceutics, Guangdong Provincial Key Laboratory of Advanced Drug Delivery, Guangdong Provincial Engineering Center of Topical Precise Drug Delivery System, Guangdong Pharmaceutical University, Guangzhou, 51006, China
| | - Qiurui Chen
- Department of Bioscience, School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 51006, China
| | - Yongjie Yang
- Laboratory of Immunology and Inflammation, Department of Biotechnology, School of Life Sciences and Biopharmaceutics, Guangdong Provincial Key Laboratory of Advanced Drug Delivery, Guangdong Provincial Engineering Center of Topical Precise Drug Delivery System, Guangdong Pharmaceutical University, Guangzhou, 51006, China
| | - Zhaoan Yu
- Laboratory of Immunology and Inflammation, Department of Biotechnology, School of Life Sciences and Biopharmaceutics, Guangdong Provincial Key Laboratory of Advanced Drug Delivery, Guangdong Provincial Engineering Center of Topical Precise Drug Delivery System, Guangdong Pharmaceutical University, Guangzhou, 51006, China
| | - Hao Zhang
- Laboratory of Immunology and Inflammation, Department of Biotechnology, School of Life Sciences and Biopharmaceutics, Guangdong Provincial Key Laboratory of Advanced Drug Delivery, Guangdong Provincial Engineering Center of Topical Precise Drug Delivery System, Guangdong Pharmaceutical University, Guangzhou, 51006, China
| | - Wenqian Cai
- Laboratory of Immunology and Inflammation, Department of Biotechnology, School of Life Sciences and Biopharmaceutics, Guangdong Provincial Key Laboratory of Advanced Drug Delivery, Guangdong Provincial Engineering Center of Topical Precise Drug Delivery System, Guangdong Pharmaceutical University, Guangzhou, 51006, China
| | - Yan Li
- Laboratory of Immunology and Inflammation, Department of Biotechnology, School of Life Sciences and Biopharmaceutics, Guangdong Provincial Key Laboratory of Advanced Drug Delivery, Guangdong Provincial Engineering Center of Topical Precise Drug Delivery System, Guangdong Pharmaceutical University, Guangzhou, 51006, China
| | - Han Shen
- Department of Bioscience, School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 51006, China
| | - Li Liu
- Department of Radiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA
| | - Rongxin Zhang
- Laboratory of Immunology and Inflammation, Department of Biotechnology, School of Life Sciences and Biopharmaceutics, Guangdong Provincial Key Laboratory of Advanced Drug Delivery, Guangdong Provincial Engineering Center of Topical Precise Drug Delivery System, Guangdong Pharmaceutical University, Guangzhou, 51006, China
| |
Collapse
|
20
|
Liu YY, Wang RJ, Ru SS, Gao F, Liu W, Zhang X. Comparative analysis of phosphorylated proteomes between plerocercoid and adult Spirometra mansoni reveals phosphoproteomic profiles of the medical tapeworm. Parasit Vectors 2024; 17:371. [PMID: 39217359 PMCID: PMC11366163 DOI: 10.1186/s13071-024-06454-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND Plerocercoid larvae of the tapeworm Spirometra mansoni can infect both humans and animals, leading to severe parasitic zoonosis worldwide. Despite ongoing research efforts, our understanding of the developmental process of S. mansoni remains inadequate. To better characterize posttranslational regulation associated with parasite growth, development, and reproduction, a comparative phosphoproteomic study was conducted on the plerocercoid and adult stages of S. mansoni. METHODS In this study, site-specific phosphoproteomic analysis was conducted via 4D label-free quantitative analysis technology to obtain primary information about the overall phosphorylation status of plerocercoids and adults. RESULTS A total of 778 differentially abundant proteins (DAPs) were detected between adults and plerocercoids, of which 704 DAPs were upregulated and only 74 were downregulated. DAPs involved in metabolic activity were upregulated in plerocercoid larvae compared with adults, whereas DAPs associated with binding were upregulated in adults. Gene Ontology (GO) and Kyoto Encyclopedia of Genes (KEGG) analyses indicated that most DAPs involved in signal transduction and environmental information processing pathways were highly active in adults. DAPs upregulated in the plerocercoid group were enriched mainly in metabolic activities. The kinases PKACA, GSK3B, and smMLCK closely interact, suggesting potential active roles in the growth and development of S. mansoni. CONCLUSIONS The dataset presented in this study offers a valuable resource for forthcoming research on signaling pathways as well as new insights into functional studies on the molecular mechanisms of S. mansoni.
Collapse
Affiliation(s)
- Yong Yan Liu
- Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- Department of Clinical Microbiology, The People's Hospital of Xixian, Xinyang, 464300, Henan, China
| | - Rui Jie Wang
- Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Si Si Ru
- Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Fei Gao
- Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Wei Liu
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, China.
| | - Xi Zhang
- Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
| |
Collapse
|
21
|
Zhu H, Liu Q, Meng Q, Zhang L, Ju S, Lang J, Zhu D, Chen Y, Aishan N, Ouyang X, Zhang S, Jin L, Xiao L, Wang L, Li L, Ji F. CCT3/ACTN4/TFRC axis protects hepatocellular carcinoma cells from ferroptosis by inhibiting iron endocytosis. J Exp Clin Cancer Res 2024; 43:245. [PMID: 39210442 PMCID: PMC11360757 DOI: 10.1186/s13046-024-03169-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
Sorafenib is widely used in treating advanced hepatocellular carcinoma (HCC). However, its effectiveness in prolonging patient survival is limited by the development of drug resistance. To systematically investigate the resistance mechanisms of Sorafenib, an integrative analysis combining posttranslational modification (PTM) omics and CRISPR/Cas9 knockout library screening was conducted. This analysis identified ubiquitination at lysine 21 (K21) on chaperonin-containing TCP1 subunit 3 (CCT3) as being associated with Sorafenib resistance. Transcriptomic data from HCC patients treated with Sorafenib revealed that CCT3 expression was lower in responders compared to non-responders. Experimentally, inhibiting the expression of CCT3 sensitized HCC cells to Sorafenib and enhanced Sorafenib-induced ferroptosis. Additionally, CCT3 was found to interact with ACTN4, hindering the recycling of transferrin receptor protein 1 (TFRC) to the cell membrane, thus obstructing iron endocytosis. Mechanistically, the inhibition of ferroptosis by CCT3 depends on the deubiquitination of K6-linked non-degradative ubiquitination at its K21, which occurs upon Sorafenib treatment. Moreover, CCT3 knockdown enhanced the anti-tumor effects of Sorafenib in nude mice. In summary, we have identified a novel function of the chaperone protein. Targeting the CCT3/ACTN4/TFRC axis offers a promising strategy to enhance ferroptosis and overcome Sorafenib resistance in HCC.
Collapse
Affiliation(s)
- Huihui Zhu
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China
| | - Qiuhong Liu
- Department of Infectious Diseases, Affiliated Hangzhou First People's Hospital, Westlake University School of Medicine, Hangzhou, 310000, Zhejiang, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China
| | - Qinna Meng
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, 310000, Zhejiang, China
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China
- Provincial Clinical Research Center for CANCER, Hangzhou, 310000, Zhejiang, China
| | - Lingjian Zhang
- Department of Infectious Diseases, Affiliated Hangzhou First People's Hospital, Westlake University School of Medicine, Hangzhou, 310000, Zhejiang, China
| | - Siwei Ju
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China
- Provincial Clinical Research Center for CANCER, Hangzhou, 310000, Zhejiang, China
| | - Jiaheng Lang
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China
- Provincial Clinical Research Center for CANCER, Hangzhou, 310000, Zhejiang, China
| | - Danhua Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China
| | - Yongxia Chen
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China
- Provincial Clinical Research Center for CANCER, Hangzhou, 310000, Zhejiang, China
| | - Nadire Aishan
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China
- Provincial Clinical Research Center for CANCER, Hangzhou, 310000, Zhejiang, China
| | - Xiaoxi Ouyang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China
| | - Sainan Zhang
- Shulan (Hangzhou) Hospital Affiliated to Zhejiang Shuren University Shulan International Medical College, Hangzhou, 310000, Zhejiang, China
| | - Lidan Jin
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China
- Provincial Clinical Research Center for CANCER, Hangzhou, 310000, Zhejiang, China
| | - Lanlan Xiao
- Department of Rheumatology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China
| | - Linbo Wang
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, 310000, Zhejiang, China.
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China.
- Provincial Clinical Research Center for CANCER, Hangzhou, 310000, Zhejiang, China.
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China.
| | - Feiyang Ji
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China.
- Provincial Clinical Research Center for CANCER, Hangzhou, 310000, Zhejiang, China.
| |
Collapse
|
22
|
Zhang X, Li M, Zhang N, Li Y, Teng F, Li Y, Zhang X, Xu X, Li H, Zhu Y, Wang Y, Jia Y, Qin C, Wang B, Guo S, Wang Y, Yu X. SARS-CoV-2 Evolution: Immune Dynamics, Omicron Specificity, and Predictive Modeling in Vaccinated Populations. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2402639. [PMID: 39206813 DOI: 10.1002/advs.202402639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 07/25/2024] [Indexed: 09/04/2024]
Abstract
Host immunity is central to the virus's spread dynamics, which is significantly influenced by vaccination and prior infection experiences. In this work, we analyzed the co-evolution of SARS-CoV-2 mutation, angiotensin-converting enzyme 2 (ACE2) receptor binding, and neutralizing antibody (NAb) responses across various variants in 822 human and mice vaccinated with different non-Omicron and Omicron vaccines is analyzed. The link between vaccine efficacy and vaccine type, dosing, and post-vaccination duration is revealed. The classification of immune protection against non-Omicron and Omicron variants is co-evolved with genetic mutations and vaccination. Additionally, a model, the Prevalence Score (P-Score) is introduced, which surpasses previous algorithm-based models in predicting the potential prevalence of new variants in vaccinated populations. The hybrid vaccination combining the wild-type (WT) inactivated vaccine with the Omicron BA.4/5 mRNA vaccine may provide broad protection against both non-Omicron variants and Omicron variants, albeit with EG.5.1 still posing a risk. In conclusion, these findings enhance understanding of population immunity variations and provide valuable insights for future vaccine development and public health strategies.
Collapse
Affiliation(s)
- Xiaohan Zhang
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, 102206, China
- School of Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Mansheng Li
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Nana Zhang
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Yunhui Li
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
| | - Fei Teng
- Emergency Medicine Clinical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing Key Laboratory of Cardiopulmonary Cerebral Resuscitation, Beijing, 100020, China
| | - Yongzhe Li
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, 100730, China
| | - Xiaomei Zhang
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Xingming Xu
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Haolong Li
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, 100730, China
| | - Yunping Zhu
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Yumin Wang
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Yan Jia
- ProteomicsEra Medical Co., Ltd., Beijing, 102206, China
| | - Chengfeng Qin
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Bingwei Wang
- School of Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Shubin Guo
- Emergency Medicine Clinical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing Key Laboratory of Cardiopulmonary Cerebral Resuscitation, Beijing, 100020, China
| | - Yajie Wang
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
| | - Xiaobo Yu
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, 102206, China
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| |
Collapse
|
23
|
Li W, Mei W, Jiang H, Wang J, Li X, Quan L, Diao Y, Ma Y, Fan S, Xie Z, Gong M, Zhu H, Bi D, Zhang F, Ma L, Zhang J, Gao Y, Paschalidis A, Lin H, Liu F, Liu K, Ye M, Zhao Z, Duan Y, Chen Z, Xu Y, Xiao W, Tao S, Zhu L, Li H. Blocking the PD-1 signal transduction by occupying the phosphorylated ITSM recognition site of SHP-2. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-024-2706-2. [PMID: 39235560 DOI: 10.1007/s11427-024-2706-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Accepted: 08/07/2024] [Indexed: 09/06/2024]
Abstract
Targeting the PD-1/PD-L1 axis with small-molecular inhibitors is a promising approach for immunotherapy. Here, we identify a natural pentacyclic triterpenoid, Pygenic Acid A (PA), as a PD-1 signaling inhibitor. PA exerts anti-tumor activity in hPD-1 knock-in C57BL/6 mice and enhances effector functions of T cells to promote immune responses by disrupting the PD-1 signaling transduction. Furthermore, we identify SHP-2 as the direct molecular target of PA for inhibiting the PD-1 signaling transduction. Subsequently, mechanistic studies suggest that PA binds to a new druggable site in the phosphorylated PD-1 ITSM recognition site of SHP-2, inhibiting the recruitment of SHP-2 by PD-1. Taken together, our findings demonstrate that PA has a potential application in cancer immunotherapy and occupying the phosphorylated ITSM recognition site of SHP-2 may serve as an alternative strategy to develop PD-1 signaling inhibitors. In addition, our success in target recognition provides a paradigm of target identification and confirmation for natural products.
