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Su C, Su C, Zheng C. Identifying a Ubiquitinated Adaptor Protein by a Viral E3 Ligase Through Co-immunoprecipitation. Methods Mol Biol 2025; 2854:35-40. [PMID: 39192116 DOI: 10.1007/978-1-0716-4108-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Abstract
Co-immunoprecipitation is a technique widely utilized to isolate protein complexes and study protein-protein interactions. Ubiquitinated proteins could be identified by combining co-immunoprecipitation with SDS-PAGE followed by immunoblotting. In this chapter, we use Herpes Simplex Virus 1 immediate-early protein ICP0-mediated polyubiquitination of p50 as an example to describe the method to identify a ubiquitinated adaptor protein by a viral E3 ligase by co-immunoprecipitation.
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Affiliation(s)
- Chenhe Su
- State Key Laboratory of Antiviral Drugs, Pingyuan Laboratory, NMPA Key Laboratory for Research and Evaluation of Innovative Drug, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan, China
| | - Chenhao Su
- Department of Nephrology and Rheumatology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Chunfu Zheng
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
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2
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Su C, Su C, Zheng C. Identifying an Abnormal Phosphorylated Adaptor by Viral Kinase Using Mass Spectrometry. Methods Mol Biol 2025; 2854:29-34. [PMID: 39192115 DOI: 10.1007/978-1-0716-4108-8_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Abstract
Mass spectrometers are widely used to identify protein phosphorylation sites. The process usually involves selective isolation of phosphoproteins and subsequent fragmentation to identify both the peptide sequence and phosphorylation site. Immunoprecipitation could capture and purify the protein of interest, greatly reducing sample complexity before submitting it for mass spectrometry analysis. This chapter describes a method to identify an abnormal phosphorylated site of the adaptor protein by a viral kinase through immunoprecipitation followed by LC-MS/MS.
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Affiliation(s)
- Chenhe Su
- State Key Laboratory of Antiviral Drugs, Pingyuan Laboratory, NMPA Key Laboratory for Research and Evaluation of Innovative Drug, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan, China
| | - Chenhao Su
- Department of Nephrology and Rheumatology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Chunfu Zheng
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
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3
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Akbarzadeh S, Coşkun Ö, Günçer B. Studying protein-protein interactions: Latest and most popular approaches. J Struct Biol 2024; 216:108118. [PMID: 39214321 DOI: 10.1016/j.jsb.2024.108118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 08/20/2024] [Accepted: 08/23/2024] [Indexed: 09/04/2024]
Abstract
PPIs, or protein-protein interactions, are essential for many biological processes. According to the findings, abnormal PPIs have been linked to several diseases, such as cancer and infectious and neurological disorders. Consequently, focusing on PPIs is a path toward disease treatment and a crucial tool for producing novel medications. Many methods exist to investigate PPIs, including low- and high-throughput studies. Since many PPIs have been discovered using in vitro and in vivo experimental approaches, the use of computational methods to predict PPIs has grown as a result of the expanding scale of PPI data and the intrinsic complexity of interacting mechanisms. Recognizing PPI networks offers a systematic means of predicting protein functions, and pathways that they are included. These investigations can help uncover the underlying molecular mechanisms of complex phenotypes and clarify the biological processes related to health and diseases. Therefore, our goal in this study is to provide an overview of the latest and most popular approaches for investigating PPIs. We also overview some important clinical approaches carried out based on the PPIs and how these interactions can be targeted.
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Affiliation(s)
- Sama Akbarzadeh
- Department of Biophysics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Türkiye; Institute of Graduate Studies in Health Sciences, Istanbul University, Istanbul, Türkiye
| | - Özlem Coşkun
- Department of Biophysics, Faculty of Medicine, Çanakkale Onsekiz Mart University, Çanakkale, Türkiye
| | - Başak Günçer
- Department of Biophysics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Türkiye.
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4
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Du J, Liu W, Li M, Li Z, Li X, Dai Y, Liu G, Wang X, Zhu P, Gladyshev VN, Zhou X. Comparative time-series multi-omics analyses suggest H1.2 involvement in anoxic adaptation and cancer resistance. PLoS Biol 2024; 22:e3002778. [PMID: 39178313 DOI: 10.1371/journal.pbio.3002778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 07/31/2024] [Indexed: 08/25/2024] Open
Abstract
The naked mole rat (NMR), Heterocephalus glaber, is known as the longest-lived rodent and is extraordinarily resistant to hypoxia and cancer. Here, both NMR embryonic fibroblasts (NEFs) and their mouse counterparts (MEFs) were subjected to anoxic conditions (0% O2, 5% CO2). A combination of comparative transcriptomics and proteomics was then employed to identify differentially expressed genes (DEGs). Notably, we observed distinct levels of histone H1.2 (encoded by HIST1H1C) accumulation between NEFs and MEFs. Subsequent mechanistic analyses showed that higher H1.2 expression in NEFs was associated with the lower expression of its inhibitor, PARP1. Additionally, we discovered that H1.2 can directly interact with HIF-1α PAS domains, thereby promoting the expression of HIF-1α through facilitating the dimerization with HIF-1β. The overexpression of H1.2 was also found to trigger autophagy and to suppress the migration of cancer cells, as well as the formation of xenograft tumors, via the NRF2/P62 signaling pathway. Moreover, an engineered H1.2 knock-in mouse model exhibited significantly extended survival in hypoxic conditions (4% O2) and showed a reduced rate of tumor formation. Collectively, our results indicate a potential mechanistic link between H1.2 and the dual phenomena of anoxic adaptation and cancer resistance.
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Affiliation(s)
- Juan Du
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chaoyang District, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Weiqiang Liu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chaoyang District, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Meng Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chaoyang District, Beijing, China
| | - Zihao Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chaoyang District, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xuanjing Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chaoyang District, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yichen Dai
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chaoyang District, Beijing, China
| | - Gaoming Liu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chaoyang District, Beijing, China
| | - Xiao Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chaoyang District, Beijing, China
| | - Pingfen Zhu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chaoyang District, Beijing, China
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Xuming Zhou
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chaoyang District, Beijing, China
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5
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Gao Q, Zhang C, Li M, Yu T. Protein-Protein Interaction Prediction Model Based on ProtBert-BiGRU-Attention. J Comput Biol 2024. [PMID: 39069885 DOI: 10.1089/cmb.2023.0297] [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: 07/30/2024] Open
Abstract
The physiological activities within cells are mainly regulated through protein-protein interactions (PPI). Therefore, studying protein interactions has become an essential part of researching protein function and mechanisms. Traditional biological experiments required for PPI prediction are expensive and time consuming. For this reason, many methods based on predicting PPI from protein sequences have been proposed in recent years. However, existing computational methods usually require the combination of evolutionary feature information of proteins to predict PPI docking situations. Because different relevant features of selected proteins are chosen, there may be differences in the predicted results for PPI. This article proposes a PPI prediction method based on the pretrained protein sequence model ProtBert, combined with the Bidirectional Gated Recurrent Unit (BiGRU) and attention mechanism. Only using protein sequence information and leveraging ProtBert's powerful ability to capture amino acid feature information, BiGRU is used for further feature extraction of the amino acid vectors output by ProtBert. The attention mechanism is then applied to enhance the focus on different amino acid features and improve the expression ability of protein sequence features, ultimately obtaining binary classification results for protein interactions. Experimental results show that our proposed ProtBert-BiGRU-Attention model has good predictive performance for PPI. Through relevant comparative experiments, it has been proven that our model performs well in protein binary prediction. Furthermore, through the ablation experiment of the model, different deep learning modules' contributions to the prediction have been demonstrated.
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Affiliation(s)
- Qian Gao
- College of Computer and Control Engineering, Qiqihar University, Qiqihar, China
| | - Chi Zhang
- College of Computer and Control Engineering, Qiqihar University, Qiqihar, China
| | - Ming Li
- College of Computer and Control Engineering, Qiqihar University, Qiqihar, China
| | - Tianfei Yu
- College of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar, China
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6
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Liao Y, Peng X, Yang Y, Zhou G, Chen L, Yang Y, Li H, Chen X, Guo S, Zuo Q, Zou J. Exploring ABHD5 as a Lipid-Related Biomarker in Idiopathic Pulmonary Fibrosis: Integrating Machine Learning, Bioinformatics, and In Vitro Experiments. Inflammation 2024:10.1007/s10753-024-02107-1. [PMID: 39046603 DOI: 10.1007/s10753-024-02107-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 07/14/2024] [Accepted: 07/16/2024] [Indexed: 07/25/2024]
Abstract
Recent studies increasingly suggest a connection between lipids and idiopathic pulmonary fibrosis (IPF). This study was aimed at exploring potential lipid-related biomarkers for IPF and uncovering the mechanisms underlying pulmonary fibrosis. IPF-related datasets were retrieved from the GEO database, and the ComBat algorithm was used to merge multiple datasets and eliminate batch effects. Weighted gene co-expression network analysis (WGCNA) was utilized to identify modules and genes associated with IPF. Potential hub genes were determined by intersecting these genes with lipid-related genes from the GeneCards database. A machine learning-based integrative approach was developed to construct diagnostic and prognostic signatures, which were validated across several datasets. Additionally, single-cell sequencing data was used to validate the expression differences of core IPF-related genes across various cell types. The effect of ABHD5 on fibroblasts was assessed using the cell counting kit-8, 5-ethynyl-2'-deoxyuridine, and cell scratch assays. The expression levels of fibrotic factors were measured using real-time quantitative polymerase chain reaction and western blot analysis. WGCNA identified a red module potentially related to IPF, and the intersection with lipid-related genes yielded 51 hub genes. These genes were used to build diagnostic and prognostic models that demonstrated robust validation capabilities across multiple datasets. Single-cell sequencing analysis revealed low expression of ABHD5 in the lung tissues of IPF patients, with a higher proportion of fibroblasts exhibiting low ABHD5 expression. Cell experiments showed that under the influence of TGF-β1, knockdown of ABHD5 slightly promoted fibroblast proliferation. Additionally, fibroblasts with low ABHD5 expression exhibited enhanced migratory capabilities and secreted more fibrotic factors. Lipid-related diagnostic and prognostic models for IPF were developed, and ABHD5 may serve as a potential biomarker. Low ABHD5 expression could potentially accelerate the progression of pulmonary fibrosis.
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Affiliation(s)
- Yi Liao
- Department of Respiratory and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Xiaying Peng
- Department of Respiratory and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yan Yang
- Department of Respiratory and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Guanghong Zhou
- Department of Respiratory and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Lijuan Chen
- Department of Respiratory and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yang Yang
- Department of Respiratory and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Hongyan Li
- Department of Respiratory and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Xianxia Chen
- Department of Respiratory and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Shujin Guo
- Department of Health Management &, Institute of Health Management, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Qiunan Zuo
- Department of Geriatric Respiratory, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Jun Zou
- Department of Respiratory and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China.
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Tian H, Tang L, Yang Z, Xiang Y, Min Q, Yin M, You H, Xiao Z, Shen J. Current understanding of functional peptides encoded by lncRNA in cancer. Cancer Cell Int 2024; 24:252. [PMID: 39030557 PMCID: PMC11265036 DOI: 10.1186/s12935-024-03446-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 07/09/2024] [Indexed: 07/21/2024] Open
Abstract
Dysregulated gene expression and imbalance of transcriptional regulation are typical features of cancer. RNA always plays a key role in these processes. Human transcripts contain many RNAs without long open reading frames (ORF, > 100 aa) and that are more than 200 bp in length. They are usually regarded as long non-coding RNA (lncRNA) which play an important role in cancer regulation, including chromatin remodeling, transcriptional regulation, translational regulation and as miRNA sponges. With the advancement of ribosome profiling and sequencing technologies, increasing research evidence revealed that some ORFs in lncRNA can also encode peptides and participate in the regulation of multiple organ tumors, which undoubtedly opens a new chapter in the field of lncRNA and oncology research. In this review, we discuss the biological function of lncRNA in tumors, the current methods to evaluate their coding potential and the role of functional small peptides encoded by lncRNA in cancers. Investigating the small peptides encoded by lncRNA and understanding the regulatory mechanisms of these functional peptides may contribute to a deeper understanding of cancer and the development of new targeted anticancer therapies.
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Affiliation(s)
- Hua Tian
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy and Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
- School of Nursing, Chongqing College of Humanities, Science & Technology, Chongqing, China
| | - Lu Tang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy and Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Zihan Yang
- Department of Pathology, The Affiliated Hospital of Southwest Medical University, Luzhou, China, 646000
| | - Yanxi Xiang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy and Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Qi Min
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy and Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Mengshuang Yin
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy and Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Huili You
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy and Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Zhangang Xiao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China.
- Cell Therapy and Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China.
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China.
- Gulin Traditional Chinese Medicine Hospital, Luzhou, China.
- Department of Pharmacology, School of Pharmacy, Sichuan College of Traditional Chinese Medicine, Mianyang, China.
| | - Jing Shen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China.
- Cell Therapy and Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China.
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China.
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Clayworth K, Gilbert M, Auld V. Cell Biology Techniques for Studying Drosophila Peripheral Glial Cells. Cold Spring Harb Protoc 2024; 2024:pdb.top108159. [PMID: 37399179 DOI: 10.1101/pdb.top108159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
Glial cells are essential for the proper development and functioning of the peripheral nervous system (PNS). The ability to study the biology of glial cells is therefore critical for our ability to understand PNS biology and address PNS maladies. The genetic and proteomic pathways underlying vertebrate peripheral glial biology are understandably complex, with many layers of redundancy making it sometimes difficult to study certain facets of PNS biology. Fortunately, many aspects of vertebrate peripheral glial biology are conserved with those of the fruit fly, Drosophila melanogaster With simple and powerful genetic tools and fast generation times, Drosophila presents an accessible and versatile model for studying the biology of peripheral glia. We introduce here three techniques for studying the cell biology of peripheral glia of Drosophila third-instar larvae. With fine dissection tools and common laboratory reagents, third-instar larvae can be dissected, with extraneous tissues removed, revealing the central nervous system (CNS) and PNS to be processed using a standard immunolabeling protocol. To improve the resolution of peripheral nerves in the z-plane, we describe a cryosectioning method to achieve 10- to 20-µm thick coronal sections of whole larvae, which can then be immunolabeled using a modified version of standard immunolabeling techniques. Finally, we describe a proximity ligation assay (PLA) for detecting close proximity between two proteins-thus inferring protein interaction-in vivo in third-instar larvae. These methods, further described in our associated protocols, can be used to improve our understanding of Drosophila peripheral glia biology, and thus our understanding of PNS biology.
