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Ren L, Zhang T, Zhang J. Recent advances in dietary androgen receptor inhibitors. Med Res Rev 2024; 44:1446-1500. [PMID: 38279967 DOI: 10.1002/med.22019] [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: 10/20/2022] [Revised: 12/07/2023] [Accepted: 01/10/2024] [Indexed: 01/29/2024]
Abstract
As a nuclear transcription factor, the androgen receptor (AR) plays a crucial role not only in normal male sexual differentiation and growth of the prostate, but also in benign prostatic hyperplasia, prostatitis, and prostate cancer. Multiple population-based epidemiological studies demonstrated that prostate cancer risk was inversely associated with increased dietary intakes of green tea, soy products, tomato, and so forth. Therefore, this review aimed to summarize the structure and function of AR, and further illustrate the structural basis for antagonistic mechanisms of the currently clinically available antiandrogens. Due to the limitations of these antiandrogens, a series of natural AR inhibitors have been identified from edible plants such as fruits and vegetables, as well as folk medicines, health foods, and nutritional supplements. Hence, this review mainly focused on recent experimental, epidemiological, and clinical studies about natural AR inhibitors, particularly the association between dietary intake of natural antiandrogens and reduced risk of prostatic diseases. Since natural products offer multiple advantages over synthetic antiandrogens, this review may provide a comprehensive and updated overview of dietary-derived AR inhibitors, as well as their potential for the nutritional intervention against prostatic disorders.
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Affiliation(s)
- Li Ren
- College of Food Science and Engineering, Jilin University, Changchun, China
| | - Tiehua Zhang
- College of Food Science and Engineering, Jilin University, Changchun, China
| | - Jie Zhang
- College of Food Science and Engineering, Jilin University, Changchun, China
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2
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Pratt SJP, Plunkett CM, Kuzu G, Trinh T, Barbara J, Choconta P, Quackenbush D, Huynh T, Smith A, Barnes SW, New J, Pierce J, Walker JR, Mainquist J, King FJ, Elliott J, Hammack S, Decker RS. A high throughput cell stretch device for investigating mechanobiology in vitro. APL Bioeng 2024; 8:026129. [PMID: 38938688 PMCID: PMC11210978 DOI: 10.1063/5.0206852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/31/2024] [Indexed: 06/29/2024] Open
Abstract
Mechanobiology is a rapidly advancing field, with growing evidence that mechanical signaling plays key roles in health and disease. To accelerate mechanobiology-based drug discovery, novel in vitro systems are needed that enable mechanical perturbation of cells in a format amenable to high throughput screening. Here, both a mechanical stretch device and 192-well silicone flexible linear stretch plate were designed and fabricated to meet high throughput technology needs for cell stretch-based applications. To demonstrate the utility of the stretch plate in automation and screening, cell dispensing, liquid handling, high content imaging, and high throughput sequencing platforms were employed. Using this system, an assay was developed as a biological validation and proof-of-concept readout for screening. A mechano-transcriptional stretch response was characterized using focused gene expression profiling measured by RNA-mediated oligonucleotide Annealing, Selection, and Ligation with Next-Gen sequencing. Using articular chondrocytes, a gene expression signature containing stretch responsive genes relevant to cartilage homeostasis and disease was identified. The possibility for integration of other stretch sensitive cell types (e.g., cardiovascular, airway, bladder, gut, and musculoskeletal), in combination with alternative phenotypic readouts (e.g., protein expression, proliferation, or spatial alignment), broadens the scope of high throughput stretch and allows for wider adoption by the research community. This high throughput mechanical stress device fills an unmet need in phenotypic screening technology to support drug discovery in mechanobiology-based disease areas.
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Affiliation(s)
- Stephen J. P. Pratt
- Novartis, Biomedical Research 10675 John Jay Hopkins Dr, San Diego, California 92121, USA
| | | | - Guray Kuzu
- Novartis, Biomedical Research 10675 John Jay Hopkins Dr, San Diego, California 92121, USA
| | - Ton Trinh
- Novartis, Biomedical Research 10675 John Jay Hopkins Dr, San Diego, California 92121, USA
| | - Joshua Barbara
- Novartis, Biomedical Research 10675 John Jay Hopkins Dr, San Diego, California 92121, USA
| | - Paula Choconta
- Novartis, Biomedical Research 10675 John Jay Hopkins Dr, San Diego, California 92121, USA
| | - Doug Quackenbush
- Novartis, Biomedical Research 10675 John Jay Hopkins Dr, San Diego, California 92121, USA
| | - Truc Huynh
- Novartis, Biomedical Research 10675 John Jay Hopkins Dr, San Diego, California 92121, USA
| | - Anders Smith
- Novartis, Biomedical Research 10675 John Jay Hopkins Dr, San Diego, California 92121, USA
| | - S. Whitney Barnes
- Novartis, Biomedical Research 10675 John Jay Hopkins Dr, San Diego, California 92121, USA
| | - Joel New
- Novartis, Biomedical Research 10675 John Jay Hopkins Dr, San Diego, California 92121, USA
| | - James Pierce
- Novartis, Biomedical Research 10675 John Jay Hopkins Dr, San Diego, California 92121, USA
| | - John R. Walker
- Novartis, Biomedical Research 10675 John Jay Hopkins Dr, San Diego, California 92121, USA
| | - James Mainquist
- Novartis, Biomedical Research 10675 John Jay Hopkins Dr, San Diego, California 92121, USA
| | - Frederick J. King
- Novartis, Biomedical Research 10675 John Jay Hopkins Dr, San Diego, California 92121, USA
| | - Jimmy Elliott
- Novartis, Biomedical Research 10675 John Jay Hopkins Dr, San Diego, California 92121, USA
| | - Scott Hammack
- Novartis, Biomedical Research 10675 John Jay Hopkins Dr, San Diego, California 92121, USA
| | - Rebekah S. Decker
- Novartis, Biomedical Research 10675 John Jay Hopkins Dr, San Diego, California 92121, USA
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Wang Y, Wang H, Shao W, Chen Y, Gui Y, Hu C, Yi X, Huang L, Li S, Wang D. Large-scale loss-of-function perturbations reveal a comprehensive epigenetic regulatory network in breast cancer. Cancer Biol Med 2023; 21:j.issn.2095-3941.2023.0276. [PMID: 38062748 PMCID: PMC10875281 DOI: 10.20892/j.issn.2095-3941.2023.0276] [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: 07/27/2023] [Accepted: 10/26/2023] [Indexed: 02/16/2024] Open
Abstract
OBJECTIVE Epigenetic abnormalities have a critical role in breast cancer by regulating gene expression; however, the intricate interrelationships and key roles of approximately 400 epigenetic regulators in breast cancer remain elusive. It is important to decipher the comprehensive epigenetic regulatory network in breast cancer cells to identify master epigenetic regulators and potential therapeutic targets. METHODS We employed high-throughput sequencing-based high-throughput screening (HTS2) to effectively detect changes in the expression of 2,986 genes following the knockdown of 400 epigenetic regulators. Then, bioinformatics analysis tools were used for the resulting gene expression signatures to investigate the epigenetic regulations in breast cancer. RESULTS Utilizing these gene expression signatures, we classified the epigenetic regulators into five distinct clusters, each characterized by specific functions. We discovered functional similarities between BAZ2B and SETMAR, as well as CLOCK and CBX3. Moreover, we observed that CLOCK functions in a manner opposite to that of HDAC8 in downstream gene regulation. Notably, we constructed an epigenetic regulatory network based on the gene expression signatures, which revealed 8 distinct modules and identified 10 master epigenetic regulators in breast cancer. CONCLUSIONS Our work deciphered the extensive regulation among hundreds of epigenetic regulators. The identification of 10 master epigenetic regulators offers promising therapeutic targets for breast cancer treatment.
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Affiliation(s)
- Yumei Wang
- School of Basic Medical Sciences, State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Haiyan Wang
- Department of Pathology, School of Medicine, Qinghai University, Xining 810001, China
| | - Wei Shao
- Omics Biosciences Inc, Beijing 100871, China
| | - Yuhui Chen
- School of Basic Medical Sciences, State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Yu Gui
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Chao Hu
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Xiaohong Yi
- School of Basic Medical Sciences, State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Lijun Huang
- School of Basic Medical Sciences, State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Shasha Li
- Department of Endocrinology and Metabolism, Guangdong Provincial Key Laboratory of Diabetology & Guangzhou Municipal Key Laboratory of Mechanistic and Translational Obesity Research, Medical Center for Comprehensive Weight Control, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China
| | - Dong Wang
- School of Basic Medical Sciences, State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
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Nguyen TB, Miramontes R, Chillon-Marinas C, Maimon R, Vazquez-Sanchez S, Lau AL, McClure NR, England WE, Singha M, Stocksdale JT, Jang KH, Jung S, McKnight JI, Ho LN, Faull RLM, Steffan JS, Reidling JC, Jang C, Lee G, Cleveland DW, Lagier-Tourenne C, Spitale RC, Thompson LM. Aberrant splicing in Huntington's disease via disrupted TDP-43 activity accompanied by altered m6A RNA modification. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.31.565004. [PMID: 37961595 PMCID: PMC10635028 DOI: 10.1101/2023.10.31.565004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Huntington's disease (HD) is a neurodegenerative disorder caused by a CAG repeat expansion in the first exon of the HTT gene encoding huntingtin. Prior reports have established a correlation between CAG expanded HTT and altered gene expression. However, the mechanisms leading to disruption of RNA processing in HD remain unclear. Here, our analysis of the reported HTT protein interactome identifies interactions with known RNA-binding proteins (RBPs). Total, long-read sequencing and targeted RASL-seq of RNAs from cortex and striatum of the HD mouse model R6/2 reveals increased exon skipping which is confirmed in Q150 and Q175 knock-in mice and in HD human brain. We identify the RBP TDP-43 and the N6-methyladenosine (m6A) writer protein methyltransferase 3 (METTL3) to be upstream regulators of exon skipping in HD. Along with this novel mechanistic insight, we observe decreased nuclear localization of TDP-43 and cytoplasmic accumulation of phosphorylated TDP-43 in HD mice and human brain. In addition, TDP-43 co-localizes with HTT in human HD brain forming novel nuclear aggregate-like bodies distinct from mutant HTT inclusions or previously observed TDP-43 pathologies. Binding of TDP-43 onto RNAs encoding HD-associated differentially expressed and aberrantly spliced genes is decreased. Finally, m6A RNA modification is reduced on RNAs abnormally expressed in striatum from HD R6/2 mouse brain, including at clustered sites adjacent to TDP-43 binding sites. Our evidence supports TDP-43 loss of function coupled with altered m6A modification as a novel mechanism underlying alternative splicing/unannotated exon usage in HD and highlights the critical nature of TDP-43 function across multiple neurodegenerative diseases.
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Tan X, Ma X, Dai Y, An J, Yu X, Li S, Liao Y, Pei T, Tang Y, Gui Y, Zhou S, Guo D, Deng Y, Hu K, Wang D. A large-scale transcriptional analysis reveals herb-derived ginsenoside F2 suppressing hepatocellular carcinoma via inhibiting STAT3. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 120:155031. [PMID: 37666060 DOI: 10.1016/j.phymed.2023.155031] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 06/15/2023] [Accepted: 08/15/2023] [Indexed: 09/06/2023]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a common type of cancer that shows great morbidity and mortality rates. However, there are limited available drugs to treat HCC. AIM The present work focused on discovering the potential anti-HCC compounds from traditional Chinese medicine (TCM) by employing high-throughput sequencing-based high-throughput screening (HTS2) together with the liver cancer pathway-associated gene signature. METHODS HTS2 assay was adopted for identifying herbs. Protein-protein interaction (PPI) network analysis and computer-aided drug design (CADD) were used to identify key targets and screen the candidate natural products of herbs. Molecular docking, network pharmacology analysis, western blotting, immunofluorescent staining, subcellular fractionation experiment, dual-luciferase reporter gene assay, surface plasmon resonance (SPR) as well as nuclear magnetic resonance (NMR) were performed to validate the ability of compound binding with key target and inhibiting its function. Moreover, cell viability, colony-forming, cell cycle assay and animal experiments were performed to examine the inhibitory effect of compound on HCC. RESULTS We examined the perturbation of 578 herb extracts on the expression of 84 genes from the liver cancer pathway, and identified the top 20 herbs significantly reverting the gene expression of this pathway. Signal transducer and activator of transcription 3 (STAT3) was identified as one of the key targets of the liver cancer pathway by PPI network analysis. Then, by analyzing compounds from top 20 herbs utilizing CADD, we found ginsenoside F2 (GF2) binds to STAT3 with high affinity, which was further validated by the results from molecular docking, SPR and NMR. Additionally, our results showed that GF2 suppresses the phosphorylation of Y705 of STAT3, inhibits its nuclear translocation, decreases its transcriptional activity and inhibits the growth of HCC in vitro and in vivo. CONCLUSION Based on this large-scale transcriptional study, a number of anti-HCC herbs were identified. GF2, a compound derived from TCM, was found to be a chemical basis of these herbs in treating HCC. The present work also discovered that GF2 is a new STAT3 inhibitor, which is able to suppress HCC. As such, GF2 represents a new potential anti-HCC therapeutic strategy.
