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Huang X, Wu B, Zhang F, Chen F, Zhang Y, Guo H, Zhang H. Epigenetic Biomarkers Screening of Non-Coding RNA and DNA Methylation Based on Peripheral Blood Monocytes in Smokers. Front Genet 2022; 13:766553. [PMID: 35233217 PMCID: PMC8882369 DOI: 10.3389/fgene.2022.766553] [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: 11/11/2021] [Accepted: 01/17/2022] [Indexed: 11/13/2022] Open
Abstract
This study aims to use bioinformatics methods to determine the epigenetic changes in microRNA expression and DNA methylation caused by cigarette smoking. The data of mRNA, miRNA expression, and methylation microarray were obtained from the GEO database to filter differentially expressed genes (DEGs), differentially expressed miRNAs (DEMs), and methylated CpG probes (DMPs) through the limma package. The R clusterProfile package was used for functional annotation and enrichment analysis. The protein-protein interaction (PPI) network was constructed by the String database and visualized in Cytoscape software. Starbase database was employed to predict lncRNA and CirRNA based on the sequence of miRNA, and to establish a regulatory network of ceRNA. By overlapping DEG and DEM, 107 down-miRNA-targeted up-regulated genes and 65 up-miRNA-target down-regulated genes were obtained, which were mainly enriched in autophagy signaling pathways and protein ubiquitination pathways, respectively. In addition, 324 genes with low methylation and high expression and 204 genes with high methylation and low expression were respectively related to the degeneration of the nervous system and the function of the cardiovascular system. Interestingly, 43 genes were up-regulated under the dual regulation of reduced miRNA and hypomethylation, while 14 genes were down-regulated under the dual regulation of increased miRNA and hypermethylation. Ten chemicals have been identified as putative therapeutic agents for pathological conditions caused by smoking. In addition, among these genes, HSPA4, GRB2, PRKCA, and BCL2L1 could play a fundamental role in related diseases caused by smoking and may be used as the biomarkers for precise diagnosis and targets for future therapies of smoking-related diseases.
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Affiliation(s)
- Xiaowei Huang
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Bian Wu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Fangxue Zhang
- Knee Surgery Department of the Institute of Sports Medicine, Beijing Key Laboratory of Sports Injuries, Peking University Third Hospital, Peking University, Beijing, China
| | - Fancheng Chen
- Department of Orthopaedics, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yong Zhang
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Huizhi Guo
- The First Institute of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Hongtao Zhang
- Department of Orthopedics, The First Affiliated Hospital of Soochow University, Suzhou, China
- *Correspondence: Hongtao Zhang,
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2
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Zhang R, Wei Y, Li M, Cai M, Gu R, Ma Y, Chen L, Wang J. Melanogenesis effects of rice protein hydrolysate and its characteristic peptides Leu-Leu-Lys, Leu-Pro-Lys, and pyroGlu-Lys on UVB-induced human epidermal melanocyte cells. Food Funct 2021; 11:8757-8767. [PMID: 32955075 DOI: 10.1039/d0fo01808b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This study assessed the melanogenesis effects of rice protein hydrolysate (RPH) and explored the underlying molecular mechanism of its characteristic peptides. In this investigation, human epidermal melanocyte (PIG1) cells were used to establish a UVB-induced model to evaluate the effect of RPH on melanin content, tyrosinase activity, and reactive oxygen species (ROS) levels. High performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) was employed to identify the peptide composition (2-4 amino acids) in RPH. Enzymatic hydrolysis was employed to screen the characteristic peptides Leu-Leu-Lys (LLK), Leu-Pro-Lys (LPK), and pyroGlu-Lys (pEK), while their effect on the molecular mechanism involved in the melanin synthesis process was further explored using quantitative real-time polymerase chain reaction (PCR) and western blotting. The results indicated that RPH reduced the melanin content, tyrosinase activity, and ROS production in PIG1 cells. The selected peptides LLK, LPK, and pEK from RPH reduced the expression of tyrosinase-related protein 1 (TRP-1) and tyrosinase-related protein 2 (TRP-2) and affected melanin synthesis by regulating the JNK/β-Trcp/NFκB-p65/MITF signaling pathway at the mRNA and protein levels. This study shows that RPH plays a vital role in the melanogenesis process, therefore, providing a theoretical basis for the use of RPH as a novel additive product.
