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Ochoa-Alejo N, Gómez-Jiménez MC, Martínez O. Editorial: Transcriptomics of fruit growth, development and ripening. Front Plant Sci 2024; 15:1399376. [PMID: 38645390 PMCID: PMC11026863 DOI: 10.3389/fpls.2024.1399376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 03/27/2024] [Indexed: 04/23/2024]
Affiliation(s)
- Neftali Ochoa-Alejo
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Irapuato, Guanajuato, Mexico
| | | | - Octavio Martínez
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, Mexico
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Augustijn HE, Karapliafis D, Joosten KMM, Rigali S, van Wezel GP, Medema MH. LogoMotif: A Comprehensive Database of Transcription Factor Binding Site Profiles in Actinobacteria. J Mol Biol 2024:168558. [PMID: 38580076 DOI: 10.1016/j.jmb.2024.168558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/28/2024] [Accepted: 03/30/2024] [Indexed: 04/07/2024]
Abstract
Actinobacteria undergo a complex multicellular life cycle and produce a wide range of specialized metabolites, including the majority of the antibiotics. These biological processes are controlled by intricate regulatory pathways, and to better understand how they are controlled we need to augment our insights into the transcription factor binding sites. Here, we present LogoMotif (https://logomotif.bioinformatics.nl), an open-source database for characterized and predicted transcription factor binding sites in Actinobacteria, along with their cognate position weight matrices and hidden Markov models. Genome-wide predictions of binding site locations in Streptomyces model organisms are supplied and visualized in interactive regulatory networks. In the web interface, users can freely access, download and investigate the underlying data. With this curated collection of actinobacterial regulatory interactions, LogoMotif serves as a basis for binding site predictions, thus providing users with clues on how to elicit the expression of genes of interest and guide genome mining efforts.
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Affiliation(s)
- Hannah E Augustijn
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands; Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | | | - Kristy M M Joosten
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Sébastien Rigali
- InBioS - Center for Protein Engineering, University of Liège, Institut de Chimie, B-4000 Liège, Belgium
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands.
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands; Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands.
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3
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Li L, Jin M, Tan J, Xiao B. NcRNAs: A synergistically antiapoptosis therapeutic tool in Alzheimer's disease. CNS Neurosci Ther 2024; 30:e14476. [PMID: 37735992 PMCID: PMC11017435 DOI: 10.1111/cns.14476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/22/2023] [Accepted: 09/08/2023] [Indexed: 09/23/2023] Open
Abstract
AIMS The aim of this review is to systematically summarize and analyze the noncoding RNAs (ncRNAs), especially microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs), in the cell apoptosis among Alzheimer's disease (AD) in recent years to demonstrate their value in the diagnosis and treatment of AD. METHODS We systematically summarized in vitro and in vivo studies focusing on the ncRNAs in the regulation of cell apoptosis among AD in PubMed, ScienceDirect, and Google Scholar. RESULTS We discover three patterns of ncRNAs (including 'miRNA-mRNA', 'lncRNA-miRNA-mRNA', and 'circRNA-miRNA-mRNA') form the ncRNA-based regulatory networks in regulating cell apoptosis in AD. CONCLUSIONS This review provides a future diagnosis and treatment strategy for AD patients based on ncRNAs.
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Affiliation(s)
- Liangxian Li
- Laboratory of Respiratory DiseaseAffiliated Hospital of Guilin Medical UniversityGuilinChina
- Guangxi Key Laboratory of Brain and Cognitive NeuroscienceGuilin Medical UniversityGuilinChina
| | - Mingyue Jin
- Guangxi Key Laboratory of Brain and Cognitive NeuroscienceGuilin Medical UniversityGuilinChina
| | - Jie Tan
- Guangxi Key Laboratory of Brain and Cognitive NeuroscienceGuilin Medical UniversityGuilinChina
| | - Bo Xiao
- Laboratory of Respiratory DiseaseAffiliated Hospital of Guilin Medical UniversityGuilinChina
- Guangxi Key Laboratory of Brain and Cognitive NeuroscienceGuilin Medical UniversityGuilinChina
- Key Laboratory of Respiratory DiseasesEducation Department of Guangxi Zhuang Autonomous RegionGuilinChina
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Yang F, Sun X, Wu G, He X, Liu W, Wang Y, Sun Q, Zhao Y, Xu D, Dai X, Ma W, Zeng J. Genome-Wide Identification and Expression Profiling of the ABF Transcription Factor Family in Wheat ( Triticum aestivum L.). Int J Mol Sci 2024; 25:3783. [PMID: 38612594 PMCID: PMC11011718 DOI: 10.3390/ijms25073783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Members of the abscisic acid (ABA)-responsive element (ABRE) binding factor (ABF) and ABA-responsive element binding protein (AREB) families play essential roles in the regulation of ABA signaling pathway activity and shape the ability of plants to adapt to a range of stressful environmental conditions. To date, however, systematic genome-wide analyses focused on the ABF/AREB gene family in wheat are lacking. Here, we identified 35 ABF/AREB genes in the wheat genome, designated TaABF1-TaABF35 according to their chromosomal distribution. These genes were further classified, based on their phylogenetic relationships, into three groups (A-C), with the TaABF genes in a given group exhibiting similar motifs and similar numbers of introns/exons. Cis-element analyses of the promoter regions upstream of these TaABFs revealed large numbers of ABREs, with the other predominant elements that were identified differing across these three groups. Patterns of TaABF gene expansion were primarily characterized by allopolyploidization and fragment duplication, with purifying selection having played a significant role in the evolution of this gene family. Further expression profiling indicated that the majority of the TaABF genes from groups A and B were highly expressed in various tissues and upregulated following abiotic stress exposure such as drought, low temperature, low nitrogen, etc., while some of the TaABF genes in group C were specifically expressed in grain tissues. Regulatory network analyses revealed that four of the group A TaABFs (TaABF2, TaABF7, TaABF13, and TaABF19) were centrally located in protein-protein interaction networks, with 13 of these TaABF genes being regulated by 11 known miRNAs, which play important roles in abiotic stress resistance such as drought and salt stress. The two primary upstream transcription factor types found to regulate TaABF gene expression were BBR/BPC and ERF, which have previously been reported to be important in the context of plant abiotic stress responses. Together, these results offer insight into the role that the ABF/AREB genes play in the responses of wheat to abiotic stressors, providing a robust foundation for future functional studies of these genes.
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Affiliation(s)
- Fuhui Yang
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Xuelian Sun
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Gang Wu
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Xiaoyan He
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Wenxing Liu
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Yongmei Wang
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Qingyi Sun
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Yan Zhao
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Dengan Xu
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Xuehuan Dai
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Wujun Ma
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
- Academy of Dongying Efficient Agricultural Technology and Industry on Saline and Alkaline Land in Collaboration with Qingdao Agricultural University, Dongying 257347, China
| | - Jianbin Zeng
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
- Academy of Dongying Efficient Agricultural Technology and Industry on Saline and Alkaline Land in Collaboration with Qingdao Agricultural University, Dongying 257347, China
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Xu G, Yang Y, Lin Y, Bai Y. GEO dataset mining analysis reveals novel Staphylococcus aureus virulence gene regulatory networks and diagnostic targets in mice. Front Mol Biosci 2024; 11:1381334. [PMID: 38606287 PMCID: PMC11007229 DOI: 10.3389/fmolb.2024.1381334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 03/18/2024] [Indexed: 04/13/2024] Open
Abstract
Staphylococcus (S.) aureus infection is a serious, worldwide health concern, particularly in many communities and hospitals. Understanding the S. aureus pathogenetic regulatory network will provide significant insights into diagnostic target screening to improve clinical treatment of diseases caused by S. aureus. We screened differentially expressed genes between normal mice and S. aureus-infected mice. We used the Gene Expression Omnibus (GEO) DataSets database for functional analysis (GO-analysis) and the DAVID and KEGG databases for signaling pathway analyses. We next integrated the gene and pathway analyses with Transcriptional Regulatory Element Database (TRED) to build an antimicrobial resistance gene regulatory network of S. aureus. We performed association analysis of network genes and diseases using DAVID online annotation tools. We identified a total of 437 virulence genes and 15 transcription factors (TFs), as well as 444 corresponding target genes, in the S. aureus TF regulatory network. We screened seven key network nodes (Met, Mmp13, Il12b, Il4, Tnf, Ptgs2, and Ctsl), four key transcription factors (Jun, C3, Spil, and Il6) and an important signaling pathway (TNF). We hypothesized that the cytokine activity and growth factor activity of S. aureus are combinatorically cross-regulated by Met, Mmp13, Il12b, Il4, Tnf, Ptgs2, and Ctsl genes, the TFs Jun, C3, Spi1, and Il6, as well as the immune response, cellular response to lipopolysaccharide, and inflammatory response. Our study provides information and reference values for the molecular understanding of the S. aureus pathogenetic gene regulatory network.