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Affiliation(s)
- Xue Tan
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Xiaofang Ma
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Yifei Dai
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Jun An
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Xiankuo Yu
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Shengrong Li
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Yile Liao
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Tianli Pei
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Yuqin Tang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; Clinical Bioinformatics Experimental Center, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou 450003, China
| | - Yu Gui
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Shiyi Zhou
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Dale Guo
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Yun Deng
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Kaifeng Hu
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
| | - Dong Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
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Li J, Chi J, Yang Y, Song Z, Yang Y, Zhou X, Liu Y, Zhao Y. PHDs-seq: a large-scale phenotypic screening method for drug discovery through parallel multi-readout quantification. CELL REGENERATION (LONDON, ENGLAND) 2023; 12:22. [PMID: 37264282 DOI: 10.1186/s13619-023-00164-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 04/15/2023] [Indexed: 06/03/2023]
Abstract
High-throughput phenotypic screening is a cornerstone of drug development and the main technical approach for stem cell research. However, simultaneous detection of activated core factors responsible for cell fate determination and accurate assessment of directional cell transition are difficult using conventional screening methods that focus on changes in only a few biomarkers. The PHDs-seq (Probe Hybridization based Drug screening by sequencing) platform was developed to evaluate compound function based on their transcriptional effects in a wide range of signature biomarkers. In this proof-of-concept demonstration, several sets of markers related to cell fate determination were profiled in adipocyte reprogramming from dermal fibroblasts. After validating the accuracy, sensitivity and reproducibility of PHDs-seq data in molecular and cellular assays, a panel of 128 signalling-related compounds was screened for the ability to induce reprogramming of keloid fibroblasts (KF) into adipocytes. Notably, the potent ATP-competitive VEGFR/PDGFR inhibitor compound, ABT869, was found to promote the transition from fibroblasts to adipocytes. This study highlights the power and accuracy of the PHDs-seq platform for high-throughput drug screening in stem cell research, and supports its use in basic explorations of the molecular mechanisms underlying disease development.
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Affiliation(s)
- Jun Li
- State Key Laboratory of Natural and Biomimetic Drugs, MOE Key Laboratory of Cell Proliferation and Differentiation, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Jun Chi
- Plastech Pharmaceutical Technology Ltd, Nanjing, 210031, China
| | - Yang Yang
- State Key Laboratory of Natural and Biomimetic Drugs, MOE Key Laboratory of Cell Proliferation and Differentiation, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, 100871, China
- Plastech Pharmaceutical Technology Ltd, Nanjing, 210031, China
| | - Zhongya Song
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Yong Yang
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Xin Zhou
- Department of General Surgery, Peking University Third Hospital, Beijing, 100191, China
| | - Yang Liu
- State Key Laboratory of Natural and Biomimetic Drugs, MOE Key Laboratory of Cell Proliferation and Differentiation, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, 100871, China.
- Plastech Pharmaceutical Technology Ltd, Nanjing, 210031, China.
| | - Yang Zhao
- State Key Laboratory of Natural and Biomimetic Drugs, MOE Key Laboratory of Cell Proliferation and Differentiation, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, 100871, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
- Plastech Pharmaceutical Technology Ltd, Nanjing, 210031, China.
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Baloglu E. Hypoxic Stress-Dependent Regulation of Na,K-ATPase in Ischemic Heart Disease. Int J Mol Sci 2023; 24:ijms24097855. [PMID: 37175562 PMCID: PMC10177966 DOI: 10.3390/ijms24097855] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
In cardiomyocytes, regular activity of the Na,K-ATPase (NKA) and its Na/K pump activity is essential for maintaining ion gradients, excitability, propagation of action potentials, electro-mechanical coupling, trans-membrane Na+ and Ca2+ gradients and, thus, contractility. The activity of NKA is impaired in ischemic heart disease and heart failure, which has been attributed to decreased expression of the NKA subunits. Decreased NKA activity leads to intracellular Na+ and Ca2+ overload, diastolic dysfunction and arrhythmias. One signal likely related to these events is hypoxia, where hypoxia-inducible factors (HIF) play a critical role in the adaptation of cells to low oxygen tension. HIF activity increases in ischemic heart, hypertension, heart failure and cardiac fibrosis; thus, it might contribute to the impaired function of NKA. This review will mainly focus on the regulation of NKA in ischemic heart disease in the context of stressed myocardium and the hypoxia-HIF axis and argue on possible consequences of treatment.
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Affiliation(s)
- Emel Baloglu
- Department of Medical Pharmacology, School of Medicine, Acibadem Mehmet Ali Aydinlar University, 34752 Istanbul, Turkey
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Pei T, Dai Y, Tan X, Geng A, Li S, Gui Y, Hu C, An J, Yu X, Bao X, Wang D. Yupingfeng San exhibits anticancer effect in hepatocellular carcinoma cells via the MAPK pathway revealed by HTS 2 technology. JOURNAL OF ETHNOPHARMACOLOGY 2023; 306:116134. [PMID: 36627003 DOI: 10.1016/j.jep.2023.116134] [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: 10/01/2022] [Revised: 12/07/2022] [Accepted: 01/01/2023] [Indexed: 06/17/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Yupingfeng San (YPFS) is a classic rousing prescription in Chinese medicine, with widly clinical application and remarkably curative effect. It consists of three herbs named Astragalus mongholicus Bunge (Huangqi), Atractylodes rubra Dekker (Baizhu) and Saposhnikovia divaricata (Turcz.) Schischk. (Fangfeng), and has a variety of pharmacological activities including immune regulation, antioxidant, anti-tumor, regulation of cytokines, etc. AIM OF THE STUDY: It has been proved that YPFS exerts its anti-tumor effect through enhancing the systemic and local immune responses in tumor patients, moreover, it has the direct tumor-suppressing effect and can reduce the adverse reactions caused by radiotherapy and chemotherapy drugs. Therefore, in this study, we explored the potential anti-HCC mechanism of YPFS based on HTS2 technology and systems pharmacology, aiming to provide a scientific basis for the clinical application of YPFS and a new strategy for Chinese medicine research. MATERIALS AND METHODS In this study, systems pharmacology plus high throughput sequencing-based high throughput screening (HTS2) technology, and experimental validation were used to investigate the therapeutic mechanisms and the chemical basis of YPFS in HCC treatment. Firstly, the potential therapeutic targets and signaling pathways of YPFS in the treatment of HCC were obtained through systems pharmacology. Subsequently, HTS2 technology combined with PPI network analysis were used to reveal potential therapeutic targets. Finally, the anti-HCC effects and underlying mechanisms of YPFS were further verified in vitro in human hepatocellular carcinoma cell lines. Moreover, the possible chemical basis was explored by drug target verification and molecular docking technology. RESULTS In total, 183 active ingredients were predicted by YPFS screening and 49 anti-HCC targets were further identified. Most of these targets were enriched into the "MAPK pathway", and the expression of 37 genes was significantly changed after herb treatment. Among them, 5 key targets, including VEGFA, GRB2, JUN, PDGFRB and CDC42, were predicted by protein-protein interaction (PPI) network analysis. According to our results, YPFS inhibited the proliferation, induced the apoptosis and caused cell cycle arrest of HCC cells. In addition, YPFS significantly reduced P38 gene expression. Fangfeng, one of the three herbs in YPFS, significantly down-regulated the expression of more target genes than that of the other two herbs. Lastly, as revealed by molecular docking analysis, 4'-O-glucosyl-5-O-methylvisamminol, an active ingredient identified in Fangfeng, showed a high affinity for P38. CONCLUSION Taken together, this study shows that YPFS possesses the activities of anti-proliferation and pro-apoptosis in treating HCC, which are achieved by inhibiting the MAPK signaling pathway. P38 is one of the critical targets of YPFS in treating HCC, which may be directly bound and inhibited by 4'-O-glucosyl-5-O-methylvisamminol, a compound derived from YPFS.
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Affiliation(s)
- Tianli Pei
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Yifei Dai
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Xue Tan
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Aiai Geng
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Shengrong Li
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Yu Gui
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Chao Hu
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Jun An
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Xiankuo Yu
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Xilinqiqige Bao
- Medical Innovation Center for Nationalities, Inner Mongolia Medical University, Hohhot City, 010110, China.
| | - Dong Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
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9
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Chang C, Yang H, Bi W, Huang C, Xu Z. Cryopreservable Through-Hole Arrays for the High-Throughput Three-Dimensional Smartphone-Based Cell Colorimetric Assay. ACS Sens 2023; 8:543-554. [PMID: 36705290 DOI: 10.1021/acssensors.2c01564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In vitro assays are an important platform for cancer research as they allow high-throughput experimentation that is not possible using in vivo animals. Although various in vitro assays are developed to study cell viability or migration, many of these assays are often limited to two dimensions, involving complex procedures or relying specialized equipment, etc. Here, we designed a simple colorimetric assay that accommodates automatic liquid samples loading, high-throughput generation of chemical concentration gradient, three-dimensional (3D) cell culture establishment, and smartphone-based colorimetric readouts. This assay is based on through-hole arrays in the poly(methyl methacrylate) (PMMA) layers. Liquid samples can be automatically loaded into through-hole arrays in PMMA layers by capillary force. Different drug concentrations can be generated by aligning and stacking to mix the contents of the corresponding through-holes with different volumes. 3D culture of cancer cells can be established by the rapid absorption of cell suspensions into the macroporous gels. After exposing the 3D cultured cells to different drug concentrations, the number of viable cells and migrated cells was reflected by the color change of Alamar blue, which enable on-site readout by a smartphone. This assay can study cell viability as well as cell migration, the two main characteristics of cancer cells, using one device. Interestingly, HeLa cells remained with high viability after cryopreservation at -80 °C, which allows for storage and distribution using dry ice. The simple protocol, along with the cryopreservability at -80 °C facilitates its ease of use to study cell viability together with cell migration in common laboratories or clinical settings.
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Affiliation(s)
- Chunqi Chang
- School of Biomedical Engineering Health Science Center, Shenzhen University, Shenzhen 518060, China.,Guangdong Provincial Key Laboratory of Biomedical Measurements and Ultrasound Imaging, Shenzhen University, Shenzhen 518060, China
| | - Haoyi Yang
- School of Biomedical Engineering Health Science Center, Shenzhen University, Shenzhen 518060, China.,Guangdong Provincial Key Laboratory of Biomedical Measurements and Ultrasound Imaging, Shenzhen University, Shenzhen 518060, China
| | - Wenchuan Bi
- School of Biomedical Engineering Health Science Center, Shenzhen University, Shenzhen 518060, China.,Guangdong Provincial Key Laboratory of Biomedical Measurements and Ultrasound Imaging, Shenzhen University, Shenzhen 518060, China
| | - Cuier Huang
- School of Biomedical Engineering Health Science Center, Shenzhen University, Shenzhen 518060, China.,Guangdong Provincial Key Laboratory of Biomedical Measurements and Ultrasound Imaging, Shenzhen University, Shenzhen 518060, China
| | - Zhen Xu
- School of Biomedical Engineering Health Science Center, Shenzhen University, Shenzhen 518060, China.,Guangdong Provincial Key Laboratory of Biomedical Measurements and Ultrasound Imaging, Shenzhen University, Shenzhen 518060, China.,Guangdong Key Laboratory of Nanomedicine, Shenzhen Engineering Laboratory of Nanomedicine and Nanoformulations, CAS-HK Joint Lab for Biomaterials, Research Laboratory for Biomedical Optics and Molecular Imaging, Shenzhen Key Laboratory for Molecular Imaging, CAS Key Lab for Health Informatics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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10
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Malik J, Ahmed S, Momin SS, Shaikh S, Alafnan A, Alanazi J, Said Almermesh MH, Anwar S. Drug Repurposing: A New Hope in Drug Discovery for Prostate Cancer. ACS OMEGA 2023; 8:56-73. [PMID: 36643505 PMCID: PMC9835086 DOI: 10.1021/acsomega.2c05821] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/24/2022] [Indexed: 06/12/2023]
Abstract
Prostate cancer (PCA), the most common cancer in men, accounted for 1.3 million new incidences in 2018. An increase in incidences is an issue of concern that should be addressed. Of all the reported prostate cancers, 85% were detected in stages III and IV, making them difficult to treat. Conventional drugs gradually lose their efficacy due to the developed resistance against them, thus requiring newer therapeutic agents to be used as monotherapy or combination. Recent research regarding treatment options has attained remarkable speed and development. Therefore, in this context, drug repurposing comes into the picture, which is defined as the "investigation of the off-patent, approved and marketed drugs for a novel therapeutic indication" which saves at least 30% of the time and cost, reducing the cost of treatment for patients, which usually runs high in cancer patients. The anticancer property of cardiac glycosides in cancers was tested in the early 1980s. The trend then shifts toward treating prostate cancer by repurposing other cardiovascular drugs. The current review mainly emphasizes the advantageous antiprostate cancer profile of conventional CVS drugs like cardiac glycosides, RAAS inhibitors, statins, heparin, and beta-blockers with underlying mechanisms.