Collapse
Affiliation(s)
- Wenjie Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Wenyi Mei
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Hewei Jiang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240, China
- Lingang Laboratory, Shanghai, 200031, China
| | - Jie Wang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Xiaoli Li
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Characteristic Plant Extraction Laboratory, Yunnan Provincial Center for Research & Development of Natural Products, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Pharmacy and School of Chemical Science and Technology, Yunnan University, Kunming, 650500, China
| | - Lina Quan
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Yanyan Diao
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Yanni Ma
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Sisi Fan
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Zhuwei Xie
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Mengdie Gong
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Huan Zhu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Dewen Bi
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Characteristic Plant Extraction Laboratory, Yunnan Provincial Center for Research & Development of Natural Products, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Pharmacy and School of Chemical Science and Technology, Yunnan University, Kunming, 650500, China
| | - Feng Zhang
- Department of Cardiology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Lei Ma
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Jian Zhang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Yufeng Gao
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Aris Paschalidis
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Honghuang Lin
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Fangfang Liu
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Science, College of Medicine, Zhengzhou University, Zhengzhou, 450001, China
| | - Kangdong Liu
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Science, College of Medicine, Zhengzhou University, Zhengzhou, 450001, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Zhenjiang Zhao
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Yajun Duan
- Department of Cardiology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Zhuo Chen
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Yufang Xu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Weilie Xiao
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Characteristic Plant Extraction Laboratory, Yunnan Provincial Center for Research & Development of Natural Products, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Pharmacy and School of Chemical Science and Technology, Yunnan University, Kunming, 650500, China.
| | - Shengce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Lili Zhu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China.
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China.
- Innovation Center for AI and Drug Discovery, East China Normal University, Shanghai, 200062, China.
- Lingang Laboratory, Shanghai, 200031, China.
| |
Collapse
|
24
|
Zhang W, Niu D, Zhao Y, Hu L, Guan C, Chai R. Discovery and demonstration of the temperature stress response functions of Dermatophagoides farinae proteins 1 and 2. BMC Genomics 2024; 25:811. [PMID: 39198731 PMCID: PMC11351518 DOI: 10.1186/s12864-024-10715-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Accepted: 08/16/2024] [Indexed: 09/01/2024] Open
Abstract
BACKGROUND Dermatophagoides farinae proteins (DFPs) are abundantly expressed in D. farinae; however, their functions remain unknown. Our previous transcriptome sequencing analyses revealed that the basal expression of DFP1 and DFP2 in D. farinae was high and, more importantly, upregulated under temperature stress. Therefore, DFPs were speculated to exert a temperature stress response function. RESULTS Real-time quantitative polymerase chain reaction detection revealed that both DFP1 and DFP2 were significantly upregulated under temperature stress. Particularly, DFP1 was upregulated under cold stress. Electrophoresis of D. farinae total proteins revealed an increased abundance of DFP1 and DFP2 (40-55 kDa bands) under temperature stress, which was corroborated by the mass spectrometry results. After silencing DFP1 and DFP2 further, temperature stress led to decreases in gene expression and survival rates. Moreover, DFP1 was identified as the upstream regulator of DFP2. CONCLUSION This study highlights the temperature stress response functions of DFP1 and DFP2 at the mRNA and protein levels. These results provide important insights for applying DFP1 and DFP2 as potential target genes for the molecular prevention and control of D. farinae to prevent allergic diseases. The newly established methods provide methodological guidance for the study of genes with unknown functions in mites.
Collapse
Affiliation(s)
- Wanyu Zhang
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, No.76 Yanta West Road, Xi'an, 710061, China
| | - Dongling Niu
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, No.76 Yanta West Road, Xi'an, 710061, China
- Clinical Laboratory Center, Xi'an People's Hospital, Xi'an Fourth Hospital, Affiliated People's Hospital of Northwest University, Xi'an, 710004, China
| | - Yae Zhao
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, No.76 Yanta West Road, Xi'an, 710061, China.
| | - Li Hu
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, No.76 Yanta West Road, Xi'an, 710061, China
| | - Chenglin Guan
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, No.76 Yanta West Road, Xi'an, 710061, China
| | - Rong Chai
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, No.76 Yanta West Road, Xi'an, 710061, China
| |
Collapse
|
25
|
Wang K, Zhang L, Zhang S, Liu Y, Mao J, Liu Z, Xu L, Li K, Wang J, Ma Y, Wang J, Li H, Wang Z, Li G, Cheng H, Ye M. Metabolic labeling based methylome profiling enables functional dissection of histidine methylation in C3H1 zinc fingers. Nat Commun 2024; 15:7459. [PMID: 39198440 PMCID: PMC11358137 DOI: 10.1038/s41467-024-51979-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 08/21/2024] [Indexed: 09/01/2024] Open
Abstract
Protein methylation is a functionally important post-translational modification that occurs on diverse amino acid residues. The current proteomics approaches are inefficient to discover the methylation on residues other than Arg and Lys, which hinders the deep understanding of the functional role of rare protein methylation. Herein, we present a methyl-specific metabolic labeling approach for global methylome mapping, which enable the acquisition of methylome dataset covering diverse methylation types. Interestingly, of the identified methylation events, His methylation is found to be preferably occurred in C3H1 zinc fingers (ZFs). These His methylation events are determined to be Nπ specific and catalyzed by CARNMT1. The His methylation is found to stabilize the structure of ZFs. U2AF1 is used as a proof-of-concept to highlight the functional importance of His methylation in ZFs in RNA binding and RNA metabolism. The results of this study enable novel understanding of how protein methylation regulates cellular processes.
Collapse
Grants
- This work was supported, in part, by funds from the China State Key Basic Research Program Grants (2021YFA13026012, 2019YFA0709400, 2022YFA1303300), the Strategic Priority Research Program of Chinese Academy of Sciences (XDB37040401, XDB0570100), the National Natural Science Foundation of China (21804131, 92153302, 21933010, 31925008), the innovation program (DICP I202226) of science and research from the DICP, CAS.
Collapse
Affiliation(s)
- Keyun Wang
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Zhang
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
| | - Sirui Zhang
- CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Ye Liu
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Jiawei Mao
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhen Liu
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lin Xu
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Kejia Li
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianshu Wang
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yanni Ma
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiayi Wang
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haitao Li
- MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Zefeng Wang
- CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
- School of Life Science, Southern University of Science and Technology, Shenzhen, China.
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
| | - Hong Cheng
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China.
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.
| | - Mingliang Ye
- State Key Laboratory of Medical Proteomics, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
26
|
Zheng JH, Zhu YH, Yang J, Ji PX, Zhao RK, Duan ZH, Yao HF, Jia QY, Yin YF, Hu LP, Li Q, Jiang SH, Huo YM, Liu W, Sun YW, Liu DJ. A CLIC1 network coordinates matrix stiffness and the Warburg effect to promote tumor growth in pancreatic cancer. Cell Rep 2024; 43:114633. [PMID: 39154343 DOI: 10.1016/j.celrep.2024.114633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 06/19/2024] [Accepted: 07/30/2024] [Indexed: 08/20/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) features substantial matrix stiffening and reprogrammed glucose metabolism, particularly the Warburg effect. However, the complex interplay between these traits and their impact on tumor advancement remains inadequately explored. Here, we integrated clinical, cellular, and bioinformatics approaches to explore the connection between matrix stiffness and the Warburg effect in PDAC, identifying CLIC1 as a key mediator. Elevated CLIC1 expression, induced by matrix stiffness through Wnt/β-catenin/TCF4 signaling, signifies poorer prognostic outcomes in PDAC. Functionally, CLIC1 serves as a catalyst for glycolytic metabolism, propelling tumor proliferation. Mechanistically, CLIC1 fortifies HIF1α stability by curbing hydroxylation via reactive oxygen species (ROS). Collectively, PDAC cells elevate CLIC1 levels in a matrix-stiffness-responsive manner, bolstering the Warburg effect to drive tumor growth via ROS/HIF1α signaling. Our insights highlight opportunities for targeted therapies that concurrently address matrix properties and metabolic rewiring, with CLIC1 emerging as a promising intervention point.
Collapse
Affiliation(s)
- Jia-Hao Zheng
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, P.R. China; Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
| | - Yu-Heng Zhu
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, P.R. China; Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
| | - Jian Yang
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, P.R. China; Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
| | - Pei-Xuan Ji
- Shanghai Institute of Digestive Disease, Division of Gastroenterology and Hepatology, NHC Key Laboratory of Digestive Diseases, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200001, P.R. China
| | - Rui-Kang Zhao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, P.R. China
| | - Zong-Hao Duan
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, P.R. China; Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
| | - Hong-Fei Yao
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, P.R. China; Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
| | - Qin-Yuan Jia
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, P.R. China; Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
| | - Yi-Fan Yin
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, P.R. China; Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
| | - Li-Peng Hu
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - Qing Li
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - Shu-Heng Jiang
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - Yan-Miao Huo
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, P.R. China; Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China.
| | - Wei Liu
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, P.R. China; Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China.
| | - Yong-Wei Sun
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, P.R. China; Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China.
| | - De-Jun Liu
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, P.R. China; Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China.
| |
Collapse
|
27
|
Zhang X, Zhu T, Li X, Zhao H, Lin S, Huang J, Yang B, Guo X. DNA damage-induced proteasome phosphorylation controls substrate recognition and facilitates DNA repair. Proc Natl Acad Sci U S A 2024; 121:e2321204121. [PMID: 39172782 PMCID: PMC11363268 DOI: 10.1073/pnas.2321204121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 07/18/2024] [Indexed: 08/24/2024] Open
Abstract
Upon DNA damage, numerous proteins are targeted for ubiquitin-dependent proteasomal degradation, which is an integral part of the DNA repair program. Although details of the ubiquitination processes have been intensively studied, little is known about whether and how the 26S proteasome is regulated in the DNA damage response (DDR). Here, we show that human Rpn10/PSMD4, one of the three ubiquitin receptors of the 26S proteasome, is rapidly phosphorylated in response to different types of DNA damage. The phosphorylation occurs at Rpn10-Ser266 within a conserved SQ motif recognized by ATM/ATR/DNA-PK. Blockade of S266 phosphorylation attenuates homologous recombination-mediated DNA repair and sensitizes cells to genotoxic insults. In vitro and in cellulo experiments indicate that phosphorylation of S266, located in the flexible linker between the two ubiquitin-interacting motifs (UIMs) of Rpn10, alters the configuration of UIMs, and actually reduces ubiquitin chain (substrate) binding. As a result, essential DDR proteins such as BRCA1 are spared from premature degradation and allowed sufficient time to engage in DNA repair, a scenario supported by proximity labeling and quantitative proteomic studies. These findings reveal an inherent self-limiting mechanism of the proteasome that, by controlling substrate recognition through Rpn10 phosphorylation, fine-tunes protein degradation for optimal responses under stress.