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Affiliation(s)
- Katherine Clayworth
- Department of Zoology, Cell and Developmental Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Mary Gilbert
- Department of Zoology, Cell and Developmental Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Vanessa Auld
- Department of Zoology, Cell and Developmental Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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Song D, Wang Q, Yan Z, Su M, Zhang H, Shi L, Fan Y, Zhang Q, Yang H, Zhang D, Liu Q. METTL3 promotes the progression of osteosarcoma through the N6-methyladenosine modification of MCAM via IGF2BP1. Biol Direct 2024; 19:44. [PMID: 38849910 PMCID: PMC11157866 DOI: 10.1186/s13062-024-00486-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 05/29/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND The molecular mechanisms of osteosarcoma (OS) are complex. In this study, we focused on the functions of melanoma cell adhesion molecule (MCAM), methyltransferase 3 (METTL3) and insulin like growth factor 2 mRNA binding protein 1 (IGF2BP1) in OS development. METHODS qRT-PCR assay and western blot assay were performed to determine mRNA and protein expression of MCAM, METTL3, IGF2BP1 and YY1. MTT assay and colony formation assay were conducted to assess cell proliferation. Cell apoptosis, invasion and migration were evaluated by flow cytometry analysis, transwell assay and wound-healing assay, respectively. Methylated RNA Immunoprecipitation (MeRIP), dual-luciferase reporter, Co-IP, RIP and ChIP assays were performed to analyze the relationships of MCAM, METTL3, IGF2BP1 and YY1. The functions of METTL3 and MCAM in tumor growth were explored through in vivo experiments. RESULTS MCAM was upregulated in OS, and MCAM overexpression promoted OS cell growth, invasion and migration and inhibited apoptosis. METTL3 and IGF2BP1 were demonstrated to mediate the m6A methylation of MCAM. Functionally, METTL3 or IGF2BP1 silencing inhibited OS cell progression, while MCAM overexpression ameliorated the effects. Transcription factor YY1 promoted the transcription level of METTL3 and regulated METTL3 expression in OS cells. Additionally, METTL3 deficiency suppressed tumor growth in vivo, while MCAM overexpression abated the effect. CONCLUSION YY1/METTL3/IGF2BP1/MCAM axis aggravated OS development, which might provide novel therapy targets for OS.
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Affiliation(s)
- Dongjian Song
- Department of Pediatric Surgery, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou, 450052, China.
- Institute of Molecular Cancer Surgery, Henan Province Engineering Research Center, Zhengzhou University, Zhengzhou, 450052, China.
| | - Qi Wang
- Department of Pediatric Surgery, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou, 450052, China
| | - Zechen Yan
- Institute of Molecular Cancer Surgery, Henan Province Engineering Research Center, Zhengzhou University, Zhengzhou, 450052, China
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Meng Su
- Department of Pediatric Surgery, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou, 450052, China
| | - Hui Zhang
- Department of Pediatric Surgery, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou, 450052, China
| | - Longyan Shi
- Department of Pediatric Surgery, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou, 450052, China
| | - Yingzhong Fan
- Department of Pediatric Surgery, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou, 450052, China
| | - Qian Zhang
- Department of Pediatric Surgery, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou, 450052, China
| | - Heying Yang
- Department of Pediatric Surgery, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou, 450052, China
| | - Da Zhang
- Department of Pediatric Surgery, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou, 450052, China
| | - Qiuliang Liu
- Department of Pediatric Surgery, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou, 450052, China
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10
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Zhao T, He M, Zhu Z, Zhang T, Zheng W, Qin S, Gao M, Wang W, Chen Z, Han J, Liu L, Zhou B, Wang H, Zhang H, Xia G, Wang J, Wang F, Wang C. P62 promotes FSH-induced antral follicle formation by directing degradation of ubiquitinated WT1. Cell Mol Life Sci 2024; 81:221. [PMID: 38763964 PMCID: PMC11102895 DOI: 10.1007/s00018-024-05251-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 04/15/2024] [Accepted: 04/22/2024] [Indexed: 05/21/2024]
Abstract
In females, the pathophysiological mechanism of poor ovarian response (POR) is not fully understood. Considering the expression level of p62 was significantly reduced in the granulosa cells (GCs) of POR patients, this study focused on identifying the role of the selective autophagy receptor p62 in conducting the effect of follicle-stimulating hormone (FSH) on antral follicles (AFs) formation in female mice. The results showed that p62 in GCs was FSH responsive and that its level increased to a peak and then decreased time-dependently either in ovaries or in GCs after gonadotropin induction in vivo. GC-specific deletion of p62 resulted in subfertility, a significantly reduced number of AFs and irregular estrous cycles, which were same as pathophysiological symptom of POR. By conducting mass spectrum analysis, we found the ubiquitination of proteins was decreased, and autophagic flux was blocked in GCs. Specifically, the level of nonubiquitinated Wilms tumor 1 homolog (WT1), a transcription factor and negative controller of GC differentiation, increased steadily. Co-IP results showed that p62 deletion increased the level of ubiquitin-specific peptidase 5 (USP5), which blocked the ubiquitination of WT1. Furthermore, a joint analysis of RNA-seq and the spatial transcriptome sequencing data showed the expression of steroid metabolic genes and FSH receptors pivotal for GCs differentiation decreased unanimously. Accordingly, the accumulation of WT1 in GCs deficient of p62 decreased steroid hormone levels and reduced FSH responsiveness, while the availability of p62 in GCs simultaneously ensured the degradation of WT1 through the ubiquitin‒proteasome system and autophagolysosomal system. Therefore, p62 in GCs participates in GC differentiation and AF formation in FSH induction by dynamically controlling the degradation of WT1. The findings of the study contributes to further study the pathology of POR.
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Affiliation(s)
- Ting Zhao
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Meina He
- College of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou Province, 550025, China
| | - Zijian Zhu
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Tuo Zhang
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Department of Physiology, College of Basic Medicine, Guizhou Medical University, Guiyang, Guizhou Province, 550025, China
| | - Wenying Zheng
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Shaogang Qin
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Meng Gao
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Wenji Wang
- School of Life Science, Taizhou University, Taizhou, 318000, China
| | - Ziqi Chen
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jun Han
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Longping Liu
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Bo Zhou
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Haibin Wang
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, School of Medicine, The First Affiliated Hospital of Xiamen University, Xiamen University, Xiamen, Fujian Province, 361005, China
| | - Hua Zhang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Guoliang Xia
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in the Western China, College of Life Science, Ningxia University, Yinchuan, 750021, China
| | - Jianbin Wang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Fengchao Wang
- Transgenic Animal Center, National Institute of Biological Sciences, Beijing, 102206, China
| | - Chao Wang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
- China Agricultural University, No.2 Yuan Ming Yuan West Road, Haidian District, Beijing, 100193, China.
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11
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Fu X, Zhang S, Liu P. Co-immunoprecipitation for identifying protein-protein interaction on lipid droplets. BIOPHYSICS REPORTS 2024; 10:102-110. [PMID: 38774355 PMCID: PMC11103721 DOI: 10.52601/bpr.2024.240007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 02/23/2024] [Indexed: 05/24/2024] Open
Abstract
The lipid droplet (LD) is a conserved organelle that exists in almost all organisms, ranging from bacteria to mammals. Dysfunctions in LDs are linked to a range of human metabolic syndromes. The formation of protein complexes on LDs is crucial for maintaining their function. Investigating how proteins interact on LDs is essential for understanding the role of LDs. We have developed an effective method to uncover protein-protein interactions and protein complexes specifically on LDs. In this method, we conduct co-immunoprecipitation (co-IP) experiments using LD proteins extracted directly from isolated LDs, rather than utilizing proteins from cell lysates. To elaborate, we begin by purifying LDs with high-quality and extracting LD-associated proteins. Subsequently, the co-IP experiment is performed on these LD-associated proteins directly, which would enhance the co-IP experiment specificity of LD-associated proteins. This method enables researchers to directly unveil protein complexes on LDs and gain deeper insights into the functional roles of proteins associated with LDs.
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Affiliation(s)
- Xiaochuan Fu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuyan Zhang
- Institute of Infectious Diseases, Beijing Key Laboratory of Emerging Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
- Beijing Institute of Infectious Diseases, Beijing 100015, China
| | - Pingsheng Liu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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12
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Zhang X, Cheng Z, Fan G, Zhu D, Tan B, Jiang T, Chen S. Transcription Factor McHB7 Improves Ice Plant Drought Tolerance through ABA Signaling Pathway. Int J Mol Sci 2024; 25:4569. [PMID: 38674154 PMCID: PMC11050535 DOI: 10.3390/ijms25084569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
As global climate change continues, drought episodes have become increasingly frequent. Studying plant stress tolerance is urgently needed to ensure food security. The common ice plant is one of the model halophyte plants for plant stress biology research. This study aimed to investigate the functions of a newly discovered transcription factor, Homeobox 7 (HB7), from the ice plant in response to drought stress. An efficient Agrobacterium-mediated transformation method was established in the ice plant, where ectopic McHB7 expression may be sustained for four weeks. The McHB7 overexpression (OE) plants displayed drought tolerance, and the activities of redox enzymes and chlorophyll content in the OE plants were higher than the wild type. Quantitative proteomics revealed 1910 and 495 proteins significantly changed in the OE leaves compared to the wild type under the control and drought conditions, respectively. Most increased proteins were involved in the tricarboxylic acid cycle, photosynthesis, glycolysis, pyruvate metabolism, and oxidative phosphorylation pathways. Some were found to participate in abscisic acid signaling or response. Furthermore, the abscisic acid levels increased in the OE compared with the wild type. McHB7 was revealed to bind to the promoter motifs of Early Responsive to Dehydration genes and abscisic acid-responsive genes, and protein-protein interaction analysis revealed candidate proteins responsive to stresses and hormones (e.g., abscisic acid). To conclude, McHB7 may contribute to enhance plant drought tolerance through abscisic acid signaling.
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Affiliation(s)
- Xuemei Zhang
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, China; (X.Z.); (Z.C.)
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (G.F.); (T.J.)
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL 32610, USA; (D.Z.); (B.T.)
| | - Zihan Cheng
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, China; (X.Z.); (Z.C.)
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (G.F.); (T.J.)
| | - Gaofeng Fan
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (G.F.); (T.J.)
| | - Dan Zhu
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL 32610, USA; (D.Z.); (B.T.)
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Bowen Tan
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL 32610, USA; (D.Z.); (B.T.)
- Department of Biology, University of Mississippi, Oxford, MS 38677, USA
| | - Tingbo Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (G.F.); (T.J.)
| | - Sixue Chen
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL 32610, USA; (D.Z.); (B.T.)
- Department of Biology, University of Mississippi, Oxford, MS 38677, USA
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13
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Long MJC, Aye Y. Climbing into their Skin to Understand Contextual Protein-Protein Associations and Localizations: Functional Investigations in Transgenic Live Model Organisms. Chembiochem 2024; 25:e202400005. [PMID: 38511872 DOI: 10.1002/cbic.202400005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/07/2024] [Indexed: 03/22/2024]
Abstract
Borrowing some quotes from Harper Lee's novel "To Kill A Mockingbird" to help frame our manuscript, we discuss methods to profile local proteomes. We initially focus on chemical biology regimens that function in live organisms and use reactive biotin species for this purpose. We then consider ways to add new dimensions to these experimental regimens, principally by releasing less reactive (i. e., more selective) (preter)natural electrophiles. Although electrophile release methods may have lower resolution and label fewer proteins than biotinylation methods, their ability to probe simultaneously protein function and locale raises new and interesting possibilities for the field.
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Affiliation(s)
| | - Yimon Aye
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, 1015, Switzerland
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14
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Ding Y, Jiang Y, Zeng H, Zhou M, Zhou X, Yu Z, Pan J, Geng X, Zhu Y, Zheng H, Huang S, Gong Y, Huang H, Xiong C, Huang D. Identification of a robust biomarker LAPTM4A for glioma based on comprehensive computational biology and experimental verification. Aging (Albany NY) 2024; 16:6954-6989. [PMID: 38613802 PMCID: PMC11087115 DOI: 10.18632/aging.205736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 03/03/2024] [Indexed: 04/15/2024]
Abstract
BACKGROUND Glioma, a highly invasive and deadly form of human neoplasm, presents a pressing need for the exploration of potential therapeutic targets. While the lysosomal protein transmembrane 4A (LATPM4A) has been identified as a risk factor in pancreatic cancer patients, its role in glioma remains unexplored. METHODS The analysis of differentially expressed genes (DEG) was conducted from The Cancer Genome Atlas (TCGA) glioma dataset and the Genotype Tissue Expression (GTEx) dataset. Through weighted gene co-expression network analysis (WGCNA), the key glioma-related genes were identified. Among these, by using Kaplan-Meier (KM) analysis and univariate/multivariate COX methods, LAPTM4A emerged as the most influential gene. Moreover, the bioinformatics methods and experimental verification were employed to analyze its relationships with diagnosis, clinical parameters, epithelial-mesenchymal transition (EMT), metastasis, immune cell infiltration, immunotherapy, drug sensitivity, and ceRNA network. RESULTS Our findings revealed that LAPTM4A was up-regulated in gliomas and was associated with clinicopathological features, leading to poor prognosis. Furthermore, functional enrichment analysis demonstrated that LATPM4A played a role in the immune system and cancer progression. In vitro experiments indicated that LAPTM4A may influence metastasis through the EMT pathway in glioma. Additionally, we found that LAPTM4A was associated with the tumor microenvironment (TME) and immunotherapy. Notably, drug sensitivity analysis revealed that patients with high LAPTM4A expression were sensitive to doxorubicin, which contributed to a reduction in LAPTM4A expression. Finally, we uncovered the FGD5-AS1-hsa-miR-103a-3p-LAPTM4A axis as a facilitator of glioma progression. CONCLUSIONS In conclusion, our study identifies LATPM4A as a promising biomarker for prognosis and immune characteristics in glioma.