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Affiliation(s)
- Jonaid
Ahmad Malik
- Department
of Pharmacology and Toxicology, National
Institute of Pharmaceutical Education and Research, Guwahati 781003, India
- Biomedical
Engineering, Indian Institute of Technology
(IIT), Ropar, Punjab 140001, India
| | - Sakeel Ahmed
- Department
of Pharmacology and Toxicology, National
Institute of Pharmaceutical Education and Research, Ahmedabad, Gujarat 382355, India
| | - Sadiya Sikandar Momin
- Department
of Pharmaceutics, Annasaheb Dange College of B. Pharmacy, Ashta, Shivaji University, Sangli, Maharastra 416301, India
| | - Sijal Shaikh
- Sandip Institute
of Pharmaceutical Sciences, Savitribai Phule
Pune University, Nashik, Maharashtra 422213, India
| | - Ahmed Alafnan
- Department
of Pharmacology and Toxicology, University
of Hail, Hail 81422, Saudi Arabia
| | - Jowaher Alanazi
- Department
of Pharmacology and Toxicology, University
of Hail, Hail 81422, Saudi Arabia
| | | | - Sirajudheen Anwar
- Department
of Pharmacology and Toxicology, University
of Hail, Hail 81422, Saudi Arabia
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11
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Hao Y, Zhang S, Shao C, Li J, Zhao G, Zhang DE, Fu XD. ZetaSuite: computational analysis of two-dimensional high-throughput data from multi-target screens and single-cell transcriptomics. Genome Biol 2022; 23:162. [PMID: 35879727 PMCID: PMC9310463 DOI: 10.1186/s13059-022-02729-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 07/07/2022] [Indexed: 11/10/2022] Open
Abstract
AbstractTwo-dimensional high-throughput data have become increasingly common in functional genomics studies, which raises new challenges in data analysis. Here, we introduce a new statistic called Zeta, initially developed to identify global splicing regulators from a two-dimensional RNAi screen, a high-throughput screen coupled with high-throughput functional readouts, and ZetaSuite, a software package to facilitate general application of the Zeta statistics. We compare our approach with existing methods using multiple benchmarked datasets and then demonstrate the broad utility of ZetaSuite in processing public data from large-scale cancer dependency screens and single-cell transcriptomics studies to elucidate novel biological insights.
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12
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Wang Y, Wu X, Yang K, Liu Q, Jiang B, Yang R, Xiao P, He C. Integrating network pharmacology analysis and pharmacodynamic evaluation for exploring the active components and molecular mechanism of moutan seed coat extract to improve cognitive impairment. Front Pharmacol 2022; 13:952876. [PMID: 36034803 PMCID: PMC9411852 DOI: 10.3389/fphar.2022.952876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
Paeonia suffruticosa (Moutan) is a traditional medicinal plant in China. Its seed coat is rich in resveratrol oligomer, especially suffruticosol B (SB). Previous studies had shown that the seed coat extracts of Paeonia suffruticosa (PSCE) had good cholinesterase inhibitory activity and neuroprotective effect, but the effective dose range was unknown, and the pharmacodynamic components and molecular mechanism of PSCE had not been discussed. The current study aimed to screen the pharmacodynamic components in PSCE and investigate the improvement effect of PSCE and the selected SB on scopolamine-induced cognitive dysfunction in mice and its mechanism. The results of high-throughput sequencing and bioinformatics analysis showed that suffruticosol B (SB) and trans-gnetin H (GH) might be the main active components of PSCE; PSCE might improve cognitive dysfunction through p53, HIF-1, MAPK, and PI3K-Akt signaling pathways, while SB and GH might improve cognitive dysfunction through HIF-1 signaling pathway. SB and GH had good molecular docking activity with the target of HIF-1 signaling pathway. The pharmacodynamic activities of PSCE and SB were further verified by behavioral experiments. PSCE and SB could improve the recognition ability of familiar and new objects and shorten the escape latency in the Morris Water Maze test (PSCE 120 mg∙kg-1, p < 0.05; SB 60 mg∙kg-1, p < 0.01); PSCE and SB could increase Ach and GSH levels, enhance the activities of ChAT, SOD and CAT, decrease the levels of IL-1β, IL-6, and TNF-α, and decrease the activity of AChE. In conclusion, the results indicated that PSCE might exert pharmacodynamic activity through multiple components, targets, and pathways, and SB and GH might be the main active components of PSCE. PSCE and SB might improve cognitive dysfunction by regulating cholinergic, antioxidant, and anti-inflammatory effects. These results indicated that PSCE and SB might be potential anti-AD drug candidates, providing a scientific basis for the development and utilization of Moutan bark.
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13
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Xie L, Zhao S, Zhang X, Huang W, Qiao L, Zhan D, Ma C, Gong W, Dang H, Lu H. Wenshenyang recipe treats infertility through hormonal regulation and inflammatory responses revealed by transcriptome analysis and network pharmacology. Front Pharmacol 2022; 13:917544. [PMID: 36003498 PMCID: PMC9393626 DOI: 10.3389/fphar.2022.917544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 07/11/2022] [Indexed: 11/15/2022] Open
Abstract
The Wenshenyang recipe (WSYR) has the effect of treating infertility, but the mechanisms underlying this activity have not been fully elucidated. In this study, network pharmacology and RNA sequencing were combined, with database-based “dry” experiments and transcriptome analysis-based “wet” experiments used conjointly to analyse the mechanism of WSYR in the treatment of infertility. In the dry analysis, 43 active compounds in WSYR and 44 therapeutic targets were obtained through a database search, 15 infertility pathways were significantly enriched, and key targets, such as ESR1, TP53, AKT1, IL-6, and IL-10 were identified. Then the wet experiments were performed to detect the expression changes of the 412 genes from 15 infertility pathways identified by dry analysis. HK-2 cells were treated with the three herbs of WSYR and subjected to targeted RNA sequencing. Based on the results, 92 of the 412 genes in 15 infertility pathways were identified as DEGs. Additionally, key targets, such as ESR2, STAT1, STAT3, and IL6, were also identified in the wet experiments. RT-qPCR experiments further verified that WSYR played an anti-inflammatory role by upregulating IL-4 and IL-10 and Epimedium brevicornu Maxim (Yinyanghuo) showed broader effect than Drynaria fortunei (Kunze) J. Sm (Gusuibu) and Cistanche deserticola Y.C.Ma (Roucongrong). By screening compounds of WSYR using molecular docking models of ESR1 and ESR2, it was further found that xanthogalenol in Gusuibu, arachidonate in Roucongrong, and anhydroicaritin in Yinyanghuo had good affinity for estrogen receptors. These findings provide evidence for an estrogen-regulating role of the three herbs in WSYR.
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Affiliation(s)
- Lan Xie
- Medical Systems Biology Research Center, Tsinghua University School of Medicine, Beijing, China
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
- *Correspondence: Lan Xie,
| | - Shuai Zhao
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
| | - Xiaoling Zhang
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
| | - Wenting Huang
- Medical Systems Biology Research Center, Tsinghua University School of Medicine, Beijing, China
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
| | - Liansheng Qiao
- Medical Systems Biology Research Center, Tsinghua University School of Medicine, Beijing, China
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
| | - Delin Zhan
- Medical Systems Biology Research Center, Tsinghua University School of Medicine, Beijing, China
| | - Chengmei Ma
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
| | - Wei Gong
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
| | - Honglei Dang
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
| | - Hua Lu
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
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14
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Ren J, Gao X, Guo X, Wang N, Wang X. Research Progress in Pharmacological Activities and Applications of Cardiotonic Steroids. Front Pharmacol 2022; 13:902459. [PMID: 35721110 PMCID: PMC9205219 DOI: 10.3389/fphar.2022.902459] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/11/2022] [Indexed: 12/21/2022] Open
Abstract
Cardiotonic steroids (CTS) are a group of compounds existing in animals and plants. CTS are commonly referred to cardiac glycosides (CGs) which are composed of sugar residues, unsaturated lactone rings and steroid cores. Their traditional mechanism of action is to inhibit sodium-potassium ATPase to strengthen the heart and regulate heart rate, so it is currently widely used in the treatment of cardiovascular diseases such as heart failure and tachyarrhythmia. It is worth noticing that recent studies have found an avalanche of inestimable values of CTS applications in many fields such as anti-tumor, anti-virus, neuroprotection, and immune regulation through multi-molecular mechanisms. Thus, the pharmacological activities and applications of CTS have extensive prospects, which would provide a direction for new drug research and development. Here, we review the potential applications of CTS in cardiovascular system and other systems. We also provide suggestions for new clinical practical strategies of CTS, for many diseases. Four main themes will be discussed, in relation to the impact of CTS, on 1) tumors, 2) viral infections, 3) nervous system diseases and 4) immune-inflammation-related diseases.
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Affiliation(s)
- Junwei Ren
- Key Laboratory of Cardiovascular Medicine Research, Department of Pharmacology, Ministry of Education, Harbin Medical University, Harbin, China
| | - Xinyuan Gao
- Key Laboratory of Cardiovascular Medicine Research, Department of Pharmacology, Ministry of Education, Harbin Medical University, Harbin, China
| | - Xi Guo
- Thyroid Surgery, Affiliated Cancer Hospital, Harbin Medical University, Harbin, China
| | - Ning Wang
- Key Laboratory of Cardiovascular Medicine Research, Department of Pharmacology, Ministry of Education, Harbin Medical University, Harbin, China
| | - Xin Wang
- Department of Pharmacy, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
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15
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Gui Y, Dai Y, Wang Y, Li S, Xiang L, Tang Y, Tan X, Pei T, Bao X, Wang D. Taohong Siwu Decoction exerts anticancer effects on breast cancer via regulating MYC, BIRC5, EGF and PIK3R1 revealed by HTS2 technology. Comput Struct Biotechnol J 2022; 20:3461-3472. [PMID: 35860405 PMCID: PMC9278046 DOI: 10.1016/j.csbj.2022.06.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 11/03/2022] Open
Abstract
Taohong Siwu Decoction (TSD), a classical gynecological prescription that was firstly reported 600 years ago, has been widely used in the adjuvant treatment of breast cancer (BRCA) in China. However, the mechanism of action of TSD in treating BRCA has remained unclear. Here, high-throughput sequencing-based high-throughput screening (HTS2) technology was used to reveal the molecular mechanism of TSD, combination with bioinformatics and systems pharmacology in this study. Firstly, our results showed that TSD exerts an anticancer effect on BRCA cells by inhibiting cell proliferation, migration and inducing apoptosis as well as cell-cycle arrest. And our results from HTS2 suggested that herbs of TSD could significantly inhibit KRAS pathway and pathway in cancer, and activate apoptosis pathway, p53 pathway and hypoxia pathway, which may lead to the anticancer function of TSD. Further, we found that TSD clearly regulates MYC, BIRC5, EGF, and PIK3R1 genes, which play an important role in the development and progression of tumor and have significant correlation with overall survival in BRCA patients. By molecular docking, we discovered that Pentagalloylglucose, a compound derived from TSD, might directly bind to and inhibit the function of BRD4, which is a reported transcriptional activator of MYC gene, and thus repress the expression of MYC. Taken together, this study explores the mechanism of TSD in anti-BRCA by combining HTS2 technology, bioinformatics analysis and systems pharmacology.
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16
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Luo K, Huang W, Qiao L, Zhang X, Yan D, Ning Z, Ma C, Dang H, Wang D, Guo H, Xie L, Cheng J. Dendrocalamus latiflorus and its component rutin exhibit glucose-lowering activities by inhibiting hepatic glucose production via AKT activation. Acta Pharm Sin B 2022; 12:2239-2251. [PMID: 35646547 PMCID: PMC9136573 DOI: 10.1016/j.apsb.2021.11.017] [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: 09/21/2021] [Revised: 11/07/2021] [Accepted: 11/08/2021] [Indexed: 11/29/2022] Open
Abstract
The potential medicinal value of Ma bamboo (Dendrocalamus latiflorus), one of the most popular and economically important bamboo species in China, has been underestimated. In the present study, we found that D. latiflorus leaf extract (DLE) reduced fasting blood glucose levels, body weight, and low-density lipoprotein cholesterol with low liver toxicity in db/db mice. In addition, gene expression profiling was performed and pathway enrichment analysis showed that DLE affected metabolic pathways. Importantly, DLE activated the AKT signaling pathway and reduced glucose production by downregulating glucose-6-phosphatase (G6PC) and phosphoenolpyruvate carboxykinase 1 (PCK1) expression. Moreover, network pharmacology analysis identified rutin as an active component in DLE through targeting insulin growth factor 1 receptor (IGF1R), an upstream signaling transducer of AKT. Due to its hypoglycemic effects and low toxicity, DLE may be considered an adjuvant treatment option for type 2 diabetes patients.