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Affiliation(s)
- Guangyu Xu
- College of Pharmacy, Beihua University, Jilin, China
| | - Yue Yang
- College of Pharmacy, Beihua University, Jilin, China
| | - Yan Lin
- School of Basic Medical Sciences, Beihua University, Jilin, China
| | - Yu Bai
- College of Pharmacy, Jilin Medical University, Jilin, China
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Li X, Li Z, Wei Y, Chen Z, Xie S. Identification and characterization of the TetR family transcriptional regulator NffT in Rhizobium johnstonii. Appl Environ Microbiol 2024; 90:e0185123. [PMID: 38426790 PMCID: PMC10952539 DOI: 10.1128/aem.01851-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 02/02/2024] [Indexed: 03/02/2024] Open
Abstract
Symbiotic nitrogen fixation (SNF) by rhizobia is not only the main natural bionitrogen-source for organisms but also a green process leveraged to increase the fertility of soil for agricultural production. However, an insufficient understanding of the regulatory mechanism of SNF hinders its practical application. During SNF, nifA-fixA signaling is essential for the biosynthesis of nitrogenases and electron transfer chain proteins. In the present study, the TetR regulator NffT, whose mutation increased fixA expression, was discovered through a fixA-promoter-β-glucuronidase fusion assay performed with Rhizobium johnstonii. Real-time quantitative PCR analysis showed that nffT deletion increased the expression of symbiotic genes including nifA and fixA in nifA-fixA signaling, and fixL, fixK, fnrN, and fixN9 in fixL-fixN signaling. nffT overexpression resulted in disordered nodules and reduced nitrogen-fixing efficiency. Electrophoretic mobility shift assays revealed that NffT directly regulated the transcription of RL0091-93, which encode an ATP-binding ABC transporter predicted to be involved in carbohydrate transport. Purified His-tagged NffT bound to a 68 bp DNA sequence located -32 to -99 bp upstream of RL0091-93 and NffT deletion significantly increased the expression of RL0091-93. nffT-promoter-β-glucuronidase fusion assay indicated that nffT expression was regulated by the cobNTS genes and cobalamin. Mutations in cobNTS significantly decreased the expression of nffT, and cobalamin restored its expression. These results revealed that NffT affects nodule development and nitrogen-fixing reaction by participating in a complex regulatory network of symbiotic and carbohydrate metabolic genes and, thus, plays a pivotal regulatory role during symbiosis of R. johnstonii-Pisum sativum.IMPORTANCESymbiotic nitrogen fixation (SNF) by rhizobia is a green way to maintain soil fertility without causing environmental pollution or consuming chemical energy. A detailed understanding of the regulatory mechanism of this complex process is essential for promoting sustainable agriculture. In this study, we discovered the TetR-type regulator NffT, which suppressed the expression of fixA in Rhizobium johnstonii. Furthermore, NffT was confirmed to play pleiotropic roles in R. johnstonii-Pisum sativum symbiosis; specifically, it inhibited rhizobial growth, nodule differentiation, and nitrogen-fixing reactions. We revealed that NffT indirectly affected R. johnstonii-P. sativum symbiosis by participating in a complex regulatory network of symbiotic and carbohydrate metabolic genes. Furthermore, cobalamin, a chemical molecule, was reported for the first time to be involved in TetR-type protein transcription during symbiosis. Thus, NffT identification connects SNF regulation with genetic, metabolic, and chemical signals and provides new insights into the complex regulation of SNF, laying an experimental basis for the targeted construction of rhizobial strains with highly efficient nitrogen-fixing capacity.
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Affiliation(s)
- Xiaofang Li
- Institute of Biopharmaceuticals, School of Pharmaceutical Sciences, Taizhou University, Taizhou, Zhejiang, China
| | - Zhangqun Li
- Institute of Biopharmaceuticals, School of Pharmaceutical Sciences, Taizhou University, Taizhou, Zhejiang, China
| | - Yajuan Wei
- Institute of Biopharmaceuticals, School of Pharmaceutical Sciences, Taizhou University, Taizhou, Zhejiang, China
| | - Zirui Chen
- Institute of Biopharmaceuticals, School of Pharmaceutical Sciences, Taizhou University, Taizhou, Zhejiang, China
| | - Shijie Xie
- Institute of Biopharmaceuticals, School of Pharmaceutical Sciences, Taizhou University, Taizhou, Zhejiang, China
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Chen L, Tang Z, Fu L, Xie Y, Xu J, Xia H, Xia T, Wang M. The Critical Role of Pyroptosis in Peri-Implantitis. J Inflamm Res 2024; 17:1621-1642. [PMID: 38495343 PMCID: PMC10944294 DOI: 10.2147/jir.s450706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 03/05/2024] [Indexed: 03/19/2024] Open
Abstract
Background Peri-implantitis (PI) is a prevalent complication of implant treatment. Pyroptosis, a distinctive inflammatory programmed cell death, is crucial to the pathophysiology of PI. Despite its importance, the pyroptosis-related genes (PRGs) influencing PI's progression remain largely unexplored. Methods This study conducted histological staining and transcriptome analyze from three datasets. The intersection of differentially expressed genes (DEGs) and PRGs was identified as pyroptosis-related differentially expressed genes (PRDEGs). Functional enrichment analyses were conducted to shed light on potential underlying mechanisms. Weighted Gene Co-expression Network Analysis (WGCNA) and a pyroptotic macrophage model were utilized to identify and validate hub PRDEGs. Immune cell infiltration in PI and its relationship with hub PRDEGs were also examined. Furthermore, consensus clustering was performed to identify new PI subtypes. Protein-protein interaction (PPI) network, competing endogenous RNA (ceRNA) network, mRNA-mRNA binding protein regulatory (RBP) network, and mRNA-drugs regulatory network of hub PRDEGs were also analyzed. Results Eight hub PRDEGs were identified: PGF, DPEP1, IL36B, IFIH1, TCEA3, RIPK3, NET7, and TLR3, which are instrumental in the PI's progression. Two PI subtypes were distinguished, with Cluster 1 exhibiting higher immune cell activation. The exploration of regulatory networks provided novel mechanisms and therapeutic targets in PI. Conclusion Our research highlights the critical role of pyroptosis and identifies eight hub PRDEGs in PI's progression, offering insights into novel immunotherapy targets and laying the foundation for advanced diagnostic and treatment strategies. This contributes to our understanding of PI and underscores the potential for personalized clinical management.
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Affiliation(s)
- Liangwen Chen
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, People’s Republic of China
- Center for Prosthodontics and Implant Dentistry, Optics Valley Branch, School and Hospital of Stomatology, Wuhan University, Wuhan, People’s Republic of China
| | - Ziqiao Tang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, People’s Republic of China
| | - Liangliang Fu
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, People’s Republic of China
| | - Yang Xie
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, People’s Republic of China
| | - Junyi Xu
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, People’s Republic of China
| | - Haibin Xia
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, People’s Republic of China
- Department of Oral Implantology, School & Hospital of Stomatology, Wuhan University, Wuhan, People’s Republic of China
| | - Ting Xia
- Department of Oral Implantology, School & Hospital of Stomatology, Wuhan University, Wuhan, People’s Republic of China
| | - Min Wang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Wuhan University, Wuhan, People’s Republic of China
- Department of Oral Implantology, School & Hospital of Stomatology, Wuhan University, Wuhan, People’s Republic of China
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Li T, Wang J, Zhang Z, Fan Y, Qin H, Yin Y, Dai G, Cao Y, Tang L. Anthocyanin biosynthesis in goji berry is inactivated by deletion in a bHLH transcription factor LrLAN1b promoter. Plant Physiol 2024:kiae122. [PMID: 38431527 DOI: 10.1093/plphys/kiae122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/27/2023] [Accepted: 10/08/2023] [Indexed: 03/05/2024]
Abstract
Black goji berry (Lycium ruthenicum Murray) contains a rich source of health-promoting anthocyanins which are used in herbal medicine and nutraceutical foods in China. A natural variant producing white berries allowed us to identify two key genes involved in the regulation of anthocyanin biosynthesis in goji berries: one encoding a MYB transcription factor (LrAN2-like) and one encoding a basic helix-loop-helix (bHLH) transcription factor (LrAN1b). We previously found that LrAN1b expression was lost in the white berry variant, but the molecular basis for this phenotype was unknown. Here, we identified the molecular mechanism for loss of anthocyanins in white goji berries. In white goji, the LrAN1b promoter region has a 229-bp deletion that removes 3 MYB-binding elements and 1 bHLH-binding element, which are key to its expression. Complementation of the white goji berry LrAN1b allele with the LrAN1b promoter restored pigmentation. Virus-induced gene silencing of LrAN1b in black goji berry reduced fruit anthocyanin biosynthesis. Molecular analyses showed that LrAN2-like and another bHLH transcription factor LrJAF13 can activate LrAN1b by binding directly to the MYB-recognizing element (MRE) and bHLH-recognizing element (BRE) of its promoter-deletion region. LrAN1b expression is enhanced by the interaction of LrAN2-like with LrJAF13 and the WD40 protein LrAN11. LrAN2-like and LrAN11 interact with either LrJAF13 or LrAN1b to form two MYB-bHLH-WD40 (MBW) complexes, which hierarchically regulate anthocyanin biosynthesis in black goji berry. This study on a natural variant builds a comprehensive anthocyanin regulatory network that may be manipulated to tailor goji berry traits.