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Affiliation(s)
- Yongqi Ding
- Department of Thyroid Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Yike Jiang
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Hong Zeng
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Minqin Zhou
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Xuanrui Zhou
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Zichuan Yu
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Jingying Pan
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Xitong Geng
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Yanting Zhu
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Hao Zheng
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Shuhan Huang
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Yiyang Gong
- Second College of Clinical Medicine, Nanchang University, Nanchang, Jiangxi 330006, China
| | - Huabin Huang
- Department of Radiology, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
| | - Chengfeng Xiong
- Department of Thyroid Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
| | - Da Huang
- Department of Thyroid Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
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15
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Liang CT, Roscow O, Zhang W. Generation and Characterization of Engineered Ubiquitin Variants to Modulate the Ubiquitin Signaling Cascade. Cold Spring Harb Protoc 2024; 2024:107784. [PMID: 36997275 DOI: 10.1101/pdb.over107784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The ubiquitin signaling cascade plays a crucial role in human cells. Consistent with this, malfunction of ubiquitination and deubiquitination is implicated in the initiation and progression of numerous human diseases, including cancer. Therefore, the development of potent and specific modulators of ubiquitin signal transduction has been at the forefront of drug development. In the past decade, a structure-based combinatorial protein-engineering approach has been used to generate ubiquitin variants (UbVs) as protein-based modulators of multiple components in the ubiquitin-proteasome system. Here, we review the design and generation of phage-displayed UbV libraries, including the processes of binder selection and library improvement. We also provide a comprehensive overview of the general in vitro and cellular methodologies involved in characterizing UbV binders. Finally, we describe two recent applications of UbVs for developing molecules with therapeutic potential.
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Affiliation(s)
- Chen T Liang
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, Ontario N1G2W1, Canada
| | - Olivia Roscow
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, Ontario N1G2W1, Canada
| | - Wei Zhang
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, Ontario N1G2W1, Canada
- CIFAR Azrieli Global Scholars Program, Canadian Institute for Advanced Research, MaRS Centre, Toronto, Ontario M5G1M1, Canada
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16
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Chen H, Zhang H, Li AM, Liu YT, Liu Y, Zhang W, Yang C, Song N, Zhan M, Yang S. VDR regulates mitochondrial function as a protective mechanism against renal tubular cell injury in diabetic rats. Redox Biol 2024; 70:103062. [PMID: 38320454 PMCID: PMC10850784 DOI: 10.1016/j.redox.2024.103062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 01/19/2024] [Accepted: 01/25/2024] [Indexed: 02/08/2024] Open
Abstract
PURPOSE To investigate the regulatory effect and mechanism of Vitamin D receptor (VDR) on mitochondrial function in renal tubular epithelial cell under diabetic status. METHODS The diabetic rats induced by streptozotocin (STZ) and HK-2 cells under high glocose(HG)/transforming growth factor beta (TGF-β) stimulation were used in this study. Calcitriol was administered for 24 weeks. Renal tubulointerstitial injury and some parameters of mitochondrial function including mitophagy, mitochondrial fission, mitochondrial ROS, mitochondrial membrane potential (MMP), mitochondrial ATP, Complex V activity and mitochondria-associated ER membranes (MAMs) integrity were examined. Additionally, paricalcitol, 3-MA (an autophagy inhibitor), VDR over-expression plasmid, VDR siRNA and Mfn2 siRNA were applied in vitro. RESULTS The expression of VDR, Pink1, Parkin, Fundc1, LC3II, Atg5, Mfn2, Mfn1 in renal tubular cell of diabetic rats were decreased significantly. Calcitriol treatment reduced the levels of urinary albumin, serum creatinine and attenuated renal tubulointerstitial fibrosis in STZ induced diabetic rats. In addition, VDR agonist relieved mitophagy dysfunction, MAMs integrity, and inhibited mitochondrial fission, mitochondrial ROS. Co-immunoprecipitation analysis demonstrated that VDR interacted directly with Mfn2. Mitochondrial function including mitophagy, mitochondrial membrane potential (MMP), mitochondrial Ca2+, mitochondrial ATP and Complex V activity were decreased dramatically in HK-2 cells under HG/TGF-β ambience. In vitro pretreatment of HK-2 cells with autophagy inhibitor 3-MA, VDR siRNA or Mfn2 siRNA negated the activating effects of paricalcitol on mitochondrial function. Pricalcitol and VDR over-expression plasmid activated Mfn2 and then partially restored the MAMs integrity. Additionally, VDR restored mitophagy was partially associated with MAMs integrity through Fundc1. CONCLUSION Activated VDR could contribute to restore mitophagy through Mfn2-MAMs-Fundc1 pathway in renal tubular cell. VDR could recover mitochondrial ATP, complex V activity and MAMs integrity, inhibit mitochondrial fission and mitochondrial ROS. It indicating that VDR agonists ameliorate renal tubulointerstitial fibrosis in diabetic rats partially via regulation of mitochondrial function.
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Affiliation(s)
- Hong Chen
- Department of Nephrology, The Third Xiangya Hospital, The Critical Kidney Disease Research Center, Central South University, China.
| | - Hao Zhang
- Department of Nephrology, The Third Xiangya Hospital, The Critical Kidney Disease Research Center, Central South University, China.
| | - Ai-Mei Li
- Department of Nephrology, The Third Xiangya Hospital, The Critical Kidney Disease Research Center, Central South University, China.
| | - Yu-Ting Liu
- Department of Nephrology, The Third Xiangya Hospital, The Critical Kidney Disease Research Center, Central South University, China.
| | - Yan Liu
- Department of Nephrology, The Third Xiangya Hospital, The Critical Kidney Disease Research Center, Central South University, China.
| | - Wei Zhang
- Department of Nephrology, The Third Xiangya Hospital, The Critical Kidney Disease Research Center, Central South University, China.
| | - Cheng Yang
- Department of Nephrology, The Third Xiangya Hospital, The Critical Kidney Disease Research Center, Central South University, China.
| | - Na Song
- Department of Nephrology, The Third Xiangya Hospital, The Critical Kidney Disease Research Center, Central South University, China.
| | - Ming Zhan
- Department of Nephrology, The First Affiliated Hospital of Ningbo University, China.
| | - Shikun Yang
- Department of Nephrology, The Third Xiangya Hospital, The Critical Kidney Disease Research Center, Central South University, China.
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17
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Hinmon JA, King JM, Mayo LJ, Faries CR, Lockett YT, Crawford DW, Beardslee PC, Hendricks A, McNaughton BR. Cell surface β-lactamase recruitment: A facile selection to identify protein-protein interactions. Protein Sci 2024; 33:e4919. [PMID: 38501433 PMCID: PMC10949332 DOI: 10.1002/pro.4919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/17/2023] [Accepted: 01/25/2024] [Indexed: 03/20/2024]
Abstract
Protein-protein interactions (PPIs) are central to many cellular processes, and the identification of novel PPIs is a critical step in the discovery of protein therapeutics. Simple methods to identify naturally existing or laboratory evolved PPIs are therefore valuable research tools. We have developed a facile selection that links PPI-dependent β-lactamase recruitment on the surface of Escherichia coli with resistance to ampicillin. Bacteria displaying a protein that forms a complex with a specific protein-β-lactamase fusion are protected from ampicillin-dependent cell death. In contrast, bacteria that do not recruit β-lactamase to the cell surface are killed by ampicillin. Given its simplicity and tunability, we anticipate this selection will be a valuable addition to the palette of methods for illuminating and interrogating PPIs.
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Affiliation(s)
- Jordan A. Hinmon
- Department of Biological SciencesDelaware State UniversityDoverDelawareUSA
| | - Jade M. King
- Department of Biological SciencesDelaware State UniversityDoverDelawareUSA
| | - Latrina J. Mayo
- Department of Biological SciencesDelaware State UniversityDoverDelawareUSA
| | - Cierra R. Faries
- Department of Biological SciencesDelaware State UniversityDoverDelawareUSA
| | - Ya'hnis T. Lockett
- Department of Biological SciencesDelaware State UniversityDoverDelawareUSA
| | - David W. Crawford
- Department of ChemistryColorado State UniversityFort CollinsColoradoUSA
| | | | | | - Brian R. McNaughton
- Department of Biological SciencesDelaware State UniversityDoverDelawareUSA
- Department of ChemistryColorado State UniversityFort CollinsColoradoUSA
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18
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Buva K, Kumbhar GM, Deshmukh A, Ladke VS. The assessment of the mechanism of action of lauric acid in the context of oral cancer through integrative approach combining network pharmacology and molecular docking technology. JOURNAL OF COMPLEMENTARY & INTEGRATIVE MEDICINE 2024; 21:101-112. [PMID: 38353231 DOI: 10.1515/jcim-2023-0262] [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: 09/15/2023] [Accepted: 01/03/2024] [Indexed: 03/22/2024]
Abstract
OBJECTIVES Lauric acid has been investigated for its effects on various human cancer cell types, although limited research has been dedicated to its impact on oral cancer. In light of this, the objective of our study was to comprehensively assess the anticancer properties of lauric acid specifically in the context of oral cancer. This evaluation was achieved through an in-silico approach, leveraging network analysis techniques. By employing this methodology, we aimed to gain valuable insights into the potential therapeutic benefits of lauric acid for treating oral cancer. METHODS The in-silico analysis involved determination of drug-likeness prediction, prediction of common targets between oral cancer and LA, protein-protein interactions (PPI), hub genes, top 10 associated pathways by gene ontology (GO), Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway, molecular docking experiments. RESULTS Our study pinpointed 23 common genes involved in critical cellular processes, including proliferation, apoptosis regulation, PI3K AKT cascade, and cell cycle control. Among them, CXCL8, MMP9, PPARA, MAPK1, and AR stood out in the top 10 pathways, particularly in the PI3K/AKT signaling pathway. This highlights the potential role of lauric acid in oral cancer treatment through the PI3K/AKT pathway and calls for further exploration of this mechanism. CONCLUSIONS Our study highlights lauric acid's promising anticancer properties through computational analysis, offering a foundation for future research in cancer treatment development. This approach combines molecular insights with in-silico methods, paving the way for identifying therapeutic compounds and understanding their mechanisms. Lauric acid holds potential as a chemotherapeutic agent, opening up new avenues for cancer therapy exploration.
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Affiliation(s)
- Kirti Buva
- Department of Oral Pathology and Microbiology, Bharti Vidyapeeth, Deemed to be University, Dental College and Hospital, Navi Mumbai, India
| | - Gauri M Kumbhar
- Dr. D. Y. Patil Dental College and Hospital, Dr. D. Y. Patil Vidyapeeth, Pimpri, Pune, India
| | | | - Vaibhav Sunil Ladke
- Dr. D. Y. Patil Medical College, Hospital and Research Center, Dr. D. Y. Patil Vidyapeeth, Pimpri, Pune, India
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19
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Jiang Y, Shen L, Wang B. Non-electrophysiological techniques targeting transient receptor potential (TRP) gene of gastrointestinal tract. Int J Biol Macromol 2024; 262:129551. [PMID: 38367416 DOI: 10.1016/j.ijbiomac.2024.129551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/10/2024] [Accepted: 01/15/2024] [Indexed: 02/19/2024]
Abstract
Transient receptor potential (TRP) channels are cation channels related to a wide range of physical and chemical stimuli, they are expressed all along the gastrointestinal system, and a myriad of diseases are often associated with aberrant expression or mutation of the TRP gene, suggesting that TRPs are promising targets for drug therapy. Therefore, a better understanding of the information of TRPs in health and disease could facilitate the development of effective drugs for the treatment of gastrointestinal diseases like IBD. But there are very few generalizations about the experimental techniques studied in this field. In view of the promise of TRP as a therapeutic target, we discuss experimental methods that can be used for TRPs including their distribution, function and interaction with other proteins, as well as some promising emerging technologies to provide experimental methods for future studies.
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Affiliation(s)
- Yuting Jiang
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Center for Pharmaceutics Research, Shanghai Institute of Materia Medica Chinese Academy of Sciences, Shanghai 201203, China
| | - Lan Shen
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| | - Bing Wang
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; Center for Pharmaceutics Research, Shanghai Institute of Materia Medica Chinese Academy of Sciences, Shanghai 201203, China.