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Affiliation(s)
- Kun Luo
- State Key Laboratory of Membrane Biology, School of Medicine, Tsinghua University, Beijing 100084, China
- Medical Systems Biology Research Center, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Wenting Huang
- State Key Laboratory of Membrane Biology, School of Medicine, Tsinghua University, Beijing 100084, China
- Medical Systems Biology Research Center, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Liansheng Qiao
- State Key Laboratory of Membrane Biology, School of Medicine, Tsinghua University, Beijing 100084, China
- Medical Systems Biology Research Center, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xiaoling Zhang
- National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, China
| | - Di Yan
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Zhiyu Ning
- State Key Laboratory of Membrane Biology, School of Medicine, Tsinghua University, Beijing 100084, China
- Medical Systems Biology Research Center, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Chengmei Ma
- National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, China
| | - Honglei Dang
- National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, China
| | - Dong Wang
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Hongyan Guo
- National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, China
| | - Lan Xie
- State Key Laboratory of Membrane Biology, School of Medicine, Tsinghua University, Beijing 100084, China
- Medical Systems Biology Research Center, School of Medicine, Tsinghua University, Beijing 100084, China
- National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, China
- Corresponding authors. Tel.: +86 10 80726868; fax: +86 10 80726898
| | - Jing Cheng
- State Key Laboratory of Membrane Biology, School of Medicine, Tsinghua University, Beijing 100084, China
- Medical Systems Biology Research Center, School of Medicine, Tsinghua University, Beijing 100084, China
- National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, China
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- Corresponding authors. Tel.: +86 10 80726868; fax: +86 10 80726898
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17
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Cistrome and transcriptome analysis identifies unique androgen receptor (AR) and AR-V7 splice variant chromatin binding and transcriptional activities. Sci Rep 2022; 12:5351. [PMID: 35354884 PMCID: PMC8969163 DOI: 10.1038/s41598-022-09371-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/14/2022] [Indexed: 12/13/2022] Open
Abstract
The constitutively active androgen receptor (AR) splice variant, AR-V7, plays an important role in resistance to androgen deprivation therapy in castration resistant prostate cancer (CRPC). Studies seeking to determine whether AR-V7 is a partial mimic of the AR, or also has unique activities, and whether the AR-V7 cistrome contains unique binding sites have yielded conflicting results. One limitation in many studies has been the low level of AR variant compared to AR. Here, LNCaP and VCaP cell lines in which AR-V7 expression can be induced to match the level of AR, were used to compare the activities of AR and AR-V7. The two AR isoforms shared many targets, but overall had distinct transcriptomes. Optimal induction of novel targets sometimes required more receptor isoform than classical targets such as PSA. The isoforms displayed remarkably different cistromes with numerous differential binding sites. Some of the unique AR-V7 sites were located proximal to the transcription start sites (TSS). A de novo binding motif similar to a half ARE was identified in many AR-V7 preferential sites and, in contrast to conventional half ARE sites that bind AR-V7, FOXA1 was not enriched at these sites. This supports the concept that the AR isoforms have unique actions with the potential to serve as biomarkers or novel therapeutic targets.
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18
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Huang L, Yi X, Yu X, Wang Y, Zhang C, Qin L, Guo D, Zhou S, Zhang G, Deng Y, Bao X, Wang D. High-Throughput Strategies for the Discovery of Anticancer Drugs by Targeting Transcriptional Reprogramming. Front Oncol 2021; 11:762023. [PMID: 34660328 PMCID: PMC8518531 DOI: 10.3389/fonc.2021.762023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 09/15/2021] [Indexed: 12/28/2022] Open
Abstract
Transcriptional reprogramming contributes to the progression and recurrence of cancer. However, the poorly elucidated mechanisms of transcriptional reprogramming in tumors make the development of effective drugs difficult, and gene expression signature is helpful for connecting genetic information and pharmacologic treatment. So far, there are two gene-expression signature-based high-throughput drug discovery approaches: L1000, which measures the mRNA transcript abundance of 978 "landmark" genes, and high-throughput sequencing-based high-throughput screening (HTS2); they are suitable for anticancer drug discovery by targeting transcriptional reprogramming. L1000 uses ligation-mediated amplification and hybridization to Luminex beads and highlights gene expression changes by detecting bead colors and fluorescence intensity of phycoerythrin signal. HTS2 takes advantage of RNA-mediated oligonucleotide annealing, selection, and ligation, high throughput sequencing, to quantify gene expression changes by directly measuring gene sequences. This article summarizes technological principles and applications of L1000 and HTS2, and discusses their advantages and limitations in anticancer drug discovery.
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Affiliation(s)
- Lijun Huang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xiaohong Yi
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xiankuo Yu
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yumei Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Chen Zhang
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Lixia Qin
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Dale Guo
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Shiyi Zhou
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Guanbin Zhang
- Department of Infectious Diseases, 404 Hospital of Mianyang, Mianyang, China.,National Engineering Research Center for Beijing Biochip Technology, Beijing, China
| | - Yun Deng
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xilinqiqige Bao
- Medical Innovation Center for Nationalities, Inner Mongolia Medical University, Hohhot, China
| | - Dong Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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19
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Del Olmo B, Merkurjev D, Yao L, Pinsach-Abuin ML, Garcia-Bassets I, Almenar-Queralt A. Analysis of Clonal Composition in Human iPSC and ESC and Derived 2D and 3D Differentiated Cultures. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2454:31-47. [PMID: 34505265 DOI: 10.1007/7651_2021_414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Human induced pluripotent and embryonic stem cell cultures (hiPSC/hESC) are phenotypically heterogeneous and prone to clonal deviations during subculturing and differentiation. Clonal deviations often emerge unnoticed, but they can change the biology of the cell culture with a negative impact on experimental reproducibility. Here, we describe a computational workflow to profile the bulk clonal composition in a hiPSC/hESC culture that can also be used to infer clonal deviations. This workflow processes data obtained with two versions of the same method. The two versions-epigenetic and transcriptomic-rely on a mechanism of stochastic H3K4me3 deposition during hiPSC/hESC derivation. This mechanism generates a signature of ten or more H3K4me3-enriched clustered protocadherin (PCDH) promoters distinct in every single cell. The aggregate of single-cell signatures provides an identificatory feature in every hiPSC/hESC line. This feature is stably transmitted to the cell progeny of the culture even after differentiation unless there is a clonal deviation event that changes the internal balance of single-cell signatures. H3K4me3 signatures can be profiled by chromatin immunoprecipitation and next-generation sequencing (ChIP-seq). Alternatively, an equivalent PCDH-expression version can be profiled by RNA-seq in PCDH-expressing hiPSC/hESC-derived cells (such as neurons, astrocytes, and cardiomyocytes; and, in long-term cultures, such as cerebral organoids). Notably, our workflow can also distinguish genetically identical hiPSC/hESC lines derived from the same patient or generated in the same editing process. Together, we propose a method to improve data sharing and reproducibility in the hiPSC and hESC fields.
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Affiliation(s)
- Bernat Del Olmo
- Visiting Scholar Program, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Daria Merkurjev
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Statistics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Likun Yao
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Mel Lina Pinsach-Abuin
- Visiting Scholar Program, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Ivan Garcia-Bassets
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA.
| | - Angels Almenar-Queralt
- Department of Cellular and Molecular Medicine, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA.
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20
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Rens C, Shapira T, Peña-Diaz S, Chao JD, Pfeifer T, Av-Gay Y. Apoptosis assessment in high-content and high-throughput screening assays. Biotechniques 2021; 70:309-318. [PMID: 34114488 DOI: 10.2144/btn-2020-0164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Here the authors describe the development of AUTOptosis, an economical and rapid apoptosis monitoring method suitable for high-content and high-throughput screening assays. AUTOptosis is based on the quantification of nuclei intensity via staining with Hoechst 33342. First, the authors calibrated the method using standard apoptosis inducers in multiple cell lines. Next, the authors validated the applicability of this approach to high-content screening using a small library of compounds and compared it with the terminal deoxynucleotidyl transferase dUTP nick end labeling gold standard. Finally, the authors demonstrated the specificity of the method by using AUTOposis to detect apoptosis triggered by Mycobacterium tuberculosis intracellular infections.
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Affiliation(s)
- Céline Rens
- Department of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Tirosh Shapira
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, Canada
| | - Sandra Peña-Diaz
- Department of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Joseph D Chao
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, Canada
| | - Tom Pfeifer
- Biofactorial High-Throughput Biology Facility, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Yossef Av-Gay
- Department of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, Canada.,Department of Microbiology & Immunology, University of British Columbia, Vancouver, Canada
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21
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Zhou W, Lai X, Wang X, Yao X, Wang W, Li S. Network pharmacology to explore the anti-inflammatory mechanism of Xuebijing in the treatment of sepsis. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2021; 85:153543. [PMID: 33799226 DOI: 10.1016/j.phymed.2021.153543] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 02/24/2021] [Accepted: 03/05/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Xuebijing (XBJ) is a traditional Chinese patent medicine for sepsis. However, the mechanism of action (MoA) of XBJ on sepsis remain unclear. PURPOSE Elucidate the MoA of XBJ for treating sepsis based on network pharmacology. STUDY DESIGN Integrate computational prediction, experimental validation and literature reported clinical results analysis based on network pharmacology. METHODS Computationally, representative compounds of XBJ were characterized by LC-MS/MS and the target profiles of each compound were identified using network-based method. Compounds from XBJ were compared with FDA approved drugs or experimental agents for sepsis by hierarchical clustering of target profile. Key biological functional modules of XBJ for treating sepsis were identified by enrichment analysis. Differential expressed analysis for each biological functional module was conducted from sepsis related public omics datasets. Herb-biological functional module network was constructed to reveal part of the traditional combinatorial rules of herbs for modules. Experimentally, the action of XBJ compounds on genes in biological functional module was validated by detecting quantitative transcriptional profiling and sepsis animal model. Clinically, combined with the clinical results recorded in literature, computational and experimental results were used to interpret the anti-inflammatory effect of XBJ for treating sepsis. RESULTS The target profiles of compound cover most of the compound's related biomolecules reported in literature, which can characterize the comprehensive function of compound. XBJ has similar pharmacological effect as FDA approved drugs or experimental agents. Four key biological functional modules including inflammation, immune, cell apoptosis and coagulation of XBJ for treating sepsis were identified. Cell line experimental results show that part of ingredients in XBJ regulate the expression of genes in inflammation modules as predicted. Animal experiments show that compounds from XBJ could reduce the expression level of IL-1β. Combined with literature reported clinical results, XBJ was found to exert anti-inflammatory effect through regulating the NF-kappa B signaling pathway. CONCLUSION The network pharmacology framework integrating computational prediction, experimental validation and literature reported clinical results analysis provides a novel approach for analyzing MoA of XBJ for treating sepsis.
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Affiliation(s)
- Wuai Zhou
- Institute for TCM-X, MOE Key Laboratory of Bioinformatics, Bioinformatics Division, BNRist, Department of Automation, Tsinghua University, 100084 Beijing, China
| | - Xinxing Lai
- Institute for TCM-X, MOE Key Laboratory of Bioinformatics, Bioinformatics Division, BNRist, Department of Automation, Tsinghua University, 100084 Beijing, China; Institute for Brain Disorders, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Xin Wang
- Institute for TCM-X, MOE Key Laboratory of Bioinformatics, Bioinformatics Division, BNRist, Department of Automation, Tsinghua University, 100084 Beijing, China
| | - Xiaoqing Yao
- Tianjin Chase Sun Pharmaceutical Co. LTD, Tianjin, China
| | - Weihua Wang
- Center of Pharmaceutical Technology, Tsinghua University, China
| | - Shao Li
- Institute for TCM-X, MOE Key Laboratory of Bioinformatics, Bioinformatics Division, BNRist, Department of Automation, Tsinghua University, 100084 Beijing, China.
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22
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Dai Y, Qiang W, Gui Y, Tan X, Pei T, Lin K, Cai S, Sun L, Ning G, Wang J, Guo H, Sun Y, Cheng J, Xie L, Lan X, Wang D. A large-scale transcriptional study reveals inhibition of COVID-19 related cytokine storm by traditional Chinese medicines. Sci Bull (Beijing) 2021; 66:884-888. [PMID: 33457042 PMCID: PMC7803147 DOI: 10.1016/j.scib.2021.01.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/25/2020] [Accepted: 01/07/2021] [Indexed: 12/19/2022]
Affiliation(s)
- Yifei Dai
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.,Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Weijie Qiang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Yu Gui
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Xue Tan
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Tianli Pei
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Kequan Lin
- High Performance Computing Department, National Supercomputing Center in Shenzhen, Shenzhen 518055, China
| | - Siwei Cai
- Department of Electronic and Computer Engineering, College of Engineering, Drexel University, Philadelphia 19104, USA
| | - Liang Sun
- Dongli District Jinqiao Street Community Health Service Center, Tianjin 300300, China
| | - Guochen Ning
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Jianxun Wang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Hongyan Guo
- National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, China
| | - Yimin Sun
- National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, China
| | - Jing Cheng
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.,National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, China.,State Key Laboratory of Membrane Biology, School of Medicine, Tsinghua University, Beijing 100084, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China.,Medical Systems Biology Research Center, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Lan Xie
- National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, China.,State Key Laboratory of Membrane Biology, School of Medicine, Tsinghua University, Beijing 100084, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China.,Medical Systems Biology Research Center, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xun Lan
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Dong Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
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23
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Wang H, Li S, Wang Q, Jin Z, Shao W, Gao Y, Li L, Lin K, Zhu L, Wang H, Liao X, Wang D. Tumor immunological phenotype signature-based high-throughput screening for the discovery of combination immunotherapy compounds. SCIENCE ADVANCES 2021; 7:eabd7851. [PMID: 33523948 DOI: 10.1126/sciadv.abd7851] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 12/04/2020] [Indexed: 02/05/2023]
Abstract
Combination immunotherapy is promising to overcome the limited objective response rates of immune checkpoint blockade (ICB) therapy. Here, a tumor immunological phenotype (TIP) gene signature and high-throughput sequencing-based high-throughput screening (HTS2) were combined to identify combination immunotherapy compounds. We firstly defined a TIP gene signature distinguishing "cold" tumors from "hot" tumors. After screening thousands of compounds, we identified that aurora kinase inhibitors (AKIs) could reprogram the expression pattern of TIP genes in triple-negative breast cancer (TNBC) cells. AKIs treatments up-regulate expression of chemokine genes CXCL10 and CXCL11 through inhibiting aurora kinase A (AURKA)-signal transducer and activator of transcription 3 (STAT3) signaling pathway, which promotes effective T cells infiltrating into tumor microenvironment and improves anti-programmed cell death 1 (PD-1) efficacy in preclinical models. Our study established a novel strategy to discover combination immunotherapy compounds and suggested the therapeutic potential of combining AKIs with ICB for the treatment of TNBC.