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Affiliation(s)
- Tingting Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Sichuan Province, Chengdu 610065, China
| | - Jingjin Wang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Sichuan Province, Chengdu 610065, China
| | - Zihan Zhang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Sichuan Province, Chengdu 610065, China
| | - Yunfang Fan
- Institute of Wolfberry Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, Ningxia Hui Autonomous Region, Yinchuan 750002, China
- National Wolfberry Engineering Research Center, Ningxia Hui Autonomous Region, Yinchuan 750002, China
| | - Huan Qin
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Sichuan Province, Chengdu 610065, China
| | - Yue Yin
- Institute of Wolfberry Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, Ningxia Hui Autonomous Region, Yinchuan 750002, China
- National Wolfberry Engineering Research Center, Ningxia Hui Autonomous Region, Yinchuan 750002, China
| | - Guoli Dai
- Institute of Wolfberry Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, Ningxia Hui Autonomous Region, Yinchuan 750002, China
- National Wolfberry Engineering Research Center, Ningxia Hui Autonomous Region, Yinchuan 750002, China
| | - Youlong Cao
- Institute of Wolfberry Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, Ningxia Hui Autonomous Region, Yinchuan 750002, China
- National Wolfberry Engineering Research Center, Ningxia Hui Autonomous Region, Yinchuan 750002, China
| | - Lin Tang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Sichuan Province, Chengdu 610065, China
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Liu D, Dong Y, Gao J, Wu Z, Zhang L, Wang B. Role of the circular RNA regulatory network in the pathogenesis of biliary atresia. Exp Ther Med 2024; 27:95. [PMID: 38313582 PMCID: PMC10831818 DOI: 10.3892/etm.2024.12383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 11/13/2023] [Indexed: 02/06/2024] Open
Abstract
Circular RNAs (circRNAs) serve an essential role in the occurrence and development of cholangiocarcinoma, but the expression and function of circRNA in biliary atresia (BA) is not clear. In the present study, circRNA expression profiles were investigated in the liver tissues of patients with BA as well as in the choledochal cyst (CC) tissues of control patients using RNA sequencing. A total of 78 differentially expressed circRNAs (DECs) were identified between the BA and CC tissues. The expression levels of eight circRNAs (hsa_circ_0006137, hsa_circ_0079422, hsa_circ_0007375, hsa_circ_0005597, hsa_circ_0006961, hsa_circ_0081171, hsa_circ_0084665 and hsa_circ_0075828) in the liver tissues of the BA group and control group were measured using reverse transcription-quantitative polymerase chain reaction. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis demonstrated that the identified DECs are involved in a variety of biological processes, including apoptosis and metabolism. In addition, based on the GO and KEGG pathway enrichment analyses, it was revealed that target genes that can be affected by circRNAs regulatory network were enriched in the TGF-β signaling pathway, EGFR tyrosine kinase inhibitor resistance pathway and transcription factor regulation pathway as well as other pathways that may be associated with the pathogenesis of BA. The present study revealed that circRNAs are potentially implicated in the pathogenesis of BA and could help to find promising targets and biomarkers for BA.
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Affiliation(s)
- Dong Liu
- Department of General Surgery, Shenzhen Children's Hospital, Shenzhen, Guangdong 518000, P.R. China
| | - Yinghui Dong
- Department of Ultrasound, Shenzhen People's Hospital, Shenzhen, Guangdong 518000, P.R. China
| | - Jiahui Gao
- Department of General Surgery, Shenzhen Children's Hospital, Shenzhen, Guangdong 518000, P.R. China
| | - Zhouguang Wu
- Department of General Surgery, Shenzhen Children's Hospital, Shenzhen, Guangdong 518000, P.R. China
| | - Lihui Zhang
- Department of Traditional Chinese Medicine, Shenzhen Children's Hospital, Shenzhen, Guangdong 518000, P.R. China
| | - Bin Wang
- Department of General Surgery, Shenzhen Children's Hospital, Shenzhen, Guangdong 518000, P.R. China
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Li S, Zhao B, Yang H, Dai K, Cai Y, Xu H, Chen P, Wang F, Zhang Y. Comprehensive transcriptomic analysis revealing the regulatory dynamics and networks of the pituitary-testis axis in sheep across developmental stages. Front Vet Sci 2024; 11:1367730. [PMID: 38440388 PMCID: PMC10909840 DOI: 10.3389/fvets.2024.1367730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 02/05/2024] [Indexed: 03/06/2024] Open
Abstract
Spermatogenesis is a complex process intricately regulated by the hypothalamic-pituitary-testis (HPT) axis. However, research on the regulatory factors governing the HPT axis remains limited. This study addresses this gap by conducting a comprehensive analysis of transcriptomes from the pituitary and testis tissues across various developmental stages, encompassing embryonic day (E120), neonatal period (P0), pre-puberty (P90), and post-puberty day (P270). Utilizing edgeR and WGCNA, we identified stage-specific genes in both the pituitary and testis throughout the four developmental stages. Notably, 380, 242, 34, and 479 stage-specific genes were identified in the pituitary, while 886, 297, 201, and 3,678 genes were identified in the testis. Subsequent analyses unveiled associations between these stage-specific genes and crucial pathways such as the cAMP signaling pathway, GnRH secretion, and male gamete generation. Furthermore, leveraging single-cell data from the pituitary and testis, we identified some signaling pathways involving BMP, HGF, IGF, and TGF-β, highlighting mutual regulation between the pituitary and testis at different developmental stages. This study sheds light on the pivotal role of the pituitary-testis axis in the reproductive process of sheep across four distinct developmental stages. Additionally, it delves into the intricate regulatory networks governing reproduction, offering novel insights into the dynamics of the pituitary-testis axis within the reproductive system.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Yanli Zhang
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing, China
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11
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Ingham V, Nagi S. Genomic Profiling of Insecticide Resistance in Malaria Vectors: Insights into Molecular Mechanisms. Res Sq 2024:rs.3.rs-3910702. [PMID: 38410472 PMCID: PMC10896400 DOI: 10.21203/rs.3.rs-3910702/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Malaria control faces challenges from widespread insecticide resistance in major Anopheles species. This study, employing a cross-species approach, integrates RNA-Sequencing, whole-genome sequencing, and microarray data to elucidate drivers of insecticide resistance in Anopheles gambiae complex and An. funestus. Findings show an inverse relationship between genetic diversity and gene expression, with highly expressed genes experiencing stronger purifying selection. These genes cluster physically in the genome, revealing potential coordinated regulation. We identified known and novel candidate insecticide resistance genes, enriched in metabolic, cuticular, and behavioural functions. We also present AnoExpress, a Python package, and an online interface for user-friendly exploration of resistance candidate expression. Despite millions of years of speciation, convergent gene expression responses to insecticidal selection pressures are observed across Anopheles species, providing crucial insights for malaria vector control. This study culminates in a rich dataset that allows us to understand molecular mechanisms, better enabling us to combat insecticide resistance effectively.
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12
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Song Y, Zhang H, Liu S, Chang Y, Zhang Y, Feng H, Zhang X, Sun M, Sha W, Li Y, Dai S. Na2CO3-responsive mechanism insight from quantitative proteomics and SlRUB gene function in Salix linearistipularis seedlings. Tree Physiol 2024; 44:tpae011. [PMID: 38263488 DOI: 10.1093/treephys/tpae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/28/2023] [Accepted: 01/07/2024] [Indexed: 01/25/2024]
Abstract
Mongolian willow (Salix linearistipularis) is a naturally occurring woody dioecious plant in the saline soils of north-eastern China, which has a high tolerance to alkaline salts. Although transcriptomics studies have identified a large number of salinity-responsive genes, the mechanism of salt tolerance in Mongolian willow is not clear. Here, we found that in response to Na2CO3 stress, Mongolian willow regulates osmotic homeostasis by accumulating proline and soluble sugars and scavenges reactive oxygen species (ROS) by antioxidant enzymes and non-enzymatic antioxidants. Our quantitative proteomics study identified 154 salt-sensitive proteins mainly involved in maintaining the stability of the photosynthetic system and ROS homeostasis to cope with Na2CO3 stress. Among them, Na2CO3-induced rubredoxin (RUB) was predicted to be associated with 122 proteins for the modulation of these processes. The chloroplast-localized S. linearistipularis rubredoxin (SlRUB) was highly expressed in leaves and was significantly induced under Na2CO3 stress. Phenotypic analysis of overexpression, mutation and complementation materials of RUB in Arabidopsis suggests that SlRUB is critical for the regulation of photosynthesis, ROS scavenging and other metabolisms in the seedlings of Mongolian willow to cope with Na2CO3 stress. This provides more clues to better understand the alkali-responsive mechanism and RUB functions in the woody Mongolian willow.
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Affiliation(s)
- Yingying Song
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, No. 26 Hexing Road, Xiangfang District, Harbin 150040, China
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, No. 100 Guilin Road, Xuhui District, Shanghai 200234, China
| | - Heng Zhang
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, No. 100 Guilin Road, Xuhui District, Shanghai 200234, China
| | - Shijia Liu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, No. 26 Hexing Road, Xiangfang District, Harbin 150040, China
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, No. 100 Guilin Road, Xuhui District, Shanghai 200234, China
| | - Yu Chang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, No. 26 Hexing Road, Xiangfang District, Harbin 150040, China
| | - Yongxue Zhang
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, No. 100 Guilin Road, Xuhui District, Shanghai 200234, China
| | - Huiting Feng
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, No. 26 Hexing Road, Xiangfang District, Harbin 150040, China
| | - Xuebin Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, No. 1 Jinming Avenue, Longting District, Kaifeng 475001, China
| | - Meihong Sun
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, No. 100 Guilin Road, Xuhui District, Shanghai 200234, China
| | - Wei Sha
- College of Life Sciences and Agriculture and Forestry, Qiqihar University, No. 42 Wenhua Street, Jianhua District, Qiqihar 161006, China
| | - Ying Li
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, No. 26 Hexing Road, Xiangfang District, Harbin 150040, China
| | - Shaojun Dai
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, No. 100 Guilin Road, Xuhui District, Shanghai 200234, China
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13
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Bai Q, Shi L, Li K, Xu F, Zhang W. The Construction of lncRNA/circRNA-miRNA-mRNA Networks Reveals Functional Genes Related to Growth Traits in Schima superba. Int J Mol Sci 2024; 25:2171. [PMID: 38396847 PMCID: PMC10888550 DOI: 10.3390/ijms25042171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/05/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Schima superba is a precious timber and fire-resistant tree species widely distributed in southern China. Currently, there is little knowledge related to its growth traits, especially with respect to molecular breeding. The lack of relevant information has delayed the development of modern breeding. The purpose is to identify probable functional genes involved in S. superba growth through whole transcriptome sequencing. In this study, a total of 32,711 mRNAs, 525 miRNAs, 54,312 lncRNAs, and 1522 circRNAs were identified from 10 S. superba individuals containing different volumes of wood. Four possible regulators, comprising three lncRNAs, one circRNA, and eleven key miRNAs, were identified from the regulatory networks of lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA to supply information on ncRNAs. Several candidate genes involved in phenylpropane and cellulose biosynthesis pathways, including Ss4CL2, SsCSL1, and SsCSL2, and transcription factors, including SsDELLA2 (SsSLR), SsDELLA3 (SsSLN), SsDELLA5 (SsGAI-like2), and SsNAM1, were identified to reveal the molecular regulatory mechanisms regulating the growth traits of S. superba. The results not merely provide candidate functional genes related to S. superba growth trait and will be useful to carry out molecular breeding, but the strategy and method also provide scientists with an effective approach to revealing mechanisms behind important economic traits in other species.