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Affiliation(s)
- Ruixue Zhang
- Beijing Engineering Research Center of Protein & Functional Peptides, China National Research Institute of Food and Fermentation Industries, Beijing 100015, PR China.
| | - Ying Wei
- Beijing Engineering Research Center of Protein & Functional Peptides, China National Research Institute of Food and Fermentation Industries, Beijing 100015, PR China.
| | - Mingliang Li
- Beijing Engineering Research Center of Protein & Functional Peptides, China National Research Institute of Food and Fermentation Industries, Beijing 100015, PR China.
| | - Muyi Cai
- Beijing Engineering Research Center of Protein & Functional Peptides, China National Research Institute of Food and Fermentation Industries, Beijing 100015, PR China.
| | - Ruizeng Gu
- Beijing Engineering Research Center of Protein & Functional Peptides, China National Research Institute of Food and Fermentation Industries, Beijing 100015, PR China.
| | - Yong Ma
- Beijing Engineering Research Center of Protein & Functional Peptides, China National Research Institute of Food and Fermentation Industries, Beijing 100015, PR China.
| | - Liang Chen
- Beijing Engineering Research Center of Protein & Functional Peptides, China National Research Institute of Food and Fermentation Industries, Beijing 100015, PR China.
| | - Jing Wang
- Beijing Engineering Research Center of Protein & Functional Peptides, China National Research Institute of Food and Fermentation Industries, Beijing 100015, PR China.
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Zheng F, Guo J, Khan AJ, Miao P, Zhang F. Coassemble dopamine and GHK tripeptide into fluorescent nanoparticles for pH sensing. LUMINESCENCE 2020; 36:28-34. [PMID: 32598511 DOI: 10.1002/bio.3907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 12/12/2022]
Abstract
Fluorescent nanostructures have been widely applied to biomedical researches and clinical diagnosis such as biolabeling/imaging/sensing and have even acted as therapy reagents. Peptide-based fluorescent nanostructures attract recent interest from biomedical researchers. Inspired by the natural existence of GHK-Cu complex with a growth factor-like effect in human blood, here we have developed a novel approach for designing nanosensors through the co-assembling of two kinds of biomolecules. By making best use of both π-π stacking between carbon rings and the easy-oxidation property of an important transmitter molecule, dopamine (DA), we successfully built up a supersensitive and robust fluorescent pH nanosensor by co-assembling oxidized DA (DAox ) with a tripeptide GHK. The GHK-DAox nanostructures have a quantum yield of 20.82%, which might be the brightest one among all the current co-assembling structures merely through unmodified biomolecules. We envision this approach could open a new avenue for not only hybrid nanostructure construction, but also may inspire the bioengineering of in vivo luminescent probes.
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Affiliation(s)
- Fan Zheng
- Biomedical Nanocenter, School of Life Science, Inner Mongolia Agricultural University, 29 East Erdos Street, Hohhot, P. R. China
| | - Jun Guo
- Terahertz Technology Innovation Research Institute, Shanghai Key Laboratory of Modern Optical System, Terahertz Science Cooperative Innovation Center, University of Shanghai for Science and Technology, 516 Jungong Road, Shanghai, P. R. China
| | - Abdul Jamil Khan
- Biomedical Nanocenter, School of Life Science, Inner Mongolia Agricultural University, 29 East Erdos Street, Hohhot, P. R. China
| | - Pandeng Miao
- Biomedical Nanocenter, School of Life Science, Inner Mongolia Agricultural University, 29 East Erdos Street, Hohhot, P. R. China.,Terahertz Technology Innovation Research Institute, Shanghai Key Laboratory of Modern Optical System, Terahertz Science Cooperative Innovation Center, University of Shanghai for Science and Technology, 516 Jungong Road, Shanghai, P. R. China
| | - Feng Zhang
- Biomedical Nanocenter, School of Life Science, Inner Mongolia Agricultural University, 29 East Erdos Street, Hohhot, P. R. China.,State Key Laboratory of Respiratory Disease, Key Laboratory of Oral Medicine, Guangzhou Institute of Oral Disease, Stomatology Hospital, Department of Biomedical Engineering, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