Collapse
Affiliation(s)
- Xiaomei Zhang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang310058, China
| | - Tianyi Zhu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang310058, China
| | - Xuemei Li
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang310058, China
| | - Hongxia Zhao
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang310058, China
| | - Shixian Lin
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang310058, China
| | - Jun Huang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang310058, China
| | - Bing Yang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang310058, China
| | - Xing Guo
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang310058, China
| |
Collapse
|
28
|
Tan J, Li Y, Li X, Zhu X, Liu L, Huang H, Wei J, Wang H, Tian Y, Wang Z, Zhang Z, Zhu B. Pramel15 facilitates zygotic nuclear DNMT1 degradation and DNA demethylation. Nat Commun 2024; 15:7310. [PMID: 39181896 PMCID: PMC11344788 DOI: 10.1038/s41467-024-51614-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 08/13/2024] [Indexed: 08/27/2024] Open
Abstract
In mammals, global passive demethylation contributes to epigenetic reprogramming during early embryonic development. At this stage, the majority of DNA-methyltransferase 1 (DNMT1) protein is excluded from nucleus, which is considered the primary cause. However, whether the remaining nuclear activity of DNMT1 is regulated by additional mechanisms is unclear. Here, we report that nuclear DNMT1 abundance is finetuned through proteasomal degradation in mouse zygotes. We identify a maternal factor, Pramel15, which targets DNMT1 for degradation via Cullin-RING E3 ligases. Loss of Pramel15 elevates DNMT1 levels in the zygote pronuclei, impairs zygotic DNA demethylation, and causes a stochastic gain of DNA methylation in early embryos. Thus, Pramel15 can modulate the residual level of DNMT1 in the nucleus during zygotic DNA replication, thereby ensuring efficient DNA methylation reprogramming in early embryos.
Collapse
Affiliation(s)
- Jiajun Tan
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences, Beijing, China
- New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yingfeng Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences, Beijing, China
- New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xiang Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xiaoxiao Zhu
- Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences, Beijing, China
| | - Liping Liu
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hua Huang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Jiahua Wei
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences, Beijing, China
- New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Hailing Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yong Tian
- Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences, Beijing, China
| | - Zhigao Wang
- Center for Regenerative Medicine, Heart Institute, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Zhuqiang Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences, Beijing, China.
- New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
| | - Bing Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences, Beijing, China.
- New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
29
|
Sun R, A J, Yu H, Wang Y, He M, Tan L, Cheng H, Zhang J, Wang Y, Sun X, Lyu M, Qu M, Huang L, Li Z, Zhang W, Ma K, Dong Z, Ge W, Zhang Y, Ding X, Yang B, Hou J, Xu C, Wang L, Zhu Y, Guo T, Gao X, Yang C. Proteomic landscape profiling of primary prostate cancer reveals a 16-protein panel for prognosis prediction. Cell Rep Med 2024; 5:101679. [PMID: 39168102 PMCID: PMC11384950 DOI: 10.1016/j.xcrm.2024.101679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 06/13/2024] [Accepted: 07/16/2024] [Indexed: 08/23/2024]
Abstract
Prostate cancer (PCa) is the most common malignant tumor in men. Currently, there are few prognosis indicators for predicting PCa outcomes and guiding treatments. Here, we perform comprehensive proteomic profiling of 918 tissue specimens from 306 Chinese patients with PCa using data-independent acquisition mass spectrometry (DIA-MS). We identify over 10,000 proteins and define three molecular subtypes of PCa with significant clinical and proteomic differences. We develop a 16-protein panel that effectively predicts biochemical recurrence (BCR) for patients with PCa, which is validated in six published datasets and one additional 99-biopsy-sample cohort by targeted proteomics. Interestingly, this 16-protein panel effectively predicts BCR across different International Society of Urological Pathology (ISUP) grades and pathological stages and outperforms the D'Amico risk classification system in BCR prediction. Furthermore, double knockout of NUDT5 and SEPTIN8, two components from the 16-protein panel, significantly suppresses the PCa cells to proliferate, invade, and migrate, suggesting the combination of NUDT5 and SEPTIN8 may provide new approaches for PCa treatment.
Collapse
Affiliation(s)
- Rui Sun
- School of Medicine, Westlake University, Hangzhou, Zhejiang Province, China; Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province 310030, China; Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang 310030, China; Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, China
| | - Jun A
- School of Medicine, Westlake University, Hangzhou, Zhejiang Province, China; Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province 310030, China; Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang 310030, China; Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, China
| | - Haolan Yu
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China; CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yan Wang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China; Department of Pathology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Miaoxia He
- Department of Pathology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Lingling Tan
- Westlake Omics (Hangzhou) Biotechnology Co., Ltd., Hangzhou 310024, China
| | - Honghan Cheng
- School of Medicine, Westlake University, Hangzhou, Zhejiang Province, China; Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province 310030, China; Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang 310030, China; Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, China
| | - Jili Zhang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Yingrui Wang
- School of Medicine, Westlake University, Hangzhou, Zhejiang Province, China; Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province 310030, China; Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang 310030, China; Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, China
| | - Xiaochen Sun
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China; CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Mengge Lyu
- School of Medicine, Westlake University, Hangzhou, Zhejiang Province, China; Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province 310030, China; Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang 310030, China; Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, China
| | - Min Qu
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Lingling Huang
- School of Medicine, Westlake University, Hangzhou, Zhejiang Province, China; Westlake Omics (Hangzhou) Biotechnology Co., Ltd., Hangzhou 310024, China
| | - Zijian Li
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Wenhui Zhang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Kunpeng Ma
- School of Medicine, Westlake University, Hangzhou, Zhejiang Province, China; Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province 310030, China; Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang 310030, China; Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, China
| | - Zhenyang Dong
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Weigang Ge
- Westlake Omics (Hangzhou) Biotechnology Co., Ltd., Hangzhou 310024, China
| | - Yun Zhang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Xuan Ding
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province 310030, China; Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang 310030, China; Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, China
| | - Bo Yang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Jianguo Hou
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Chuanliang Xu
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China; Shanghai Key Laboratory of Cell Engineering, Shanghai 200433, China
| | - Linhui Wang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China; Shanghai Key Laboratory of Cell Engineering, Shanghai 200433, China
| | - Yi Zhu
- School of Medicine, Westlake University, Hangzhou, Zhejiang Province, China; Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province 310030, China; Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang 310030, China; Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, China
| | - Tiannan Guo
- School of Medicine, Westlake University, Hangzhou, Zhejiang Province, China; Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province 310030, China; Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang 310030, China; Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, China.
| | - Xu Gao
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China; Shanghai Key Laboratory of Cell Engineering, Shanghai 200433, China.
| | - Chenghua Yang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China; Shanghai Key Laboratory of Cell Engineering, Shanghai 200433, China.
| |
Collapse
|
30
|
Su D, Wang R, Chen G, Ding C, Liu Y, Tao J, Wang Y, Qiu J, Luo W, Weng G, Yang G, Zhang T. FBXO32 Stimulates Protein Synthesis to Drive Pancreatic Cancer Progression and Metastasis. Cancer Res 2024; 84:2607-2625. [PMID: 38775804 DOI: 10.1158/0008-5472.can-23-3638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 03/16/2024] [Accepted: 05/15/2024] [Indexed: 08/16/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the leading causes of cancer-related death worldwide, primarily due to its rapid progression. The current treatment options for PDAC are limited, and a better understanding of the underlying mechanisms responsible for PDAC progression is required to identify improved therapeutic strategies. In this study, we identified FBXO32 as an oncogenic driver in PDAC. FBXO32 was aberrantly upregulated in PDAC, and high FBXO32 expression was significantly associated with an unfavorable prognosis in patients with PDAC. FRG1 deficiency promoted FBXO32 upregulation in PDAC. FBXO32 promoted cell migration and invasion in vitro and tumor growth and metastasis in vivo. Mechanistically, FBXO32 directly interacted with eEF1A1 and promoted its polyubiquitination at the K273 site, leading to enhanced activity of eEF1A1 and increased protein synthesis in PDAC cells. Moreover, FBXO32-catalyzed eEF1A1 ubiquitination boosted the translation of ITGB5 mRNA and activated focal adhesion kinase (FAK) signaling, thereby facilitating focal adhesion assembly and driving PDAC progression. Importantly, interfering with the FBXO32-eEF1A1 axis or pharmaceutical inhibition of FAK by defactinib, an FDA-approved FAK inhibitor, substantially inhibited PDAC growth and metastasis driven by aberrantly activated FBXO32-eEF1A1 signaling. Overall, this study uncovers a mechanism by which PDAC cells rely on FBXO32-mediated eEF1A1 activation to drive progression and metastasis. FBXO32 may serve as a promising biomarker for selecting eligible patients with PDAC for treatment with defactinib. Significance: FBXO32 upregulation in pancreatic cancer induced by FRG1 deficiency increases eEF1A1 activity to promote ITGB5 translation and stimulate FAK signaling, driving cancer progression and sensitizing tumors to the FAK inhibitor defactinib.
Collapse
Affiliation(s)
- Dan Su
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Clinical Immunology Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ruobing Wang
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Clinical Immunology Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Guangyu Chen
- Department of Breast Surgery, The Affiliated Hospital of Guizhou Medical University, Guizhou Medical University, Guiyang, China
| | - Chen Ding
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Clinical Immunology Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yueze Liu
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Clinical Immunology Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jinxin Tao
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Clinical Immunology Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuanyang Wang
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Clinical Immunology Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiangdong Qiu
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Clinical Immunology Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wenhao Luo
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Clinical Immunology Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Guihu Weng
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Clinical Immunology Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Gang Yang
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Clinical Immunology Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Taiping Zhang
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Clinical Immunology Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| |
Collapse
|
31
|
Mabrouk I, Song Y, Liu Q, Ma J, Zhou Y, Yu J, Hou J, Hu X, Li X, Xue G, Cao H, Ma X, Xu J, Wang J, Pan H, Hua G, Hu J, Sun Y. Novel insights into the mechanisms of seasonal cyclicity of testicles by proteomics and transcriptomics analyses in goose breeder lines. Poult Sci 2024; 103:104213. [PMID: 39190991 PMCID: PMC11396066 DOI: 10.1016/j.psj.2024.104213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 07/08/2024] [Accepted: 08/08/2024] [Indexed: 08/29/2024] Open
Abstract
Spermatogenesis is a crucial indicator of geese reproduction performance and production. The testis is the main organ responsible for sperm production, and the egg-laying cycle in geese is a complex physiological process that demands precise orchestration of hormonal cues and cellular events within the testes, however, the seasonal changes in the transcriptomic and proteomic profiles of goose testicles remain unclear. To explore various aspects of the mechanisms of the seasonal cyclicity of testicles in different goose breeds, in this study, we used an integrative transcriptomic and proteomic approach to screen the key genes and proteins in the testes of 2 goose males, the Hungarian white goose and the Wanxi white goose, at 3 different periods of the laying cycle: beginning of laying cycle (BLC), peak of laying cycle (PLC), and end of laying cycle (ELC). The results showed that a total of 9,273 differentially expressed genes and 4,543 differentially expressed proteins were identified in the geese testicles among the comparison groups. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis suggested that the DEGs, in the comparison groups, were mainly enrichment in metabolic pathways, neuroactive ligand-receptor interaction, cyctokine-cyctokine receptor interaction, calcium signaling pathway, apelin signaling pathway, ether lipid metabolism, cysteine, and methionine metabolism. While the DEPs, in the 3 comparison groups, were mainly involved in the ribosome, metabolic pathways, carbon metabolism, proteasome, endocytosis, lysosome, regulation of actin cytoskeleton, oxidative phosphorylation, nucleocytoplasmic transport, and tight junction. The protein-protein interaction network analysis (PPI) indicated that selected DEPs, such as CHD1L, RAB18, FANCM, TAF5, TSC1/2, PHLDB2, DNAJA2, NCOA5, DEPTOR, TJP1, and RAPGEF2, were highly associated with male reproductive regulation. Further, the expression trends of 4 identified DEGs were validated by qRT-PCR. In conclusion, this work offers a new perspective on comprehending the molecular mechanisms and pathways involved in the seasonal cyclicity of testicles in the Hungarian white goose and the Wanxi white goose, as well as contributing to improving goose reproductive performance.