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Affiliation(s)
- Qingsong Bai
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, China
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14
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Chen C, Cruz-Ramirez A, Zhang Y, Ishikawa M. Editorial: Molecular basis of stem cells underlying plant vitality. Front Plant Sci 2024; 15:1371814. [PMID: 38384758 PMCID: PMC10879608 DOI: 10.3389/fpls.2024.1371814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 01/30/2024] [Indexed: 02/23/2024]
Affiliation(s)
- Chunli Chen
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Alfredo Cruz-Ramirez
- Molecular & Developmental Complexity Group, Unit of Advanced Genomics, LANGEBIO-CINVESTAV, Irapuato, Mexico
| | - Yonghong Zhang
- Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medicine, Hubei University of Medicine, Shiyan, China
| | - Masaki Ishikawa
- Division of Evolutionary Biology, National Institute for Basic Biology, Okazaki, Japan
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15
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Tan M, Andersen LJ, Bruun NE, Lindholm MG, Tan Q, Snoer M. Transcription Factor Regulation of Gene Expression Network by ZNF385D and HAND2 in Carotid Atherosclerosis. Genes (Basel) 2024; 15:213. [PMID: 38397203 PMCID: PMC10888454 DOI: 10.3390/genes15020213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/01/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
Carotid intima-media thickness (CIMT) is a surrogate indicator for atherosclerosis and has been shown to predict cardiovascular risk in multiple large studies. Identification of molecular markers for carotid atheroma plaque formation can be critical for early intervention and prevention of atherosclerosis. This study performed transcription factor (TF) network analysis of global gene expression data focusing on two TF genes, ZNF385D and HAND2, whose polymorphisms have been recently reported to show association with CIMT. Genome-wide gene expression data were measured from pieces of carotid endarterectomy collected from 34 hypertensive patients (atheroma plaque of stages IV and above according to the Stary classification) each paired with one sample of distant macroscopically intact tissue (stages I and II). Transcriptional regulation networks or the regulons were reconstructed for ZNF385D (5644 target genes) and HAND2 (781 target genes) using network inference. Their association with the progression of carotid atheroma was examined using gene-set enrichment analysis with extremely high statistical significance for regulons of both ZNF385D and HAND2 (p < 6.95 × 10-7) suggesting the involvement of expression quantitative loci (eQTL). Functional annotation of the regulon genes found heavy involvement in the immune system's response to inflammation and infection in the development of atherosclerosis. Detailed examination of the regulation and correlation patterns suggests that activities of the two TF genes could have high clinical and interventional impacts on impairing carotid atheroma plaque formation and preventing carotid atherosclerosis.
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Affiliation(s)
- Ming Tan
- Department of Cardiology, Zealand University Hospital, 4000 Roskilde, Denmark; (M.T.); (L.J.A.); (N.E.B.); (M.G.L.); (M.S.)
| | - Lars Juel Andersen
- Department of Cardiology, Zealand University Hospital, 4000 Roskilde, Denmark; (M.T.); (L.J.A.); (N.E.B.); (M.G.L.); (M.S.)
| | - Niels Eske Bruun
- Department of Cardiology, Zealand University Hospital, 4000 Roskilde, Denmark; (M.T.); (L.J.A.); (N.E.B.); (M.G.L.); (M.S.)
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Department of Clinical Medicine, University of Aalborg, 9260 Aalborg, Denmark
| | - Matias Greve Lindholm
- Department of Cardiology, Zealand University Hospital, 4000 Roskilde, Denmark; (M.T.); (L.J.A.); (N.E.B.); (M.G.L.); (M.S.)
| | - Qihua Tan
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, Faculty of Health Science, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
- Unit of Human Genetics, Department of Clinical Research, Faculty of Health Science, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Martin Snoer
- Department of Cardiology, Zealand University Hospital, 4000 Roskilde, Denmark; (M.T.); (L.J.A.); (N.E.B.); (M.G.L.); (M.S.)
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16
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Zhu L, Li F, Xie T, Li Z, Tian T, An X, Wei X, Long Y, Jiao Z, Wan X. Receptor-like kinases and their signaling cascades for plant male fertility: loyal messengers. New Phytol 2024; 241:1421-1434. [PMID: 38174365 DOI: 10.1111/nph.19527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024]
Abstract
Receptor-like kinases (RLKs) are evolved for plant cell-cell communications. The typical RLK protein contains an extracellular and hypervariable N-terminus to perceive various signals, a transmembrane domain to anchor into plasma membrane, and a cytoplasmic, highly conserved kinase domain to phosphorylate target proteins. To date, RLKs have manifested their significance in a myriad of biological processes during plant reproductive growth, especially in male fertility. This review first summarizes a recent update on RLKs and their interacting protein partners controlling anther and pollen development, pollen release from dehisced anther, and pollen function during pollination and fertilization. Then, regulatory networks of RLK signaling pathways are proposed. In addition, we predict RLKs in maize and rice genome, obtain homologs of well-studied RLKs from phylogeny of three subfamilies and then analyze their expression patterns in developing anthers of maize and rice to excavate potential RLKs regulating male fertility in crops. Finally, current challenges and future prospects regarding RLKs are discussed. This review will contribute to a better understanding of plant male fertility control by RLKs, creating potential male sterile lines, and inspiring innovative crop breeding methods.
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Affiliation(s)
- Lei Zhu
- Research Institute of Biology and Agriculture, Zhongzhi International Institute of Agricultural Biosciences, Shunde Innovation School, University of Science and Technology Beijing, Beijing, 100083, China
- Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining, 835000, China
| | - Fan Li
- Research Institute of Biology and Agriculture, Zhongzhi International Institute of Agricultural Biosciences, Shunde Innovation School, University of Science and Technology Beijing, Beijing, 100083, China
| | - Tianle Xie
- Research Institute of Biology and Agriculture, Zhongzhi International Institute of Agricultural Biosciences, Shunde Innovation School, University of Science and Technology Beijing, Beijing, 100083, China
| | - Ziwen Li
- Research Institute of Biology and Agriculture, Zhongzhi International Institute of Agricultural Biosciences, Shunde Innovation School, University of Science and Technology Beijing, Beijing, 100083, China
- Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining, 835000, China
| | - Tian Tian
- Research Institute of Biology and Agriculture, Zhongzhi International Institute of Agricultural Biosciences, Shunde Innovation School, University of Science and Technology Beijing, Beijing, 100083, China
| | - Xueli An
- Research Institute of Biology and Agriculture, Zhongzhi International Institute of Agricultural Biosciences, Shunde Innovation School, University of Science and Technology Beijing, Beijing, 100083, China
- Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining, 835000, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd, Beijing, 100192, China
| | - Xun Wei
- Research Institute of Biology and Agriculture, Zhongzhi International Institute of Agricultural Biosciences, Shunde Innovation School, University of Science and Technology Beijing, Beijing, 100083, China
- Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining, 835000, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd, Beijing, 100192, China
| | - Yan Long
- Research Institute of Biology and Agriculture, Zhongzhi International Institute of Agricultural Biosciences, Shunde Innovation School, University of Science and Technology Beijing, Beijing, 100083, China
- Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining, 835000, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd, Beijing, 100192, China
| | - Ziwei Jiao
- Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining, 835000, China
| | - Xiangyuan Wan
- Research Institute of Biology and Agriculture, Zhongzhi International Institute of Agricultural Biosciences, Shunde Innovation School, University of Science and Technology Beijing, Beijing, 100083, China
- Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining, 835000, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd, Beijing, 100192, China
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17
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An JP, Xu RR, Wang XN, Zhang XW, You CX, Han Y. MdbHLH162 connects the gibberellin and jasmonic acid signals to regulate anthocyanin biosynthesis in apple. J Integr Plant Biol 2024; 66:265-284. [PMID: 38284786 DOI: 10.1111/jipb.13608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/09/2023] [Accepted: 01/03/2024] [Indexed: 01/30/2024]
Abstract
Anthocyanins are secondary metabolites induced by environmental stimuli and developmental signals. The positive regulators of anthocyanin biosynthesis have been reported, whereas the anthocyanin repressors have been neglected. Although the signal transduction pathways of gibberellin (GA) and jasmonic acid (JA) and their regulation of anthocyanin biosynthesis have been investigated, the cross-talk between GA and JA and the antagonistic mechanism of regulating anthocyanin biosynthesis remain to be investigated. In this study, we identified the anthocyanin repressor MdbHLH162 in apple and revealed its molecular mechanism of regulating anthocyanin biosynthesis by integrating the GA and JA signals. MdbHLH162 exerted passive repression by interacting with MdbHLH3 and MdbHLH33, which are two recognized positive regulators of anthocyanin biosynthesis. MdbHLH162 negatively regulated anthocyanin biosynthesis by disrupting the formation of the anthocyanin-activated MdMYB1-MdbHLH3/33 complexes and weakening transcriptional activation of the anthocyanin biosynthetic genes MdDFR and MdUF3GT by MdbHLH3 and MdbHLH33. The GA repressor MdRGL2a antagonized MdbHLH162-mediated inhibition of anthocyanins by sequestering MdbHLH162 from the MdbHLH162-MdbHLH3/33 complex. The JA repressors MdJAZ1 and MdJAZ2 interfered with the antagonistic regulation of MdbHLH162 by MdRGL2a by titrating the formation of the MdRGL2a-MdbHLH162 complex. Our findings reveal that MdbHLH162 integrates the GA and JA signals to negatively regulate anthocyanin biosynthesis. This study provides new information for discovering more anthocyanin biosynthesis repressors and explores the cross-talk between hormone signals.
