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Shi H, Cui W, Qin Y, Chen L, Yu T, Lv J. A glimpse into novel acylations and their emerging role in regulating cancer metastasis. Cell Mol Life Sci 2024; 81:76. [PMID: 38315203 PMCID: PMC10844364 DOI: 10.1007/s00018-023-05104-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 02/07/2024]
Abstract
Metastatic cancer is a major cause of cancer-related mortality; however, the complex regulation process remains to be further elucidated. A large amount of preliminary investigations focus on the role of epigenetic mechanisms in cancer metastasis. Notably, the posttranslational modifications were found to be critically involved in malignancy, thus attracting considerable attention. Beyond acetylation, novel forms of acylation have been recently identified following advances in mass spectrometry, proteomics technologies, and bioinformatics, such as propionylation, butyrylation, malonylation, succinylation, crotonylation, 2-hydroxyisobutyrylation, lactylation, among others. These novel acylations play pivotal roles in regulating different aspects of energy mechanism and mediating signal transduction by covalently modifying histone or nonhistone proteins. Furthermore, these acylations and their modifying enzymes show promise regarding the diagnosis and treatment of tumors, especially tumor metastasis. Here, we comprehensively review the identification and characterization of 11 novel acylations, and the corresponding modifying enzymes, highlighting their significance for tumor metastasis. We also focus on their potential application as clinical therapeutic targets and diagnostic predictors, discussing the current obstacles and future research prospects.
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Affiliation(s)
- Huifang Shi
- Clinical Laboratory, The Rizhao People's Hospital Affiliated to Jining Medical University, No. 126 Taian Road, Rizhao, 276826, Shandong, China
| | - Weigang Cui
- Central Laboratory, The Rizhao People's Hospital Affiliated to Jining Medical University, No. 126 Taian Road, Rizhao, 276826, Shandong, China
| | - Yan Qin
- Clinical Laboratory, The Rizhao People's Hospital Affiliated to Jining Medical University, No. 126 Taian Road, Rizhao, 276826, Shandong, China
| | - Lei Chen
- Clinical Laboratory, The Rizhao People's Hospital Affiliated to Jining Medical University, No. 126 Taian Road, Rizhao, 276826, Shandong, China
| | - Tao Yu
- Center for Regenerative Medicine, Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, No. 16 Jiangsu Road, Qingdao, 266000, China.
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, No. 16 Jiangsu Road, Qingdao, 266000, China.
| | - Jie Lv
- Clinical Laboratory, The Rizhao People's Hospital Affiliated to Jining Medical University, No. 126 Taian Road, Rizhao, 276826, Shandong, China.
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2
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Jia J, Chen J, Wang G, Li M, Zheng Q, Li D. Progress of research into the pharmacological effect and clinical application of the traditional Chinese medicine Rehmanniae Radix. Biomed Pharmacother 2023; 168:115809. [PMID: 37907043 DOI: 10.1016/j.biopha.2023.115809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/18/2023] [Accepted: 10/26/2023] [Indexed: 11/02/2023] Open
Abstract
The traditional Chinese medicine (TCM) Rehmanniae Radix (RR) refers to the fresh or dried root tuber of the plant Rehmannia glutinosa Libosch of the family Scrophulariaceae. As a traditional Chinese herbal medicine (CHM), it possesses multiple effects, including analgesia, sedation, anti-inflammation, antioxidation, anti-tumor, immunomodulation, cardiovascular and cerebrovascular regulation, and nerve damage repair, and it has been widely used in clinical practice. In recent years, scientists have extensively studied the active components and pharmacological effects of RR. Active ingredients mainly include iridoid glycosides (such as catalpol and aucuboside), phenylpropanoid glycosides (such as acteoside), other saccharides, and unsaturated fatty acids. In addition, the Chinese patent medicine (CPM) and Chinese decoction related to RR have also become major research subjects for TCM practitioners; one example is the Bolus of Six Drugs, which includes Rehmannia, Lily Bulb and Rehmannia Decoction, and Siwu Decoction. This article reviews recent literature on RR; summarizes the studies on its chemical constituents, pharmacological effects, and clinical applications; and analyzes the progress and limitations of current investigations to provide reference for further exploration and development of RR.