Collapse
Affiliation(s)
- Ichraf Mabrouk
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Yupu Song
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Qiuyuan Liu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Jingyun Ma
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Yuxuan Zhou
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Jin Yu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Jiahui Hou
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Xiangman Hu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Xinyue Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Guizhen Xue
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Heng Cao
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Xiaoming Ma
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Jing Xu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Jingbo Wang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Hongxiao Pan
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Guoqing Hua
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Jingtao Hu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Yongfeng Sun
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China; Key Laboratory of Animal Production, Product Quality and Security, Jilin Agricultural University, Ministry of Education, Changchun, 130118, China; Joint Laboratory of Modern Agricultural Technology International Cooperation, Ministry of Education, Jilin Agricultural University, Changchun, 130118, China.
| |
Collapse
|
32
|
Guo Z, Zhang Y, Wang H, Liao L, Ma L, Zhao Y, Yang R, Li X, Niu J, Chu Q, Fu Y, Li B, Yang C. Hypoxia-induced downregulation of PGK1 crotonylation promotes tumorigenesis by coordinating glycolysis and the TCA cycle. Nat Commun 2024; 15:6915. [PMID: 39134530 PMCID: PMC11319824 DOI: 10.1038/s41467-024-51232-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 08/02/2024] [Indexed: 08/15/2024] Open
Abstract
Protein post-translational modifications (PTMs) are crucial for cancer cells to adapt to hypoxia; however, the functional significance of lysine crotonylation (Kcr) in hypoxia remains unclear. Herein we report a quantitative proteomics analysis of global crotonylome under normoxia and hypoxia, and demonstrate 128 Kcr site alterations across 101 proteins in MDA-MB231 cells. Specifically, we observe a significant decrease in K131cr, K156cr and K220cr of phosphoglycerate kinase 1 (PGK1) upon hypoxia. Enoyl-CoA hydratase 1 (ECHS1) is upregulated and interacts with PGK1, leading to the downregulation of PGK1 Kcr under hypoxia. Abolishment of PGK1 Kcr promotes glycolysis and suppresses mitochondrial pyruvate metabolism by activating pyruvate dehydrogenase kinase 1 (PDHK1). A low PGK1 K131cr level is correlated with malignancy and poor prognosis of breast cancer. Our findings show that PGK1 Kcr is a signal in coordinating glycolysis and the tricarboxylic acid (TCA) cycle and may serve as a diagnostic indicator for breast cancer.
Collapse
Affiliation(s)
- Zihao Guo
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Yang Zhang
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Haoyue Wang
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Liming Liao
- Westlake Four-Dimensional Dynamic Metabolomics (Meta4D) Laboratory, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, China
| | - Lingdi Ma
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Yiliang Zhao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Ronghui Yang
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Xuexue Li
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Jing Niu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Qiaoyun Chu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Yanxia Fu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Binghui Li
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China.
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China.
- Department of Cancer Cell Biology and National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China.
| | - Chuanzhen Yang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China.
- Westlake Four-Dimensional Dynamic Metabolomics (Meta4D) Laboratory, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, China.
| |
Collapse
|
33
|
Bao L, Zhu J, Shi T, Jiang Y, Li B, Huang J, Ji X. Increased transcriptional elongation and RNA stability of GPCR ligand binding genes unveiled via RNA polymerase II degradation. Nucleic Acids Res 2024; 52:8165-8183. [PMID: 38842922 DOI: 10.1093/nar/gkae478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 05/01/2024] [Accepted: 05/31/2024] [Indexed: 06/07/2024] Open
Abstract
RNA polymerase II drives mRNA gene expression, yet our understanding of Pol II degradation is limited. Using auxin-inducible degron, we degraded Pol II's RPB1 subunit, resulting in global repression. Surprisingly, certain genes exhibited increased RNA levels post-degradation. These genes are associated with GPCR ligand binding and are characterized by being less paused and comprising polycomb-bound short genes. RPB1 degradation globally increased KDM6B binding, which was insufficient to explain specific gene activation. In contrast, RPB2 degradation repressed nearly all genes, accompanied by decreased H3K9me3 and SUV39H1 occupancy. We observed a specific increase in serine 2 phosphorylated Pol II and RNA stability for RPB1 degradation-upregulated genes. Additionally, α-amanitin or UV treatment resulted in RPB1 degradation and global gene repression, unveiling subsets of upregulated genes. Our findings highlight the activated transcription elongation and increased RNA stability of signaling genes as potential mechanisms for mammalian cells to counter RPB1 degradation during stress.
Collapse
Affiliation(s)
- Lijun Bao
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Junyi Zhu
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Tingxin Shi
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yongpeng Jiang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Boyuan Li
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Jie Huang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Beijing Advanced Center of RNA Biology (BEACON), Peking University, Beijing 100871, China
| | - Xiong Ji
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| |
Collapse
|
34
|
Li Z, Shi B, Li N, Sun J, Zeng X, Huang R, Bok S, Chen X, Han J, Yallowitz AR, Debnath S, Cung M, Ling Z, Zhong CQ, Hong Y, Li G, Koenen M, Cohen P, Su X, Lu H, Greenblatt MB, Xu R. Bone controls browning of white adipose tissue and protects from diet-induced obesity through Schnurri-3-regulated SLIT2 secretion. Nat Commun 2024; 15:6697. [PMID: 39107299 PMCID: PMC11303806 DOI: 10.1038/s41467-024-51155-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 07/31/2024] [Indexed: 08/10/2024] Open
Abstract
The skeleton has been suggested to function as an endocrine organ controlling whole organism energy balance, however the mediators of this effect and their molecular links remain unclear. Here, utilizing Schnurri-3-/- (Shn3-/-) mice with augmented osteoblast activity, we show Shn3-/-mice display resistance against diet-induced obesity and enhanced white adipose tissue (WAT) browning. Conditional deletion of Shn3 in osteoblasts but not adipocytes recapitulates lean phenotype of Shn3-/-mice, indicating this phenotype is driven by skeleton. We further demonstrate osteoblasts lacking Shn3 can secrete cytokines to promote WAT browning. Among them, we identify a C-terminal fragment of SLIT2 (SLIT2-C), primarily secreted by osteoblasts, as a Shn3-regulated osteokine that mediates WAT browning. Lastly, AAV-mediated Shn3 silencing phenocopies the lean phenotype and augmented glucose metabolism. Altogether, our findings establish a novel bone-fat signaling axis via SHN3 regulated SLIT2-C production in osteoblasts, offering a potential therapeutic target to address both osteoporosis and metabolic syndrome.
Collapse
Affiliation(s)
- Zan Li
- State Key Laboratory of Cellular Stress Biology, Cancer Research Center, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, People's Republic of China
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Sports Medicine, Xiangya Hospital, Central South University, Changsha, People's Republic of China
- PET Center, Department of Nuclear Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Baohong Shi
- State Key Laboratory of Cellular Stress Biology, Cancer Research Center, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, People's Republic of China
- Xiamen Key Laboratory of Regeneration Medicine, Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Xiamen University, Xiamen, China
| | - Na Li
- State Key Laboratory of Cellular Stress Biology, Cancer Research Center, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, People's Republic of China
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Xiamen Key Laboratory of Regeneration Medicine, Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Xiamen University, Xiamen, China
| | - Jun Sun
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Xiangchen Zeng
- State Key Laboratory of Cellular Stress Biology, Cancer Research Center, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, People's Republic of China
| | - Rui Huang
- State Key Laboratory of Cellular Stress Biology, Cancer Research Center, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, People's Republic of China
| | - Seoyeon Bok
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Xiaohui Chen
- State Key Laboratory of Cellular Stress Biology, Cancer Research Center, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, People's Republic of China
- Xiamen Key Laboratory of Regeneration Medicine, Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Xiamen University, Xiamen, China
| | - Jie Han
- State Key Laboratory of Cellular Stress Biology, Cancer Research Center, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, People's Republic of China
| | - Alisha R Yallowitz
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Shawon Debnath
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Michelle Cung
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Zheng Ling
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Chuan-Qi Zhong
- College of Life Science, Xiamen University, Xiamen, China
| | - Yixang Hong
- Xiamen Cardiovascular Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Gang Li
- Xiamen Cardiovascular Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Mascha Koenen
- Laboratory of Molecular Metabolism, The Rockefeller University, New York, NY, USA
| | - Paul Cohen
- Laboratory of Molecular Metabolism, The Rockefeller University, New York, NY, USA
| | - Xinhui Su
- PET Center, Department of Nuclear Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hongbin Lu
- Department of Sports Medicine, Xiangya Hospital, Central South University, Changsha, People's Republic of China.
- Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Changsha, China.
- Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.
| | - Matthew B Greenblatt
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
- Research Division, Hospital for Special Surgery, New York, NY, USA.
| | - Ren Xu
- State Key Laboratory of Cellular Stress Biology, Cancer Research Center, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, People's Republic of China.
- Xiamen Key Laboratory of Regeneration Medicine, Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Xiamen University, Xiamen, China.
| |
Collapse
|
35
|
Hua R, Zhao K, Xu Z, Zheng Y, Wu C, Zhang L, Teng Y, Wang J, Wang M, Hu J, Chen L, Yuan D, Dong W, Cheng X, Xia Y. Stratifin-mediated activation of AKT signaling and therapeutic targetability in hepatocellular carcinoma progression. CELL INSIGHT 2024; 3:100178. [PMID: 39027058 PMCID: PMC11254524 DOI: 10.1016/j.cellin.2024.100178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 07/20/2024]
Abstract
Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related deaths worldwide and presents a significant threat to human health. Despite its prevalence, the underlying regulatory mechanisms of HCC remain unclear. In this study, we integrated RNA-seq datasets, proteome dataset and survival analysis and unveiled Stratifin (SFN) as a potential prognostic biomarker for HCC. SFN knockdown inhibited HCC progression in cell cultures and mouse models. Conversely, ectopic expression of Sfn in primary mouse HCC model accelerated HCC progression. Mechanistically, SFN acted as an adaptor protein, activating AKT1 signaling by fostering the interaction between PDK1 and AKT1, with the R56 and R129 sites on SFN proving to be crucial for this binding. In the syngeneic implantation model, the R56A/R129A mutant of SFN inhibited Akt signaling activation and impeded HCC growth. Additionally, peptide inhibitors designed based on the binding motif of AKT1 to SFN significantly inhibited HCC progression. In summary, our findings establish that SFN promotes HCC progression by activating AKT signaling through the R56 and R129 binding sites. This discovery opens new avenues for a promising therapeutic strategy for the treatment of HCC.