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Affiliation(s)
- Jian-Ping An
- Apple technology innovation center of Shandong Province, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, China
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, 430074, China
| | - Rui-Rui Xu
- College of Biology and Oceanography, Weifang University, Weifang, 261061, China
| | - Xiao-Na Wang
- Apple technology innovation center of Shandong Province, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, China
| | - Xiao-Wei Zhang
- Apple technology innovation center of Shandong Province, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, China
| | - Chun-Xiang You
- Apple technology innovation center of Shandong Province, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, China
| | - Yuepeng Han
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, 430074, China
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18
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An Y, Tan S, Yang J, Gao T, Dong Y. The potential role of Hippo pathway regulates cellular metabolism via signaling crosstalk in disease-induced macrophage polarization. Front Immunol 2024; 14:1344697. [PMID: 38274792 PMCID: PMC10808647 DOI: 10.3389/fimmu.2023.1344697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024] Open
Abstract
Macrophages polarized into distinct phenotypes play vital roles in inflammatory diseases by clearing pathogens, promoting tissue repair, and maintaining homeostasis. Metabolism serves as a fundamental driver in regulating macrophage polarization, and understanding the interplay between macrophage metabolism and polarization is crucial for unraveling the mechanisms underlying inflammatory diseases. The intricate network of cellular signaling pathway plays a pivotal role in modulating macrophage metabolism, and growing evidence indicates that the Hippo pathway emerges as a central player in network of cellular metabolism signaling. This review aims to explore the impact of macrophage metabolism on polarization and summarize the cell signaling pathways that regulate macrophage metabolism in diseases. Specifically, we highlight the pivotal role of the Hippo pathway as a key regulator of cellular metabolism and reveal its potential relationship with metabolism in macrophage polarization.
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Affiliation(s)
- Yina An
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Shuyu Tan
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jingjing Yang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Ting Gao
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yanjun Dong
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
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19
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Wang H, Chi X, Zhang D. Potential Regulatory Gene Network Associated with the Ameliorative Effect of Oat Antibacterial Peptides on Rat Colitis. Foods 2024; 13:236. [PMID: 38254536 PMCID: PMC10814071 DOI: 10.3390/foods13020236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/28/2023] [Accepted: 01/06/2024] [Indexed: 01/24/2024] Open
Abstract
Oat protein is unstable in intestinal fluid digestion, and it is easily degraded by trypsin and chymotrypsin, producing low molecular weight peptides. Endopeptidase hydrolysis can improve the bioavailability of active peptides and avoid further digestion in the gastrointestinal tract. Antimicrobial peptides (AMPs) can effectively improve host immunity, but most related studies focus on physiology and ecology, and there are few reports on their molecular level. Therefore, in this article, oat peptides were prepared via the simulated digestion method in vitro, and the main metabolites and action factors affecting colitis were screened by using the multi-omics methods in a high-throughput mode to analyze the effect and mechanism of colitis. Firstly, oat antimicrobial peptides were prepared from cationic resin combined with HPLC, and the anti-inflammatory effects of antimicrobial peptides were analyzed in vitro through the use of human colon epithelial (HCoEpiC) anti-inflammatory cells. In vivo experiments using rats have verified that AMPs can effectively prevent colitis caused by dextran sodium sulfate (DSS), reduce intestinal inflammatory cell infiltration and glandular disappearance in the colon, and reduce the apoptosis rate of colon cells. Secondly, metabolomics and transcriptomics were combined to analyze the mechanism of preventing enteritis, and it was found that oat antimicrobial peptides can promote DAG diglycerol production and inhibit the activation of T helper cells (TH), resulting in the down-regulation of key factors in the main downstream pathways of TH1, TH2 and TH17, and inhibit the production of inflammatory cells. At the same time, AMP can activate the wnt pathway, improve the expression of key genes of wnt and frizzled, promote the generation of intestinal stem cells, facilitate the differentiation and repair of intestinal epithelial cells, and prevent the generation of enteritis. Finally, the underlying genetic regulatory network of the important pathway was constructed from the effect of AMP on rat colitis.
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Affiliation(s)
- Helin Wang
- College of Food Science, Hei Long Jiang Bayi Agricultrue University, Daqing 163319, China; (H.W.); (D.Z.)
| | - Xiaoxing Chi
- College of Food Science, Hei Long Jiang Bayi Agricultrue University, Daqing 163319, China; (H.W.); (D.Z.)
- Key Laboratory of Agro-Products Processing and Quality Safety of Heilongjiang Province, Daqing 163319, China
- Coarse Cereals Engineering Research Center, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Dongjie Zhang
- College of Food Science, Hei Long Jiang Bayi Agricultrue University, Daqing 163319, China; (H.W.); (D.Z.)
- Key Laboratory of Agro-Products Processing and Quality Safety of Heilongjiang Province, Daqing 163319, China
- Coarse Cereals Engineering Research Center, Heilongjiang Bayi Agricultural University, Daqing 163319, China
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20
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Li H, Feng YH, Xia C, Chen Y, Lu XY, Wei Y, Qian LL, Zhu MY, Gao GY, Meng YF, You YL, Tian Q, Liang KQ, Li YT, Lv CT, Rui XY, Wei MY, Zhang B. Physiological and transcriptomic analysis dissects the molecular mechanism governing meat quality during postmortem aging in Hu sheep ( Ovis aries). Front Nutr 2024; 10:1321938. [PMID: 38249602 PMCID: PMC10799347 DOI: 10.3389/fnut.2023.1321938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 12/11/2023] [Indexed: 01/23/2024] Open
Abstract
Introduction Hu sheep, known for its high quality and productivity, lack fundamental scientific research in China. Methods This study focused on the effects of 24 h postmortem aging on the meat physiological and transcriptomic alteration in Hu sheep. Results The results showed that the 24 h aging process exerts a substantial influence on the mutton color, texture, and water content as compared to untreated group. Transcriptomic analysis identified 1,668 differentially expressed genes. Functional enrichment analysis highlighted the importance of glycolysis metabolism, protein processing in endoplasmic reticulum, and the FcγR-mediated phagocytosis pathway in mediating meat quality modification following postmortem aging. Furthermore, protein-protein interaction analysis uncovered complex regulatory networks involving glycolysis, the MAPK signaling pathway, protein metabolism, and the immune response. Discussion Collectively, these findings offer valuable insights into the molecular mechanisms underlying meat quality changes during postmortem aging in Hu sheep, emphasizing the potential for improving quality control strategies in mutton production.
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Affiliation(s)
- Huan Li
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Yan-Hui Feng
- College of Food Engineering, Anhui Science and Technology University, Chuzhou, Anhui, China
| | - Chao Xia
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Yu Chen
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Xin-Yi Lu
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Yue Wei
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Le-Le Qian
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Meng-Yao Zhu
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Guo-Yv Gao
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Ya-Fei Meng
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Yv-Le You
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Qi Tian
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Kun-Qi Liang
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Yun-Tao Li
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Chao-Tian Lv
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Xiang-Yun Rui
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
| | - Ming-Yue Wei
- School of Ecology, Resources and Environment, Dezhou University, Dezhou, Shandong, China
| | - Bin Zhang
- College of Food and Bio-engineering, Bengbu University, Bengbu, Anhui, China
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21
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Wu C, Liu M, Liu J, Jia M, Zeng X, Fu Z, Geng Y, He Z, Zhang X, Yan H. Integrative analysis of an endoplasmic reticulum stress-related signature in multiple myeloma. J Gene Med 2024; 26:e3595. [PMID: 37730959 DOI: 10.1002/jgm.3595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 08/17/2023] [Accepted: 09/03/2023] [Indexed: 09/22/2023] Open
Abstract
BACKGROUND Multiple myeloma (MM) is a malignancy in which plasma cells proliferate abnormally, and it remains incurable. The cells are characterized by high levels of endoplasmic reticulum stress (ERS) and depend on the ERS response for survival. Thus, we aim to find an ERS-related signature of MM and assess its diagnostic value. METHODS We downloaded three datasets of MM from the Gene Expression Omnibus database. After identifying ERS-related differentially expressed genes (ERDEGs), we analyzed them using Gene Ontology enrichment analysis. A protein-protein interaction network, a transcription factor-mRNA network, a miRNA-mRNA network and a drug-mRNA network were constructed to explore the ERDEGs. The clinical application of these genes was identified by calculating the infiltration of immune cells and using receiver operating characteistic analyses. Finally, qPCR was performed to further confirm the roles of ERDEGs. RESULTS We obtained nine ERDEGs of MM. Gene Ontology enrichment indicated that the ERDEGs played a role in the endoplasmic reticulum membrane. Additionally, the protein-protein interaction network showed interaction among the ERDEGs, and there were 20 proteins, 107 transcription factors, 42 drugs or molecular compounds and 51 miRNAs which were likely to interact with the nine genes. In addition, immune cell infiltration analyses showed that there was a strong correlation between the nine genes and immune cells, and these potential biomarkers exhibited good diagnostic values. Finally, the expression of ERDEGs in MM cells was different from that in healthy donor samples. CONCLUSION The nine ERS-related genes, CR2, DHCR7, DNAJC3, KDELR2, LPL, OSBPL3, PINK1, VCAM1 and XBP1 are potential biomarkers of MM, and this supports further clinical development of the diagnosis and treatment of MM.