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Affiliation(s)
- Jinhao Jia
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai 264003, Shandong, PR China
| | - Jianfei Chen
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai 264003, Shandong, PR China
| | - Guoli Wang
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai 264003, Shandong, PR China
| | - Minjing Li
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai 264003, Shandong, PR China
| | - Qiusheng Zheng
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai 264003, Shandong, PR China; Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, School of Pharmacy, Shihezi University, Shihezi 832003 Xinjiang, PR China.
| | - Defang Li
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Integrated Traditional Chinese and Western Medicine, Binzhou Medical University, Yantai 264003, Shandong, PR China; Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, School of Pharmacy, Shihezi University, Shihezi 832003 Xinjiang, PR China.
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3
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Liu J, Liu S, Yu M, Li J, Xie Z, Gao B, Liu Y. Anti-inflammatory effect and mechanism of catalpol in various inflammatory diseases. Drug Dev Res 2023; 84:1376-1394. [PMID: 37534768 DOI: 10.1002/ddr.22096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/21/2023] [Accepted: 07/17/2023] [Indexed: 08/04/2023]
Abstract
Catalpol is a kind of iridoid glucoside, widely found in a variety of plants, mostly extracted from the rhizome of the traditional medicinal herb rehmanniae. It has various biological activities such as anti-inflammatory, antioxidant, and antitumor. The anti-inflammatory effects of catalpol have been demonstrated in a variety of diseases, such as neurological diseases, atherosclerosis, renal diseases, respiratory diseases, digestive diseases, bone and joint diseases, eye diseases, and periodontitis. The purpose of this review is to summarize the existing literature on the anti-inflammatory effects of catalpol in a variety of inflammatory diseases over the last decade and to focus on the anti-inflammatory mechanisms of catalpol.
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Affiliation(s)
- Jinyao Liu
- Department of Endodontics, Hospital of Stomatology, Jilin University, Changchun, China
| | - Shuang Liu
- Department of Endodontics, Hospital of Stomatology, Jilin University, Changchun, China
| | - Mingyue Yu
- Department of Endodontics, Hospital of Stomatology, Jilin University, Changchun, China
| | - Jianing Li
- Department of Endodontics, Hospital of Stomatology, Jilin University, Changchun, China
| | - Zunxuan Xie
- Department of Endodontics, Hospital of Stomatology, Jilin University, Changchun, China
| | - Boyang Gao
- Department of Endodontics, Hospital of Stomatology, Jilin University, Changchun, China
| | - Yuyan Liu
- Department of Endodontics, Hospital of Stomatology, Jilin University, Changchun, China
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4
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Qu J, Li P, Sun Z. Histone lactylation regulates cancer progression by reshaping the tumor microenvironment. Front Immunol 2023; 14:1284344. [PMID: 37965331 PMCID: PMC10641494 DOI: 10.3389/fimmu.2023.1284344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/13/2023] [Indexed: 11/16/2023] Open
Abstract
As a major product of glycolysis and a vital signaling molecule, many studies have reported the key role of lactate in tumor progression and cell fate determination. Lactylation is a newly discovered post-translational modification induced by lactate. On the one hand, lactylation introduced a new era of lactate metabolism in the tumor microenvironment (TME), and on the other hand, it provided a key breakthrough point for elucidation of the interaction between tumor metabolic reprogramming and epigenetic modification. Studies have shown that the lactylation of tumor cells, tumor stem cells and tumor-infiltrating immune cells in TME can participate in the development of cancer through downstream transcriptional regulation, and is a potential and promising tumor treatment target. This review summarized the discovery and effects of lactylation, as well as recent research on histone lactylation regulating cancer progression through reshaping TME. We also focused on new strategies to enhance anti-tumor effects via targeting lactylation. Finally, we discussed the limitations of existing studies and proposed new perspectives for future research in order to further explore lactylation targets. It may provide a new way and direction to improve tumor prognosis.