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20
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Liu Y, Jiang N, Chen W, Zhang W, Shen X, Jia B, Chen G. TRIM59-mediated ferroptosis enhances neuroblastoma development and chemosensitivity through p53 ubiquitination and degradation. Heliyon 2024; 10:e26014. [PMID: 38434050 PMCID: PMC10906161 DOI: 10.1016/j.heliyon.2024.e26014] [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: 04/27/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 03/05/2024] Open
Abstract
Neuroblastoma, predominantly afflicting young individuals, is characterized as an embryonal tumor, with poor prognosis primarily attributed to chemoresistance. This study delved into the impact of tripartite motif (TRIM) 59, an E3 ligase, on neuroblastoma development and chemosensitivity through mediating ferroptosis and the involvement of the tumor suppressor p53. Clinical samples were assessed for TRIM59 and p53 levels to explore their correlation with neuroblastoma differentiation. In neuroblastoma cells, modulation of TRIM59 expression, either through overexpression or knockdown, was coupled with doxorubicin hydrochloride (DOX) or ferrostatin-1 (Fer-1) therapy. In vivo assessments examined the influence of TRIM59 knockdown on neuroblastoma chemosensitivity to DOX. Co-immunoprecipitation and ubiquitination assays investigated the association between TRIM59 and p53. Proliferation was gauged with Cell Counting Kit-8, lipid reactive oxygen species (ROS) were assessed via flow cytometry, and protein levels were determined by Western blotting. TRIM59 expression was inversely correlated with neuroblastoma differentiation and positively linked to cell proliferation in response to DOX. Moreover, TRIM59 impeded lipid ROS generation and ferroptosis by directly interacting with p53, promoting its ubiquitination and degradation in DOX-exposed neuroblastoma cells. Fer-1 countered the impact of TRIM59 knockdown on neuroblastoma, while TRIM59 knockdown enhanced the therapeutic efficacy of DOX in xenograph mice. This study underscores TRIM59 as an oncogene in neuroblastoma, fostering growth and chemoresistance by suppressing ferroptosis through p53 ubiquitination and degradation. TRIM59 emerges as a potential strategy for neuroblastoma therapy.
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Affiliation(s)
| | | | - Weicheng Chen
- Department of Cardiothoracic Surgery, Children's Hospital of Fudan University. No.399, Wanyuan Road, Minhang District, Shanghai, 201102, China
| | - Wenbo Zhang
- Department of Cardiothoracic Surgery, Children's Hospital of Fudan University. No.399, Wanyuan Road, Minhang District, Shanghai, 201102, China
| | - Xiao Shen
- Department of Cardiothoracic Surgery, Children's Hospital of Fudan University. No.399, Wanyuan Road, Minhang District, Shanghai, 201102, China
| | - Bing Jia
- Department of Cardiothoracic Surgery, Children's Hospital of Fudan University. No.399, Wanyuan Road, Minhang District, Shanghai, 201102, China
| | - Gang Chen
- Department of Cardiothoracic Surgery, Children's Hospital of Fudan University. No.399, Wanyuan Road, Minhang District, Shanghai, 201102, China
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21
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Czerczak-Kwiatkowska K, Kaminska M, Fraczyk J, Majsterek I, Kolesinska B. Searching for EGF Fragments Recreating the Outer Sphere of the Growth Factor Involved in Receptor Interactions. Int J Mol Sci 2024; 25:1470. [PMID: 38338748 PMCID: PMC10855902 DOI: 10.3390/ijms25031470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
The aims of this study were to determine whether it is possible to use peptide microarrays obtained using the SPOT technique (immobilized on cellulose) and specific polyclonal antibodies to select fragments that reconstruct the outer sphere of proteins and to ascertain whether the selected peptide fragments can be useful in the study of their protein-protein and/or peptide-protein interactions. Using this approach, epidermal growth factor (EGF) fragments responsible for the interaction with the EGF receptor were searched. A library of EGF fragments immobilized on cellulose was obtained using triazine condensing reagents. Experiments on the interactions with EGFR confirmed the high affinity of the selected peptide fragments. Biological tests on cells showed the lack of cytotoxicity of the EGF fragments. Selected EGF fragments can be used in various areas of medicine.
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Affiliation(s)
- Katarzyna Czerczak-Kwiatkowska
- Faculty of Chemistry, Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland; (K.C.-K.); (J.F.)
| | - Marta Kaminska
- Division of Biophysics, Institute of Materials Science and Engineering, Lodz University of Technology, Stefanowskiego 1/15, 90-924 Lodz, Poland;
| | - Justyna Fraczyk
- Faculty of Chemistry, Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland; (K.C.-K.); (J.F.)
| | - Ireneusz Majsterek
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, Narutowicza 60, 90-136 Lodz, Poland;
| | - Beata Kolesinska
- Faculty of Chemistry, Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland; (K.C.-K.); (J.F.)
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22
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Hosseini S, Golding GB, Ilie L. Seq-InSite: sequence supersedes structure for protein interaction site prediction. Bioinformatics 2024; 40:btad738. [PMID: 38212995 PMCID: PMC10796176 DOI: 10.1093/bioinformatics/btad738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 11/17/2023] [Accepted: 01/10/2024] [Indexed: 01/13/2024] Open
Abstract
MOTIVATION Proteins accomplish cellular functions by interacting with each other, which makes the prediction of interaction sites a fundamental problem. As experimental methods are expensive and time consuming, computational prediction of the interaction sites has been studied extensively. Structure-based programs are the most accurate, while the sequence-based ones are much more widely applicable, as the sequences available outnumber the structures by two orders of magnitude. Ideally, we would like a tool that has the quality of the former and the applicability of the latter. RESULTS We provide here the first solution that achieves these two goals. Our new sequence-based program, Seq-InSite, greatly surpasses the performance of sequence-based models, matching the quality of state-of-the-art structure-based predictors, thus effectively superseding the need for models requiring structure. The predictive power of Seq-InSite is illustrated using an analysis of evolutionary conservation for four protein sequences. AVAILABILITY AND IMPLEMENTATION Seq-InSite is freely available as a web server at http://seq-insite.csd.uwo.ca/ and as free source code, including trained models and all datasets used for training and testing, at https://github.com/lucian-ilie/Seq-InSite.
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Affiliation(s)
- SeyedMohsen Hosseini
- Department of Computer Science, University of Western Ontario, London, ON N6A 5B7, Canada
| | - G Brian Golding
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Lucian Ilie
- Department of Computer Science, University of Western Ontario, London, ON N6A 5B7, Canada
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23
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Bloemers D, Carmo-Silva E. Antibody Design for the Quantification of Photosynthetic Proteins and Their Isoforms. Methods Mol Biol 2024; 2790:405-416. [PMID: 38649583 DOI: 10.1007/978-1-0716-3790-6_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Antibodies are a valuable research tool, with uses including detection and quantification of specific proteins. By using peptide fragments to raise antibodies, they can be designed to differentiate between structurally similar proteins, or to bind conserved motifs in divergent proteins. Peptide sequence selection and antibody validation are crucial to ensure reliable results from antibody-based experiments. This chapter describes the steps for the identification of peptide sequences to produce protein- or isoform-specific antibodies using recombinant technologies as well as the subsequent validation of such antibodies. The photosynthetic protein Rubisco activase is used as a case study to explain the various steps involved and key aspects to take into consideration.
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Affiliation(s)
- Duncan Bloemers
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
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24
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Huang M, Yu X, Li B. Co-immunoprecipitation Assays to Detect Protein-Protein Interactions. Methods Mol Biol 2024; 2724:225-233. [PMID: 37987909 DOI: 10.1007/978-1-0716-3485-1_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Proteins usually do not function as monomers but rather perform their functions by interacting with themselves or other proteins. Co-immunoprecipitation is an essential assay for detecting protein interactions in vivo. In this chapter, we describe how to use co-immunoprecipitation to detect protein interactions in Arabidopsis protoplasts, seedlings, and Nicotiana benthamiana leaves. When using co-immunoprecipitation assays to detect protein interactions, it is necessary to pay attention to the design of the experimental and control groups.
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Affiliation(s)
- Mengling Huang
- National Key Laboratory of Agricultural Microbiology, Hubei Key Lab of Plant Pathology, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xiao Yu
- National Key Laboratory of Agricultural Microbiology, Hubei Key Lab of Plant Pathology, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Bo Li
- National Key Laboratory of Agricultural Microbiology, Hubei Key Lab of Plant Pathology, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China.
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25
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Caron C, Bertolin G. Cristae shaping and dynamics in mitochondrial function. J Cell Sci 2024; 137:jcs260986. [PMID: 38197774 DOI: 10.1242/jcs.260986] [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] [Indexed: 01/11/2024] Open
Abstract
Mitochondria are multifunctional organelles of key importance for cell homeostasis. The outer mitochondrial membrane (OMM) envelops the organelle, and the inner mitochondrial membrane (IMM) is folded into invaginations called cristae. As cristae composition and functions depend on the cell type and stress conditions, they recently started to be considered as a dynamic compartment. A number of proteins are known to play a role in cristae architecture, such as OPA1, MIC60, LETM1, the prohibitin (PHB) complex and the F1FO ATP synthase. Furthermore, phospholipids are involved in the maintenance of cristae ultrastructure and dynamics. The use of new technologies, including super-resolution microscopy to visualize cristae dynamics with superior spatiotemporal resolution, as well as high-content techniques and datasets have not only allowed the identification of new cristae proteins but also helped to explore cristae plasticity. However, a number of open questions remain in the field, such as whether cristae-resident proteins are capable of changing localization within mitochondria, or whether mitochondrial proteins can exit mitochondria through export. In this Review, we present the current view on cristae morphology, stability and composition, and address important outstanding issues that might pave the way to future discoveries.
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Affiliation(s)
- Claire Caron
- Univ. Rennes, CNRS, IGDR (Institute of Genetics and Development of Rennes), UMR 6290, F-35000 Rennes, France
| | - Giulia Bertolin
- Univ. Rennes, CNRS, IGDR (Institute of Genetics and Development of Rennes), UMR 6290, F-35000 Rennes, France
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26
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Joo EE, Olson MF. BioID Analysis of Actin-Binding Proteins. Methods Mol Biol 2024; 2794:95-104. [PMID: 38630223 DOI: 10.1007/978-1-0716-3810-1_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Proteins often exist and function as part of higher-order complexes or networks. A challenge is to identify the universe of proximal and interacting partners for a given protein. We describe how the high-activity promiscuous biotin ligase called TurboID is fused to the actin-binding peptide LifeAct to label by biotinylation proteins that bind, or are in close proximity, to actin. The rapid enzyme kinetics of TurboID allows the profiles of actin-binding proteins to be compared under different conditions, such as acute disruption of filamentous actin structures with cytochalasin D.
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Affiliation(s)
- E Emily Joo
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, ON, Canada
| | - Michael F Olson
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, ON, Canada.
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27
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Metwally H, Elbrashy MM. Analysis of Protein Interactions in Patient-Derived Xenografts Using Immunoprecipitation. Methods Mol Biol 2024; 2806:219-227. [PMID: 38676806 DOI: 10.1007/978-1-0716-3858-3_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2024]
Abstract
Proteins are large, complex molecules that regulate multiple functions within the cell. The protein rarely functions as a single molecule, but rather interacts with one or more other proteins forming a dynamic network. Protein-protein interactions are critical for regulating the cell's response toward various stimuli from outside and inside the cell. Identification of protein-protein interactions enhanced our understanding of various biological processes in the living cell. Immunoprecipitation (IP) has been one of the standard and most commonly used biochemical methods to identify and confirm protein-protein interactions. IP uses a target protein-specific antibody conjugated with protein A/G affinity beads to identify molecules interacting with the target protein. Here, we describe the principle, procedure and challenges of the IP assay.
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Affiliation(s)
- Hozaifa Metwally
- Laboratory of Immune Regulation, Immunology Frontier Research Center, Osaka University, Osaka, Japan.
| | - Maha M Elbrashy
- Laboratory of Immune Regulation, Immunology Frontier Research Center, Osaka University, Osaka, Japan
- Biochemistry Department, Biotechnology Research Institute, National Research Center, Giza, Egypt
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28
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Luo Y, Cheng J, Fu Y, Zhang M, Gou M, Li J, Li X, Bai J, Zhou Y, Zhang L, Gao D. D-allose Inhibits TLR4/PI3K/AKT Signaling to Attenuate Neuroinflammation and Neuronal Apoptosis by Inhibiting Gal-3 Following Ischemic Stroke. Biol Proced Online 2023; 25:30. [PMID: 38017376 PMCID: PMC10683335 DOI: 10.1186/s12575-023-00224-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/01/2023] [Indexed: 11/30/2023] Open
Abstract
BACKGROUND Ischemic stroke (IS) occurs when a blood vessel supplying the brain becomes obstructed, resulting in cerebral ischemia. This type of stroke accounts for approximately 87% of all strokes. Globally, IS leads to high mortality and poor prognosis and is associated with neuroinflammation and neuronal apoptosis. D-allose is a bio-substrate of glucose that is widely expressed in many plants. Our previous study showed that D-allose exerted neuroprotective effects against acute cerebral ischemic/reperfusion (I/R) injury by reducing neuroinflammation. Here, we aimed to clarify the beneficial effects D-allose in suppressing IS-induced neuroinflammation damage, cytotoxicity, neuronal apoptosis and neurological deficits and the underlying mechanism in vitro and in vivo. METHODS In vivo, an I/R model was induced by middle cerebral artery occlusion and reperfusion (MCAO/R) in C57BL/6 N mice, and D-allose was given by intraperitoneal injection within 5 min after reperfusion. In vitro, mouse hippocampal neuronal cells (HT-22) with oxygen-glucose deprivation and reperfusion (OGD/R) were established as a cell model of IS. Neurological scores, some cytokines, cytotoxicity and apoptosis in the brain and cell lines were measured. Moreover, Gal-3 short hairpin RNAs, lentiviruses and adeno-associated viruses were used to modulate Gal-3 expression in neurons in vitro and in vivo to reveal the molecular mechanism. RESULTS D-allose alleviated cytotoxicity, including cell viability, LDH release and apoptosis, in HT-22 cells after OGD/R, which also alleviated brain injury, as indicated by lesion volume, brain edema, neuronal apoptosis, and neurological functional deficits, in a mouse model of I/R. Moreover, D-allose decreased the release of inflammatory factors, such as IL-1β, IL-6 and TNF-α. Furthermore, the expression of Gal-3 was increased by I/R in wild-type mice and HT-22 cells, and this factor further bound to TLR4, as confirmed by three-dimensional structure prediction and Co-IP. Silencing the Gal-3 gene with shRNAs decreased the activation of TLR4 signaling and alleviated IS-induced neuroinflammation, apoptosis and brain injury. Importantly, the loss of Gal-3 enhanced the D-allose-mediated protection against I/R-induced HT-22 cell injury, inflammatory insults and apoptosis, whereas activation of TLR4 by the selective agonist LPS increased the degree of neuronal injury and abolished the protective effects of D-allose. CONCLUSIONS In summary, D-allose plays a crucial role in inhibiting inflammation after IS by suppressing Gal-3/TLR4/PI3K/AKT signaling pathway in vitro and in vivo.
