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Wang K, Xiao Y, Zheng R, Cheng Y. Immune cell infiltration and drug response in glioblastoma multiforme: insights from oxidative stress-related genes. Cancer Cell Int 2024; 24:123. [PMID: 38566075 PMCID: PMC10986133 DOI: 10.1186/s12935-024-03316-2] [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: 12/13/2023] [Accepted: 03/27/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND GBM, also known as glioblastoma multiforme, is the most prevalent and lethal type of brain cancer. The cell proliferation, invasion, angiogenesis, and treatment of gliomas are significantly influenced by oxidative stress. Nevertheless, the connection between ORGs and GBM remains poorly comprehended. The objective of this research is to investigate the predictive significance of ORGs in GBM and their potential as targets for therapy. METHODS We identified differentially expressed genes in glioma and ORGs from public databases. A risk model was established using LASSO regression and Cox analysis, and its performance was evaluated with ROC curves. We then performed consistent cluster analysis on the model, examining its correlation with immunity and drug response. Additionally, PCR, WB and IHC were employed to validate key genes within the prognostic model. RESULTS 9 ORGs (H6PD, BMP2, SPP1, HADHA, SLC25A20, TXNIP, ACTA1, CCND1, EEF1A1) were selected via differential expression analysis, LASSO and Cox analysis, and incorporated into the risk model with high predictive accuracy. Enrichment analyses using GSVA and GSEA focused predominantly on malignancy-associated pathways. Subtype C of GBM had the best prognosis with the lowest risk score. Furthermore, the model exhibited a strong correlation with the infiltration of immune cells and had the capability to pinpoint potential targeted therapeutic medications for GBM. Ultimately, we selected HADHA for in vitro validation. The findings indicated that GBM exhibits a significant upregulation of HADHA. Knockdown of HADHA inhibited glioma cell proliferation and diminished their migration and invasion capacities and influenced the tumor growth in vivo. CONCLUSION The risk model, built upon 9 ORGs and the identification of GBM subtypes, suggests that ORGs have a broad application prospect in the clinical immunotherapy and targeted drug treatment of GBM. HADHA significantly influences the development of gliomas, both in vivo and in vitro.
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Affiliation(s)
- Kan Wang
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin City, 150001, Heilongjiang Province, China
| | - Yifei Xiao
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin City, 150001, Heilongjiang Province, China
| | - Ruipeng Zheng
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin City, 150001, Heilongjiang Province, China
| | - Yu Cheng
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin City, 150001, Heilongjiang Province, China.
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Zhang C, Lai G, Deng J, Li K, Chen L, Zhong X, Xie B. Integrating Machine Learning and Mendelian Randomization Determined a Functional Neurotrophin-Related Gene Signature in Patients with Lower-Grade Glioma. Mol Biotechnol 2024:10.1007/s12033-023-01045-x. [PMID: 38261152 DOI: 10.1007/s12033-023-01045-x] [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: 11/13/2023] [Accepted: 12/15/2023] [Indexed: 01/24/2024]
Abstract
Recent researches reported that neurotrophins can promote glioma growth/invasion but the relevant model for predicting patients' survival in Lower-Grade Gliomas (LGGs) lacked. In this study, we adopted univariate Cox analysis, LASSO regression, and multivariate Cox analysis to determine a signature including five neurotrophin-related genes (NTGs), CLIC1, SULF2, TGIF1, TTF2, and WEE1. Two-sample Mendelian Randomization (MR) further explored whether these prognostic-related genes were genetic variants that increase the risk of glioma. A total of 1306 patients have been included in this study, and the results obtained from the training set can be verified by four independent validation sets. The low-risk subgroup had longer overall survival in five datasets, and its AUC values all reached above 0.7. The risk groups divided by the NTGs signature exhibited a distinct difference in targeted therapies from the copy-number variation, somatic mutation, LGG's surrounding microenvironment, and drug response. MR corroborated that TGIF1 was a potential causal target for increasing the risk of glioma. Our study identified a five-NTGs signature that presented an excellent survival prediction and potential biological function, providing new insight for the selection of LGGs therapy.