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Affiliation(s)
- Chengyu Wu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mei Liu
- Department of General Practice, Wuxi Branch of Ruijin Hospital, Jiangsu, China
| | - Jia Liu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mingyuan Jia
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xinyi Zeng
- Department of Hematology, Huadong Hospital Affiliated with Fudan University, Shanghai, China
| | - Ze Fu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yanlai Geng
- Department of General Practice, Wuxi Branch of Ruijin Hospital, Jiangsu, China
| | - Ziqi He
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xian Zhang
- Department of General Practice, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hua Yan
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of General Practice, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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22
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Qian H, Zhang Z, Tao Z, Xie Y, Yin Y, He W, Zhang L. Association of Circular RNAs levels in blood and Essential Hypertension with Carotid Plaque. Clin Exp Hypertens 2023; 45:2180020. [PMID: 36843004 DOI: 10.1080/10641963.2023.2180020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
Abstract
BACKGROUND As one of the essential hypertension (EH)-mediated target organ damage, carotid plaque is a crucial subclinical precursor for cardiovascular events. Therefore, it is vital to identify the risk factors and pathogenesis for EH with carotid plaque. METHODS Based on our previous microarray analysis, we selected four circRNAs as the candidate circRNAs and detected their expression levels in blood of 192 subjects (64 healthy controls, 64 EH patients, and 64 EH patients with carotid plaque) by qRT-PCR analysis. The regulatory mechanism of circRNAs involved in carotid plaque was predicted by bioinformatics analysis. RESULTS The level of hsa_circ_0124782 increased significantly and the levels of hsa_circ_0131618 and hsa_circ_0127342 decreased significantly in the EH group and EH with carotid plaque group compared with the control group (P < .05). Functional enrichment analysis showed that three circRNAs might be implicated in pathogenesis for carotid plaque. CONCLUSION Our study revealed the relationship between three circRNAs and carotid plaque, suggesting that they may serve as potential biomarkers for EH with carotid plaque.
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Affiliation(s)
- Haiyan Qian
- Department of Preventive Medicine, School of Medicine, Ningbo University, Ningbo, China
| | - Zebo Zhang
- Department of Preventive Medicine, School of Medicine, Ningbo University, Ningbo, China
| | - Zhenbo Tao
- Department of Preventive Medicine, School of Medicine, Ningbo University, Ningbo, China.,Ningbo Municipal Centre for Disease Control and Prevention, Ningbo, China
| | - Yanqing Xie
- Institute of Geriatrics, the Affiliated Hospital of Medical School, Ningbo University, Ningbo, China
| | - Yueqi Yin
- Department of Preventive Medicine, School of Medicine, Ningbo University, Ningbo, China
| | - Wenming He
- Institute of Geriatrics, the Affiliated Hospital of Medical School, Ningbo University, Ningbo, China
| | - Lina Zhang
- Department of Preventive Medicine, School of Medicine, Ningbo University, Ningbo, China.,Institute of Geriatrics, the Affiliated Hospital of Medical School, Ningbo University, Ningbo, China
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23
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Zhou B, Zheng B, Wu W. The ncRNAs Involved in the Regulation of Abiotic Stress-Induced Anthocyanin Biosynthesis in Plants. Antioxidants (Basel) 2023; 13:55. [PMID: 38247480 PMCID: PMC10812613 DOI: 10.3390/antiox13010055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/16/2023] [Accepted: 12/19/2023] [Indexed: 01/23/2024] Open
Abstract
Plants have evolved complicated defense and adaptive systems to grow in various abiotic stress environments such as drought, cold, and salinity. Anthocyanins belong to the secondary metabolites of flavonoids with strong antioxidant activity in response to various abiotic stress and enhance stress tolerance. Anthocyanin accumulation often accompanies the resistance to abiotic stress in plants to scavenge reactive oxygen species (ROS). Recent research evidence showed that many regulatory pathways such as osmoregulation, antioxidant response, plant hormone response, photosynthesis, and respiration regulation are involved in plant adaption to stress. However, the molecular regulatory mechanisms involved in controlling anthocyanin biosynthesis in relation to abiotic stress response have remained obscure. Here, we summarize the current research progress of specific regulators including small RNAs, and lncRNAs involved in the molecular regulation of abiotic stress-induced anthocyanin biosynthesis. In addition, an integrated regulatory network of anthocyanin biosynthesis controlled by microRNAs (miRNAs), long non-coding RNAs (lncRNAs), transcription factors, and stress response factors is also discussed. Understanding molecular mechanisms of anthocyanin biosynthesis for ROS scavenging in various abiotic stress responses will benefit us for resistance breeding in crop plants.
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Affiliation(s)
- Bo Zhou
- College of Life Science, Northeast Forestry University, Harbin 150040, China;
| | - Baojiang Zheng
- College of Life Science, Northeast Forestry University, Harbin 150040, China;
| | - Weilin Wu
- Agricultural College, Yanbian University, Yanji 133002, China
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24
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Fu Y, Song Y, Jiang D, Pan J, Li W, Zhang X, Chen W, Tian Y, Shen X, Huang Y. Comprehensive Transcriptomic and Metabolomic Analysis Revealed the Functional Differences in Pigeon Lactation between Male and Female during the Reproductive Cycle. Animals (Basel) 2023; 14:75. [PMID: 38200806 PMCID: PMC10778231 DOI: 10.3390/ani14010075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/07/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Lactation is a unique reproductive behavior in pigeons, with the crop serving as the organ responsible for secreting pigeon milk. Both male and female pigeons can produce crop milk and rear their offspring through a division of labor. Since the time of the secretion of pigeon crop milk is different in the process of feeding the young, whether the metabolism and formation of pigeon milk use the same mechanism is a very interesting scientific question. However, the metabolic dynamics and underlying genetic mechanisms involved in the formation of pigeon crop milk remain unclear, particularly during the incubation-feeding reproductive cycle. In this study, we integrated lactation-associated metabolism and transcriptome data from the crop tissues of both male and female pigeons during the brooding and feeding stages. We mapped the changes in metabolites related to milk formation in the crop tissues during these stages. Through metabolome profiling, we identified 1413 metabolites among 18 crop tissues. During the breeding cycles, the concentrations of estrone, L-ergothioneine, and L-histidine exhibited the most dynamic changes in females. In contrast, estrone, L-anserine, 1-methylhistidine, homovanillate, oxidized glutathione, and reducing glutathione showed the most dynamic changes in males. Gender-specific differences were observed in the metabolome, with several metabolites significantly differing between males and females, many of which were correlated with cytokine binding, immunity, and cytochrome P450 activity. Using this dataset, we constructed complex regulatory networks, enabling us to identify important metabolites and key genes involved in regulating the formation of pigeon milk in male and female pigeons, respectively. Additionally, we investigated gender-associated differences in the crop metabolites of pigeons. Our study revealed differences in the modulation of pigeon crop milk metabolism between males and females and shed light on the potential functions of male and female pigeon milk in the growth, development, and immunity of young pigeons, an area that has not been previously explored. In conclusion, our results provide new insights into the metabolic regulation of pigeon crop milk formation during the brooding and breeding stages. Furthermore, our findings lay the foundation for the accurate development of artificial pigeon milk.
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Affiliation(s)
- Yuting Fu
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510225, China; (Y.F.); (Y.S.); (D.J.); (J.P.); (W.L.); (X.Z.); (W.C.); (Y.T.)
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Waterfowl Healthy Breeding Engineering Research Center, Guangdong Higher Education Institute, Guangzhou 510225, China
| | - Yan Song
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510225, China; (Y.F.); (Y.S.); (D.J.); (J.P.); (W.L.); (X.Z.); (W.C.); (Y.T.)
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Waterfowl Healthy Breeding Engineering Research Center, Guangdong Higher Education Institute, Guangzhou 510225, China
| | - Danli Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510225, China; (Y.F.); (Y.S.); (D.J.); (J.P.); (W.L.); (X.Z.); (W.C.); (Y.T.)
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Waterfowl Healthy Breeding Engineering Research Center, Guangdong Higher Education Institute, Guangzhou 510225, China
| | - Jianqiu Pan
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510225, China; (Y.F.); (Y.S.); (D.J.); (J.P.); (W.L.); (X.Z.); (W.C.); (Y.T.)
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Waterfowl Healthy Breeding Engineering Research Center, Guangdong Higher Education Institute, Guangzhou 510225, China
| | - Wanyan Li
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510225, China; (Y.F.); (Y.S.); (D.J.); (J.P.); (W.L.); (X.Z.); (W.C.); (Y.T.)
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Waterfowl Healthy Breeding Engineering Research Center, Guangdong Higher Education Institute, Guangzhou 510225, China
| | - Xumeng Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510225, China; (Y.F.); (Y.S.); (D.J.); (J.P.); (W.L.); (X.Z.); (W.C.); (Y.T.)
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Waterfowl Healthy Breeding Engineering Research Center, Guangdong Higher Education Institute, Guangzhou 510225, China
| | - Wenbin Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510225, China; (Y.F.); (Y.S.); (D.J.); (J.P.); (W.L.); (X.Z.); (W.C.); (Y.T.)
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Yunbo Tian
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510225, China; (Y.F.); (Y.S.); (D.J.); (J.P.); (W.L.); (X.Z.); (W.C.); (Y.T.)
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Waterfowl Healthy Breeding Engineering Research Center, Guangdong Higher Education Institute, Guangzhou 510225, China
| | - Xu Shen
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510225, China; (Y.F.); (Y.S.); (D.J.); (J.P.); (W.L.); (X.Z.); (W.C.); (Y.T.)
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Waterfowl Healthy Breeding Engineering Research Center, Guangdong Higher Education Institute, Guangzhou 510225, China
| | - Yunmao Huang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510225, China; (Y.F.); (Y.S.); (D.J.); (J.P.); (W.L.); (X.Z.); (W.C.); (Y.T.)