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Affiliation(s)
- Yaowen Luo
- Department of Neurosurgery, Xijing Hospital, Air Force Medical University, Changle West Road NO.127, Xi'an, China
| | - Junkai Cheng
- Department of Neurosurgery, Xijing Hospital, Air Force Medical University, Changle West Road NO.127, Xi'an, China
| | - Yihao Fu
- Department of Neurosurgery, Xijing Hospital, Air Force Medical University, Changle West Road NO.127, Xi'an, China
| | - Min Zhang
- Department of Neurosurgery, Xijing Hospital, Air Force Medical University, Changle West Road NO.127, Xi'an, China
| | - Maorong Gou
- Department of Neurosurgery, Xijing Hospital, Air Force Medical University, Changle West Road NO.127, Xi'an, China
| | - Juan Li
- Department of Neurosurgery, Xijing Hospital, Air Force Medical University, Changle West Road NO.127, Xi'an, China
| | - Xiaobing Li
- Department of Neurology, Xijing Hospital, Air Force Medical University, Changle West Road 127, Xi'an, China
| | - Jing Bai
- Department of Neurology, Xijing Hospital, Air Force Medical University, Changle West Road 127, Xi'an, China
| | - Yuefei Zhou
- Department of Neurosurgery, Xijing Hospital, Air Force Medical University, Changle West Road NO.127, Xi'an, China
| | - Lei Zhang
- Department of Neurosurgery, Xijing Hospital, Air Force Medical University, Changle West Road NO.127, Xi'an, China.
| | - Dakuan Gao
- Department of Neurosurgery, Xijing Hospital, Air Force Medical University, Changle West Road NO.127, Xi'an, China.
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29
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Santos TG, Silva KS, Lima RM, Silva LC, Pereira M. State of the art in protein-protein interactions within the fungi kingdom. Future Microbiol 2023; 18:1119-1131. [PMID: 37540069 DOI: 10.2217/fmb-2022-0274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023] Open
Abstract
Proteins rarely exert their function by themselves. Protein-protein interactions (PPIs) regulate virtually every biological process that takes place in a cell. Such interactions are targets for new therapeutic agents against all sorts of diseases, through the screening and design of a variety of inhibitors. Here we discuss several aspects of PPIs that contribute to prediction of protein function and drug discovery. As the high-throughput techniques continue to release biological data, targets for fungal therapeutics that rely on PPIs are being proposed worldwide. Computational approaches have reduced the time taken to develop new therapeutic approaches. The near future brings the possibility of developing new PPI and interaction network inhibitors and a revolution in the way we treat fungal diseases.
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Affiliation(s)
- Thaynara G Santos
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, 74 000, Brazil
| | - Kleber Sf Silva
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, 74 000, Brazil
| | - Raisa M Lima
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, 74 000, Brazil
| | - Lívia C Silva
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, 74 000, Brazil
| | - Maristela Pereira
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, 74 000, Brazil
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30
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Guo J, Guo S, Lu S, Gong J, Wang L, Ding L, Chen Q, Liu W. The development of proximity labeling technology and its applications in mammals, plants, and microorganisms. Cell Commun Signal 2023; 21:269. [PMID: 37777761 PMCID: PMC10544124 DOI: 10.1186/s12964-023-01310-1] [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: 07/31/2023] [Accepted: 09/07/2023] [Indexed: 10/02/2023] Open
Abstract
Protein‒protein, protein‒RNA, and protein‒DNA interaction networks form the basis of cellular regulation and signal transduction, making it crucial to explore these interaction networks to understand complex biological processes. Traditional methods such as affinity purification and yeast two-hybrid assays have been shown to have limitations, as they can only isolate high-affinity molecular interactions under nonphysiological conditions or in vitro. Moreover, these methods have shortcomings for organelle isolation and protein subcellular localization. To address these issues, proximity labeling techniques have been developed. This technology not only overcomes the limitations of traditional methods but also offers unique advantages in studying protein spatial characteristics and molecular interactions within living cells. Currently, this technique not only is indispensable in research on mammalian nucleoprotein interactions but also provides a reliable approach for studying nonmammalian cells, such as plants, parasites and viruses. Given these advantages, this article provides a detailed introduction to the principles of proximity labeling techniques and the development of labeling enzymes. The focus is on summarizing the recent applications of TurboID and miniTurbo in mammals, plants, and microorganisms. Video Abstract.
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Affiliation(s)
- Jieyu Guo
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Shuang Guo
- Medicine Research Institute, Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Siao Lu
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Jun Gong
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Long Wang
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Liqiong Ding
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Qingjie Chen
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China.
| | - Wu Liu
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, 437000, China.
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31
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Luo X, Wang L, Hu P, Hu L. Predicting Protein-Protein Interactions Using Sequence and Network Information via Variational Graph Autoencoder. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:3182-3194. [PMID: 37155405 DOI: 10.1109/tcbb.2023.3273567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Protein-protein interactions (PPIs) play a critical role in the proteomics study, and a variety of computational algorithms have been developed to predict PPIs. Though effective, their performance is constrained by high false-positive and false-negative rates observed in PPI data. To overcome this problem, a novel PPI prediction algorithm, namely PASNVGA, is proposed in this work by combining the sequence and network information of proteins via variational graph autoencoder. To do so, PASNVGA first applies different strategies to extract the features of proteins from their sequence and network information, and obtains a more compact form of these features using principal component analysis. In addition, PASNVGA designs a scoring function to measure the higher-order connectivity between proteins and so as to obtain a higher-order adjacency matrix. With all these features and adjacency matrices, PASNVGA trains a variational graph autoencoder model to further learn the integrated embeddings of proteins. The prediction task is then completed by using a simple feedforward neural network. Extensive experiments have been conducted on five PPI datasets collected from different species. Compared with several state-of-the-art algorithms, PASNVGA has been demonstrated as a promising PPI prediction algorithm.
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32
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Yamada K, Soga F, Tokunaga S, Nagaoka H, Ozawa T, Kishi H, Takashima E, Sawasaki T. GATS tag system is compatible with biotin labelling methods for protein analysis. Sci Rep 2023; 13:10243. [PMID: 37353572 PMCID: PMC10290147 DOI: 10.1038/s41598-023-36858-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 06/11/2023] [Indexed: 06/25/2023] Open
Abstract
Polypeptide tags and biotin labelling technologies are widely used for protein analyses in biochemistry and cell biology. However, many peptide tag epitopes contain lysine residues (or amino acids) that are masked after biotinylation. Here, we propose the GATS tag system without a lysine residue and with high sensitivity and low non-specific binding using a rabbit monoclonal antibody against Plasmodium falciparum glycosylphosphatidylinositol (GPI)-anchored micronemal antigen (PfGAMA). From 14 monoclonal clones, an Ra3 clone was selected as it recognized an epitope-TLSVGVQNTF-without a lysine residue; this antibody and epitope tag set was called the GATS tag system. Surface plasmon resonance analysis showed that the tag system had a high affinity of 8.71 × 10-9 M. GATS tag indicated a very low background with remarkably high sensitivity and specificity in immunoblotting using the lysates of mammalian cells. It also showed a high sensitivity for immunoprecipitation and immunostaining of cultured human cells. The tag system was highly sensitive in both biotin labelling methods for proteins using NHS-Sulfo-biotin and BioID (proximity-dependent biotin identification) in the human cells, as opposed to a commercially available tag system having lysine residues, which showed reduced sensitivity. These results showed that the GATS tag system is suitable for methods such as BioID involving labelling lysine residues.
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Affiliation(s)
- Kohdai Yamada
- Division of Cell-Free Life Science, Proteo-Science Center, Ehime University, 3 Bunkyo-Cho, Matsuyama, Ehime, 790-8577, Japan
| | - Fumiya Soga
- Division of Cell-Free Life Science, Proteo-Science Center, Ehime University, 3 Bunkyo-Cho, Matsuyama, Ehime, 790-8577, Japan
| | - Soh Tokunaga
- Division of Cell-Free Life Science, Proteo-Science Center, Ehime University, 3 Bunkyo-Cho, Matsuyama, Ehime, 790-8577, Japan
| | - Hikaru Nagaoka
- Division of Malaria Research, Proteo-Science Center, 3 Bunkyo-Cho, Matsuyama, Ehime, 790-8577, Japan
| | - Tatsuhiko Ozawa
- Department of Immunology, Faculty of Medicine, Academic Assembly, Advanced Antibody Drug Development Center, University of Toyama, Toyama, 930-0194, Japan
| | - Hiroyuki Kishi
- Department of Immunology, Faculty of Medicine, Academic Assembly, Advanced Antibody Drug Development Center, University of Toyama, Toyama, 930-0194, Japan
| | - Eizo Takashima
- Division of Malaria Research, Proteo-Science Center, 3 Bunkyo-Cho, Matsuyama, Ehime, 790-8577, Japan
| | - Tatsuya Sawasaki
- Division of Cell-Free Life Science, Proteo-Science Center, Ehime University, 3 Bunkyo-Cho, Matsuyama, Ehime, 790-8577, Japan.
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33
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Chen J, Luo M, Hands P, Rolland V, Zhang J, Li Z, Outram M, Dodds P, Ayliffe M. A split GAL4 RUBY assay for visual in planta detection of protein-protein interactions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:1209-1226. [PMID: 37323061 DOI: 10.1111/tpj.16234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/23/2023] [Accepted: 03/28/2023] [Indexed: 06/17/2023]
Abstract
Protein-protein interactions (PPIs) are a fundamental process in cellular biogenesis. Here we have developed a split GAL4 RUBY assay that enables macroscopically visual PPI detection in plant leaves in real time. Candidate interacting protein partners are fused to specific domains of the yeast GAL4 and herpes simplex virus VP16 transcription factors and transiently expressed in Nicotiana benthamina leaves by Agrobacterium infiltration. PPI, that may be either direct or indirect, results in transcriptional activation of a RUBY reporter gene leading to the production of the highly visual metabolite, betalain, in leaf tissue of living plants. Samples require no processing for in planta visual qualitative assessment, but with very simple processing steps the assay is quantitative. Its accuracy is demonstrated using a series of known interacting protein partners and mutant derivatives including transcription factors, signalling molecules and plant resistance proteins with cognate pathogen effectors. Using this assay, association between the wheat Sr27 stem rust disease resistance protein and corresponding AvrSr27 avirulence effector family produced by the rust pathogen is detected. Interaction is also observed between this resistance protein and the effector encoded by the corresponding avrSr27-3 virulence allele. However, this association appears weaker in the split GAL4 RUBY assay, which coupled with lower avrSr27-3 expression during stem rust infection, likely enables virulent races of the rust pathogen to avoid Sr27-mediated detection.
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Affiliation(s)
- Jian Chen
- CSIRO Agriculture and Food, Box 1700, Clunies Ross St, Canberra, Australia, 2601
| | - Ming Luo
- CSIRO Agriculture and Food, Box 1700, Clunies Ross St, Canberra, Australia, 2601
| | - Phillip Hands
- CSIRO Agriculture and Food, Box 1700, Clunies Ross St, Canberra, Australia, 2601
| | - Vivien Rolland
- CSIRO Agriculture and Food, Box 1700, Clunies Ross St, Canberra, Australia, 2601
| | - Jianping Zhang
- CSIRO Agriculture and Food, Box 1700, Clunies Ross St, Canberra, Australia, 2601
| | - Zhao Li
- Australian National University, Canberra, Australia, 2601
| | - Megan Outram
- CSIRO Agriculture and Food, Box 1700, Clunies Ross St, Canberra, Australia, 2601
| | - Peter Dodds
- CSIRO Agriculture and Food, Box 1700, Clunies Ross St, Canberra, Australia, 2601
| | - Michael Ayliffe
- CSIRO Agriculture and Food, Box 1700, Clunies Ross St, Canberra, Australia, 2601
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34
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Celesia A, Franzò M, Di Liberto D, Lauricella M, Carlisi D, D'Anneo A, Notaro A, Allegra M, Giuliano M, Emanuele S. Oncogenic BRAF and p53 Interplay in Melanoma Cells and the Effects of the HDAC Inhibitor ITF2357 (Givinostat). Int J Mol Sci 2023; 24:ijms24119148. [PMID: 37298104 DOI: 10.3390/ijms24119148] [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: 04/19/2023] [Revised: 05/17/2023] [Accepted: 05/21/2023] [Indexed: 06/12/2023] Open
Abstract
Oncogenic BRAF mutations have been widely described in melanomas and promote tumour progression and chemoresistance. We previously provided evidence that the HDAC inhibitor ITF2357 (Givinostat) targets oncogenic BRAF in SK-MEL-28 and A375 melanoma cells. Here, we show that oncogenic BRAF localises to the nucleus of these cells, and the compound decreases BRAF levels in both the nuclear and cytosolic compartments. Although mutations in the tumour suppressor p53 gene are not equally frequent in melanomas compared to BRAF, the functional impairment of the p53 pathway may also contribute to melanoma development and aggressiveness. To understand whether oncogenic BRAF and p53 may cooperate, a possible interplay was considered in the two cell lines displaying a different p53 status, being p53 mutated into an oncogenic form in SK-MEL-28 and wild-type in A375 cells. Immunoprecipitation revealed that BRAF seems to preferentially interact with oncogenic p53. Interestingly, ITF2357 not only reduced BRAF levels but also oncogenic p53 levels in SK-MEL-28 cells. ITF2357 also targeted BRAF in A375 cells but not wild-type p53, which increased, most likely favouring apoptosis. Silencing experiments confirmed that the response to ITF2357 in BRAF-mutated cells depends on p53 status, thus providing a rationale for melanoma-targeted therapy.