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Affiliation(s)
- Cong Zhang
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Yixue Road, Chongqing, 400016, China
| | - Guichuan Lai
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Yixue Road, Chongqing, 400016, China
| | - Jielian Deng
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Yixue Road, Chongqing, 400016, China
| | - Kangjie Li
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Yixue Road, Chongqing, 400016, China
| | - Liuyi Chen
- The Fifth People's Hospital of Chongqing, Renji Road, Chongqing, 400062, China
| | - Xiaoni Zhong
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Yixue Road, Chongqing, 400016, China.
| | - Biao Xie
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Yixue Road, Chongqing, 400016, China.
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Jane EP, Reslink MC, Gatesman TA, Halbert ME, Miller TA, Golbourn BJ, Casillo SM, Mullett SJ, Wendell SG, Obodo U, Mohanakrishnan D, Dange R, Michealraj A, Brenner C, Agnihotri S, Premkumar DR, Pollack IF. Targeting mitochondrial energetics reverses panobinostat- and marizomib-induced resistance in pediatric and adult high-grade gliomas. Mol Oncol 2023; 17:1821-1843. [PMID: 37014128 PMCID: PMC10483615 DOI: 10.1002/1878-0261.13427] [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: 11/08/2022] [Revised: 02/22/2023] [Accepted: 04/03/2023] [Indexed: 04/05/2023] Open
Abstract
In previous studies, we demonstrated that panobinostat, a histone deacetylase inhibitor, and bortezomib, a proteasomal inhibitor, displayed synergistic therapeutic activity against pediatric and adult high-grade gliomas. Despite the remarkable initial response to this combination, resistance emerged. Here, in this study, we aimed to investigate the molecular mechanisms underlying the anticancer effects of panobinostat and marizomib, a brain-penetrant proteasomal inhibitor, and the potential for exploitable vulnerabilities associated with acquired resistance. RNA sequencing followed by gene set enrichment analysis (GSEA) was employed to compare the molecular signatures enriched in resistant compared with drug-naïve cells. The levels of adenosine 5'-triphosphate (ATP), nicotinamide adenine dinucleotide (NAD)+ content, hexokinase activity, and tricarboxylic acid (TCA) cycle metabolites required for oxidative phosphorylation to meet their bioenergetic needs were analyzed. Here, we report that panobinostat and marizomib significantly depleted ATP and NAD+ content, increased mitochondrial permeability and reactive oxygen species generation, and promoted apoptosis in pediatric and adult glioma cell lines at initial treatment. However, resistant cells exhibited increased levels of TCA cycle metabolites, which required for oxidative phosphorylation to meet their bioenergetic needs. Therefore, we targeted glycolysis and the electron transport chain (ETC) with small molecule inhibitors, which displayed substantial efficacy, suggesting that resistant cell survival is dependent on glycolytic and ETC complexes. To verify these observations in vivo, lonidamine, an inhibitor of glycolysis and mitochondrial function, was chosen. We produced two diffuse intrinsic pontine glioma (DIPG) models, and lonidamine treatment significantly increased median survival in both models, with particularly dramatic effects in panobinostat- and marizomib-resistant cells. These data provide new insights into mechanisms of treatment resistance in gliomas.