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Waterfowl Healthy Breeding Engineering Research Center, Guangdong Higher Education Institute, Guangzhou 510225, China
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25
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Wang Y, Wang H, Shao W, Chen Y, Gui Y, Hu C, Yi X, Huang L, Li S, Wang D. Large-scale loss-of-function perturbations reveal a comprehensive epigenetic regulatory network in breast cancer. Cancer Biol Med 2023; 21:j.issn.2095-3941.2023.0276. [PMID: 38062748 PMCID: PMC10875281 DOI: 10.20892/j.issn.2095-3941.2023.0276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/26/2023] [Indexed: 02/16/2024] Open
Abstract
OBJECTIVE Epigenetic abnormalities have a critical role in breast cancer by regulating gene expression; however, the intricate interrelationships and key roles of approximately 400 epigenetic regulators in breast cancer remain elusive. It is important to decipher the comprehensive epigenetic regulatory network in breast cancer cells to identify master epigenetic regulators and potential therapeutic targets. METHODS We employed high-throughput sequencing-based high-throughput screening (HTS2) to effectively detect changes in the expression of 2,986 genes following the knockdown of 400 epigenetic regulators. Then, bioinformatics analysis tools were used for the resulting gene expression signatures to investigate the epigenetic regulations in breast cancer. RESULTS Utilizing these gene expression signatures, we classified the epigenetic regulators into five distinct clusters, each characterized by specific functions. We discovered functional similarities between BAZ2B and SETMAR, as well as CLOCK and CBX3. Moreover, we observed that CLOCK functions in a manner opposite to that of HDAC8 in downstream gene regulation. Notably, we constructed an epigenetic regulatory network based on the gene expression signatures, which revealed 8 distinct modules and identified 10 master epigenetic regulators in breast cancer. CONCLUSIONS Our work deciphered the extensive regulation among hundreds of epigenetic regulators. The identification of 10 master epigenetic regulators offers promising therapeutic targets for breast cancer treatment.
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Affiliation(s)
- Yumei Wang
- School of Basic Medical Sciences, State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Haiyan Wang
- Department of Pathology, School of Medicine, Qinghai University, Xining 810001, China
| | - Wei Shao
- Omics Biosciences Inc, Beijing 100871, China
| | - Yuhui Chen
- School of Basic Medical Sciences, State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Yu Gui
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Chao Hu
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Xiaohong Yi
- School of Basic Medical Sciences, State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Lijun Huang
- School of Basic Medical Sciences, State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Shasha Li
- Department of Endocrinology and Metabolism, Guangdong Provincial Key Laboratory of Diabetology & Guangzhou Municipal Key Laboratory of Mechanistic and Translational Obesity Research, Medical Center for Comprehensive Weight Control, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China
| | - Dong Wang
- School of Basic Medical Sciences, State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
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Lin W, Liu S, Xiao X, Sun W, Lu X, Gao Y, He J, Zhu Z, Wu Q, Zhang X. Integrative Analysis of Metabolome and Transcriptome Provides Insights into the Mechanism of Flower Induction in Pineapple ( Ananas comosus (L.) Merr.) by Ethephon. Int J Mol Sci 2023; 24:17133. [PMID: 38138962 PMCID: PMC10742410 DOI: 10.3390/ijms242417133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/22/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
Exogenous ethylene is commonly utilized to initiate flower induction in pineapple (Ananas comosus (L.) Merr.). However, the molecular mechanisms and metabolic changes involved are not well understood. In this study, we explored the genetic network and metabolic shifts in the 'Comte de Paris' pineapple variety during ethylene-induced flowering. This was achieved through an integrative analysis of metabolome and transcriptome profiles at vegetative shoot apexes (0 d after ethephon treatment named BL_0d), the stage of bract primordia (8 d after ethephon treatment named BL_8d), stage of flower primordia (18 d after ethephon treatment named BL_18d), and the stage of stopped floret differentiation (34 d after ethephon treatment named BL_34d). We isolated and identified 804 metabolites in the pineapple shoot apex and inflorescence, categorized into 24 classes. Notably, 29, 31, and 46 metabolites showed significant changes from BL_0d to BL_8d, BL_8d to BL_18d, and BL_18d to BL_34d, respectively. A marked decrease in indole was observed, suggesting its role as a characteristic metabolite during flower induction. Transcriptomic analysis revealed 956, 1768, and 4483 differentially expressed genes (DEGs) for BL_0d vs. BL_8d, BL_8d vs. BL_18d, and BL_18d vs. BL_34d, respectively. These DEGs were significantly enriched in carbohydrate metabolism and hormone signaling pathways, indicating their potential involvement in flower induction. Integrating metabolomic and transcriptomic data, we identified several candidate genes, such as Agamous-Like9 (AGL9), Ethylene Insensitive 3-like (ETIL3), Apetala2 (AP2), AP2-like ethylene-responsive transcription factor ANT (ANT), and Sucrose synthase 2 (SS2), that play potentially crucial roles in ethylene-induced flower induction in pineapple. We also established a regulatory network for pineapple flower induction, correlating metabolites and DEGs, based on the Arabidopsis thaliana pathway as a reference. Overall, our findings offer a deeper understanding of the metabolomic and molecular mechanisms driving pineapple flowering.
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Affiliation(s)
- Wenqiu Lin
- South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China; (W.L.)
- Laboratory of Tropical Fruit Biology, Ministry of Agriculture, Zhanjiang 524091, China
- Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
| | - Shenghui Liu
- South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China; (W.L.)
- Laboratory of Tropical Fruit Biology, Ministry of Agriculture, Zhanjiang 524091, China
- Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
| | - Xiou Xiao
- South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China; (W.L.)
| | - Weisheng Sun
- South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China; (W.L.)
- Laboratory of Tropical Fruit Biology, Ministry of Agriculture, Zhanjiang 524091, China
| | - Xinhua Lu
- South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China; (W.L.)
- Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
| | - Yuyao Gao
- South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China; (W.L.)
- Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
| | - Junjun He
- South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China; (W.L.)
| | - Zhuying Zhu
- South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China; (W.L.)
| | - Qingsong Wu
- South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China; (W.L.)
- Laboratory of Tropical Fruit Biology, Ministry of Agriculture, Zhanjiang 524091, China
- Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
| | - Xiumei Zhang
- South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China; (W.L.)
- Laboratory of Tropical Fruit Biology, Ministry of Agriculture, Zhanjiang 524091, China
- Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
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Zeng YL, Gao F, Zhang C, Ren PP, Ma L, Wang X, Wang R, Kang Y, Li K. USF1 modulates transcription and cellular functions by regulating multiple transcription factors in Huh7 cells. Oncol Lett 2023; 26:532. [PMID: 38020298 PMCID: PMC10655063 DOI: 10.3892/ol.2023.14119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/28/2023] [Indexed: 12/01/2023] Open
Abstract
Liver cancer, including hepatocellular carcinoma (HCC), is a malignant tumor that has high rates of metastasis and mortality worldwide. Upstream transcription factor 1 (USF1) is a canonical transcription factor (TF) and is associated with the pathogenesis of several cancers, but its biological functions and molecular targets in HCC remain unclear. Huh7 cells that overexpress USF1 were used with whole transcriptome profiling through RNA sequencing and chromatin immunoprecipitation (ChIP) sequencing methods to investigate the downstream targets of USF1. Reverse transcription-quantitative PCR was then used to validate the downstream targets. The results showed that USF1 significantly regulates 350 differentially expressed genes (DEGs). The upregulated DEGs were primarily protein-coding genes enriched in immune and inflammation response pathways, while the downregulated DEGs were mainly coding long non-coding (lnc)RNAs, indicating the regulatory function of USF1. It was also demonstrated that USF1 directly binds to the promoter region of 2,492 genes, which may be involved in the viral progression and cell proliferation pathways. By integrating these two datasets, 16 overlapped genes were detected, including downregulated lncRNA-NEAT1 and upregulated TF-ETV5. The downregulated lncRNA-NEAT1 showed reverse expression pattern and prognosis result compared with that of USF1 in patients with liver cancer, while upregulated TF-ETV5 showed consistent results with USF1. Promoter region motif analysis indicated that ETV5 has more binding motifs and genes than USF1 itself for USF1-regulated DEGs, indicating that USF1 may indirectly modulate gene expression by regulating ETV5 expression in Huh7 cells. The study also validated the direct interaction between USF1 and the promoter of ETV5 using ChIP-qPCR. In summary, the results demonstrated that USF1 binds to the promoter region of thousands of genes and affects a large part of DEGs indirectly. Downstream genes, including lncRNA-NEAT1 and TF-ETV5, may also have potential functions in the regulated network by USF1 and have potential functions in the progression of HCC. The present findings suggested that USF1 and its downstream targets could be potential targets for HCC therapy in the future.