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Affiliation(s)
- Haiyan Wang
- Department of Pathology, School of Medicine, Qinghai University, Xining 810001, China
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Shasha Li
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Qianyu Wang
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhengshuo Jin
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Wei Shao
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yan Gao
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Lu Li
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Kequan Lin
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Lin Zhu
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Huili Wang
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xuebin Liao
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Dong Wang
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China.
- Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Sichuan 610041, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
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24
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Yu Z, Feng H, Zhuo Y, Li M, Zhu X, Huang L, Zhang X, Zhou Z, Zheng C, Jiang Y, Le F, Yu DY, Cheng AS, Sun X, Gao Y. Bufalin inhibits hepatitis B virus-associated hepatocellular carcinoma development through androgen receptor dephosphorylation and cell cycle-related kinase degradation. Cell Oncol (Dordr) 2020; 43:1129-1145. [PMID: 32623699 DOI: 10.1007/s13402-020-00546-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2020] [Indexed: 12/30/2022] Open
Abstract
PURPOSE Hepatitis B virus (HBV)-associated hepatocellular carcinoma (HCC), which has a male predominance, lacks effective therapeutic options. Previously, the cardiac glycoside analogue bufalin has been found to inhibit HBV infection and HCC development. As yet, however, its molecular role in HBV-associated HCC has remained obscure. METHODS Colony formation and soft agar assays, xenograft and orthotopic mouse models and HBV X protein (HBx) transgenic mice with exposure to diethylnitrosamine were used to evaluate the effect of bufalin on HBV-associated HCC growth and tumorigenicity. HBx-induced oncogenic signaling regulated by bufalin was assessed using PCR array, chromatin immunoprecipitation, site-directed mutagenesis, luciferase reporter, transcription and protein expression assays. Synergistic HCC therapeutic effects were examined using combinations of bufalin and sorafenib. RESULTS We found that bufalin exerted a more profound effect on inhibiting the proliferation of HBV-associated HCC cells than of non HBV-associated HCC cells. Bufalin significantly inhibited HBx-induced malignant transfromation in vitro and tumorigenicity in vivo. Androgen receptor (AR) signaling was found to be a target of bufalin resistance to HBV-associated hepatocarcinogenesis. We also found that bufalin induced both AR dephosphorylation and cell cycle-related kinase (CCRK) degradation to inhibit β-catenin/TCF signaling, which subsequently led to cell cycle arrest via cyclin D1 down-regulation and p21 up-regulation, resulting in HCC regression. Furthermore, we found that bufalin reduced > 60% diethylnitrosamine-induced hepatocarcinogenesis in HBx transgenic mice, and improved the sensitivity of refractory HBV-associated HCC cells to sorafenib treatment. CONCLUSION Our results indicate that bufalin acts as a potential anti-HCC therapeutic candidate to block HBx-induced AR/CCRK/β-catenin signaling by targeting AR and CCRK, which may provide a novel strategy for the treatment of HBV-associated HCC.
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Affiliation(s)
- Zhuo Yu
- Liver Disease Department, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, No.528. Zhangheng Road, Pudong New District, Shanghai, People's Republic of China.
| | - Hai Feng
- Department of pharmacology, School of Pharmacy, Harbin Medical University, Harbin, People's Republic of China
| | - Yunhui Zhuo
- Liver Disease Department, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, No.528. Zhangheng Road, Pudong New District, Shanghai, People's Republic of China
| | - Man Li
- Laboratory of Cellular Immunity, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, People's Republic of China
| | - Xiaojun Zhu
- Liver Disease Department, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, No.528. Zhangheng Road, Pudong New District, Shanghai, People's Republic of China
| | - Lingying Huang
- Liver Disease Department, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, No.528. Zhangheng Road, Pudong New District, Shanghai, People's Republic of China
| | - Xin Zhang
- Laboratory of Cellular Immunity, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, People's Republic of China
| | - Zhenhua Zhou
- Laboratory of Cellular Immunity, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, People's Republic of China
| | - Chao Zheng
- Liver Disease Department, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, No.528. Zhangheng Road, Pudong New District, Shanghai, People's Republic of China
| | - Yun Jiang
- Liver Disease Department, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, No.528. Zhangheng Road, Pudong New District, Shanghai, People's Republic of China
| | - Fan Le
- Liver Disease Department, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, No.528. Zhangheng Road, Pudong New District, Shanghai, People's Republic of China
| | - Dae-Yeul Yu
- Disease Model Research Laboratory, Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Republic of Korea
| | - Alfred Szelok Cheng
- School of Biomedical Sciences, State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, SAR, People's Republic of China
| | - Xuehua Sun
- Liver Disease Department, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, No.528. Zhangheng Road, Pudong New District, Shanghai, People's Republic of China.
| | - Yueqiu Gao
- Liver Disease Department, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, No.528. Zhangheng Road, Pudong New District, Shanghai, People's Republic of China. .,Laboratory of Cellular Immunity, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, People's Republic of China.
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25
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Telpoukhovskaia MA, Liu K, Sayed FA, Etchegaray JI, Xie M, Zhan L, Li Y, Zhou Y, Le D, Bahr BA, Bogyo M, Ding S, Gan L. Discovery of small molecules that normalize the transcriptome and enhance cysteine cathepsin activity in progranulin-deficient microglia. Sci Rep 2020; 10:13688. [PMID: 32792571 PMCID: PMC7426857 DOI: 10.1038/s41598-020-70534-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 07/17/2020] [Indexed: 12/11/2022] Open
Abstract
Patients with frontotemporal dementia (FTD) resulting from granulin (GRN) haploinsufficiency have reduced levels of progranulin and exhibit dysregulation in inflammatory and lysosomal networks. Microglia produce high levels of progranulin, and reduction of progranulin in microglia alone is sufficient to recapitulate inflammation, lysosomal dysfunction, and hyperproliferation in a cell-autonomous manner. Therefore, targeting microglial dysfunction caused by progranulin insufficiency represents a potential therapeutic strategy to manage neurodegeneration in FTD. Limitations of current progranulin-enhancing strategies necessitate the discovery of new targets. To identify compounds that can reverse microglial defects in Grn-deficient mouse microglia, we performed a compound screen coupled with high throughput sequencing to assess key transcriptional changes in inflammatory and lysosomal pathways. Positive hits from this initial screen were then further narrowed down based on their ability to rescue cathepsin activity, a critical biochemical readout of lysosomal capacity. The screen identified nor-binaltorphimine dihydrochloride (nor-BNI) and dibutyryl-cAMP, sodium salt (DB-cAMP) as two phenotypic modulators of progranulin deficiency. In addition, nor-BNI and DB-cAMP also rescued cell cycle abnormalities in progranulin-deficient cells. These data highlight the potential of a transcription-based platform for drug screening, and advance two novel lead compounds for FTD.
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Affiliation(s)
- Maria A Telpoukhovskaia
- Gladstone Institute of Neurological Disease, San Francisco, CA, 94158, USA.,Department of Neurology, University of California, San Francisco, CA, 94158, USA
| | - Kai Liu
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA, 94158, USA
| | - Faten A Sayed
- Gladstone Institute of Neurological Disease, San Francisco, CA, 94158, USA.,Department of Neurology, University of California, San Francisco, CA, 94158, USA.,Neuroscience Graduate Program, University of California, San Francisco, CA, 94158, USA
| | | | - Min Xie
- Gladstone Institute of Neurological Disease, San Francisco, CA, 94158, USA.,Gladstone Institute of Cardiovascular Disease, San Francisco, CA, 94158, USA
| | - Lihong Zhan
- Gladstone Institute of Neurological Disease, San Francisco, CA, 94158, USA.,Department of Neurology, University of California, San Francisco, CA, 94158, USA
| | - Yaqiao Li
- Gladstone Institute of Neurological Disease, San Francisco, CA, 94158, USA
| | - Yungui Zhou
- Gladstone Institute of Neurological Disease, San Francisco, CA, 94158, USA
| | - David Le
- Gladstone Institute of Neurological Disease, San Francisco, CA, 94158, USA
| | - Ben A Bahr
- Biotechnology Research and Training Center, University of North Carolina At Pembroke, Pembroke, NC, 28372, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
| | - Sheng Ding
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA, 94158, USA
| | - Li Gan
- Gladstone Institute of Neurological Disease, San Francisco, CA, 94158, USA. .,Department of Neurology, University of California, San Francisco, CA, 94158, USA. .,Helen and Robert Appel Alzheimer's Disease Research Institute, Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, 10021, USA.
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26
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Dai Y, Qiang W, Yu X, Cai S, Lin K, Xie L, Lan X, Wang D. Guizhi Fuling Decoction inhibiting the PI3K and MAPK pathways in breast cancer cells revealed by HTS 2 technology and systems pharmacology. Comput Struct Biotechnol J 2020; 18:1121-1136. [PMID: 32489526 PMCID: PMC7260686 DOI: 10.1016/j.csbj.2020.05.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 04/25/2020] [Accepted: 05/06/2020] [Indexed: 02/07/2023] Open
Abstract
As one of the classical traditional Chinese medicine (TCM) prescriptions in treating gynecological tumors, Guizhi Fuling Decoction (GFD) has been used to treat breast cancer (BRCA). Nonetheless, the potential molecular mechanism remains unclear so far. Therefore, systems pharmacology was used in combination with high throughput sequencing-based high throughput screening (HTS2) assay and bioinformatic technologies in this study to investigate the molecular mechanisms of GFD in treating BRCA. By computationally analyzing 76 active ingredients in GFD, 38 potential therapeutic targets were predicted and significantly enriched in the "pathways in cancer". Meanwhile, experimental analysis was carried out to examine changes in the expression levels of 308 genes involved in the "pathways in cancer" in BRCA cells treated by five herbs of GFD utilizing HTS2 platform, and 5 key therapeutic targets, including HRAS, EGFR, PTK2, SOS1, and ITGB1, were identified. The binding mode of active compounds to these five targets was analyzed by molecular docking and molecular dynamics simulation. It was found after integrating the computational and experimental data that, GFD possessed the anti-proliferation, pro-apoptosis, and anti-angiogenesis activities mainly through regulating the PI3K and the MAPK signaling pathways to inhibit BRCA. Besides, consistent with the TCM theory about the synergy of Cinnamomi Ramulus (Guizhi) by Cortex Moutan (Mudanpi) in GFD, both of these two herbs acted on the same targets and pathways. Taken together, the combined application of computational systems pharmacology techniques and experimental HTS2 platform provides a practical research strategy to investigate the functional and biological mechanisms of the complicated TCM prescriptions.
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Affiliation(s)
- Yifei Dai
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Weijie Qiang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Xiankuo Yu
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Siwei Cai
- Department of Electronic and Computer Engineering, College of Engineering, Drexel University, Philadelphia 19104, USA
| | - Kequan Lin
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Lan Xie
- Medical Systems Biology Research Center, School of Medicine, Tsinghua University, Beijing 100084, China
- National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, China
| | - Xun Lan
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Dong Wang
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
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27
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Cardiac glycosides with target at direct and indirect interactions with nuclear receptors. Biomed Pharmacother 2020; 127:110106. [PMID: 32248001 DOI: 10.1016/j.biopha.2020.110106] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/13/2020] [Accepted: 03/17/2020] [Indexed: 12/15/2022] Open
Abstract
Cardiac glycosides are compounds isolated from plants and animals and have been known since ancient times. These compounds inhibit the activity of the sodium potassium pump in eukaryotic cells. Cardiac glycosides were used as drugs in heart ailments to increase myocardial contraction force and, at the same time, to lower frequency of this contraction. An increasing number of studies have indicated that the biological effects of these compounds are not limited to inhibition of sodium-potassium pump activity. Furthermore, an increasing number of data have shown that they are synthesized in tissues of mammals, where they may act as a new class of steroid hormones or other hormones by mimicry to modulate various signaling pathways and influence whole organisms. Thus, we discuss the interactions of cardiac glycosides with the nuclear receptor superfamily of transcription factors activated by low-weight molecular ligands (including hormones) that regulate many functions of cells and organisms. Cardiac glycosides of endogenous and exogenous origin by interacting with nuclear receptors can affect the processes regulated by these transcription factors, including hormonal management, immune system, body defense, and carcinogenesis. They can also be treated as initial structures for combinatorial chemistry to produce new compounds (including drugs) with the desired properties.
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28
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Lin K, Li L, Dai Y, Wang H, Teng S, Bao X, Lu ZJ, Wang D. A comprehensive evaluation of connectivity methods for L1000 data. Brief Bioinform 2019; 21:2194-2205. [DOI: 10.1093/bib/bbz129] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 08/26/2019] [Accepted: 09/14/2019] [Indexed: 01/08/2023] Open
Abstract
Abstract
The methodologies for evaluating similarities between gene expression profiles of different perturbagens are the key to understanding mechanisms of actions (MoAs) of unknown compounds and finding new indications for existing drugs. L1000-based next-generation Connectivity Map (CMap) data is more than a thousand-fold scale-up of the CMap pilot dataset. Although several systematic evaluations have been performed individually to assess the accuracy of the methodologies for the CMap pilot study, the performance of these methodologies needs to be re-evaluated for the L1000 data. Here, using the drug–drug similarities from the Drug Repurposing Hub database as a benchmark standard, we evaluated six popular published methods for the prediction performance of drug–drug relationships based on the partial area under the receiver operating characteristic (ROC) curve at false positive rates of 0.001, 0.005 and 0.01 (AUC0.001, AUC0.005 and AUC0.01). The similarity evaluating algorithm called ZhangScore was generally superior to other methods and exhibited the highest accuracy at the gene signature sizes ranging from 10 to 200. Further, we tested these methods with an experimentally derived gene signature related to estrogen in breast cancer cells, and the results confirmed that ZhangScore was more accurate than other methods. Moreover, based on scoring results of ZhangScore for the gene signature of TOP2A knockdown, in addition to well-known TOP2A inhibitors, we identified a number of potential inhibitors and at least two of them were the subject of previous investigation. Our studies provide potential guidelines for researchers to choose the suitable connectivity method. The six connectivity methods used in this report have been implemented in R package (https://github.com/Jasonlinchina/RCSM).