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Affiliation(s)
- Esther P. Jane
- Department of NeurosurgeryUniversity of Pittsburgh School of MedicinePAUSA
- John G. Rangos Sr. Research CenterChildren's Hospital of PittsburghPAUSA
| | - Matthew C. Reslink
- Department of NeurosurgeryUniversity of Pittsburgh School of MedicinePAUSA
| | - Taylor A. Gatesman
- Department of NeurosurgeryUniversity of Pittsburgh School of MedicinePAUSA
- John G. Rangos Sr. Research CenterChildren's Hospital of PittsburghPAUSA
| | - Matthew E. Halbert
- Department of NeurosurgeryUniversity of Pittsburgh School of MedicinePAUSA
- John G. Rangos Sr. Research CenterChildren's Hospital of PittsburghPAUSA
| | - Tracy A. Miller
- Department of NeurosurgeryUniversity of Pittsburgh School of MedicinePAUSA
| | - Brian J. Golbourn
- Department of NeurosurgeryUniversity of Pittsburgh School of MedicinePAUSA
| | - Stephanie M. Casillo
- Department of NeurosurgeryUniversity of Pittsburgh School of MedicinePAUSA
- John G. Rangos Sr. Research CenterChildren's Hospital of PittsburghPAUSA
| | - Steven J. Mullett
- Department of Pharmacology and Chemical BiologyUniversity of PittsburghPAUSA
| | - Stacy G. Wendell
- Department of Pharmacology and Chemical BiologyUniversity of PittsburghPAUSA
| | - Udochukwu Obodo
- Department of Diabetes & Cancer MetabolismCity of Hope Medical CenterDuarteCAUSA
| | | | - Riya Dange
- Department of NeurosurgeryUniversity of Pittsburgh School of MedicinePAUSA
| | - Antony Michealraj
- Department of NeurosurgeryUniversity of Pittsburgh School of MedicinePAUSA
| | - Charles Brenner
- Department of Diabetes & Cancer MetabolismCity of Hope Medical CenterDuarteCAUSA
| | - Sameer Agnihotri
- Department of NeurosurgeryUniversity of Pittsburgh School of MedicinePAUSA
- John G. Rangos Sr. Research CenterChildren's Hospital of PittsburghPAUSA
- UPMC Hillman Cancer CenterPittsburghPAUSA
| | - Daniel R. Premkumar
- Department of NeurosurgeryUniversity of Pittsburgh School of MedicinePAUSA
- John G. Rangos Sr. Research CenterChildren's Hospital of PittsburghPAUSA
- UPMC Hillman Cancer CenterPittsburghPAUSA
| | - Ian F. Pollack
- Department of NeurosurgeryUniversity of Pittsburgh School of MedicinePAUSA
- John G. Rangos Sr. Research CenterChildren's Hospital of PittsburghPAUSA
- UPMC Hillman Cancer CenterPittsburghPAUSA
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Stacpoole PW, McCall CE. The pyruvate dehydrogenase complex: Life's essential, vulnerable and druggable energy homeostat. Mitochondrion 2023; 70:59-102. [PMID: 36863425 DOI: 10.1016/j.mito.2023.02.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 01/30/2023] [Accepted: 02/13/2023] [Indexed: 03/04/2023]
Abstract
Found in all organisms, pyruvate dehydrogenase complexes (PDC) are the keystones of prokaryotic and eukaryotic energy metabolism. In eukaryotic organisms these multi-component megacomplexes provide a crucial mechanistic link between cytoplasmic glycolysis and the mitochondrial tricarboxylic acid (TCA) cycle. As a consequence, PDCs also influence the metabolism of branched chain amino acids, lipids and, ultimately, oxidative phosphorylation (OXPHOS). PDC activity is an essential determinant of the metabolic and bioenergetic flexibility of metazoan organisms in adapting to changes in development, nutrient availability and various stresses that challenge maintenance of homeostasis. This canonical role of the PDC has been extensively probed over the past decades by multidisciplinary investigations into its causal association with diverse physiological and pathological conditions, the latter making the PDC an increasingly viable therapeutic target. Here we review the biology of the remarkable PDC and its emerging importance in the pathobiology and treatment of diverse congenital and acquired disorders of metabolic integration.
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Affiliation(s)
- Peter W Stacpoole
- Department of Medicine (Division of Endocrinology, Metabolism and Diabetes), and Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, FL, United States.