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Affiliation(s)
- Adriana Celesia
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (BIND), Biochemistry Building, University of Palermo, 90127 Palermo, Italy
| | - Marzia Franzò
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (BIND), Biochemistry Building, University of Palermo, 90127 Palermo, Italy
| | - Diana Di Liberto
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (BIND), Biochemistry Building, University of Palermo, 90127 Palermo, Italy
| | - Marianna Lauricella
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (BIND), Biochemistry Building, University of Palermo, 90127 Palermo, Italy
| | - Daniela Carlisi
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (BIND), Biochemistry Building, University of Palermo, 90127 Palermo, Italy
| | - Antonella D'Anneo
- Laboratory of Biochemistry, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90127 Palermo, Italy
| | - Antonietta Notaro
- Laboratory of Biochemistry, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90127 Palermo, Italy
| | - Mario Allegra
- Laboratory of Biochemistry, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90127 Palermo, Italy
| | - Michela Giuliano
- Laboratory of Biochemistry, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90127 Palermo, Italy
| | - Sonia Emanuele
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (BIND), Biochemistry Building, University of Palermo, 90127 Palermo, Italy
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Tian S, Zeng J, Jiao H, Zhang D, Zhang L, Lei CQ, Rossiter SJ, Zhao H. Comparative analyses of bat genomes identify distinct evolution of immunity in Old World fruit bats. SCIENCE ADVANCES 2023; 9:eadd0141. [PMID: 37146151 PMCID: PMC10162675 DOI: 10.1126/sciadv.add0141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Bats have been identified as natural reservoir hosts of several zoonotic viruses, prompting suggestions that they have unique immunological adaptations. Among bats, Old World fruit bats (Pteropodidae) have been linked to multiple spillovers. To test for lineage-specific molecular adaptations in these bats, we developed a new assembly pipeline to generate a reference-quality genome of the fruit bat Cynopterus sphinx and used this in comparative analyses of 12 bat species, including six pteropodids. Our results reveal that immunity-related genes have higher evolutionary rates in pteropodids than in other bats. Several lineage-specific genetic changes were shared across pteropodids, including the loss of NLRP1, duplications of PGLYRP1 and C5AR2, and amino acid replacements in MyD88. We introduced MyD88 transgenes containing Pteropodidae-specific residues into bat and human cell lines and found evidence of dampened inflammatory responses. By uncovering distinct immune adaptations, our results could help explain why pteropodids are frequently identified as viral hosts.
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Affiliation(s)
- Shilin Tian
- College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Jiaming Zeng
- College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Hengwu Jiao
- College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Dejing Zhang
- Novogene Bioinformatics Institute, Beijing 100015, China
| | - Libiao Zhang
- Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Cao-Qi Lei
- College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Huabin Zhao
- College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
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36
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Ding Y, Gong Y, Zeng H, Zhou X, Yu Z, Pan J, Zhou M, Liu S, Lai W. Biological function analysis of ARHGAP39 as an independent prognostic biomarker in hepatocellular carcinoma. Aging (Albany NY) 2023; 15:2631-2666. [PMID: 37059586 PMCID: PMC10120899 DOI: 10.18632/aging.204635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 03/11/2023] [Indexed: 04/16/2023]
Abstract
Hepatocellular carcinoma (HCC) is the most common subtype of liver cancer, with a high morbidity and low survival rate. Rho GTPase activating protein 39 (ARHGAP39) is a crucial activating protein of Rho GTPases, a novel target in cancer therapy, and it was identified as a hub gene for gastric cancer. However, the expression and role of ARHGAP39 in hepatocellular carcinoma remain unclear. Accordingly, the cancer genome atlas (TCGA) data were used to analyze the expression and clinical value of ARHGAP39 in hepatocellular carcinoma. Further, the LinkedOmics tool suggested functional enrichment pathways for ARHGAP39. To investigate in depth the possible role of ARHGAP39 on immune infiltration, we analyzed the relationship between ARHGAP39 and chemokines in HCCLM3 cells. Finally, the GSCA website was used to explore drug resistance in patients with high ARHGAP39 expression. Studies have shown that ARHGAP39 is highly expressed in hepatocellular carcinoma and relevant to clinicopathological features. In addition, the overexpression of ARHGAP39 leads to a poor prognosis. Besides, co-expressed genes and enrichment analysis showed a correlation with the cell cycle. Notably, ARHGAP39 may worsen the survival of hepatocellular carcinoma patients by increasing the level of immune infiltration through chemokines. Moreover, N6-methyladenosine (m6A) modification-related factors and drug sensitivity were also found to be associated with ARHGAP39. In brief, ARHGAP39 is a promising prognostic factor for hepatocellular carcinoma patients that is closely related to cell cycle, immune infiltration, m6A modification, and drug resistance.
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Affiliation(s)
- Yongqi Ding
- Department of Health Management Medical, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Yiyang Gong
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Hong Zeng
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Xuanrui Zhou
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Zichuan Yu
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Jingying Pan
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Minqin Zhou
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Shiwen Liu
- Emergency Intensive Care Unit, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Wei Lai
- Department of Health Management Medical, The Second Affiliated Hospital of Nanchang University, Nanchang, China
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Mostaffa NH, Suhaimi AH, Al-Idrus A. Interactomics in plant defence: progress and opportunities. Mol Biol Rep 2023; 50:4605-4618. [PMID: 36920596 DOI: 10.1007/s11033-023-08345-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 02/15/2023] [Indexed: 03/16/2023]
Abstract
Interactomics is a branch of systems biology that deals with the study of protein-protein interactions and how these interactions influence phenotypes. Identifying the interactomes involved during host-pathogen interaction events may bring us a step closer to deciphering the molecular mechanisms underlying plant defence. Here, we conducted a systematic review of plant interactomics studies over the last two decades and found that while a substantial progress has been made in the field, plant-pathogen interactomics remains a less-travelled route. As an effort to facilitate the progress in this field, we provide here a comprehensive research pipeline for an in planta plant-pathogen interactomics study that encompasses the in silico prediction step to the validation step, unconfined to model plants. We also highlight four challenges in plant-pathogen interactomics with plausible solution(s) for each.
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Affiliation(s)
- Nur Hikmah Mostaffa
- Programme of Genetics, Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Ahmad Husaini Suhaimi
- Programme of Genetics, Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Aisyafaznim Al-Idrus
- Programme of Genetics, Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
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Li L, Shen X, Mo X, Chen Z, Yu F, Mo X, Song J, Huang G, Liang K, Luo Z, Mao N, Yang J. CEMIP-mediated hyaluronan metabolism facilitates SCLC metastasis by activating TLR2/c-Src/ERK1/2 axis. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119451. [PMID: 36931608 DOI: 10.1016/j.bbamcr.2023.119451] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 02/12/2023] [Accepted: 02/27/2023] [Indexed: 03/17/2023]
Abstract
Small-cell lung cancer (SCLC) is a highly metastatic and recalcitrant malignancy. Metastasis is the major cause of death in patients with SCLC but its mechanism remains poorly understood. An imbalance of hyaluronan catabolism in the extracellular matrix accelerates malignant progression in solid cancers due to the accumulation of low-molecular-weight HA. We previously found that CEMIP, a novel hyaluronidase, may act as a metastatic trigger in SCLC. In the present study, we found that both CEMIP and HA levels were higher in SCLC tissues than in paracancerous tissues from patient specimens and in vivo orthotopic models. Additionally, high expression of CEMIP was associated with lymphatic metastasis in patients with SCLC, and in vitro results showed that CEMIP expression was elevated in SCLC cells relative to human bronchial epithelial cells. Mechanistically, CEMIP facilitates the breakdown of HA and accumulation of LMW-HA. LMW-HA activates its receptor TLR2, and subsequently recruits c-Src to activate ERK1/2 signalling, thereby promoting F-actin rearrangement as well as migration and invasion of SCLC cells. In addition, the in vivo results verified that depletion of CEMIP attenuated HA levels and the expressions of TLR2, c-Src, and phosphorylation of ERK1/2, as well as liver and brain metastasis in SCLC xenografts. Furthermore, the application of the actin filament inhibitor latrunculin A significantly inhibited the liver and brain metastasis of SCLC in vivo. Collectively, our findings reveal the critical role of CEMIP-mediated HA degradation in SCLC metastasis and suggest its translational potential as an attractive target and a novel strategy for SCLC therapy.
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Affiliation(s)
- Li Li
- Department of Pharmacology, School of Pharmacy, Guangxi Medical University, Nanning 530021, Guangxi, PR China; Department of Pharmacology, Guangxi Institute of Chinese Medicine & Pharmaceutical Science, Nanning 530001, Guangxi, PR China; Guangxi Key Laboratory of Traditional Chinese Medicine Quality Standards, Guangxi Institute of Chinese Medicine & Pharmaceutical Science, Nanning 530001, Guangxi, PR China
| | - Xiaoju Shen
- Department of Pharmacology, School of Pharmacy, Guangxi Medical University, Nanning 530021, Guangxi, PR China
| | - Xiaoxiang Mo
- Department of Pharmacology, School of Pharmacy, Guangxi Medical University, Nanning 530021, Guangxi, PR China; Department of Pharmacology, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530021, Guangxi, PR China
| | - Zhiquan Chen
- Department of Pharmacology, School of Pharmacy, Guangxi Medical University, Nanning 530021, Guangxi, PR China.
| | - Fei Yu
- Department of Pharmacology, School of Pharmacy, Guangxi Medical University, Nanning 530021, Guangxi, PR China
| | - Xiaocheng Mo
- Department of Pharmacology, School of Pharmacy, Guangxi Medical University, Nanning 530021, Guangxi, PR China
| | - Jinjing Song
- Department of Pharmacology, School of Pharmacy, Guangxi Medical University, Nanning 530021, Guangxi, PR China; Department of Pharmacy, The First People's Hospital of Nanning, Nanning 530022, Guangxi, PR China
| | - Guolin Huang
- Department of Pharmacology, School of Pharmacy, Guangxi Medical University, Nanning 530021, Guangxi, PR China; Department of Pharmacy, The First People's Hospital of Nanning, Nanning 530022, Guangxi, PR China
| | - Kai Liang
- Department of Pharmacology, School of Pharmacy, Guangxi Medical University, Nanning 530021, Guangxi, PR China; Department of Thoracic Tumor Surgery, Guangxi Cancer Hospital and Guangxi Medical University Affiliated Cancer Hospital, Nanning 530021, Guangxi, PR China
| | - Zhuo Luo
- Department of Pharmacology, School of Pharmacy, Guangxi Medical University, Nanning 530021, Guangxi, PR China
| | - Naiquan Mao
- Department of Pharmacology, School of Pharmacy, Guangxi Medical University, Nanning 530021, Guangxi, PR China; Department of Thoracic Tumor Surgery, Guangxi Cancer Hospital and Guangxi Medical University Affiliated Cancer Hospital, Nanning 530021, Guangxi, PR China
| | - Jie Yang
- Department of Pharmacology, School of Pharmacy, Guangxi Medical University, Nanning 530021, Guangxi, PR China.
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Robinson NA, Robledo D, Sveen L, Daniels RR, Krasnov A, Coates A, Jin YH, Barrett LT, Lillehammer M, Kettunen AH, Phillips BL, Dempster T, Doeschl‐Wilson A, Samsing F, Difford G, Salisbury S, Gjerde B, Haugen J, Burgerhout E, Dagnachew BS, Kurian D, Fast MD, Rye M, Salazar M, Bron JE, Monaghan SJ, Jacq C, Birkett M, Browman HI, Skiftesvik AB, Fields DM, Selander E, Bui S, Sonesson A, Skugor S, Østbye TK, Houston RD. Applying genetic technologies to combat infectious diseases in aquaculture. REVIEWS IN AQUACULTURE 2023; 15:491-535. [PMID: 38504717 PMCID: PMC10946606 DOI: 10.1111/raq.12733] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/24/2022] [Accepted: 08/16/2022] [Indexed: 03/21/2024]
Abstract
Disease and parasitism cause major welfare, environmental and economic concerns for global aquaculture. In this review, we examine the status and potential of technologies that exploit genetic variation in host resistance to tackle this problem. We argue that there is an urgent need to improve understanding of the genetic mechanisms involved, leading to the development of tools that can be applied to boost host resistance and reduce the disease burden. We draw on two pressing global disease problems as case studies-sea lice infestations in salmonids and white spot syndrome in shrimp. We review how the latest genetic technologies can be capitalised upon to determine the mechanisms underlying inter- and intra-species variation in pathogen/parasite resistance, and how the derived knowledge could be applied to boost disease resistance using selective breeding, gene editing and/or with targeted feed treatments and vaccines. Gene editing brings novel opportunities, but also implementation and dissemination challenges, and necessitates new protocols to integrate the technology into aquaculture breeding programmes. There is also an ongoing need to minimise risks of disease agents evolving to overcome genetic improvements to host resistance, and insights from epidemiological and evolutionary models of pathogen infestation in wild and cultured host populations are explored. Ethical issues around the different approaches for achieving genetic resistance are discussed. Application of genetic technologies and approaches has potential to improve fundamental knowledge of mechanisms affecting genetic resistance and provide effective pathways for implementation that could lead to more resistant aquaculture stocks, transforming global aquaculture.