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Affiliation(s)
- Junxing Qu
- Institutes of Health Central Plains, Xinxiang Medical University, Xinxiang, China
| | - Peizhi Li
- The First People’s Hospital of Xinxiang City, The Fifth Clinical College of Xinxiang Medical University, Xinxiang, China
| | - Zhiheng Sun
- College of Life Science, Institute of Biomedical Science, Henan Normal University, Xinxiang, Henan, China
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Zheng X, Zhao D, Jin Y, Liu Y, Liu D. Role of the NLRP3 inflammasome in gynecological disease. Biomed Pharmacother 2023; 166:115393. [PMID: 37660654 DOI: 10.1016/j.biopha.2023.115393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/20/2023] [Accepted: 08/26/2023] [Indexed: 09/05/2023] Open
Abstract
The NLR family pyrin domain containing 3 (NLRP3) inflammasome is involved in the innate immune system and is a three-part macromolecular complex comprising the NLRP3 protein, apoptosis-associated speck-like protein containing a CARD (ASC) and the cysteine protease pro-caspase-1. When the NLRP3 inflammasome is activated, it can produce interleukin (IL)- 1β and IL-18 and eventually lead to inflammatory cell pyroptosis. Related studies have demonstrated that the NLRP3 inflammasome can induce an immune response and is related to the occurrence and development of gynecological diseases, such as endometriosis, polycystic ovary syndrome and breast cancer. NLRP3 inflammasome inhibitors are beneficial for maintaining cellular homeostasis and tissue health and have been found effective in targeting some gynecological diseases. However, excessive inhibitor concentrations have been found to cause adverse effects. Therefore, proper control of NLRP3 inflammasome activity is critical. This paper summarizes the structure and function of the NLRP3 inflammasome and highlights the therapeutic potential of targeting it in gynecological diseases, such as endometriosis, polycystic ovary syndrome and breast cancer The application of NLRP3 inflammasome inhibitors is also discussed.
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Affiliation(s)
- Xu Zheng
- College of Acupuncture and Massage, Changchun University of Chinese Medicine, Changchun 130117, Jilin, China
| | - Dan Zhao
- College of Acupuncture and Massage, Changchun University of Chinese Medicine, Changchun 130117, Jilin, China
| | - Ye Jin
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun 130117, Jilin, China.
| | - Yang Liu
- Acupuncture department,Affiliated Hospital of Changchun University of Chinese Medicine, Changchun 130117, Jilin, China.
| | - Da Liu
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun 130117, Jilin, China.
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6
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Rong Y, Dong F, Zhang G, Tang M, Zhao X, Zhang Y, Tao P, Cai H. The crosstalking of lactate-Histone lactylation and tumor. Proteomics Clin Appl 2023; 17:e2200102. [PMID: 36853081 DOI: 10.1002/prca.202200102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/17/2023] [Accepted: 02/23/2023] [Indexed: 03/01/2023]
Abstract
Lactate was once considered to be a by-product of energy metabolism, but its unique biological value was only gradually explored with the advent of the Warburg effect. As an end product of glycolysis, lactate can act as a substrate for energy metabolism, a signal transduction molecule, a regulator of the tumor microenvironment and immune cells, and a regulator of the deubiquitination of specific enzymes, and is involved in various biological aspects of tumor regulation, including energy shuttling, growth and invasion, angiogenesis and immune escape. Furthermore, we describe a novel lactate-dependent epigenetic modification, namely histone lactylation modification, and review the progress of its study in tumors, mainly involving the reprogramming of tumor phenotypes, regulation of related gene expression, mediation of the glycolytic process in tumor stem cells (CSCs) and influence on the tumor immune microenvironment. The study of epigenetic regulation of tumor genes by histone modification is still in its infancy, and we expect that by summarizing the effects of lactate and histone modification on tumor and related gene regulation, we will clarify the scientific significance of future histone modification studies and the problems to be solved, and open up new fields for targeted tumor therapy.