| | - Charles E McCall
- Department of Internal Medicine and Translational Sciences, and Department of Microbiology and Immunology, Wake Forest University School of Medicine, Winston-Salem, NC, United States
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The Comparative Experimental Study of Sodium and Magnesium Dichloroacetate Effects on Pediatric PBT24 and SF8628 Cell Glioblastoma Tumors Using a Chicken Embryo Chorioallantoic Membrane Model and on Cells In Vitro. Int J Mol Sci 2022; 23:ijms231810455. [PMID: 36142368 PMCID: PMC9499689 DOI: 10.3390/ijms231810455] [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: 08/16/2022] [Revised: 08/31/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
In this study, pyruvate dehydrogenase kinase-1 inhibition with dichloroacetate (DCA) was explored as an alternative cancer therapy. The study’s aim was to compare the effectiveness of NaDCA and MgDCA on pediatric glioblastoma PBT24 and SF8628 tumors and cells. The treatment effects were evaluated on xenografts growth on a chicken embryo chorioallantoic membrane. The PCNA, EZH2, p53, survivin expression in tumor, and the SLC12A2, SLC12A5, SLC5A8, CDH1, and CDH2 expression in cells were studied. The tumor groups were: control, cells treated with 10 mM and 5 mM of NaDCA, and 5 mM and 2.5 mM of MgDCA. The cells were also treated with 3 mM DCA. Both the 10 mM DCA preparations significantly reduced PBT24 and SF8624 tumor invasion rates, while 5 mM NaDCA reduced it only in the SF8628 tumors. The 5 mM MgDCA inhibited tumor-associated neoangiogenesis in PBT24; both doses of NaDCA inhibited tumor-associated neoangiogenesis in SF8628. The 10 mM DCA inhibited the expression of markers tested in PBT24 and SF8628 tumors, but the 5 mM DCA affect on their expression depended on the cation. The DCA treatment did not affect the SLC12A2, SLC12A5, and SLC5A8 expression in cells but increased CDH1 expression in SF8628. The tumor response to DCA at different doses indicated that a contrast between NaDCA and MgDCA effectiveness reflects the differences in the tested cells’ biologies.
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Fukushi A, Kim HD, Chang YC, Kim CH. Revisited Metabolic Control and Reprogramming Cancers by Means of the Warburg Effect in Tumor Cells. Int J Mol Sci 2022; 23:ijms231710037. [PMID: 36077431 PMCID: PMC9456516 DOI: 10.3390/ijms231710037] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/22/2022] [Accepted: 08/29/2022] [Indexed: 12/22/2022] Open
Abstract
Aerobic glycolysis is an emerging hallmark of many human cancers, as cancer cells are defined as a “metabolically abnormal system”. Carbohydrates are metabolically reprogrammed by its metabolizing and catabolizing enzymes in such abnormal cancer cells. Normal cells acquire their energy from oxidative phosphorylation, while cancer cells acquire their energy from oxidative glycolysis, known as the “Warburg effect”. Energy–metabolic differences are easily found in the growth, invasion, immune escape and anti-tumor drug resistance of cancer cells. The glycolysis pathway is carried out in multiple enzymatic steps and yields two pyruvate molecules from one glucose (Glc) molecule by orchestral reaction of enzymes. Uncontrolled glycolysis or abnormally activated glycolysis is easily observed in the metabolism of cancer cells with enhanced levels of glycolytic proteins and enzymatic activities. In the “Warburg effect”, tumor cells utilize energy supplied from lactic acid-based fermentative glycolysis operated by glycolysis-specific enzymes of hexokinase (HK), keto-HK-A, Glc-6-phosphate isomerase, 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase, phosphofructokinase (PFK), phosphor-Glc isomerase (PGI), fructose-bisphosphate aldolase, phosphoglycerate (PG) kinase (PGK)1, triose phosphate isomerase, PG mutase (PGAM), glyceraldehyde-3-phosphate dehydrogenase, enolase, pyruvate kinase isozyme type M2 (PKM2), pyruvate dehydrogenase (PDH), PDH kinase and lactate dehydrogenase. They are related to glycolytic flux. The key enzymes involved in glycolysis are directly linked to oncogenesis and drug resistance. Among the metabolic enzymes, PKM2, PGK1, HK, keto-HK-A and nucleoside diphosphate kinase also have protein kinase activities. Because glycolysis-generated energy is not enough, the cancer cell-favored glycolysis to produce low ATP level seems to be non-efficient for cancer growth and self-protection. Thus, the Warburg effect is still an attractive phenomenon to understand the metabolic glycolysis favored in cancer. If the basic properties of the Warburg effect, including genetic mutations and signaling shifts are considered, anti-cancer therapeutic targets can be raised. Specific therapeutics targeting metabolic enzymes in aerobic glycolysis and hypoxic microenvironments have been developed to kill tumor cells. The present review deals with the tumor-specific Warburg effect with the revisited viewpoint of recent progress.