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Affiliation(s)
- Nicholas A. Robinson
- Nofima ASTromsøNorway
- Sustainable Aquaculture Laboratory—Temperate and Tropical (SALTT)School of BioSciences, The University of MelbourneMelbourneVictoriaAustralia
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | | | - Rose Ruiz Daniels
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | | | - Andrew Coates
- Sustainable Aquaculture Laboratory—Temperate and Tropical (SALTT)School of BioSciences, The University of MelbourneMelbourneVictoriaAustralia
| | - Ye Hwa Jin
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | - Luke T. Barrett
- Sustainable Aquaculture Laboratory—Temperate and Tropical (SALTT)School of BioSciences, The University of MelbourneMelbourneVictoriaAustralia
- Institute of Marine Research, Matre Research StationMatredalNorway
| | | | | | - Ben L. Phillips
- Sustainable Aquaculture Laboratory—Temperate and Tropical (SALTT)School of BioSciences, The University of MelbourneMelbourneVictoriaAustralia
| | - Tim Dempster
- Sustainable Aquaculture Laboratory—Temperate and Tropical (SALTT)School of BioSciences, The University of MelbourneMelbourneVictoriaAustralia
| | - Andrea Doeschl‐Wilson
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | - Francisca Samsing
- Sydney School of Veterinary ScienceThe University of SydneyCamdenAustralia
| | | | - Sarah Salisbury
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | | | | | | | | | - Dominic Kurian
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | - Mark D. Fast
- Atlantic Veterinary CollegeThe University of Prince Edward IslandCharlottetownPrince Edward IslandCanada
| | | | | | - James E. Bron
- Institute of AquacultureUniversity of StirlingStirlingScotlandUK
| | - Sean J. Monaghan
- Institute of AquacultureUniversity of StirlingStirlingScotlandUK
| | - Celeste Jacq
- Blue Analytics, Kong Christian Frederiks Plass 3BergenNorway
| | | | - Howard I. Browman
- Institute of Marine Research, Austevoll Research Station, Ecosystem Acoustics GroupTromsøNorway
| | - Anne Berit Skiftesvik
- Institute of Marine Research, Austevoll Research Station, Ecosystem Acoustics GroupTromsøNorway
| | | | - Erik Selander
- Department of Marine SciencesUniversity of GothenburgGothenburgSweden
| | - Samantha Bui
- Institute of Marine Research, Matre Research StationMatredalNorway
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Liu S, Wang J, Chen S, Han Z, Wu H, Chen H, Duan Y. C/EBPβ Coupled with E2F2 Promoted the Proliferation of hESC-Derived Hepatocytes through Direct Binding to the Promoter Regions of Cell-Cycle-Related Genes. Cells 2023; 12:cells12030497. [PMID: 36766839 PMCID: PMC9914899 DOI: 10.3390/cells12030497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/09/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Human embryonic stem cells (hESCs) hold the potential to solve the problem of the shortage of functional hepatocytes in clinical applications and drug development. However, a large number of usable hepatocytes derived from hESCs cannot be effectively obtained due to the limited proliferation capacity. In this study, we found that enhancement of liver transcription factor C/EBPβ during hepatic differentiation could not only significantly promote the expression of hepatic genes, such as albumin, alpha fetoprotein, and alpha-1 antitrypsin, but also dramatically reinforce proliferation-related phenotypes, including increasing the expression of proliferative genes, such as CDC25C, CDC45L, and PCNA, and the activation of cell cycle and DNA replication pathways. In addition, the analysis of CUT&Tag sequencing further revealed that C/EBPβ is directly bound to the promoter region of proliferating genes to promote cell proliferation; this interaction between C/EBPβ and DNA sequences of the promoters was verified by luciferase assay. On the contrary, the knockdown of C/EBPβ could significantly inhibit the expression of the aforementioned proliferative genes. RNA transcriptome analysis and GSEA enrichment indicated that the E2F family was enriched, and the expression of E2F2 was changed with the overexpression or knockdown of C/EBPβ. Moreover, the results of CUT&Tag sequencing showed that C/EBPβ also directly bound the promoter of E2F2, regulating E2F2 expression. Interestingly, Co-IP analysis exhibited a direct binding between C/EBPβ and E2F2 proteins, and this interaction between these two proteins was also verified in the LO2 cell line, a hepatic progenitor cell line. Thus, our results demonstrated that C/EBPβ first initiated E2F2 expression and then coupled with E2F2 to regulate the expression of proliferative genes in hepatocytes during the differentiation of hESCs. Therefore, our findings open a new avenue to provide an in vitro efficient approach to generate proliferative hepatocytes to potentially meet the demands for use in cell-based therapeutics as well as for pharmaceutical and toxicological studies.
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Affiliation(s)
- Shoupei Liu
- Laboratory of Stem Cells and Translational Medicine, Institutes for Life Sciences, School of Medicine, South China University of Technology, Guangzhou 510006, China
| | - Jue Wang
- Laboratory of Stem Cells and Translational Medicine, Institutes for Life Sciences, School of Medicine, South China University of Technology, Guangzhou 510006, China
| | - Sen Chen
- Laboratory of Stem Cells and Translational Medicine, Institutes for Life Sciences, School of Medicine, South China University of Technology, Guangzhou 510006, China
| | - Zonglin Han
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Haibin Wu
- Laboratory of Stem Cells and Translational Medicine, Institutes for Life Sciences, School of Medicine, South China University of Technology, Guangzhou 510006, China
| | - Honglin Chen
- Laboratory of Stem Cells and Translational Medicine, Institutes for Life Sciences, School of Medicine, South China University of Technology, Guangzhou 510006, China
- Correspondence: (H.C.); (Y.D.)
| | - Yuyou Duan
- Laboratory of Stem Cells and Translational Medicine, Institutes for Life Sciences, School of Medicine, South China University of Technology, Guangzhou 510006, China
- Correspondence: (H.C.); (Y.D.)
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Wang S, Zhao J, Wang L, Zhang T, Zeng W, Lu H. METTL21C mediates lysine trimethylation of IGF2BP1 to regulate chicken myoblast proliferation. Br Poult Sci 2023; 64:74-80. [PMID: 36069737 DOI: 10.1080/00071668.2022.2121639] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
1. Methyltransferase-like 21C (METTL21C) and insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) play important roles in the proliferation of chicken myoblasts. However, it remains unclear whether there is protein-protein interaction between METTL21C and IGF2BP1 to regulate proliferation of chicken myoblasts.2. In this study, the Igf2bp1 gene was amplified from cDNA of liver tissue of Lueyang black-bone chicken to construct the overexpression vector HA-Igf2bp1. The HA-Igf2bp1 and Flag-Mettl21c vectors were individually transfected and co-transfected into HEK293T, respectively. Co-immunoprecipitation (Co-IP) assay indicated a protein-protein interaction between METTL21C and IGF2BP1.3. Using the Western blotting and LC-MS/MS, it was found that METTL21C could mediate the lysine methylation modification of IGF2BP1. Furthermore, the His-tagged overexpression vector HA-Igf2bp1-His was constructed, transfected and co-transfected with Flag-Mettl21c into HEK293T. His-tagged IGF2BP1 was purified by nickel ion affinity chromatography. Western blotting revealed that IGF2BP1 was successfully purified, and the trimethylation modification level of co-transfection group was significantly elevated compared with the single-transfection Igf2bp1 group.4. Mettl21c and Igf2bp1 overexpression vectors were transfected and co-transfected into primary chicken myoblasts, respectively. The results of 5-ethynyl-2'-deoxyuridine assay and the expression level of Pax7 and MyoD indicated that overexpression of Igf2bp1 alone inhibited the chicken myoblast proliferation, whereas co-expression of Mettl21c and Igf2bp1 eliminated the inhibitory effects of Igf2bp1, thereby favouring cell proliferation and differentiation.5. The results, for the first time, revealed that METTL21C mediated the lysine trimethylation modification of IGF2BP1 to regulate the proliferation of chicken myoblasts, which provided a new insight into in-depth analysis of the molecular mechanism of METTL21C methylation involved in regulating the growth and development of skeletal muscle in Lueyang black-bone chicken.
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Affiliation(s)
- S Wang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi, China
- Qinba State Key Laboratory of Biological Resources and Ecological Environment, Shaanxi University of Technology, Hanzhong, Shaanxi, China
| | - J Zhao
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi, China
| | - L Wang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi, China
- Qinba State Key Laboratory of Biological Resources and Ecological Environment, Shaanxi University of Technology, Hanzhong, Shaanxi, China
| | - T Zhang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi, China
- Department of Biology, QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C., Hanzhong, Shaanxi, China
| | - W Zeng
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi, China
- Department of Biology, QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C., Hanzhong, Shaanxi, China
| | - H Lu
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi, China
- Qinba State Key Laboratory of Biological Resources and Ecological Environment, Shaanxi University of Technology, Hanzhong, Shaanxi, China
- Shaanxi Province Key Laboratory of Bio-resources, Shaanxi University of Technology, Hanzhong, Shaanxi, China
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Xue K, Chen S, Chai J, Yan W, Zhu X, Ji D, Wu Y, Liu H, Wang W. Nitration of cAMP-Response Element Binding Protein Participates in Myocardial Infarction-Induced Myocardial Fibrosis via Accelerating Transcription of Col1a2 and Cxcl12. Antioxid Redox Signal 2023; 38:709-730. [PMID: 36324232 DOI: 10.1089/ars.2021.0273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Aims: Myocardial fibrosis after myocardial infarction (MI) leads to heart failure. Nitration of protein can alter its function. cAMP-response element binding protein (CREB) is a key transcription factor involved in fibrosis. However, little is known about the role of nitrated CREB in MI-induced myocardial fibrosis. Meanwhile, downstream genes of transcription factor CREB in myocardial fibrosis have not been identified. This study aims to verify the hypothesis that nitrated CREB promotes MI-induced myocardial fibrosis via regulating the transcription of Col1a2 and Cxcl12. Results: Our study showed that (1) the level of nitrative stress was elevated and nitrated CREB was higher in the myocardium after MI. Tyr182, 307, and 336 were the nitration sites of CREB; (2) with the administration of peroxynitrite (ONOO-) scavengers, CREB phosphorylation, nuclear translocation, and binding activity to TORC2 (transducers of regulated CREB-2) were attenuated; (3) the expressions of extracellular matrix (ECM) proteins were upregulated and downregulated in accordance with the expression alteration of CREB both in vitro and in vivo; (4) CREB accelerated transcription of Col1a2 and Cxcl12 after MI directly. With the administration of ONOO- scavengers, ECM protein expressions were attenuated; meanwhile, the messenger RNA (mRNA) levels of Col1a2 and Cxcl12 were alleviated as well. Innovation and Conclusion: Nitration of transcription factor CREB participates in MI-induced myocardial fibrosis through enhancing its phosphorylation, nuclear translocation, and binding activity to TORCs, among which CREB transcripts Col1a2 and Cxcl12 directly. These data indicated that nitrated CREB might be a potential therapeutic target against MI-induced myocardial fibrosis.
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Affiliation(s)
- Ke Xue
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China.,Beijing Key Laboratory for Metabolic Disorder-Related Cardiovascular Diseases, Beijing, China.,Department of Pathology, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Shuai Chen
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China.,Beijing Key Laboratory for Metabolic Disorder-Related Cardiovascular Diseases, Beijing, China
| | - Jiayin Chai
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China.,Beijing Key Laboratory for Metabolic Disorder-Related Cardiovascular Diseases, Beijing, China
| | - Wenjing Yan
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China.,Beijing Key Laboratory for Metabolic Disorder-Related Cardiovascular Diseases, Beijing, China
| | - Xinyu Zhu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China.,Beijing Key Laboratory for Metabolic Disorder-Related Cardiovascular Diseases, Beijing, China
| | - Dengyu Ji
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China.,Beijing Key Laboratory for Metabolic Disorder-Related Cardiovascular Diseases, Beijing, China
| | - Ye Wu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China.,Beijing Key Laboratory for Metabolic Disorder-Related Cardiovascular Diseases, Beijing, China
| | - Huirong Liu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China.,Beijing Key Laboratory for Metabolic Disorder-Related Cardiovascular Diseases, Beijing, China
| | - Wen Wang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing, China.,Beijing Key Laboratory for Metabolic Disorder-Related Cardiovascular Diseases, Beijing, China
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Zhang H, Liu C, Zhu D, Zhang Q, Li J. Medicinal Chemistry Strategies for the Development of Inhibitors Disrupting β-Catenin's Interactions with Its Nuclear Partners. J Med Chem 2023; 66:1-31. [PMID: 36583662 DOI: 10.1021/acs.jmedchem.2c01016] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Dysregulation of the Wnt/β-catenin signaling pathway is strongly associated with various aspects of cancer, including tumor initiation, proliferation, and metastasis as well as antitumor immunity, and presents a promising opportunity for cancer therapy. Wnt/β-catenin signaling activation increases nuclear dephosphorylated β-catenin levels, resulting in β-catenin binding to TCF and additional cotranscription factors, such as BCL9, CBP, and p300. Therefore, directly disrupting β-catenin's interactions with these nuclear partners holds promise for the effective and selective suppression of the aberrant activation of Wnt/β-catenin signaling. Herein, we summarize recent advances in biochemical techniques and medicinal chemistry strategies used to identify potent peptide-based and small-molecule inhibitors that directly disrupt β-catenin's interactions with its nuclear binding partners. We discuss the challenges involved in developing drug-like inhibitors that target the interactions of β-catenin and its nuclear binding partner into therapeutic agents.