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Affiliation(s)
- Yao Rong
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou, China
- General Surgery Clinical Medical Center, Gansu Provincial Hospital, Lanzhou, China
- Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province, Gansu Provincial Hospital, Gansu, China
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou, China
| | - Fengyuan Dong
- Geriatrics Department, Lianyungang First People's Hospital, Lianyugang, China
| | - Guiqian Zhang
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou, China
- General Surgery Clinical Medical Center, Gansu Provincial Hospital, Lanzhou, China
- Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province, Gansu Provincial Hospital, Gansu, China
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou, China
| | - Mingzheng Tang
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou, China
- General Surgery Clinical Medical Center, Gansu Provincial Hospital, Lanzhou, China
- Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province, Gansu Provincial Hospital, Gansu, China
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou, China
| | - Xiashuang Zhao
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou, China
- General Surgery Clinical Medical Center, Gansu Provincial Hospital, Lanzhou, China
- Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province, Gansu Provincial Hospital, Gansu, China
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou, China
| | - Yan Zhang
- Cadre Ward of General Surgery Department, Gansu Provincial Hospital, Lanzhou, China
| | - Pengxian Tao
- Cadre Ward of General Surgery Department, Gansu Provincial Hospital, Lanzhou, China
| | - Hui Cai
- General Surgery Clinical Medical Center, Gansu Provincial Hospital, Lanzhou, China
- Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province, Gansu Provincial Hospital, Gansu, China
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou, China
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Ainembabazi D, Zhang Y, Turchi JJ. The mechanistic role of cardiac glycosides in DNA damage response and repair signaling. Cell Mol Life Sci 2023; 80:250. [PMID: 37584722 PMCID: PMC10432338 DOI: 10.1007/s00018-023-04910-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 08/17/2023]
Abstract
Cardiac glycosides (CGs) are a class of bioactive organic compounds well-known for their application in treating heart disease despite a narrow therapeutic window. Considerable evidence has demonstrated the potential to repurpose CGs for cancer treatment. Chemical modification of these CGs has been utilized in attempts to increase their anti-cancer properties; however, this has met limited success as their mechanism of action is still speculative. Recent studies have identified the DNA damage response (DDR) pathway as a target of CGs. DDR serves to coordinate numerous cellular pathways to initiate cell cycle arrest, promote DNA repair, regulate replication fork firing and protection, or induce apoptosis to avoid the survival of cells with DNA damage or cells carrying mutations. Understanding the modus operandi of cardiac glycosides will provide critical information to better address improvements in potency, reduced toxicity, and the potential to overcome drug resistance. This review summarizes recent scientific findings of the molecular mechanisms of cardiac glycosides affecting the DDR signaling pathway in cancer therapeutics from 2010 to 2022. We focus on the structural and functional differences of CGs toward identifying the critical features for DDR targeting of these agents.
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Affiliation(s)
- Diana Ainembabazi
- Department of Medicine, School of Medicine, Joseph E Walther Hall, Indiana University, 980 W. Walnut St, C560, R3-C560, Indianapolis, IN 46202 USA
| | - Youwei Zhang
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106 USA
| | - John J. Turchi
- Department of Medicine, School of Medicine, Joseph E Walther Hall, Indiana University, 980 W. Walnut St, C560, R3-C560, Indianapolis, IN 46202 USA
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Ndongwe T, Witika BA, Mncwangi NP, Poka MS, Skosana PP, Demana PH, Summers B, Siwe-Noundou X. Iridoid Derivatives as Anticancer Agents: An Updated Review from 1970-2022. Cancers (Basel) 2023; 15. [PMID: 36765728 DOI: 10.3390/cancers15030770] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 01/28/2023] Open
Abstract
The rise of cancer cases has coincided with the urgent need for the development of potent chemical entities and/or modification of existing commodities to improve their efficacy. Increasing evidence suggests that cancer remains one of the leading causes of death globally, with colon cancer cases alone likely to rise exponentially by 2030. The exponential rise in cancer prevalence is largely attributable to the growing change toward a sedentary lifestyle and modern diets, which include genetically modified foods. At present, the prominent treatments for cancer are chemotherapy, surgery, and radiation. Despite slowing cancer progression, these treatments are known to have devastating side effects that may deteriorate the health of the patient, thus, have a low risk-benefit ratio. In addition, many cancer drugs have low bioavailability, thereby limiting their therapeutic effects in cancer patients. Moreover, the drastic rise in the resistance of neoplastic cells to chemotherapeutic agents is rendering the use of some drugs ineffective, thereby signaling the need for more anticancer chemical entities. As a result, the use of natural derivatives as anticancer agents is gaining considerable attention. Iridoids have the potential to form conjugates with other anticancer, antidiabetic, antileishmanial, and antimalarial drugs, which synergistically have the potential to increase their effects. Published studies have identified the role of iridoids, which, if fully explored, may result in cheaper and less toxic alternative/adjuvant cancer drugs. The subject of this article is natural and synthetic iridoid derivatives and their potential therapeutic roles as anticancer agents.