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Affiliation(s)
- Kequan Lin
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Lu Li
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yifei Dai
- School of Medicine, Tsinghua University, Beijing 100084, China
| | - Huili Wang
- School of Medicine, Tsinghua University, Beijing 100084, China
| | - Shuaishuai Teng
- School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xilinqiqige Bao
- International Mongolian Hospital of Inner Mongolia, Hohhot 010065, China
| | - Zhi John Lu
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- Center of Synthetic & Systems Biology, Tsinghua University, Beijing 100084, China
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
| | - Dong Wang
- School of Medicine, Tsinghua University, Beijing 100084, China
- Center of Synthetic & Systems Biology, Tsinghua University, Beijing 100084, China
- National Collaborative Innovation Center for Biotherapy, Tsinghua University, Beijing 100084, China
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
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29
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Lyu P, Kwok HF. High-throughput Strategy Accelerates the Progress of Marine Anticancer Peptide Drug Development. Recent Pat Anticancer Drug Discov 2018; 14:2-4. [PMID: 30474536 DOI: 10.2174/1574892813999181114152127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Peng Lyu
- Cancer Centre, Faculty of Health Sciences, University of Macau, University Avenue, Taipa, Macau, P.R, China
| | - Hang F Kwok
- Cancer Centre, Faculty of Health Sciences, University of Macau, University Avenue, Taipa, Macau, P.R, China
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30
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Zheng J, Wu M, Wang H, Li S, Wang X, Li Y, Wang D, Li S. Network Pharmacology to Unveil the Biological Basis of Health-Strengthening Herbal Medicine in Cancer Treatment. Cancers (Basel) 2018; 10:cancers10110461. [PMID: 30469422 PMCID: PMC6266222 DOI: 10.3390/cancers10110461] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 11/05/2018] [Accepted: 11/16/2018] [Indexed: 12/15/2022] Open
Abstract
Health-strengthening (Fu-Zheng) herbs is a representative type of traditional Chinese medicine (TCM) widely used for cancer treatment in China, which is in contrast to pathogen eliminating (Qu-Xie) herbs. However, the commonness in the biological basis of health-strengthening herbs remains to be holistically elucidated. In this study, an innovative high-throughput research strategy integrating computational and experimental methods of network pharmacology was proposed, and 22 health-strengthening herbs were selected for the investigation. Additionally, 25 pathogen-eliminating herbs were included for comparison. First, based on network-based, large-scale target prediction, we analyzed the target profiles of 1446 TCM compounds. Next, the actions of 166 compounds on 420 antitumor or immune-related genes were measured using a unique high-throughput screening strategy by high-throughput sequencing, referred to as HTS2. Furthermore, the structural information and the antitumor activity of the compounds in health-strengthening and pathogen-eliminating herbs were compared. Using network pharmacology analysis, we discovered that: (1) Functionally, the predicted targets of compounds from health strengthening herbs were enriched in both immune-related and antitumor pathways, similar to those of pathogen eliminating herbs. As a case study, galloylpaeoniflorin, a compound in a health strengthening herb Radix Paeoniae Alba (Bai Shao), was found to exert antitumor effects both in vivo and in vitro. Yet the inhibitory effects of the compounds from pathogen eliminating herbs on tumor cells proliferation as a whole were significantly stronger than those in health-strengthening herbs (p < 0.001). Moreover, the percentage of assay compounds in health-strengthening herbs with the predicted targets enriched in the immune-related pathways (e.g., natural killer cell mediated cytotoxicity and antigen processing and presentation) were significantly higher than that in pathogen-eliminating herbs (p < 0.05). This finding was supported by the immune-enhancing effects of a group of compounds from health-strengthening herbs indicated by differentially expressed genes in the HTS2 results. (2) Compounds in the same herb may exhibit the same or distinguished mechanisms in cancer treatment, which was demonstrated as the compounds influence pathway gene expressions in the same or opposite directions. For example, acetyl ursolic acid and specnuezhenide in a health-strengthening herb Fructus Ligustri lucidi (Nv Zhen Zi) both upregulated gene expressions in T cell receptor signaling pathway. Together, this study suggested greater potentials in tumor immune microenvironment regulation and tumor prevention than in direct killing tumor cells of health-strengthening herbs generally, and provided a systematic strategy for unveiling the commonness in the biological basis of health-strengthening herbs in cancer treatment.
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Affiliation(s)
- Jiahui Zheng
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division Biology/Center for TCM-X, BNRist, TFIDT/Department of Automation, Tsinghua University, 100084 Beijing, China.
| | - Min Wu
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division Biology/Center for TCM-X, BNRist, TFIDT/Department of Automation, Tsinghua University, 100084 Beijing, China.
| | - Haiyan Wang
- Department of Basic Medicine, School of Medicine, Tsinghua University, 100084 Beijing, China.
| | - Shasha Li
- Department of Basic Medicine, School of Medicine, Tsinghua University, 100084 Beijing, China.
| | - Xin Wang
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division Biology/Center for TCM-X, BNRist, TFIDT/Department of Automation, Tsinghua University, 100084 Beijing, China.
| | - Yan Li
- State Key Laboratory of Bioactive Substances and Functions of Nature Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, 100730 Beijing, China.
| | - Dong Wang
- Department of Basic Medicine, School of Medicine, Tsinghua University, 100084 Beijing, China.
| | - Shao Li
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division Biology/Center for TCM-X, BNRist, TFIDT/Department of Automation, Tsinghua University, 100084 Beijing, China.
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Chemical genomics reveals inhibition of breast cancer lung metastasis by Ponatinib via c-Jun. Protein Cell 2018; 10:161-177. [PMID: 29667003 PMCID: PMC6338618 DOI: 10.1007/s13238-018-0533-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 03/14/2018] [Indexed: 02/05/2023] Open
Abstract
Metastasis is the leading cause of human cancer deaths. Unfortunately, no approved drugs are available for anti-metastatic treatment. In our study, high-throughput sequencing-based high-throughput screening (HTS2) and a breast cancer lung metastasis (BCLM)-associated gene signature were combined to discover anti-metastatic drugs. After screening of thousands of compounds, we identified Ponatinib as a BCLM inhibitor. Ponatinib significantly inhibited the migration and mammosphere formation of breast cancer cells in vitro and blocked BCLM in multiple mouse models. Mechanistically, Ponatinib represses the expression of BCLM-associated genes mainly through the ERK/c-Jun signaling pathway by inhibiting the transcription of JUN and accelerating the degradation of c-Jun protein. Notably, JUN expression levels were positively correlated with BCLM-associated gene expression and lung metastases in breast cancer patients. Collectively, we established a novel approach for the discovery of anti-metastatic drugs, identified Ponatinib as a new drug to inhibit BCLM and revealed c-Jun as a crucial factor and potential drug target for BCLM. Our study may facilitate the therapeutic treatment of BCLM as well as other metastases.
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Almassalha LM, Bauer GM, Wu W, Cherkezyan L, Zhang D, Kendra A, Gladstein S, Chandler JE, VanDerway D, Seagle BLL, Ugolkov A, Billadeau DD, O'Halloran TV, Mazar AP, Roy HK, Szleifer I, Shahabi S, Backman V. Macrogenomic engineering via modulation of the scaling of chromatin packing density. Nat Biomed Eng 2017; 1:902-913. [PMID: 29450107 DOI: 10.1038/s41551-017-0153-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Many human diseases result from the dysregulation of the complex interactions between tens to thousands of genes. However, approaches for the transcriptional modulation of many genes simultaneously in a predictive manner are lacking. Here, through the combination of simulations, systems modelling and in vitro experiments, we provide a physical regulatory framework based on chromatin packing-density heterogeneity for modulating the genomic information space. Because transcriptional interactions are essentially chemical reactions, they depend largely on the local physical nanoenvironment. We show that the regulation of the chromatin nanoenvironment allows for the predictable modulation of global patterns in gene expression. In particular, we show that the rational modulation of chromatin density fluctuations can lead to a decrease in global transcriptional activity and intercellular transcriptional heterogeneity in cancer cells during chemotherapeutic responses to achieve near-complete cancer cell killing in vitro. Our findings represent a 'macrogenomic engineering' approach to modulating the physical structure of chromatin for whole-scale transcriptional modulation.
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Affiliation(s)
- Luay M Almassalha
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Greta M Bauer
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Wenli Wu
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Lusik Cherkezyan
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Di Zhang
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Alexis Kendra
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Scott Gladstein
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - John E Chandler
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - David VanDerway
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Brandon-Luke L Seagle
- Department of Obstetrics and Gynecology, Prentice Women's Hospital, Northwestern University, Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Andrey Ugolkov
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
| | - Daniel D Billadeau
- Schulze Center for Novel Therapeutics, Division of Oncology Research, Mayo Clinic, Rochester, MN, 55905, USA
| | - Thomas V O'Halloran
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA.,Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA.,Department of Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | | | - Hemant K Roy
- Section of Gastroenterology, Boston Medical Center/Boston University School of Medicine, Boston, MA, 02118, USA
| | - Igal Szleifer
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA. .,Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA. .,Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA.
| | - Shohreh Shahabi
- Department of Obstetrics and Gynecology, Prentice Women's Hospital, Northwestern University, Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA. .,Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA.
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Behrsing H, Raabe H, Tice R, Devlin R, Pinkerton K, Oberdörster G, Wright C, Wieczorek R, Aufderheide M, Steiner S, Krebs T, Asgharian B, Corley R, Oldham M, Adamson J, Li X, Rahman I, Grego S, Chu PH, McCullough S, Hill E, Curren R, Curren R. In vitro exposure systems and dosimetry assessment tools for inhaled tobacco products: Workshop proceedings, conclusions and paths forward for in vitro model use. Altern Lab Anim 2017; 45:117-158. [PMID: 28816053 PMCID: PMC9878375 DOI: 10.1177/026119291704500305] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In 2009, the passing of the Family Smoking Prevention and Tobacco Control Act facilitated the establishment of the FDA Center for Tobacco Products (CTP), and gave it regulatory authority over the marketing, manufacture and distribution of tobacco products, including those termed 'modified risk'. On 4-6 April 2016, the Institute for In Vitro Sciences, Inc. (IIVS) convened a workshop conference entitled, In Vitro Exposure Systems and Dosimetry Assessment Tools for Inhaled Tobacco Products, to bring together stakeholders representing regulatory agencies, academia and industry to address the research priorities articulated by the FDA CTP. Specific topics were covered to assess the status of current in vitro smoke and aerosol/vapour exposure systems, as well as the various approaches and challenges to quantifying the complex exposures in in vitro pulmonary models developed for evaluating adverse pulmonary events resulting from tobacco product exposures. The four core topics covered were: a) Tobacco Smoke and E-Cigarette Aerosols; b) Air-Liquid Interface-In Vitro Exposure Systems; c) Dosimetry Approaches for Particles and Vapours/In Vitro Dosimetry Determinations; and d) Exposure Microenvironment/Physiology of Cells. The 2.5-day workshop included presentations from 20 expert speakers, poster sessions, networking discussions, and breakout sessions which identified key findings and provided recommendations to advance these technologies. Here, we will report on the proceedings, recommendations, and outcome of the April 2016 technical workshop, including paths forward for developing and validating non-animal test methods for tobacco product smoke and next generation tobacco product aerosol/vapour exposures. With the recent FDA publication of the final deeming rule for the governance of tobacco products, there is an unprecedented necessity to evaluate a very large number of tobacco-based products and ingredients. The questionable relevance, high cost, and ethical considerations for the use of in vivo testing methods highlight the necessity of robust in vitro approaches to elucidate tobacco-based exposures and how they may lead to pulmonary diseases that contribute to lung exposure-induced mortality worldwide.