Collapse
Affiliation(s)
- Rong Hua
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Kaitao Zhao
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Zaichao Xu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Yingcheng Zheng
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Chuanjian Wu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Lu Zhang
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Yan Teng
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Jingjing Wang
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Mengfei Wang
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Jiayu Hu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Lang Chen
- Department of Immunology, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Detian Yuan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Wei Dong
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, China
- Hubei Province for the Clinical Medicine Research Center of Hepatic Surgery, Wuhan, Hubei, China
- Key Laboratory of Organ Transplantation, Ministry of Education, NHC Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, Hubei, China
| | - Xiaoming Cheng
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
- Wuhan University Center for Pathology and Molecular Diagnostics, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, China
- Hubei Jiangxia Laboratory, Wuhan, China
| | - Yuchen Xia
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, China
- Hubei Jiangxia Laboratory, Wuhan, China
- Pingyuan Laboratory, Henan, China
| |
Collapse
|
36
|
Tang Y, Chu C, Bu S, Sun Q, Liu A, Xie J, Qiao S, Huang L, Wang H. Integrated multi-omics profiling landscape of organising pneumonia. Clin Transl Med 2024; 14:e1782. [PMID: 39083563 PMCID: PMC11290555 DOI: 10.1002/ctm2.1782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 07/09/2024] [Accepted: 07/11/2024] [Indexed: 08/02/2024] Open
Abstract
BACKGROUND Organising pneumonia (OP) is one of the most common and lethal diseases in the category of interstitial pneumonia, along with lung cancer. Reprogramming of lipid metabolism is a newly recognized hallmark of many diseases including cancer, cardiovascular disorders, as well as liver fibrosis and sclerosis. Increased levels of ceramides composed of sphingosine and fatty acid, are implicated in the development of both acute and chronic lung diseases. However, their pathophysiological significance in OP is unclear. The aim of this study was to investigate the role of lipid metabolism reprogramming in OP, focusing on inflammation and fibrosis. METHODS Comprehensive multi-omics profiling approaches, including single-cell RNA sequencing, Visium CytAssist spatial transcriptomics, proteomics, metabolomics and mass spectrometry, were employed to analyze the tissues. OP mice model was utilized and molecular mechanisms were investigated in macrophages. RESULTS The results revealed a significant association between OP and lipid metabolism reprogramming, characterized by an abnormal expression of several genes related to lipid metabolism, including CD36, SCD1, and CES1 mainly in macrophages. CD36 deficiency in alveolar macrophages, led to an increased expression of C16/24 ceramides that accumulated in mitochondria, resulting in mitophagy or mitochondrial dysfunction. The number of alveolar macrophages in OP was significantly reduced, which was probably due to the ferroptosis signaling pathway involving GSH/SLC3A2/GPX4 through CD36 downregulation in OP. Furthermore, macrophage secretion of DPP7 and FABP4 influenced epithelial cell fibrosis. CONCLUSIONS CD36 inhibited the ferroptosis pathway involving SLC3A2/GPX4 in alveolar macrophages of OP tissue by regulating lipid metabolism, thus representing a new anti-ferroptosis and anti-fibrosis effect of CD36 mediated, at least in part, by ceramides. HIGHLIGHTS Our findings reveal a significant association between organising pneumonia and lipid metabolism reprogramming and will make a substantial contribution to the understanding of the mechanism of organising pneumonia in patients.
Collapse
Affiliation(s)
- Ying Tang
- Jiangsu Provincial Key Laboratory of Critical Care MedicineDepartment of Critical Care MedicineZhongda HospitalSchool of MedicineSoutheast UniversityNanjingChina
| | - Cuilin Chu
- Jiangsu Provincial Key Laboratory of Critical Care MedicineDepartment of Critical Care MedicineZhongda HospitalSchool of MedicineSoutheast UniversityNanjingChina
| | - Siyuan Bu
- Jiangsu Provincial Key Laboratory of Critical Care MedicineDepartment of Critical Care MedicineZhongda HospitalSchool of MedicineSoutheast UniversityNanjingChina
- Shaanxi University of Chinese MedicineXianyangChina
| | - Qin Sun
- Jiangsu Provincial Key Laboratory of Critical Care MedicineDepartment of Critical Care MedicineZhongda HospitalSchool of MedicineSoutheast UniversityNanjingChina
| | - Airan Liu
- Jiangsu Provincial Key Laboratory of Critical Care MedicineDepartment of Critical Care MedicineZhongda HospitalSchool of MedicineSoutheast UniversityNanjingChina
| | - Jianfeng Xie
- Jiangsu Provincial Key Laboratory of Critical Care MedicineDepartment of Critical Care MedicineZhongda HospitalSchool of MedicineSoutheast UniversityNanjingChina
| | - Sen Qiao
- Assisted Reproduction CenterNorthwest Women's and Children's HospitalXi'anChina
| | - Lingyan Huang
- Department of PathologicalGeneral Hospital of Ningxia Medical UniversityYinchuanChina
| | - Hongmei Wang
- Jiangsu Provincial Key Laboratory of Critical Care MedicineDepartment of Critical Care MedicineZhongda HospitalSchool of MedicineSoutheast UniversityNanjingChina
- Shaanxi University of Chinese MedicineXianyangChina
| |
Collapse
|
37
|
Liu H, Wuren T, Ge RL. DATA in BRIEF of: Adaptative mechanisms indicated by placental protein expression changes in high-altitude Tibetan women during vaginal delivery. Data Brief 2024; 55:110542. [PMID: 38948405 PMCID: PMC11214193 DOI: 10.1016/j.dib.2024.110542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 05/08/2024] [Accepted: 05/13/2024] [Indexed: 07/02/2024] Open
Abstract
Over a period of 30,000 to 40,000 years, high-altitude Tibetans have physiologically and genetically adapted to conditions such as hypoxia, low temperature, and high-intensity ultraviolet radiation. Based on the unique physiological and morphological characteristics of the Tibetan people, they have outstanding hypoxia adaptation skills and can continue to thrive in plateau hypoxia. The placenta of high-altitude Tibetans is protected from oxidative stress during delivery; however, little is known about changes in placental protein expression during vaginal delivery. In this study, we aimed to reveal these adaptive mechanisms by studying changes in placental protein expression during vaginal delivery in high-altitude Tibetans, low-altitude Tibetans, and low-altitude Han populations. Studying the changing mechanisms of maternal responses to hypoxia at high altitudes can reveal the molecular mechanisms of maternal and fetal adaptation to hypoxia at high altitudes and provide theories for preventing and treating maternal hypoxia and intrauterine growth and development restriction caused by other diseases.
Collapse
Affiliation(s)
- Huifang Liu
- Key Laboratory of Plateau Medicine of Ministry of Education, Plateau Medicine Research Center, Qinghai University, China
- Qinghai Key Laboratory of Plateau Medicine Application Foundation, China
- Qinghai-Utah Joint Key Laboratory of Plateau Medicine, China
- Affiliated Hospital of Qinghai University, Xining 810001, China
| | - Tana Wuren
- Key Laboratory of Plateau Medicine of Ministry of Education, Plateau Medicine Research Center, Qinghai University, China
- Qinghai Key Laboratory of Plateau Medicine Application Foundation, China
- Qinghai-Utah Joint Key Laboratory of Plateau Medicine, China
| | - Ri-li Ge
- Key Laboratory of Plateau Medicine of Ministry of Education, Plateau Medicine Research Center, Qinghai University, China
- Qinghai Key Laboratory of Plateau Medicine Application Foundation, China
- Qinghai-Utah Joint Key Laboratory of Plateau Medicine, China
| |
Collapse
|
38
|
Zhang Z, Li Y, Yang J, Li J, Lin X, Liu T, Yang S, Lin J, Xue S, Yu J, Tang C, Li Z, Liu L, Ye Z, Deng Y, Li Z, Chen K, Ding H, Luo C, Lin H. Dual-site molecular glues for enhancing protein-protein interactions of the CDK12-DDB1 complex. Nat Commun 2024; 15:6477. [PMID: 39090085 PMCID: PMC11294606 DOI: 10.1038/s41467-024-50642-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 07/18/2024] [Indexed: 08/04/2024] Open
Abstract
Protein-protein interactions (PPIs) stabilization with molecular glues plays a crucial role in drug discovery, albeit with significant challenges. In this study, we propose a dual-site approach, targeting the PPI region and its dynamic surroundings. We conduct molecular dynamics simulations to identify critical sites on the PPI that stabilize the cyclin-dependent kinase 12 - DNA damage-binding protein 1 (CDK12-DDB1) complex, resulting in further cyclin K degradation. This exploration leads to the creation of LL-K12-18, a dual-site molecular glue, which enhances the glue properties to augment degradation kinetics and efficiency. Notably, LL-K12-18 demonstrates strong inhibition of gene transcription and anti-proliferative effects in tumor cells, showing significant potency improvements in MDA-MB-231 (88-fold) and MDA-MB-468 cells (307-fold) when compared to its precursor compound SR-4835. These findings underscore the potential of dual-site approaches in disrupting CDK12 function and offer a structural insight-based framework for the design of cyclin K molecular glues.
Collapse
Affiliation(s)
- Zemin Zhang
- The School of Pharmacy, Fujian Medical University, Fuzhou, China
| | - Yuanqing Li
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Jie Yang
- Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Jiacheng Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Xiongqiang Lin
- The School of Pharmacy, Fujian Medical University, Fuzhou, China
| | - Ting Liu
- The School of Pharmacy, Fujian Medical University, Fuzhou, China
| | - Shiling Yang
- Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Jin Lin
- The School of Pharmacy, Fujian Medical University, Fuzhou, China
| | - Shengyu Xue
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Jiamin Yu
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Cailing Tang
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Ziteng Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Liping Liu
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China
| | - Zhengzheng Ye
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Yanan Deng
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Zhihai Li
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Kaixian Chen
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hong Ding
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- State Key Laboratory of Functions and Applications of Medicinal Plants, School of Pharmacy, Guizhou Medical University, Guiyang, China.
| | - Cheng Luo
- The School of Pharmacy, Fujian Medical University, Fuzhou, China.
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China.
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
- State Key Laboratory of Functions and Applications of Medicinal Plants, School of Pharmacy, Guizhou Medical University, Guiyang, China.
| | - Hua Lin
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, College of Life Sciences, Fujian Normal University, Fuzhou, China.
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China.
| |
Collapse
|
39
|
Ming J, Lin L, Li J, Wu L, Fang S, Huang T, Fu Y, Liu D, Zhang W, Li C, Yang Y, Huang Y, Qin Y, Kuang J, Huang X, Guo L, Zhang X, Liu J, Chen J, Zhao C, Wang B, Pei D. Cell fate decision by a morphogen-transcription factor-chromatin modifier axis. Nat Commun 2024; 15:6365. [PMID: 39075094 PMCID: PMC11286941 DOI: 10.1038/s41467-024-50144-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 06/28/2024] [Indexed: 07/31/2024] Open
Abstract
Cell fate decisions remain poorly understood at the molecular level. Embryogenesis provides a unique opportunity to analyze molecular details associated with cell fate decisions. Works based on model organisms have provided a conceptual framework of genes that specify cell fate control, for example, transcription factors (TFs) controlling processes from pluripotency to immunity1. How TFs specify cell fate remains poorly understood. Here we report that SALL4 relies on NuRD (nucleosome-remodeling and deacetylase complex) to interpret BMP4 signal and decide cell fate in a well-controlled in vitro system. While NuRD complex cooperates with SALL4 to convert mouse embryonic fibroblasts or MEFs to pluripotency, BMP4 diverts the same process to an alternative fate, PrE (primitive endoderm). Mechanistically, BMP4 signals the dissociation of SALL4 from NuRD physically to establish a gene regulatory network for PrE. Our results provide a conceptual framework to explore the rich landscapes of cell fate choices intrinsic to development in higher organisms involving morphogen-TF-chromatin modifier pathways.
Collapse
Affiliation(s)
- Jin Ming
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Lihui Lin
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jiajun Li
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Linlin Wu
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Shicai Fang
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Tao Huang
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Yu Fu
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Dong Liu
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Wenhui Zhang
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Chen Li
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yongzheng Yang
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yi Huang
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yue Qin
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Junqi Kuang
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, Zhejiang, China
| | - Xingnan Huang
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Liman Guo
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xiaofei Zhang
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jing Liu
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jiekai Chen
- CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Chengchen Zhao
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China.
| | - Bo Wang
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China.