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Identification of an Ultra-Short Peptide with Potent Pseudomonas aeruginosa Activity for Development as a Topical Antibacterial Agent. Int J Pept Res Ther 2018. [DOI: 10.1007/s10989-018-9678-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Screening for a Potent Antibacterial Peptide to Treat Mupirocin-Resistant MRSA Skin Infections. Int J Pept Res Ther 2017. [DOI: 10.1007/s10989-017-9580-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Ng SMS, Yap YYA, Cheong JWD, Ng FM, Lau QY, Barkham T, Teo JWP, Hill J, Chia CSB. Antifungal peptides: a potential new class of antifungals for treating vulvovaginal candidiasis caused by fluconazole-resistant Candida albicans. J Pept Sci 2017; 23:215-221. [PMID: 28105725 DOI: 10.1002/psc.2970] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Revised: 12/14/2016] [Accepted: 12/23/2016] [Indexed: 11/06/2022]
Abstract
Vulvovaginal candidiasis/candidosis is a common fungal infection afflicting approximately 75% of women globally caused primarily by the yeast Candida albicans. Fluconazole is widely regarded as the antifungal drug of choice since its introduction in 1990 due to its high oral bioavailability, convenient dosing regimen and favourable safety profile. However, its widespread use has led to the emergence of fluconazole-resistant C. albicans, posing a universal clinical concern. Coupled to the dearth of new antifungal drugs entering the market, it is imperative to introduce new drug classes to counter this threat. Antimicrobial peptides (AMPs) are potential candidates due to their membrane-disrupting mechanism of action. By specifically targeting fungal membranes and being rapidly fungicidal, they can reduce the chances of resistance development and treatment duration. Towards this goal, we conducted a head-to-head comparison of 61 short linear AMPs from the literature to identify the peptide with the most potent activity against fluconazole-resistant C. albicans. The 11-residue peptide, P11-6, was identified and assayed against a panel of clinical C. albicans isolates followed by fungicidal/static determination and a time-kill assay to gauge its potential for further drug development. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.
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Affiliation(s)
- Siew Mei Samantha Ng
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #03-01, 138669, Singapore
| | - Yi Yong Alvin Yap
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #03-01, 138669, Singapore
| | - Jin Wei Darryl Cheong
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #03-01, 138669, Singapore
| | - Fui Mee Ng
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #03-01, 138669, Singapore
| | - Qiu Ying Lau
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #03-01, 138669, Singapore
| | - Timothy Barkham
- Department of Laboratory Medicine, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, 308433, Singapore
| | - Jeanette Woon Pei Teo
- Department of Laboratory Medicine, National University Hospital, 5 Lower Kent Ridge Road, 119074, Singapore
| | - Jeffrey Hill
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #03-01, 138669, Singapore
| | - Cheng San Brian Chia
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #03-01, 138669, Singapore
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Kukowska M, Pikuła M, Kukowska-Kaszuba M, Schumacher A, Dzierzbicka K, Trzonkowski P. Synthetic lipopeptides as potential topical therapeutics in wound and skin care: in vitro studies of permeation and skin cells behaviour. RSC Adv 2016. [DOI: 10.1039/c6ra24424f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Wound healing is an extraordinarily complicated process associating with the cell aging, slowing down of cell renewal mechanism and even loss of protective function to environmentally induced oxidative stress.
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Affiliation(s)
- Monika Kukowska
- Department of Organic Chemistry
- Faculty of Chemistry
- Gdansk University of Technology
- 80-233 Gdańsk
- Poland
| | - Michał Pikuła
- Department of Clinical Immunology and Transplantology
- Faculty of Medicine
- Medical University of Gdansk
- 80-211 Gdańsk
- Poland
| | | | - Adriana Schumacher
- Department of Clinical Immunology and Transplantology
- Faculty of Medicine
- Medical University of Gdansk
- 80-211 Gdańsk
- Poland
| | - Krystyna Dzierzbicka
- Department of Organic Chemistry
- Faculty of Chemistry
- Gdansk University of Technology
- 80-233 Gdańsk
- Poland
| | - Piotr Trzonkowski
- Department of Clinical Immunology and Transplantology
- Faculty of Medicine
- Medical University of Gdansk
- 80-211 Gdańsk
- Poland
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