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Affiliation(s)
| | - Hans Raabe
- Institute for In Vitro Sciences, Inc., Gaithersburg, MD
| | | | - Robert Devlin
- US Environmental Protection Agency, Chapel Hill, North Carolina, USA
| | - Kent Pinkerton
- Center for Health and the Environment, University of California, Davis
| | | | - Chris Wright
- British American Tobacco (Investments) Ltd., Southampton, UK
| | | | | | | | | | | | | | | | - Jason Adamson
- British American Tobacco (Investments) Ltd., Southampton, UK
| | - Xiang Li
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou City, China
| | - Irfan Rahman
- University of Rochester Medical Center, Rochester, NY
| | - Sonia Grego
- RTI International, Research Triangle Park, North Carolina
| | - Pei-Hsuan Chu
- National Center for Advancing Translational Sciences/National Institutes of Health, Rockville, Maryland
| | - Shaun McCullough
- US Environmental Protection Agency, Chapel Hill, North Carolina, USA
| | - Erin Hill
- Institute for In Vitro Sciences, Inc., Gaithersburg, MD
| | - Rodger Curren
- Institute for In Vitro Sciences, Inc., Gaithersburg, MD
| | - Rodger Curren
- Institute for In Vitro Sciences, Inc., Gaithersburg, MD, USA
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Yeakley JM, Shepard PJ, Goyena DE, VanSteenhouse HC, McComb JD, Seligmann BE. A trichostatin A expression signature identified by TempO-Seq targeted whole transcriptome profiling. PLoS One 2017; 12:e0178302. [PMID: 28542535 PMCID: PMC5444820 DOI: 10.1371/journal.pone.0178302] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 05/10/2017] [Indexed: 11/18/2022] Open
Abstract
The use of gene expression signatures to classify compounds, identify efficacy or toxicity, and differentiate close analogs relies on the sensitivity of the method to identify modulated genes. We used a novel ligation-based targeted whole transcriptome expression profiling assay, TempO-Seq®, to determine whether previously unreported compound-responsive genes could be identified and incorporated into a broad but specific compound signature. TempO-Seq exhibits 99.6% specificity, single cell sensitivity, and excellent correlation with fold differences measured by RNA-Seq (R2 = 0.9) for 20,629 targets. Unlike many expression assays, TempO-Seq does not require RNA purification, cDNA synthesis, or capture of targeted RNA, and lacks a 3' end bias. To investigate the sensitivity of the TempO-Seq assay to identify significantly modulated compound-responsive genes, we derived whole transcriptome profiles from MCF-7 cells treated with the histone deacetylase inhibitor Trichostatin A (TSA) and identified more than 9,000 differentially expressed genes. The TSA profile for MCF-7 cells overlapped those for HL-60 and PC-3 cells in the Connectivity Map (cMAP) database, suggesting a common TSA-specific expression profile independent of baseline gene expression. A 43-gene cell-independent TSA signature was extracted from cMAP and confirmed in TempO-Seq MCF-7 data. Additional genes that were not previously reported to be TSA responsive in the cMAP database were also identified. TSA treatment of 5 cell types revealed 1,136 differentially expressed genes in common, including 785 genes not previously reported to be TSA responsive. We conclude that TSA induces a specific expression signature that is consistent across widely different cell types, that this signature contains genes not previously associated with TSA responses, and that TempO-Seq provides the sensitive differential expression detection needed to define such compound-specific, cell-independent, changes in expression.
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Affiliation(s)
- Joanne M. Yeakley
- BioSpyder Technologies, Incorporated, Carlsbad, California, United States of America
- * E-mail:
| | - Peter J. Shepard
- BioSpyder Technologies, Incorporated, Carlsbad, California, United States of America
| | - Diana E. Goyena
- BioSpyder Technologies, Incorporated, Carlsbad, California, United States of America
| | | | - Joel D. McComb
- BioSpyder Technologies, Incorporated, Carlsbad, California, United States of America
| | - Bruce E. Seligmann
- BioSpyder Technologies, Incorporated, Carlsbad, California, United States of America
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Abstract
Reprogramming cell fates towards pluripotent stem cells and other cell types has revolutionized our understanding of cellular plasticity. During the last decade, transcription factors and microRNAs have become powerful reprogramming factors for modulating cell fates. Recently, many efforts are focused on reprogramming cell fates by non-viral and non-integrating chemical approaches. Small molecules not only are useful in generating desired cell types in vitro for various applications, such as disease modeling and cell-based transplantation, but also hold great promise to be further developed as drugs to stimulate patients’ endogenous cells to repair and regenerate in vivo. Here we will focus on chemical approaches for generating induced pluripotent stem cells, neurons, cardiomyocytes, hepatocytes and pancreatic β cells. Significantly, the rapid and exciting advances in cellular reprogramming by small molecules will help us to achieve the long-term goal of curing devastating diseases, injuries, cancers and aging.
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Affiliation(s)
- Xiaojie Ma
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Linghao Kong
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Saiyong Zhu
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China.
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36
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He Y, Wu M, Liu Y, Li Q, Li X, Hu L, Cen S, Zhou J. Identification of Triptophenolide from Tripterygium wilfordii as a Pan-antagonist of Androgen Receptor. ACS Med Chem Lett 2016; 7:1024-1027. [PMID: 27994731 DOI: 10.1021/acsmedchemlett.6b00180] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 09/28/2016] [Indexed: 12/21/2022] Open
Abstract
A compound, triptophenolide, derived from Tripterygium wilfordii was identified as an antiandrogen. Triptophenolide inhibits the activity of both wild-type and F876L mutant androgen receptors. Triptophenolide exhibits its antiandrogenic activity through competitive binding with androgen in the hormone-binding pocket, decreasing the expression of androgen receptor, and reducing the nuclear translocation of androgen receptor.
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Affiliation(s)
- Yang He
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing, China
| | - Meng Wu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing, China
| | - Yangguang Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing, China
| | - Quanjie Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing, China
| | - Xiaoyu Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing, China
| | - Laixing Hu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing, China
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing, China
| | - Jinming Zhou
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing, China
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Feng Q, Leong WS, Liu L, Chan WI. Peruvoside, a Cardiac Glycoside, Induces Primitive Myeloid Leukemia Cell Death. Molecules 2016; 21:534. [PMID: 27110755 PMCID: PMC6273398 DOI: 10.3390/molecules21040534] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 04/15/2016] [Accepted: 04/20/2016] [Indexed: 01/08/2023] Open
Abstract
Despite the available chemotherapy and treatment, leukemia remains a difficult disease to cure due to frequent relapses after treatment. Among the heterogeneous leukemic cells, a rare population referred as the leukemic stem cell (LSC), is thought to be responsible for relapses and drug resistance. Cardiac glycosides (CGs) have been used in treating heart failure despite its toxicity. Recently, increasing evidence has demonstrated its new usage as a potential anti-cancer drug. Ouabain, one of the CGs, specifically targeted CD34⁺CD38(-) leukemic stem-like cells, but not the more mature CD34⁺CD38⁺ leukemic cells, making this type of compounds a potential treatment for leukemia. In search of other potential anti-leukemia CGs, we found that Peruvoside, a less studied CG, is more effective than Ouabain and Digitoxin at inducing cell death in primitive myeloid leukemia cells without obvious cytotoxicity on normal blood cells. Similar to Ouabain and Digitoxin, Peruvoside also caused cell cycle arrest at G₂/M stage. It up-regulates CDKN1A expression and activated the cleavage of Caspase 3, 8 and PARP, resulting in apoptosis. Thus, Peruvoside showed potent anti-leukemia effect, which may serve as a new anti-leukemia agent in the future.
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Affiliation(s)
- Qian Feng
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China.
| | - Wa Seng Leong
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China.
| | - Liang Liu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China.
| | - Wai-In Chan
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China.
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Dhayakaran R, Neethirajan S, Weng X. Investigation of the antimicrobial activity of soy peptides by developing a high throughput drug screening assay. Biochem Biophys Rep 2016; 6:149-157. [PMID: 28955872 PMCID: PMC5600318 DOI: 10.1016/j.bbrep.2016.04.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Revised: 02/01/2016] [Accepted: 04/04/2016] [Indexed: 01/10/2023] Open
Abstract
Background Antimicrobial resistance is a great concern in the medical community, as well as food industry. Soy peptides were tested against bacterial biofilms for their antimicrobial activity. A high throughput drug screening assay was developed using microfluidic technology, RAMAN spectroscopy, and optical microscopy for rapid screening of antimicrobials and rapid identification of pathogens. Methods Synthesized PGTAVFK and IKAFKEATKVDKVVVLWTA soy peptides were tested against Pseudomonas aeruginosa and Listeria monocytogenes using a microdilution assay. Microfluidic technology in combination with Surface Enhanced RAMAN Spectroscopy (SERS) and optical microscopy was used for rapid screening of soy peptides, pathogen identification, and to visualize the impact of selected peptides. Results The PGTAVFK peptide did not significantly affect P. aeruginosa, although it had an inhibitory effect on L. monocytogenes above a concentration of 625 µM. IKAFKEATKVDKVVVLWTA was effective against both P. aeruginosa and L. monocytogenes above a concentration of 37.2 µM. High throughput drug screening assays were able to reduce the screening and bacterial detection time to 4 h. SERS spectra was used to distinguish the two bacterial species. Conclusions PGTAVFK and IKAFKEATKVDKVVVLWTA soy peptides showed antimicrobial activity against P. aeruginosa and L. monocytogenes. Development of high throughput assays could streamline the drug screening and bacterial detection process. General significance The results of this study show that the antimicrobial properties, biocompatibility, and biodegradability of soy peptides could possibly make them an alternative to the ineffective antimicrobials and antibiotics currently used in the food and medical fields. High throughput drug screening assays could help hasten pre-clinical trials in the medical field. Soy peptide PGTAVFK above 312.5 µM concentrations inhibits Listeria monocytogenes. IKAFKEATKVDKVVVLWTA restricts motility and aggregation of Listeria monocytogenes. Microfluidic 3D device generate multiplex parallel drug concentration gradients. RAMAN spectroscopy microfluidics provides a high throughput drug-screening assay.
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Affiliation(s)
- Rekha Dhayakaran
- Bionano Laboratory, School of Engineering, University of Guelph, Guelph, Canada N1G 2W1
| | - Suresh Neethirajan
- Bionano Laboratory, School of Engineering, University of Guelph, Guelph, Canada N1G 2W1
| | - Xuan Weng
- Bionano Laboratory, School of Engineering, University of Guelph, Guelph, Canada N1G 2W1
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Wen Z, Christian KM, Song H, Ming GL. Modeling psychiatric disorders with patient-derived iPSCs. Curr Opin Neurobiol 2016; 36:118-27. [PMID: 26705693 PMCID: PMC4738077 DOI: 10.1016/j.conb.2015.11.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 11/11/2015] [Accepted: 11/20/2015] [Indexed: 12/22/2022]
Abstract
Psychiatric disorders are heterogeneous disorders characterized by complex genetics, variable symptomatology, and anatomically distributed pathology, all of which present challenges for effective treatment. Current treatments are often blunt tools used to ameliorate the most severe symptoms, often at the risk of disrupting functional neural systems, thus there is a pressing need to develop rational therapeutics. Induced pluripotent stem cells (iPSCs) reprogrammed from patient somatic cells offer an unprecedented opportunity to recapitulate both normal and pathologic human tissue and organ development, and provides new approaches for understanding disease mechanisms and for drug discovery with higher predictability of their effects in humans. Here we review recent progress and challenges in using human iPSCs for modeling neuropsychiatric disorders and developing novel therapeutic strategies.
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Affiliation(s)
- Zhexing Wen
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kimberly M Christian
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hongjun Song
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Guo-li Ming
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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Network and systems biology: essential steps in virtualising drug discovery and development. DRUG DISCOVERY TODAY. TECHNOLOGIES 2015; 15:33-40. [PMID: 26464088 DOI: 10.1016/j.ddtec.2015.07.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 07/06/2015] [Accepted: 07/14/2015] [Indexed: 02/08/2023]
Abstract
The biological processes that keep us healthy or cause disease, as well as the mechanisms of action of possible drugs are inherently complex. In the face of this complexity, attempts at discovering new drugs to treat diseases have alternated between trial-and-error (typically on experimental systems) and grand simplification, usually based on much too little information. We now have the chance to combine these strategies through establishment of 'virtual patient' models, centred on a detailed molecular characterisation of thousands or even, in the future, millions of patients. In doing so, we lay the foundations for truly personalised therapy, as well as a far-reaching virtualisation of drug discovery and development in oncology and other areas of medicine.
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Hong C, Manimaran S, Johnson WE. PathoQC: Computationally Efficient Read Preprocessing and Quality Control for High-Throughput Sequencing Data Sets. Cancer Inform 2015; 13:167-76. [PMID: 25983538 PMCID: PMC4429651 DOI: 10.4137/cin.s13890] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 02/09/2015] [Accepted: 02/12/2015] [Indexed: 01/18/2023] Open
Abstract
Quality control and read preprocessing are critical steps in the analysis of data sets generated from high-throughput genomic screens. In the most extreme cases, improper preprocessing can negatively affect downstream analyses and may lead to incorrect biological conclusions. Here, we present PathoQC, a streamlined toolkit that seamlessly combines the benefits of several popular quality control software approaches for preprocessing next-generation sequencing data. PathoQC provides a variety of quality control options appropriate for most high-throughput sequencing applications. PathoQC is primarily developed as a module in the PathoScope software suite for metagenomic analysis. However, PathoQC is also available as an open-source Python module that can run as a stand-alone application or can be easily integrated into any bioinformatics workflow. PathoQC achieves high performance by supporting parallel computation and is an effective tool that removes technical sequencing artifacts and facilitates robust downstream analysis. The PathoQC software package is available at http://sourceforge.net/projects/PathoScope/.