- Zhejiang University of Science and Technology, School of Information and Electronic Engineering, Hangzhou, Zhejiang, China.
- Key Laboratory of Biomedical Intelligent Computing Technology of Zhejiang Province, Hangzhou, Zhejiang, China.
| | - Duanqing Pei
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, Zhejiang, China.
| |
Collapse
|
40
|
Ye J, Xu S, Liu X, Zhang Q, Li X, Zhang H, Ma J, Leng L, Zhang S. Effect and mechanism of T lymphocytes on human induced pluripotent stem cell-derived cardiomyocytes via Proteomics. Stem Cell Res Ther 2024; 15:236. [PMID: 39075540 PMCID: PMC11288085 DOI: 10.1186/s13287-024-03791-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 06/08/2024] [Indexed: 07/31/2024] Open
Abstract
BACKGROUND Abnormalities in T cell activation play an important role in the pathogenesis of myocarditis, and persistent T cell responses can lead to autoimmunity and chronic cardiac inflammation, as well as even dilated cardiomyopathy. Although previous work has examined the role of T cells in myocarditis in animal models, the specific mechanism for human cardiomyocytes has not been investigated. METHODS In this study, we constructed the human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) and established the T cell-mediated cardiac injury model by co-culturing with activated CD4 + T or CD8 + T cells that were isolated from peripheral mononuclear blood to elucidate the pathogenesis of myocardial cell injury caused by inflammation. RESULTS By combination of quantitative proteomics with tissue and cell immunofluorescence examination, we established a proteome profile of inflammatory myocardia from hiPSC-CMs with obvious cardiomyocyte injury and increased levels of lactate dehydrogenase content, creatine kinase isoenzyme MB and cardiac troponin. A series of molecular dysfunctions of hiPSC-CMs was observed and indicated that CD4 + cells could produce direct cardiomyocyte injury by activating the NOD-like receptor signals pathway. CONCLUSIONS The data presented in our study established a proteome map of inflammatory myocardial based on hiPSC-CMs injury model. These results can provide guidance in the discovery of improved clinical treatments for myocarditis.
Collapse
Affiliation(s)
- Jin Ye
- Stem cell and Regenerative Medicine Lab, Institute of Clinical Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Translational Medicine Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Sichi Xu
- Stem cell and Regenerative Medicine Lab, Institute of Clinical Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Translational Medicine Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Xiaoqing Liu
- Stem cell and Regenerative Medicine Lab, Institute of Clinical Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Translational Medicine Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
- College of Life Sciences, Hebei University, Baoding, 071002, China
| | - Qiyu Zhang
- Stem cell and Regenerative Medicine Lab, Institute of Clinical Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Translational Medicine Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Xiao Li
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Hui Zhang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Jie Ma
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
| | - Ling Leng
- Stem cell and Regenerative Medicine Lab, Institute of Clinical Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Translational Medicine Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
| | - Shuyang Zhang
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
| |
Collapse
|
41
|
Gao J, Liu H, Li L, Guo C, Wang Z, Cheng M, Tan S, Chen L, Shi J, Wu H, Feng C, Yu G, Ding C. Comprehensive proteomic characterization of urethral stricture disease in the Chinese population. Front Mol Biosci 2024; 11:1401970. [PMID: 39130371 PMCID: PMC11310122 DOI: 10.3389/fmolb.2024.1401970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 06/26/2024] [Indexed: 08/13/2024] Open
Abstract
Background Male urethral stricture disease (USD) is predominantly characterized by scar formation. There are few effective therapeutic drugs, and comprehensive molecular characterizations of USD formation remain undefined. Methods The proteomic profiling of twelve scar tissues and five matched normal adjacent tissues (NATs). Proteomic analysis methods were applied to explore the molecular characterizations of USD formation, including uncovering mechanistic pathways and providing novel biomarkers for scar formation. Results Comparative proteomic analysis showed that the extracellular matrix (ECM) and complement cascade signaling were predominant in scar tissues. COL11A1 and CD248 significantly contributed to the accumulation of ECM components. Our study presented diverse molecular mechanisms of scar formation across different ages and suggested the potential effects of PXK in Age 1 (<45) patients. Furthermore, immune infiltration studies indicated the therapeutic potential of inhibiting the complement system (C4A, C4B) in Age 2 (≥45) patients, providing a potential clinical strategy for USD. Conclusion This study illustrated the pathogenesis of USD formation and the diverse characteristics of USD patients with different ages, enhancing our understanding of the disease's pathogenesis and providing a valuable resource for USD treatment.
Collapse
Affiliation(s)
- Jiangtao Gao
- Department of Urology, The First People’s Hospital of Zhengzhou, Henan, China
| | - Hui Liu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China
- State Key Laboratory Cell Differentiation and Regulation, Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis, (111 Project), College of Life Science, Henan Normal University, Xinxiang, China
| | - Lingling Li
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Chunmei Guo
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Zhiyong Wang
- Key Medical Laboratory of Stem Cell Transformation and Application, Department of Pathology, The First People’s Hospital of Zhengzhou, Henan, China
| | - Mengya Cheng
- Department of Urology, The First People’s Hospital of Zhengzhou, Henan, China
| | - Subei Tan
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Lu Chen
- Department of Urology, The First People’s Hospital of Zhengzhou, Henan, China
| | - Jijing Shi
- Key Medical Laboratory of Stem Cell Transformation and Application, Department of Pathology, The First People’s Hospital of Zhengzhou, Henan, China
| | - Hui Wu
- Department of Urology, The First People’s Hospital of Zhengzhou, Henan, China
| | - Chao Feng
- Department of Urology, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Guoying Yu
- State Key Laboratory Cell Differentiation and Regulation, Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis, (111 Project), College of Life Science, Henan Normal University, Xinxiang, China
| | - Chen Ding
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China
- State Key Laboratory Cell Differentiation and Regulation, Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis, (111 Project), College of Life Science, Henan Normal University, Xinxiang, China
- Institute of Cancer Research, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, China
| |
Collapse
|
42
|
Liu H, Yan P, Zhang Z, Han H, Zhou Q, Zheng J, Zhang J, Xu F, Shui W. Structural Mass Spectrometry Captures Residue-Resolved Comprehensive Conformational Rearrangements of a G Protein-Coupled Receptor. J Am Chem Soc 2024; 146:20045-20058. [PMID: 39001877 DOI: 10.1021/jacs.4c03922] [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: 07/15/2024]
Abstract
G protein-coupled receptor (GPCR) structural studies with in-solution spectroscopic approaches have offered distinctive insights into GPCR activation and signaling that highly complement those yielded from structural snapshots by crystallography or cryo-EM. While most current spectroscopic approaches allow for probing structural changes at selected residues or loop regions, they are not suitable for capturing a holistic view of GPCR conformational rearrangements across multiple domains. Herein, we develop an approach based on limited proteolysis mass spectrometry (LiP-MS) to simultaneously monitor conformational alterations of a large number of residues spanning both flexible loops and structured transmembrane domains for a given GPCR. To benchmark LiP-MS for GPCR conformational profiling, we studied the adenosine 2A receptor (A2AR) in response to different ligand binding (agonist/antagonist/allosteric modulators) and G protein coupling. Systematic and residue-resolved profiling of A2AR conformational rearrangements by LiP-MS precisely captures structural mechanisms in multiple domains underlying ligand engagement, receptor activation, and allostery, and may also reflect local conformational flexibility. Furthermore, these residue-resolution structural fingerprints of the A2AR protein allow us to readily classify ligands of different pharmacology and distinguish the G protein-coupled state. Thus, our study provides a new structural MS approach that would be generalizable to characterizing conformational transition and plasticity for challenging integral membrane proteins.
Collapse
Affiliation(s)
- Hongyue Liu
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pengfei Yan
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhaoyu Zhang
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongbo Han
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Qingtong Zhou
- Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Jie Zheng
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jian Zhang
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Fei Xu
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Wenqing Shui
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| |
Collapse
|
43
|
Wang C, Zhang X, Wu K, Liu S, Li X, Zhu C, Xiao Y, Fang Z, Liu J. Two Zn 2Cys 6-type transcription factors respond to aromatic compounds and regulate the expression of laccases in the white-rot fungus Trametes hirsuta. Appl Environ Microbiol 2024; 90:e0054524. [PMID: 38899887 PMCID: PMC11267944 DOI: 10.1128/aem.00545-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
White-rot fungi differentially express laccases when they encounter aromatic compounds. However, the underlying mechanisms are still being explored. Here, proteomics analysis revealed that in addition to increased laccase activity, proteins involved in sphingolipid metabolism and toluene degradation as well as some cytochrome P450s (CYP450s) were differentially expressed and significantly enriched during 48 h of o-toluidine exposure, in Trametes hirsuta AH28-2. Two Zn2Cys6-type transcription factors (TFs), TH8421 and TH4300, were upregulated. Bioinformatics docking and isothermal titration calorimetry assays showed that each of them could bind directly to o-toluidine and another aromatic monomer, guaiacol. Binding to aromatic compounds promoted the formation of TH8421/TH4300 heterodimers. TH8421 and TH4300 silencing in T. hirsuta AH28-2 led to decreased transcriptional levels and activities of LacA and LacB upon o-toluidine and guaiacol exposure. EMSA and ChIP-qPCR analysis further showed that TH8421 and TH4300 bound directly with the promoter regions of lacA and lacB containing CGG or CCG motifs. Furthermore, the two TFs were involved in direct and positive regulation of the transcription of some CYP450s. Together, TH8421 and TH4300, two key regulators found in T. hirsuta AH28-2, function as heterodimers to simultaneously trigger the expression of downstream laccases and intracellular enzymes. Monomeric aromatic compounds act as ligands to promote heterodimer formation and enhance the transcriptional activities of the two TFs.IMPORTANCEWhite-rot fungi differentially express laccase isoenzymes when exposed to aromatic compounds. Clarification of the molecular mechanisms underlying differential laccase expression is essential to elucidate how white-rot fungi respond to the environment. Our study shows that two Zn2Cys6-type transcription factors form heterodimers, interact with the promoters of laccase genes, and positively regulate laccase transcription in Trametes hirsuta AH28-2. Aromatic monomer addition induces faster heterodimer formation and rate of activity. These findings not only identify two new transcription factors involved in fungal laccase transcription but also deepen our understanding of the mechanisms underlying the response to aromatics exposure in white-rot fungi.
Collapse
Affiliation(s)
- Chenkai Wang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, China
| | - Xinlei Zhang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, China
| | - Kun Wu
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, China
| | - Shenglong Liu
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, China
| | - Xiang Li
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Chaona Zhu
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Yazhong Xiao
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, China
| | - Zemin Fang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, China
| | - Juanjuan Liu
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, China
| |
Collapse
|
44
|
Xu H, Zhang J, Wang F, Chen Y, Chen H, Feng Y, Hou G, Zi J, Zhang M, Zhou J, Deng L, Lin L, Zhang X, Liu S. Integration of metagenomics and metaproteomics in the intestinal lavage fluids benefits construction of discriminative model and discovery of biomarkers for HBV liver diseases. Proteomics 2024:e2400002. [PMID: 39044605 DOI: 10.1002/pmic.202400002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 06/29/2024] [Accepted: 07/15/2024] [Indexed: 07/25/2024]
Abstract
Intestinal lavage fluid (IVF) containing the mucosa-associated microbiota instead of fecal samples was used to study the gut microbiota using different omics approaches. Focusing on the 63 IVF samples collected from healthy and hepatitis B virus-liver disease (HBV-LD), a question is prompted whether omics features could be extracted to distinguish these samples. The IVF-related microbiota derived from the omics data was classified into two enterotype sets, whereas the genomics-based enterotypes were poorly overlapped with the proteomics-based one in either distribution of microbiota or of IVFs. There is lack of molecular features in these enterotypes to specifically recognize healthy or HBV-LD. Running machine learning against the omics data sought the appropriate models to discriminate the healthy and HBV-LD IVFs based on selected genes or proteins. Although a single omics dataset is basically workable in such discrimination, integration of the two datasets enhances discrimination efficiency. The protein features with higher frequencies in the models are further compared between healthy and HBV-LD based on their abundance, bringing about three potential protein biomarkers. This study highlights that integration of metaomics data is beneficial for a molecular discriminator of healthy and HBV-LD, and reveals the IVF samples are valuable for microbiome in a small cohort.