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Fu H, Li W, Weng Z, Huang Z, Liu J, Mao Q, Ding B. Water extract of cacumen platycladi promotes hair growth through the Akt/GSK3β/β-catenin signaling pathway. Front Pharmacol 2023; 14:1038039. [PMID: 36891275 PMCID: PMC9986263 DOI: 10.3389/fphar.2023.1038039] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 02/09/2023] [Indexed: 02/22/2023] Open
Abstract
Cacumen Platycladi (CP) consists of the dried needles of Platycladus orientalis L.) Franco. It was clinically demonstrated that it effectively regenerates hair, but the underlying mechanism remains unknown. Thus, we employed shaved mice to verify the hair growth-promoting capability of the water extract of Cacumen Platycladi (WECP). The morphological and histological analyses revealed that WECP application could significantly promote hair growth and hair follicles (HFs) construction, in comparison to that of control group. Additionally, the skin thickness and hair bulb diameter were significantly increased by the application of WECP in a dose-dependent manner. Besides, the high dose of WECP also showed an effect similar to that of finasteride. In an in vitro assay, WECP stimulated dermal papilla cells (DPCs) proliferation and migration. Moreover, the upregulation of cyclins (cyclin D1, cyclin-dependent kinase 2 (CDK2), and cyclin-dependent kinase 4 (CDK4)) and downregulation of P21 in WECP-treated cell assays have been evaluated. We identified the ingredients of WECP using ultra-high-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q/TOF-MS) and endeavored to predict their relevant molecular mechanisms by network analysis. We found that the Akt (serine/threonine protein kinase) signaling pathway might be a crucial target of WECP. It has been demonstrated that WECP treatment activated the phosphorylation of Akt and glycogen synthase kinase-3-beta (GSK3β), promoted β-Catenin and Wnt10b accumulation, and upregulated the expression of lymphoid enhancer-binding factor 1 (LEF1), vascular endothelial growth factor (VEGF), and insulin-like growth factor 1 (IGF1). We also found that WECP significantly altered the expression levels of apoptosis-related genes in mouse dorsal skin. The enhancement capability of WECP on DPCs proliferation and migration could be abrogated by the Akt-specific inhibitor MK-2206 2HCl. These results suggested that WECP might promote hair growth by modulating DPCs proliferation and migration through the regulation of the Akt/GSK3β/β-Catenin signaling pathway.
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Affiliation(s)
- Hangjie Fu
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou, China.,Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Wenxia Li
- The Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China
| | - Zhiwei Weng
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou, China.,Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Zhiguang Huang
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou, China.,Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jinyuan Liu
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou, China.,Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Qingqing Mao
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou, China.,Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Bin Ding
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou, China.,Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, China
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10
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Agapito G, Milano M, Cannataro M. A Python Clustering Analysis Protocol of Genes Expression Data Sets. Genes (Basel) 2022; 13:genes13101839. [PMID: 36292724 PMCID: PMC9601308 DOI: 10.3390/genes13101839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/05/2022] [Accepted: 10/08/2022] [Indexed: 11/16/2022] Open
Abstract
Gene expression and SNPs data hold great potential for a new understanding of disease prognosis, drug sensitivity, and toxicity evaluations. Cluster analysis is used to analyze data that do not contain any specific subgroups. The goal is to use the data itself to recognize meaningful and informative subgroups. In addition, cluster investigation helps data reduction purposes, exposes hidden patterns, and generates hypotheses regarding the relationship between genes and phenotypes. Cluster analysis could also be used to identify bio-markers and yield computational predictive models. The methods used to analyze microarrays data can profoundly influence the interpretation of the results. Therefore, a basic understanding of these computational tools is necessary for optimal experimental design and meaningful data analysis. This manuscript provides an analysis protocol to effectively analyze gene expression data sets through the K-means and DBSCAN algorithms. The general protocol enables analyzing omics data to identify subsets of features with low redundancy and high robustness, speeding up the identification of new bio-markers through pathway enrichment analysis. In addition, to demonstrate the effectiveness of our clustering analysis protocol, we analyze a real data set from the GEO database. Finally, the manuscript provides some best practice and tips to overcome some issues in the analysis of omics data sets through unsupervised learning.
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Affiliation(s)
- Giuseppe Agapito
- Department of Law, Economics and Social Sciences, University Magna Græcia of Catanzaro, 88100 Catanzaro, Italy
- Data Analytics Research Center, University Magna Græcia of Catanzaro, 88100 Catanzaro, Italy
- Correspondence:
| | - Marianna Milano
- Data Analytics Research Center, University Magna Græcia of Catanzaro, 88100 Catanzaro, Italy
- Department of Medical and Clinical Surgery, University Magna Græcia of Catanzaro, 88100 Catanzaro, Italy
| | - Mario Cannataro
- Data Analytics Research Center, University Magna Græcia of Catanzaro, 88100 Catanzaro, Italy
- Department of Medical and Clinical Surgery, University Magna Græcia of Catanzaro, 88100 Catanzaro, Italy
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