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Affiliation(s)
- Changjin Hong
- Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA. ; Cytogenetics/Molecular Genetics Laboratory, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Solaiappan Manimaran
- Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA
| | - William Evan Johnson
- Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA
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Zhang JD, Küng E, Boess F, Certa U, Ebeling M. Pathway reporter genes define molecular phenotypes of human cells. BMC Genomics 2015; 16:342. [PMID: 25903797 PMCID: PMC4415216 DOI: 10.1186/s12864-015-1532-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 04/13/2015] [Indexed: 12/21/2022] Open
Abstract
Background The phenotype of a living cell is determined by its pattern of active signaling networks, giving rise to a “molecular phenotype” associated with differential gene expression. Digital amplicon based RNA quantification by sequencing is a useful technology for molecular phenotyping as a novel tool to characterize the state of biological systems. Results We show here that the activity of signaling networks can be assessed based on a set of established key regulators and expression targets rather than the entire transcriptome. We compiled a panel of 917 human pathway reporter genes, representing 154 human signaling and metabolic networks for integrated knowledge- and data-driven understanding of biological processes. The reporter genes are significantly enriched for regulators and effectors covering a wide range of biological processes, and faithfully capture gene-level and pathway-level changes. We apply the approach to iPSC derived cardiomyocytes and primary human hepatocytes to describe changes in molecular phenotype during development or drug response. The reporter genes deliver an accurate pathway-centric view of the biological system under study, and identify known and novel modulation of signaling networks consistent with literature or experimental data. Conclusions A panel of 917 pathway reporter genes is sufficient to describe changes in the molecular phenotype defined by 154 signaling cascades in various human cell types. AmpliSeq-RNA based digital transcript imaging enables simultaneous monitoring of the entire pathway reporter gene panel in up to 150 samples. We propose molecular phenotyping as a useful approach to understand diseases and drug action at the network level. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1532-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jitao David Zhang
- Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Erich Küng
- Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Franziska Boess
- Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Ulrich Certa
- Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Martin Ebeling
- Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Grenzacherstrasse 124, 4070, Basel, Switzerland.
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Neto AI, Correia CR, Oliveira MB, Rial-Hermida MI, Alvarez-Lorenzo C, Reis RL, Mano JF. A novel hanging spherical drop system for the generation of cellular spheroids and high throughput combinatorial drug screening. Biomater Sci 2015. [PMID: 26222417 DOI: 10.1039/c4bm00411f] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We propose a novel hanging spherical drop system for anchoring arrays of droplets of cell suspension based on the use of biomimetic superhydrophobic flat substrates, with controlled positional adhesion and minimum contact with a solid substrate. By facing down the platform, it was possible to generate independent spheroid bodies in a high throughput manner, in order to mimic in vivo tumour models on the lab-on-chip scale. To validate this system for drug screening purposes, the toxicity of the anti-cancer drug doxorubicin in cell spheroids was tested and compared to cells in 2D culture. The advantages presented by this platform, such as feasibility of the system and the ability to control the size uniformity of the spheroid, emphasize its potential to be used as a new low cost toolbox for high-throughput drug screening and in cell or tissue engineering.
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Affiliation(s)
- A I Neto
- 3B's Research Group - Biomaterials, Biodegradables and Biomimetics, University of Minho, AvePark, 4806-90 Taipas, Guimarães, Portugal
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Larman HB, Scott ER, Wogan M, Oliveira G, Torkamani A, Schultz PG. Sensitive, multiplex and direct quantification of RNA sequences using a modified RASL assay. Nucleic Acids Res 2014; 42:9146-57. [PMID: 25063296 PMCID: PMC4132746 DOI: 10.1093/nar/gku636] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
UNLABELLED A sensitive and highly multiplex method to directly measure RNA sequence abundance without requiring reverse transcription would be of value for a number of biomedical applications, including high throughput small molecule screening, pathogen transcript detection and quantification of short/degraded RNAs. R NA A nnealing, S: election and L: igation (RASL) assays, which are based on RNA template-dependent oligonucleotide probe ligation, have been developed to meet this need, but technical limitations have impeded their adoption. Whereas DNA ligase-based RASL assays suffer from extremely low and sequence-dependent ligation efficiencies that compromise assay robustness, Rnl2 can join a fully DNA donor probe to a 3'-diribonucleotide-terminated acceptor probe with high efficiency on an RNA template strand. Rnl2-based RASL exhibits sub-femtomolar transcript detection sensitivity, and permits the rational tuning of probe signals for optimal analysis by massively parallel DNA sequencing (RASL-seq). A streamlined Rnl2-based RASL-seq protocol was assessed in a small molecule screen using 77 probe sets designed to monitor complex human B cell phenotypes during antibody class switch recombination. Our data demonstrate the robustness, cost-efficiency and broad applicability of Rnl2-based RASL assays.
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Affiliation(s)
- H Benjamin Larman
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA California Institute for Biomedical Research (Calibr), La Jolla, CA 92307, USA
| | - Erick R Scott
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA The Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Megan Wogan
- California Institute for Biomedical Research (Calibr), La Jolla, CA 92307, USA
| | - Glenn Oliveira
- The Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ali Torkamani
- The Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037, USA Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Peter G Schultz
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA California Institute for Biomedical Research (Calibr), La Jolla, CA 92307, USA
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45
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Phenotypic screening in cancer drug discovery - past, present and future. Nat Rev Drug Discov 2014; 13:588-602. [PMID: 25033736 DOI: 10.1038/nrd4366] [Citation(s) in RCA: 317] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
There has been a resurgence of interest in the use of phenotypic screens in drug discovery as an alternative to target-focused approaches. Given that oncology is currently the most active therapeutic area, and also one in which target-focused approaches have been particularly prominent in the past two decades, we investigated the contribution of phenotypic assays to oncology drug discovery by analysing the origins of all new small-molecule cancer drugs approved by the US Food and Drug Administration (FDA) over the past 15 years and those currently in clinical development. Although the majority of these drugs originated from target-based discovery, we identified a significant number whose discovery depended on phenotypic screening approaches. We postulate that the contribution of phenotypic screening to cancer drug discovery has been hampered by a reliance on 'classical' nonspecific drug effects such as cytotoxicity and mitotic arrest, exacerbated by a paucity of mechanistically defined cellular models for therapeutically translatable cancer phenotypes. However, technical and biological advances that enable such mechanistically informed phenotypic models have the potential to empower phenotypic drug discovery in oncology.
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46
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Chem-seq permits identification of genomic targets of drugs against androgen receptor regulation selected by functional phenotypic screens. Proc Natl Acad Sci U S A 2014; 111:9235-40. [PMID: 24928520 DOI: 10.1073/pnas.1404303111] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Understanding the mechanisms by which compounds discovered using cell-based phenotypic screening strategies might exert their effects would be highly augmented by new approaches exploring their potential interactions with the genome. For example, altered androgen receptor (AR) transcriptional programs, including castration resistance and subsequent chromosomal translocations, play key roles in prostate cancer pathological progression, making the quest for identification of new therapeutic agents and an understanding of their actions a continued priority. Here we report an approach that has permitted us to uncover the sites and mechanisms of action of a drug, referred to as "SD70," initially identified by phenotypic screening for inhibitors of ligand and genotoxic stress-induced translocations in prostate cancer cells. Based on synthesis of a derivatized form of SD70 that permits its application for a ChIP-sequencing-like approach, referred to as "Chem-seq," we were next able to efficiently map the genome-wide binding locations of this small molecule, revealing that it largely colocalized with AR on regulatory enhancers. Based on these observations, we performed the appropriate global analyses to ascertain that SD70 inhibits the androgen-dependent AR program, and prostate cancer cell growth, acting, at least in part, by functionally inhibiting the Jumonji domain-containing demethylase, KDM4C. Global location of candidate drugs represents a powerful strategy for new drug development by mapping genome-wide location of small molecules, a powerful adjunct to contemporary drug development strategies.
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Abstract
Small molecules that modulate stem cell fate and function offer significant opportunities that will allow the full realization of the therapeutic potential of stem cells. Rational design and screening for small molecules have identified useful compounds to probe fundamental mechanisms of stem cell self-renewal, differentiation, and reprogramming and have facilitated the development of cell-based therapies and therapeutic drugs targeting endogenous stem and progenitor cells for repair and regeneration. Here, we will discuss recent scientific and therapeutic progress, as well as new perspectives and future challenges for using chemical approaches in stem cell biology and regenerative medicine.
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Affiliation(s)
- Wenlin Li
- Department of Cell Biology, Second Military Medical University, Shanghai 200433, China
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48
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Wang Y, Zhan Y, Xu R, Shao R, Jiang J, Wang Z. Src mediates extracellular signal-regulated kinase 1/2 activation and autophagic cell death induced by cardiac glycosides in human non-small cell lung cancer cell lines. Mol Carcinog 2014; 54 Suppl 1:E26-34. [DOI: 10.1002/mc.22147] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 02/04/2014] [Accepted: 02/17/2014] [Indexed: 12/18/2022]
Affiliation(s)
- Yan Wang
- Biochemistry Department; Institute of Medicinal Biotechnology; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing P.R. China
- Pharmacology Department; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing P.R. China
| | - Yuechen Zhan
- Biochemistry Department; Institute of Medicinal Biotechnology; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing P.R. China
| | - Rong Xu
- Biochemistry Department; Institute of Medicinal Biotechnology; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing P.R. China
| | - Rongguang Shao
- Biochemistry Department; Institute of Medicinal Biotechnology; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing P.R. China
| | - Jiandong Jiang
- Biochemistry Department; Institute of Medicinal Biotechnology; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing P.R. China
- Pharmacology Department; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing P.R. China
| | - Zhen Wang
- Biochemistry Department; Institute of Medicinal Biotechnology; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing P.R. China
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49
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Li X, Zhang X, Zhao S, Wang J, Liu G, Du Y. Micro-scaffold array chip for upgrading cell-based high-throughput drug testing to 3D using benchtop equipment. LAB ON A CHIP 2014; 14:471-81. [PMID: 24287736 DOI: 10.1039/c3lc51103k] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Cell-based high throughput drug screening accelerates the pace of drug discovery which is routinely operated on planar high-density multi-well plates with sophisticated robotic liquid-dispensing systems for cell seeding and drug administration. Considerable efforts have been made to upgrade in vitro cellular models from 2D to a more biomimetic 3D configuration. For instance, in anti-cancer drug screening, tumor spheroids are increasingly applied as a gold-standard 3D model exhibiting cellular behaviors and drug responses distinguishable from the 2D counterpart. However, translation of spheroids to high throughput drug screening is challenging since pre-formation of spheroids and subsequent translocation to multi-well plates for drug testing are usually uncontrollable and time/reagent consuming and cell loss is inevitable during medium exchange for drug testing. Here we present an off-the-shelf micro-scaffold array chip which enables high throughput 3D cell culture, drug administration and quantitative in situ assays entirely on the same chip. The sponge-like micro-scaffolds functioned both as absorbents to realize parallel auto-loading of cells or drugs and as barriers to prevent cell loss during medium exchange via centrifugation. Rapid manual loading of cell suspensions or drugs into the 96 isolated micro-scaffolds on the chip was achieved in the timescale of several seconds, meanwhile with total medium consumption reduced to the order of microliters. Proof of concept demonstration of drug cytotoxicity testing was performed on multiple cancer cells using common benchtop equipment, making it accessible to most biomedical labs with basic cell culture setups. Higher cellular drug resistance was constantly obtained with this platform compared to the planar cultures, which was partially attributed to the malignant phenotype of cancer cells yielded by enhanced cell-matrix interactions in the micro-scaffolds. Interestingly, the high drug resistance of 3D cultured cells in the micro-scaffold was shown to be density-independent in contrast to the density-dependent drug response for 2D cultured cells, indicating intrinsic differences between the two culture models. This platform is expected to facilitate upgrade of the current cell-based high throughput drug testing to the 3D level and be widely applicable across various disciplines.
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Affiliation(s)
- Xiaokang Li
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, China.
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50
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Wang Y, Lonard DM, Yu Y, Chow DC, Palzkill TG, Wang J, Qi R, Matzuk AJ, Song X, Madoux F, Hodder P, Chase P, Griffin PR, Zhou S, Liao L, Xu J, O'Malley BW. Bufalin is a potent small-molecule inhibitor of the steroid receptor coactivators SRC-3 and SRC-1. Cancer Res 2014; 74:1506-1517. [PMID: 24390736 DOI: 10.1158/0008-5472.can-13-2939] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Virtually all transcription factors partner with coactivators that recruit chromatin remodeling factors and interact with the basal transcription machinery. Coactivators have been implicated in cancer cell proliferation, invasion, and metastasis, including the p160 steroid receptor coactivator (SRC) family composed of SRC-1 (NCOA1), SRC-2 (TIF2/GRIP1/NCOA2), and SRC-3 (AIB1/ACTR/NCOA3). Given their broad involvement in many cancers, they represent candidate molecular targets for new chemotherapeutics. Here, we report on the results of a high-throughput screening effort that identified the cardiac glycoside bufalin as a potent small-molecule inhibitor for SRC-3 and SRC-1. Bufalin strongly promoted SRC-3 protein degradation and was able to block cancer cell growth at nanomolar concentrations. When incorporated into a nanoparticle delivery system, bufalin was able to reduce tumor growth in a mouse xenograft model of breast cancer. Our work identifies bufalin as a potentially broad-spectrum small-molecule inhibitor for cancer.
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Affiliation(s)
- Ying Wang
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - David M Lonard
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yang Yu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dar-Chone Chow
- Department of Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Timothy G Palzkill
- Department of Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jin Wang
- Department of Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ruogu Qi
- Department of Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alexander J Matzuk
- Department of Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xianzhou Song
- Department of Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Franck Madoux
- Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Peter Hodder
- Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Peter Chase
- Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Patrick R Griffin
- Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Suoling Zhou
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lan Liao
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jianming Xu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bert W O'Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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