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Affiliation(s)
- Hao Zhang
- School of Pharmacy, Fudan University, Shanghai 201203, China.,Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai 201203, China
| | - Chenglong Liu
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Di Zhu
- School of Pharmacy, Fudan University, Shanghai 201203, China.,Department of Pharmacology, School of Basic Medical Science, Fudan University, Shanghai 201100, China
| | - Qingwei Zhang
- Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai 201203, China
| | - Jianqi Li
- Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai 201203, China
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Khan M, Djamei A. Co-immunoprecipitation-Based Identification of Effector-Host Protein Interactions from Pathogen-Infected Plant Tissue. Methods Mol Biol 2023; 2690:87-100. [PMID: 37450139 DOI: 10.1007/978-1-0716-3327-4_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Protein-protein interactions play an essential role in host-pathogen interactions. Phytopathogens secrete a cocktail of effector proteins to suppress plant immunity and reprogram host cell metabolism in their favor. Identification and characterization of effectors and their target protein complexes by co-immunoprecipitation can help to gain a deeper understanding of the functions of individual effectors during pathogenicity and can also provide new insights into the wiring of plant signaling pathways or metabolic complexes. Here we describe a detailed protocol to perform co-immunoprecipitation of effector-target protein complexes from plant extracts with an example of the Ustilago maydis/maize pathosystem for which we also provide a fungal protoplast transformation and maize seedling infection protocols.
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Affiliation(s)
- Mamoona Khan
- Department of Plant Pathology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany.
| | - Armin Djamei
- Department of Plant Pathology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
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45
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Gnanasekaran P, Pappu HR. Affinity Purification-Mass Spectroscopy (AP-MS) and Co-Immunoprecipitation (Co-IP) Technique to Study Protein-Protein Interactions. Methods Mol Biol 2023; 2690:81-85. [PMID: 37450138 DOI: 10.1007/978-1-0716-3327-4_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Affinity purification-Mass spectroscopy (AP-MS) is a biochemical technique to identify the novel protein-protein interaction that occurs in the most relevant physiological conditions, whereas co-immunoprecipitation (Co-IP) is used to study the interaction between two known protein partners that are expressed in the native physiological conditions. Both AP-MS and Co-IP techniques are based on the ability of the interacting partners to pull-down with protein of interest. In this chapter, we have explained the AP-MS and Co-IP methods to study protein-protein interactions in the plant cells.
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Affiliation(s)
- Prabu Gnanasekaran
- Department of Plant Pathology, Washington State University, Pullman, WA, USA
| | - Hanu R Pappu
- Department of Plant Pathology, Washington State University, Pullman, WA, USA.
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46
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Zheng J, Yang X, Zhang Z. Using PlaPPISite to Predict and Analyze Plant Protein-Protein Interaction Sites. Methods Mol Biol 2023; 2690:385-399. [PMID: 37450161 DOI: 10.1007/978-1-0716-3327-4_30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Proteome-wide characterization of protein-protein interactions (PPIs) is crucial to understand the functional roles of protein machinery within cells systematically. With the accumulation of PPI data in different plants, the interaction details of binary PPIs, such as the three-dimensional (3D) structural contexts of interaction sites/interfaces, are urgently demanded. To meet this requirement, we have developed a comprehensive and easy-to-use database called PlaPPISite ( http://zzdlab.com/plappisite/index.php ) to present interaction details for 13 plant interactomes. Here, we provide a clear guide on how to search and view protein interaction details through the PlaPPISite database. Firstly, the running environment of our database is introduced. Secondly, the input file format is briefly introduced. Moreover, we discussed which information related to interaction sites can be achieved through several examples. In addition, some notes about PlaPPISite are also provided. More importantly, we would like to emphasize the importance of interaction site information in plant systems biology through this user guide of PlaPPISite. In particular, the easily accessible 3D structures of PPIs in the coming post-AlphaFold2 era will definitely boost the application of plant interactome to decipher the molecular mechanisms of many fundamental biological issues.
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Affiliation(s)
- Jingyan Zheng
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xiaodi Yang
- Department of Hematology, Peking University First Hospital, Beijing, China.
| | - Ziding Zhang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, China.
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47
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Removal of nonspecific binding proteins is required in co-immunoprecipitation with nuclear proteins. Biotechniques 2022; 73:289-296. [DOI: 10.2144/btn-2022-0048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Whether protein samples should be pretreated to remove nonspecific binding proteins in co-immunoprecipitation (CO-IP) is controversial. In this work, nonspecific binding of proteins to agarose beads was found to be greater than that to magnetic beads. The nonspecific binding was increased with the decrease of ion concentrations but reduced by Nonidet P40. Western blot indicated that p65 and β-actin were present as nonspecifically bound protein to the beads. p53 and β-actin were present in the CO-IP precipitates of nuclear proteins but pretreatment cleared the nonspecifically pulled down p53 and β-actin. These data suggest that magnetic beads are better for CO-IP, but preclearing is necessary to minimize false positive regardless of which bead is used, particularly for nuclear proteins.
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Zhang Q, Bai X, Lin T, Wang X, Zhang B, Dai L, Shi J, Zhang Y, Zhao X. HMOX1 Promotes Ferroptosis in Mammary Epithelial Cells via FTH1 and Is Involved in the Development of Clinical Mastitis in Dairy Cows. Antioxidants (Basel) 2022; 11:2221. [PMID: 36421410 PMCID: PMC9686786 DOI: 10.3390/antiox11112221] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 08/26/2023] Open
Abstract
Ferroptosis is associated with inflammatory diseases as a lethal iron-dependent lipid peroxidation; its role in the development of clinical mastitis (CM) in dairy cows is not well understood. The aim of this study was to identify differentially expressed proteins (DEPs) associated with iron homeostasis and apoptosis, and to investigate further their roles in dairy cows with CM. The results suggested that ferroptosis occurs in the mammary glands of Holstein cows with CM. Using data-independent acquisition proteomics, 302 DEPs included in 11 GO terms related to iron homeostasis and apoptosis were identified. In particular, heme oxygenase-1 (HMOX1) was identified and involved in nine pathways. In addition, ferritin heavy chain 1 (FTH1) was identified and involved in the ferroptosis pathway. HMOX1 and FTH1 were located primarily in mammary epithelial cells (MECs), and displayed significantly up-regulated expression patterns compared to the control group (healthy cows). The expression levels of HMOX1 and FTH1 were up-regulated in a dose-dependent manner in LPS induced MAC-T cells with increased iron accumulation. The expression levels of HMOX1 and FTH1 and iron accumulation levels in the MAC-T cells were significantly up-regulated by using LPS, but were lower than the levels seen with Erastin (ERA). Finally, we deduced the mechanism of ferroptosis in the MECs of Holstein cows with CM. These results provide new insights for the prevention and treatment of ferroptosis-mediated clinical mastitis in dairy animals.
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Affiliation(s)
- Quanwei Zhang
- College of Life Science and Technology, Gansu Agriculture University, Lanzhou 730070, China
- College of Veterinary Medicine, Gansu Agriculture University, Lanzhou 730070, China
- Gansu Key Laboratory of Animal Reproductive Physiology and Reproductive Regulation, Lanzhou 730070, China
| | - Xu Bai
- College of Life Science and Technology, Gansu Agriculture University, Lanzhou 730070, China
- Gansu Key Laboratory of Animal Reproductive Physiology and Reproductive Regulation, Lanzhou 730070, China
| | - Ting Lin
- College of Life Science and Technology, Gansu Agriculture University, Lanzhou 730070, China
- Gansu Key Laboratory of Animal Reproductive Physiology and Reproductive Regulation, Lanzhou 730070, China
| | - Xueying Wang
- College of Veterinary Medicine, Gansu Agriculture University, Lanzhou 730070, China
- Gansu Key Laboratory of Animal Reproductive Physiology and Reproductive Regulation, Lanzhou 730070, China
| | - Bohao Zhang
- College of Veterinary Medicine, Gansu Agriculture University, Lanzhou 730070, China
- Gansu Key Laboratory of Animal Reproductive Physiology and Reproductive Regulation, Lanzhou 730070, China
| | - Lijun Dai
- College of Life Science and Technology, Gansu Agriculture University, Lanzhou 730070, China
- Gansu Key Laboratory of Animal Reproductive Physiology and Reproductive Regulation, Lanzhou 730070, China
| | - Jun Shi
- College of Life Science and Technology, Gansu Agriculture University, Lanzhou 730070, China
- Gansu Key Laboratory of Animal Reproductive Physiology and Reproductive Regulation, Lanzhou 730070, China
| | - Yong Zhang
- College of Life Science and Technology, Gansu Agriculture University, Lanzhou 730070, China
- College of Veterinary Medicine, Gansu Agriculture University, Lanzhou 730070, China
- Gansu Key Laboratory of Animal Reproductive Physiology and Reproductive Regulation, Lanzhou 730070, China
| | - Xingxu Zhao
- College of Life Science and Technology, Gansu Agriculture University, Lanzhou 730070, China
- College of Veterinary Medicine, Gansu Agriculture University, Lanzhou 730070, China
- Gansu Key Laboratory of Animal Reproductive Physiology and Reproductive Regulation, Lanzhou 730070, China
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Yadav RP, Sadhukhan S, Saha ML, Ghosh S, Das M. Exploring the mechanism of andrographolide in the treatment of gastric cancer through network pharmacology and molecular docking. Sci Rep 2022; 12:18413. [PMID: 36319798 PMCID: PMC9626486 DOI: 10.1038/s41598-022-18319-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 08/09/2022] [Indexed: 01/01/2023] Open
Abstract
Gastric cancer has emerged as a key challenge in oncology research as a malignant tumour with advanced stage detection. Apart from surgical management, a pharmacotherapeutic approach to stomach cancer treatment is an appealing option to consider. Andrographolide has been shown to have anticancer and chemosensitizer properties in a variety of solid tumors, including stomach cancer but the exact molecular mechanism is skeptical. In this study, we identified and validated pharmacological mechanism involved in the treatment of GC with integrated approach of network pharmacology and molecular docking. The targets of andrographolide and GC were obtained from databases. The intersected targets between andrographolide and GC-related genes were used to construct protein-protein interaction (PPI) network. Furthermore, mechanism of action of the targets was predicted by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Finally, these results were validated by molecular docking experiments, mRNA and protein expression level. A total of 197 targets were obtained for andrographolide treating GC. Functional enrichment analysis revealed that the target genes were exerted promising therapeutic effects on GC by HIF-1 and PI3K-Akt signaling pathway. The possible mechanism of action is by inactivation of HIF-1 signaling pathway which is dependent on the inhibition of upstream PI3K-AKT pathway. The PPI network identified SRC, AKT1, TP53, STAT3, PIK3CA, MAPK1, MAPK3, VEGFA, JUN and HSP90AA1 as potential hub targets. In addition, these results were further validated with molecular docking experiments. Survival analysis indicated that the expression levels of the hub genes were significantly associated with the clinical prognosis of GC. This study provided a novel approach to reveal the therapeutic mechanisms of andrographolide on GC, making future clinical application of andrographolide in the treatment of GC.
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Affiliation(s)
- Ravi Prakash Yadav
- grid.59056.3f0000 0001 0664 9773Department of Zoology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700 019 India
| | - Susanta Sadhukhan
- grid.59056.3f0000 0001 0664 9773Department of Zoology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700 019 India
| | - Makhan Lal Saha
- grid.414764.40000 0004 0507 4308Department of General Surgery, Institute of Post Graduate Medical Education & Research, Kolkata, 700020 India
| | - Sudakshina Ghosh
- grid.59056.3f0000 0001 0664 9773Department of Zoology, Vidyasagar College for Women, 39 Sankar Ghosh Lane, Kolkata, 700006 India
| | - Madhusudan Das
- grid.59056.3f0000 0001 0664 9773Department of Zoology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700 019 India
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50
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Bao X, Zhang Y, Li H, Teng Y, Ma L, Chen Z, Luo X, Zheng J, Zhao A, Ren J, Zuo Z. RM2Target: a comprehensive database for targets of writers, erasers and readers of RNA modifications. Nucleic Acids Res 2022; 51:D269-D279. [PMID: 36300630 PMCID: PMC9825529 DOI: 10.1093/nar/gkac945] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/21/2022] [Accepted: 10/11/2022] [Indexed: 01/29/2023] Open
Abstract
RNA modification is a dynamic and reversible process regulated by a series of writers, erasers and readers (WERs). Abnormal changes of WERs will disrupt the RNA modification homeostasis of their target genes, leading to the dysregulation of RNA metabolisms such as RNA stability and translation, and consequently to diseases such as cancer. A public repository hosting the regulatory relationships between WERs and their target genes will help in understanding the roles of RNA modifications in various physiological and pathological conditions. Previously, we developed a database named 'm6A2Target' to host targets of WERs in m6A, one of the most prevalent RNA modifications in eukaryotic cells. To host all RNA modification (RM)-related WER-target associations, we hereby present an updated database, named 'RM2Target' (http://rm2target.canceromics.org/). In this update, RM2Target encompasses 1 619 653 WER-target associations for nine RNA modifications in human and mouse, including m6A, m6Am, m5C, m5U, m1A, m7G, pseudouridine, 2'-O-Me and A-to-I. Extensive annotations of target genes are available in RM2Target, including but not limited to basic gene information, RNA modifications, RNA-RNA/RNA-protein interactions and related diseases. Altogether, we expect that RM2Target will facilitate further downstream functional and mechanistic studies in the field of RNA modification research.
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Affiliation(s)
| | | | | | - Yuyan Teng
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou 510060, China
| | - Lixia Ma
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou 510060, China
| | - Zhihang Chen
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou 510060, China
| | - Xiaotong Luo
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou 510060, China
| | - Jian Zheng
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou 510060, China
| | - An Zhao
- Correspondence may also be addressed to An Zhao.
| | - Jian Ren
- Correspondence may also be addressed to Jian Ren.
| | - Zhixiang Zuo
- To whom correspondence should be addressed. Tel: +86 02087342325;
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