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Affiliation(s)
- Abekura Fukushi
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Seoburo 2066, Suwon 16419, Korea
| | - Hee-Do Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Seoburo 2066, Suwon 16419, Korea
| | - Yu-Chan Chang
- Department of Biomedicine Imaging and Radiological Science, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
- Correspondence: (Y.-C.C.); (C.-H.K.); Fax: +82-31-290-7015 (C.-H.K.)
| | - Cheorl-Ho Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Seoburo 2066, Suwon 16419, Korea
- Samsung Advanced Institute of Health Science and Technology (SAIHST), Sungkyunkwan University, Seoul 06351, Korea
- Correspondence: (Y.-C.C.); (C.-H.K.); Fax: +82-31-290-7015 (C.-H.K.)
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Qin X, Wang R, Xu H, Tu L, Chen H, Li H, Liu N, Wang J, Li S, Yin F, Xu N, Li Z. Identification of an autoinhibitory, mitophagy-inducing peptide derived from the transmembrane domain of USP30. Autophagy 2022; 18:2178-2197. [PMID: 34989313 PMCID: PMC9397470 DOI: 10.1080/15548627.2021.2022360] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The mitochondrial-anchored deubiquitinating enzyme USP30 (ubiquitin specific peptidase 30) antagonizes PRKN/parkin-mediated mitophagy, making it a potential target for treating Parkinson disease. However, few inhibitors targeting USP30 have been reported. Here, we report a novel peptide (Q14) derived from the transmembrane (TM) domain of USP30 that can target mitochondrial-anchored USP30 directly and increase mitophagy through two intriguing and distinct mechanisms: a novel autoinhibition mechanism in USP30 and accelerated autophagosome formation via the LC3-interacting region (LIR) of the Q14 peptide. We identified the potential binding sites between the Q14 peptide and USP30 and postulated that an allosteric autoinhibition mechanism regulates USP30 activity. Furthermore, the LIR motif in the Q14 peptide offers additional binding with LC3 and accelerated autophagosome formation. The two mechanisms synergistically enhance mitophagy. Our work provides novel insight and direction to the design of inhibitors for USP30 or other deubiquitinating enzymes (DUBs).Abbreviations: 3-MA: 3-methyladenine; ATTEC: autophagosome-tethering compound; BafA1: bafilomycin A1; BNIP3: BCL2 interacting protein 3; BNIP3L/NIX: BCL2 interacting protein 3 like; CCCP: carbonyl cyanide m-chlorophenyl hydrazone; DMSO: dimethyl sulfoxide; FP: fluorescence polarization; FUNDC1: FUN14 domain containing 1; HCQ: hydroxychloroquine; LIR: LC3-interacting region; MST: microscale thermophoresis; mtDNA: mitochondrial DNA; mtPA-GFP: mitochondria-targeted photoactive fluorescence protein; OMM: outer mitochondrial membrane; PINK1: PTEN induced kinase 1; PRKN/parkin: parkin RBR E3 ubiquitin protein ligase; Rap: rapamycin; SA: streptavidin; TM: transmembrane; Ub: ubiquitin; Ub-AMC: Ub-7-amido-4-methylcoumarin; UPS: ubiquitin-protease system; USP: ubiquitin specific peptidase; USP30: ubiquitin specific peptidase 30.
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Affiliation(s)
- Xuan Qin
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Rui Wang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, China
| | - Hongkun Xu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Licheng Tu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Hailing Chen
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Heng Li
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Na Liu
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, China
| | - Jinpeng Wang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Shuiming Li
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Feng Yin
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, China,CONTACT Feng Yin Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, China
| | - Naihan Xu
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China,Naihan Xu Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China,Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, China,Zigang Li State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
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