Collapse
Affiliation(s)
- Hongkai Xu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Department of Proteomics, Beijing Genomics Institute (BGI-Shenzhen), Shenzhen, China
| | - Jiangguo Zhang
- Department of Gastroenterology, Third People's Hospital of Shenzhen, Shenzhen, China
| | - Fang Wang
- Department of Gastroenterology, Third People's Hospital of Shenzhen, Shenzhen, China
| | - Yiyang Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Department of Proteomics, Beijing Genomics Institute (BGI-Shenzhen), Shenzhen, China
| | - Hao Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Department of Proteomics, Beijing Genomics Institute (BGI-Shenzhen), Shenzhen, China
| | - Yang Feng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Department of Proteomics, Beijing Genomics Institute (BGI-Shenzhen), Shenzhen, China
| | - Guixue Hou
- Department of Proteomics, Beijing Genomics Institute (BGI-Shenzhen), Shenzhen, China
| | - Jin Zi
- Department of Proteomics, Beijing Genomics Institute (BGI-Shenzhen), Shenzhen, China
| | - Meiping Zhang
- Department of Gastroenterology, Third People's Hospital of Shenzhen, Shenzhen, China
| | - Jinfeng Zhou
- Department of Gastroenterology, Third People's Hospital of Shenzhen, Shenzhen, China
| | - Le Deng
- Department of Gastroenterology, Third People's Hospital of Shenzhen, Shenzhen, China
| | - Liang Lin
- Department of Proteomics, Beijing Genomics Institute (BGI-Shenzhen), Shenzhen, China
| | - Xiaoyin Zhang
- Department of Gastroenterology, Third People's Hospital of Shenzhen, Shenzhen, China
| | - Siqi Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Department of Proteomics, Beijing Genomics Institute (BGI-Shenzhen), Shenzhen, China
| |
Collapse
|
45
|
Hu J, Yu T, Huang K, Liang C, Li Y, Li X, Sun J, Bai W. Covalent Interactions of Anthocyanins with Proteins: Activity-Based Protein Profiling of Cyanidin-3- O-glucoside. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 39036896 DOI: 10.1021/acs.jafc.4c03869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
Anthocyanins are common natural pigments with a variety of physiological activities. Traditional perspectives attribute their molecular mechanism to noncovalent interactions influencing signaling pathways. However, this ignores the nature of its benzopyrylium skeleton, which readily reacts with the electron-rich groups of proteins. Here, we modified cyanidin-3-O-glucoside (C3G) via activity-based protein profiling technology by our previous synthesis route and prepared the covalent binding probe (C3G-Probe) and the noncovalent photoaffinity probe (C3G-Diazirine). The properties of C3G's covalent binding to proteins were also discovered by comparing the labeling of the two probes to the whole HepG2 cell proteome. We further explored its target proteins and enriched pathways in HepG2 and HeLa cells. Western blot analysis further confirmed the covalent binding of C3G to four target proteins: insulin-degrading enzyme, metal cation symporter ZIP14, spermatid perinuclear RNA-binding protein, and Cystatin-B. Pathway analysis showed that covalent targets of C3G were concentrated in metabolic pathways and several ribonucleoprotein complexes that were also coenriched. The results of this study provide new insights into the interaction of the naturally active molecule C3G with proteins.
Collapse
Affiliation(s)
- Jun Hu
- School of Chemical Engineering and Light Industry, Guangdong Provincial Key Laboratory of Plant Resources Biorefinery, Guangdong University of Technology, Guangzhou 510632, China
- Department of Food Science and Engineering, Institute of Food Safety and Nutrition, Guangdong Engineering Technology Center of Food Safety Molecular Rapid Detection, Jinan University, Guangzhou 510632, China
| | - Tingxin Yu
- Department of Food Science and Engineering, Institute of Food Safety and Nutrition, Guangdong Engineering Technology Center of Food Safety Molecular Rapid Detection, Jinan University, Guangzhou 510632, China
| | - Kuanchen Huang
- Department of Food Science and Engineering, Institute of Food Safety and Nutrition, Guangdong Engineering Technology Center of Food Safety Molecular Rapid Detection, Jinan University, Guangzhou 510632, China
| | - Chujie Liang
- School of Chemical Engineering and Light Industry, Guangdong Provincial Key Laboratory of Plant Resources Biorefinery, Guangdong University of Technology, Guangzhou 510632, China
| | - Yue Li
- Department of Food Science and Engineering, Institute of Food Safety and Nutrition, Guangdong Engineering Technology Center of Food Safety Molecular Rapid Detection, Jinan University, Guangzhou 510632, China
| | - Xusheng Li
- Department of Food Science and Engineering, Institute of Food Safety and Nutrition, Guangdong Engineering Technology Center of Food Safety Molecular Rapid Detection, Jinan University, Guangzhou 510632, China
| | - Jianxia Sun
- School of Chemical Engineering and Light Industry, Guangdong Provincial Key Laboratory of Plant Resources Biorefinery, Guangdong University of Technology, Guangzhou 510632, China
| | - Weibin Bai
- Department of Food Science and Engineering, Institute of Food Safety and Nutrition, Guangdong Engineering Technology Center of Food Safety Molecular Rapid Detection, Jinan University, Guangzhou 510632, China
| |
Collapse
|
46
|
Shang L, Jiang X, Zhao X, Huang X, Wang X, Jiang X, Kong X, Yao M, Jiang S, Wong PP. Mitochondrial DNA-boosted dendritic cell-based nanovaccination triggers antitumor immunity in lung and pancreatic cancers. Cell Rep Med 2024; 5:101648. [PMID: 38986624 PMCID: PMC11293323 DOI: 10.1016/j.xcrm.2024.101648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 04/09/2024] [Accepted: 06/17/2024] [Indexed: 07/12/2024]
Abstract
Low migratory dendritic cell (DC) levels pose a challenge in cancer immune surveillance, yet their impact on tumor immune status and immunotherapy responses remains unclear. We present clinical evidence linking reduced migratory DC levels to immune-cold tumor status, resulting in poor patient outcomes. To address this, we develop an autologous DC-based nanovaccination strategy using patient-derived organoid or cancer cell lysate-pulsed cationic nanoparticles (cNPs) to load immunogenic DC-derived microvesicles (cNPcancer cell@MVDC). This approach transforms immune-cold tumors, increases migratory DCs, activates T cells and natural killer cells, reduces tumor growth, and enhances survival in orthotopic pancreatic and lung cancer models, surpassing conventional methods. In vivo imaging reveals superior cNPcancer cell@MVDC accumulation in tumors and lymph nodes, promoting immune cell infiltration. Mechanistically, cNPs enrich mitochondrial DNA, enhancing cGAS-STING-mediated DC activation and migration. Our strategy shifts cold tumors to a hot state, enhancing antitumor immunity for potential personalized cancer treatments.
Collapse
Affiliation(s)
- Lihuan Shang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou 510120, China; Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Xue Jiang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou 510120, China; Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Xinbao Zhao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou 510120, China; Department of Ultrasound, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Xi Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou 510120, China; Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Xiaojuan Wang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou 510120, China; Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Xue Jiang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou 510120, China; Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Xiangzhan Kong
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou 510120, China; Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Mingkang Yao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou 510120, China; Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Department of Respiratory Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Shanping Jiang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou 510120, China; Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Department of Respiratory Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Ping-Pui Wong
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou 510120, China; Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.
| |
Collapse
|
47
|
Tian Y, Wang H, Pan T, Hu X, Ding J, Chen Y, Li J, Chen H, Luo T. Global proteomic analyses of lysine acetylation, malonylation, succinylation, and crotonylation in human sperm reveal their involvement in male fertility. J Proteomics 2024; 303:105213. [PMID: 38797435 DOI: 10.1016/j.jprot.2024.105213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/17/2024] [Accepted: 05/23/2024] [Indexed: 05/29/2024]
Abstract
Protein lysine modifications (PLMs) are hotspots of post-translational modifications and are involved in many diseases; however, their role in human sperm remains obscure. This study examined the presence and functional roles of a classical PLM (lysine acetylation, Kac) and three novel PLMs (lysine malonylation, Kmal; lysine succinylation, Ksucc; lysine crotonylation, Kcr) in human sperm. Immunoblotting and immunofluorescence assays revealed modified proteins (15-150 kDa) in the tails of human sperm. An immunoaffinity approach coupled with liquid chromatography/tandem mass spectrometry revealed 1423 Kac sites in 680 proteins, 196 Kmal sites in 118 proteins, 788 Ksucc sites in 251 proteins, and 1836 Kcr sites in 645 proteins. These modified proteins participate in a variety of biological processes and metabolic pathways. Crosstalk analysis demonstrated that proteins involved in the sperm energy pathways of glycolysis, oxidative phosphorylation, the citrate cycle, fatty acid oxidation, and ketone body metabolism were modified by at least one of these modifications. In addition, these modifications were found in 62 male fertility-related proteins that weave a protein-protein interaction network associated with asthenoteratozoospermia, asthenozoospermia, globozoospermia, spermatogenic failure, hypogonadotropic hypogonadism, and polycystic kidney disease. Our findings shed light on the functional role of PLMs in male reproduction. SIGNIFICANCE: Protein lysine modifications (PLMs) are hotspots of posttranslational modifications and are involved in many diseases. This study revealed the presence of a classical PLM (lysine acetylation) and three novel PLMs (lysine malonylation, lysine succinylation, and lysine crotonylation) in human sperm tails. The modified proteins participate in a variety of biological processes and metabolic pathways. In addition, these modifications were found in 62 male infertility-associated proteins and could serve as potential diagnostic markers and therapeutic targets for male infertility.
Collapse
Affiliation(s)
- Yan Tian
- Institute of Biomedical Innovation and School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330031, Jiangxi, China
| | - Hao Wang
- Department of Urology, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, Hunan, China
| | - Tingting Pan
- Institute of Biomedical Innovation and School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330031, Jiangxi, China
| | - Xiaonian Hu
- Institute of Biomedical Innovation and School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330031, Jiangxi, China
| | - Jing Ding
- Institute of Biomedical Innovation and School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330031, Jiangxi, China
| | - Ying Chen
- Institute of Biomedical Innovation and School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330031, Jiangxi, China
| | - Jia Li
- Institute of Biomedical Innovation and School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330031, Jiangxi, China
| | - Houyang Chen
- Reproductive Medical Center, Jiangxi Maternal and Child Health Hospital, Nanchang 330006, Jiangxi, China; Jiangxi Key Laboratory of Reproductive Health, Nanchang 330006, Jiangxi, China.
| | - Tao Luo
- Institute of Biomedical Innovation and School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330031, Jiangxi, China; Jiangxi Key Laboratory of Reproductive Health, Nanchang 330006, Jiangxi, China.
| |
Collapse
|
48
|
Zhang Y, Dong Q, Zhao X, Sun Y, Lin X, Zhang X, Wang T, Yang T, Jiang X, Li J, Cao Z, Cai T, Liu W, Zhang H, Bai J, Yao Q. Honeycomb-like biomimetic scaffold by functionalized antibacterial hydrogel and biodegradable porous Mg alloy for osteochondral regeneration. Front Bioeng Biotechnol 2024; 12:1417742. [PMID: 39070169 PMCID: PMC11273084 DOI: 10.3389/fbioe.2024.1417742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 06/20/2024] [Indexed: 07/30/2024] Open
Abstract
Introduction: Osteochondral repair poses a significant challenge due to its unique pathological mechanisms and complex repair processes, particularly in bacterial tissue conditions resulting from open injuries, infections, and surgical contamination. This study introduces a biomimetic honeycomb-like scaffold (Zn-AlgMA@Mg) designed for osteochondral repair. The scaffold consists of a dicalcium phosphate dihydrate (DCPD)-coated porous magnesium scaffold (DCPD Mg) embedded within a dual crosslinked sodium alginate hydrogel (Zn-AlgMA). This combination aims to synergistically exert antibacterial and osteochondral integrated repair properties. Methods: The Zn-AlgMA@Mg scaffold was fabricated by coating porous magnesium scaffolds with DCPD and embedding them within a dual crosslinked sodium alginate hydrogel. The structural and mechanical properties of the DCPD Mg scaffold were characterized using scanning electron microscopy (SEM) and mechanical testing. The microstructural features and hydrophilicity of Zn-AlgMA were assessed. In vitro studies were conducted to evaluate the controlled release of magnesium and zinc ions, as well as the scaffold's osteogenic, chondrogenic, and antibacterial properties. Proteomic analysis was performed to elucidate the mechanism of osteochondral integrated repair. In vivo efficacy was evaluated using a rabbit full-thickness osteochondral defect model, with micro-CT evaluation, quantitative analysis, and histological staining (hematoxylin-eosin, Safranin-O, and Masson's trichrome). Results: The DCPD Mg scaffold exhibited a uniform porous structure and superior mechanical properties. The Zn-AlgMA hydrogel displayed consistent microstructural features and enhanced hydrophilicity. The Zn-AlgMA@Mg scaffold provided controlled release of magnesium and zinc ions, promoting cell proliferation and vitality. In vitro studies demonstrated significant osteogenic and chondrogenic properties, as well as antibacterial efficacy. Proteomic analysis revealed the underlying mechanism of osteochondral integrated repair facilitated by the scaffold. Micro-CT evaluation and histological analysis confirmed successful osteochondral integration in the rabbit model. Discussion: The biomimetic honeycomb-like scaffold (Zn-AlgMA@Mg) demonstrated promising results for osteochondral repair, effectively addressing the challenges posed by bacterial tissue conditions. The scaffold's ability to release magnesium and zinc ions in a controlled manner contributed to its significant osteogenic, chondrogenic, and antibacterial properties. Proteomic analysis provided insights into the scaffold's mechanism of action, supporting its potential for integrated osteochondral regeneration. The successful in vivo results highlight the scaffold's efficacy, making it a promising biomaterial for future applications in osteochondral repair.
Collapse
Affiliation(s)
- Yongqiang Zhang
- Department of Orthopedic Surgery, Institute of Digital Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
- Key Lab of Additive Manufacturing Technology, Institute of Digital Medicine, Nanjing Medical University, Nanjing, China
- Research Center of Digital Medicine and 3D Printing Technology of Jiangsu Province, Nanjing, China
| | - Qiangsheng Dong
- School of Materials Science and Engineering, Jiangsu Key Laboratory of Advanced Structural Materials and Application Technology, Nanjing Institute of Technology, Nanjing, China
| | - Xiao Zhao
- Department of Orthopedic Surgery, Institute of Digital Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
- Key Lab of Additive Manufacturing Technology, Institute of Digital Medicine, Nanjing Medical University, Nanjing, China
- Research Center of Digital Medicine and 3D Printing Technology of Jiangsu Province, Nanjing, China
| | - Yuzhi Sun
- Department of Orthopedic Surgery, Institute of Digital Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
- Key Lab of Additive Manufacturing Technology, Institute of Digital Medicine, Nanjing Medical University, Nanjing, China
- Research Center of Digital Medicine and 3D Printing Technology of Jiangsu Province, Nanjing, China
| | - Xin Lin
- Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xin Zhang
- Department of Orthopedic Surgery, Institute of Digital Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
- Key Lab of Additive Manufacturing Technology, Institute of Digital Medicine, Nanjing Medical University, Nanjing, China
- Research Center of Digital Medicine and 3D Printing Technology of Jiangsu Province, Nanjing, China
| | - Tianming Wang
- Department of Orthopedic Surgery, Institute of Digital Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
- Key Lab of Additive Manufacturing Technology, Institute of Digital Medicine, Nanjing Medical University, Nanjing, China
- Research Center of Digital Medicine and 3D Printing Technology of Jiangsu Province, Nanjing, China
| | - Tianxiao Yang
- Department of Orthopedic Surgery, Institute of Digital Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
- Key Lab of Additive Manufacturing Technology, Institute of Digital Medicine, Nanjing Medical University, Nanjing, China
- Research Center of Digital Medicine and 3D Printing Technology of Jiangsu Province, Nanjing, China
| | - Xiao Jiang
- Department of Orthopedic Surgery, Institute of Digital Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
- Key Lab of Additive Manufacturing Technology, Institute of Digital Medicine, Nanjing Medical University, Nanjing, China
- Research Center of Digital Medicine and 3D Printing Technology of Jiangsu Province, Nanjing, China
| | - Jiaxiang Li
- Department of Orthopedic Surgery, Institute of Digital Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
- Key Lab of Additive Manufacturing Technology, Institute of Digital Medicine, Nanjing Medical University, Nanjing, China
- Research Center of Digital Medicine and 3D Printing Technology of Jiangsu Province, Nanjing, China
| | - Zhicheng Cao
- Department of Orthopedic Surgery, Institute of Digital Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
- Key Lab of Additive Manufacturing Technology, Institute of Digital Medicine, Nanjing Medical University, Nanjing, China
- Research Center of Digital Medicine and 3D Printing Technology of Jiangsu Province, Nanjing, China
| | - Tingwen Cai
- Department of Orthopedic Surgery, Institute of Digital Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
- Key Lab of Additive Manufacturing Technology, Institute of Digital Medicine, Nanjing Medical University, Nanjing, China
- Research Center of Digital Medicine and 3D Printing Technology of Jiangsu Province, Nanjing, China
| | - Wanshun Liu
- Department of Orthopedic Surgery, Institute of Digital Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
- Key Lab of Additive Manufacturing Technology, Institute of Digital Medicine, Nanjing Medical University, Nanjing, China
- Research Center of Digital Medicine and 3D Printing Technology of Jiangsu Province, Nanjing, China
| | - Hongjing Zhang
- Department of Orthopedic Surgery, Institute of Digital Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
- Key Lab of Additive Manufacturing Technology, Institute of Digital Medicine, Nanjing Medical University, Nanjing, China
- Research Center of Digital Medicine and 3D Printing Technology of Jiangsu Province, Nanjing, China
| | - Jing Bai
- School of Materials Science and Engineering, Southeast University, Nanjing, Jiangsu, China
- Institute of Medical Devices (Suzhou), Southeast University, Suzhou, China
| | - Qingqiang Yao
- Department of Orthopedic Surgery, Institute of Digital Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
- Key Lab of Additive Manufacturing Technology, Institute of Digital Medicine, Nanjing Medical University, Nanjing, China
- Research Center of Digital Medicine and 3D Printing Technology of Jiangsu Province, Nanjing, China
| |
Collapse
|
49
|
Yang L, Guo CW, Luo QM, Guo ZF, Chen L, Ishihama Y, Li P, Yang H, Gao W. Thermostability-assisted limited proteolysis-coupled mass spectrometry for capturing drug target proteins and sites. Anal Chim Acta 2024; 1312:342755. [PMID: 38834267 DOI: 10.1016/j.aca.2024.342755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/28/2024] [Accepted: 05/20/2024] [Indexed: 06/06/2024]
Abstract
BACKGROUND Identifying drug-binding targets and their corresponding sites is crucial for drug discovery and mechanism studies. Limited proteolysis-coupled mass spectrometry (LiP-MS) is a sophisticated method used for the detection of compound and protein interactions. However, in some cases, LiP-MS cannot identify the target proteins due to the small structure changes or the lack of enrichment of low-abundant protein. To overcome this drawback, we developed a thermostability-assisted limited proteolysis-coupled mass spectrometry (TALiP-MS) approach for efficient drug target discovery. RESULTS We proved that the novel strategy, TALiP-MS, could efficiently identify target proteins of various ligands, including cyclosporin A (a calcineurin inhibitor), geldanamycin (an HSP90 inhibitor), and staurosporine (a kinase inhibitor), with accurately recognizing drug-binding domains. The TALiP protocol increased the number of target peptides detected in LiP-MS experiments by 2- to 8-fold. Meanwhile, the TALiP-MS approach can not only identify both ligand-binding stability and destabilization proteins but also shows high complementarity with the thermal proteome profiling (TPP) and machine learning-based limited proteolysis (LiP-Quant) methods. The developed TALiP-MS approach was applied to identify the target proteins of celastrol (CEL), a natural product known for its strong antioxidant and anti-cancer angiogenesis effect. Among them, four proteins, MTHFD1, UBA1, ACLY, and SND1 were further validated for their strong affinity to CEL by using cellular thermal shift assay. Additionally, the destabilized proteins induced by CEL such as TAGLN2 and CFL1 were also validated. SIGNIFICANCE Collectively, these findings underscore the efficacy of the TALiP-MS method for identifying drug targets, elucidating binding sites, and even detecting drug-induced conformational changes in target proteins in complex proteomes.
Collapse
Affiliation(s)
- Liu Yang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, PR China
| | - Chen-Wan Guo
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, PR China
| | - Qi-Ming Luo
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, PR China
| | - Zi-Fan Guo
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, PR China
| | - Ling Chen
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, PR China
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | - Ping Li
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, PR China.
| | - Hua Yang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, PR China.
| | - Wen Gao
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, PR China; Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan.
| |
Collapse
|
50
|
Chen W, He Y, Fang C, Lu H. A rapid and convenient sample treatment method based on the dissolvable polyacrylamide gel for S-acylation proteomics. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:4590-4598. [PMID: 38920099 DOI: 10.1039/d4ay00937a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
Protein S-acylation is an important lipid modification and plays a series of biological functions. As a classic proteomic method for S-acylated proteome analysis, the acyl-biotin exchange and its derivative methods are known to be very labour-intensive and time-consuming all the time, and will result in significant sample loss. Multiple methanol-chloroform precipitations are involved in order to remove the substances that would interfere with enrichment and identification including detergents, the residual reduction and alkylation reagents. Here, we developed a rapid and convenient method for S-acylation proteomics by combining a dissolvable tube gel and the classic ABE method, a Dissolvable Gel based One-Tube sample Treatment method (DGOTT) method. The protein fixation rate, impact of the gel size on analysis performance and feasibility for analyzing complex samples were evaluated. This method enabled the alkylation and chemical substitution reactions to be conducted in a single EP tube, and convenient removal of interferents through gel washing, which could obviously simplify operations and shorten the sample treatment duration. Finally, we identified a total of 1625 potential S-acylated proteins from 800 μg of mouse brain cerebral cortex proteins. We believe that our method could offer potential for high-throughput analysis of protein S-acylation.
Collapse
Affiliation(s)
- Weiyu Chen
- Department of Chemistry and Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200438, People's Republic of China.
| | - Yufei He
- Department of Chemistry and Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200438, People's Republic of China.
| | - Caiyun Fang
- Department of Chemistry and Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200438, People's Republic of China.
| | - Haojie Lu
- Department of Chemistry and Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200438, People's Republic of China.
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, 200032, People's Republic of China
| |
Collapse
|