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Affiliation(s)
- Yan-Li Zeng
- Department of Infectious Diseases, Henan Key Laboratory for Infectious Diseases, Henan Provincial People's Hospital, Zhengzhou, Henan 450003, P.R. China
- Department of Infectious Diseases, Zhengzhou University People's Hospital, Zhengzhou, Henan 450003, P.R. China
- Department of Infectious Diseases, Henan University People's Hospital, Zhengzhou, Henan 450003, P.R. China
| | - Fei Gao
- Department of Infectious Diseases, Henan Key Laboratory for Infectious Diseases, Henan Provincial People's Hospital, Zhengzhou, Henan 450003, P.R. China
| | - Can Zhang
- Department of Infectious Diseases, Henan Key Laboratory for Infectious Diseases, Henan Provincial People's Hospital, Zhengzhou, Henan 450003, P.R. China
| | - Pei-Pei Ren
- Department of Infectious Diseases, Henan Key Laboratory for Infectious Diseases, Henan Provincial People's Hospital, Zhengzhou, Henan 450003, P.R. China
| | - Li Ma
- Department of Infectious Diseases, Henan Key Laboratory for Infectious Diseases, Henan Provincial People's Hospital, Zhengzhou, Henan 450003, P.R. China
| | - Xin Wang
- Department of Infectious Diseases, Henan University, Zhengzhou, Henan 450003, P.R. China
| | - Ruzhen Wang
- Department of Infectious Diseases, Henan Key Laboratory for Infectious Diseases, Henan Provincial People's Hospital, Zhengzhou, Henan 450003, P.R. China
| | - Yi Kang
- Department of Infectious Diseases, Henan Key Laboratory for Infectious Diseases, Henan Provincial People's Hospital, Zhengzhou, Henan 450003, P.R. China
| | - Ke Li
- Department of Infectious Diseases, Henan Key Laboratory for Infectious Diseases, Henan Provincial People's Hospital, Zhengzhou, Henan 450003, P.R. China
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Guo Y, Qi Y, Feng Y, Yang Y, Xue L, El-Kassaby YA, Wang G, Fu F. Inferring the Regulatory Network of miRNAs on Terpene Trilactone Biosynthesis Affected by Environmental Conditions. Int J Mol Sci 2023; 24:17002. [PMID: 38069325 PMCID: PMC10707241 DOI: 10.3390/ijms242317002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
As a medicinal tree species, ginkgo (Ginkgo biloba L.) and terpene trilactones (TTLs) extracted from its leaves are the main pharmacologic activity constituents and important economic indicators of its value. The accumulation of TTLs is known to be affected by environmental stress, while the regulatory mechanism of environmental response mediated by microRNAs (miRNAs) at the post-transcriptional levels remains unclear. Here, we focused on grafted ginkgo grown in northwestern, southwestern, and eastern-central China and integrally analyzed RNA-seq and small RNA-seq high-throughput sequencing data as well as metabolomics data from leaf samples of ginkgo clones grown in natural environments. The content of bilobalide was highest among detected TTLs, and there was more than a twofold variation in the accumulation of bilobalide between growth conditions. Meanwhile, transcriptome analysis found significant differences in the expression of 19 TTL-related genes among ginkgo leaves from different environments. Small RNA sequencing and analysis showed that 62 of the 521 miRNAs identified were differentially expressed among different samples, especially the expression of miRN50, miR169h/i, and miR169e was susceptible to environmental changes. Further, we found that transcription factors (ERF, MYB, C3H, HD-ZIP, HSF, and NAC) and miRNAs (miR319e/f, miRN2, miRN54, miR157, miR185, and miRN188) could activate or inhibit the expression of TTL-related genes to participate in the regulation of terpene trilactones biosynthesis in ginkgo leaves by weighted gene co-regulatory network analysis. Our findings provide new insights into the understanding of the regulatory mechanism of TTL biosynthesis but also lay the foundation for ginkgo leaves' medicinal value improvement under global change.
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Affiliation(s)
- Ying Guo
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Y.Q.); (Y.F.)
| | - Yongli Qi
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Y.Q.); (Y.F.)
| | - Yangfan Feng
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Y.Q.); (Y.F.)
| | - Yuting Yang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Y.Q.); (Y.F.)
| | - Liangjiao Xue
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Y.Q.); (Y.F.)
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada;
| | - Guibin Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Y.Q.); (Y.F.)
| | - Fangfang Fu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Y.Q.); (Y.F.)
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Meng Q, Zhou Q, Chen X, Chen J. Prognostic hub gene CBX2 drives a cancer stem cell-like phenotype in HCC revealed by multi-omics and multi-cohorts. Aging (Albany NY) 2023; 15:12817-12851. [PMID: 37980163 DOI: 10.18632/aging.205173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/07/2023] [Indexed: 11/20/2023]
Abstract
Hepatocellular carcinoma (HCC) is a malignant tumor with a high prevalence and fatality rate. CBX2 has been demonstrated to impact the development and advancement of various cancers, albeit it has received limited attention in relation to HCC. In this study, CBX2 and CEP55 were screened out with the refined triple regulatory networks constructed by total RNA-seq datasets (TCGA-LIHC, GSE140845) and a robust prognostic model. Aberrantly higher expression levels of CBX2 and CEP55 in HCC may be caused by CNV alterations, promoter hypo-methylation, open chromatin accessibility, and greater active marks such as H3K4me3, H3K4me1, and H3K27ac. Functionally, CBX2, which was highly correlated with CD44, shaped a cancer stem cell-like phenotype by positively regulating cell-cycle progression, proliferation, invasion, metastasis, wound healing, and radiation resistance, revealed by combining bulk RNA-seq and scRNA-seq datasets. CBX2 knockdown validated its role in affecting the cell cycle. Importantly, we revealed CBX2 could activate gene by cooperating with co-regulators or not rather than a recognizer of the repressive mark H3K27me3. For instance, we uncovered CBX2 bound to promoter of CTNNB1 and CEP55 to augment their expressions. CBX2 showed a highly positive correlation with CEP55 at pan-cancer level. In addition, CBX2 and CEP55 may enhance extracellular matrix reprograming via cancer-associated fibroblast. Surprisingly, patients with high expression of CBX2 or CEP55 exhibited a higher response to immunotherapy, indicating that CBX2 and CEP55 may be promising therapeutic targets for HCC patients.
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Affiliation(s)
- Qingren Meng
- National Clinical Research Center for Infectious Diseases, The Third People’s Hospital of Shenzhen, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen 518000, Guangdong, China
- School of Medicine, Southern University of Science and Technology, Shenzhen 518100, Guangdong, China
| | - Qian Zhou
- International Cancer Center, Shenzhen University Medical School, Shenzhen 518100, Guangdong, China
| | - Xi Chen
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518100, Guangdong, China
| | - Jun Chen
- National Clinical Research Center for Infectious Diseases, The Third People’s Hospital of Shenzhen, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen 518000, Guangdong, China
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dos Santos EC, Rohan P, Binato R, Abdelhay E. Integrated Network Analysis of microRNAs, mRNAs, and Proteins Reveals the Regulatory Interaction between hsa-mir-200b and CFL2 Associated with Advanced Stage and Poor Prognosis in Patients with Intestinal Gastric Cancer. Cancers (Basel) 2023; 15:5374. [PMID: 38001634 PMCID: PMC10670725 DOI: 10.3390/cancers15225374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/07/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
Intestinal gastric cancer (IGC) carcinogenesis results from a complex interplay between environmental and molecular factors, ultimately contributing to disease development. We used integrative bioinformatic analysis to investigate IGC high-throughput molecular data to uncover interactions among differentially expressed genes, microRNAs, and proteins and their roles in IGC. An integrated network was generated based on experimentally validated microRNA-gene/protein interaction data, with three regulatory circuits involved in a complex network contributing to IGC progression. Key regulators were determined, including 23 microRNA and 15 gene/protein hubs. The regulatory circuit networks were associated with hallmarks of cancer, e.g., cell death, apoptosis and the cell cycle, the immune response, and epithelial-to-mesenchymal transition, indicating that different mechanisms of gene regulation impact similar biological functions. Altered expression of hubs was related to the clinicopathological characteristics of IGC patients and showed good performance in discriminating tumors from adjacent nontumor tissues and in relation to T stage and overall survival (OS). Interestingly, expression of upregulated hub hsa-mir-200b and its downregulated target hub gene/protein CFL2 were related not only to pathological T staging and OS but also to changes during IGC carcinogenesis. Our study suggests that regulation of CFL2 by hsa-miR-200b is a dynamic process during tumor progression and that this control plays essential roles in IGC development. Overall, the results indicate that this regulatory interaction is an important component in IGC pathogenesis. Also, we identified a novel molecular interplay between microRNAs, proteins, and genes associated with IGC in a complex biological network and the hubs closely related to IGC carcinogenesis as potential biomarkers.
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Affiliation(s)
- Everton Cruz dos Santos
- Stem Cell Laboratory, Division of Specialized Laboratories, Instituto Nacional de Câncer (INCA), Rio de Janeiro 20230-130, RJ, Brazil; (P.R.); (R.B.); (E.A.)
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Cai X, Yang R, Shi W, Cai Y, Ma Z. Exploration of the common pathogenic link between COVID-19 and diabetic foot ulcers: An in silico approach. Health Sci Rep 2023; 6:e1686. [PMID: 37936615 PMCID: PMC10626003 DOI: 10.1002/hsr2.1686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/09/2023] [Accepted: 10/23/2023] [Indexed: 11/09/2023] Open
Abstract
Background and Aims The Coronavirus Disease-19 (COVID-19) is posing an ongoing threat to human health. Patients of diabetic foot ulcer (DFU) are susceptible to COVID-19-induced adverse outcomes. Nevertheless, investigations into their mutual molecular mechanisms have been limited to date. In the present work, we tried to uncover the shared pathogenesis and regulatory gene targets of COVID-19 and DFU. Methods In this study, we chose GSE161281 as the COVID-19 data set, which contained severe acute respiratory syndrome coronavirus 2 infected human induced embryonic stem cell-derived peripheral neurons (n = 2) with uninfected controls (n = 2). The GSE134431 designated as the DFU data set, comprising full-thickness DFU (n = 13) and diabetic foot skin (n = 8) samples from diabetic patients. The differential expressed genes (DEGs) were identified from GSE161281 and GSE134431, and the common DEGs between COVID-19 and DFU were extracted. Multifactor regulatory network and co-expression network of the common DEGs were analyzed, along with candidate drug prediction. Results Altogether, six common DEGs (dickkopf-related protein 1 [DKK1], serine proteinase inhibitor A3 [SERPINA3], ras homolog family member D [RHOD], myelin protein zero like 3 [MPZL3], Claudin-11 [CLDN11], and epidermal growth factor receptor pathway substrate 8-like 1 [EPS8L1]) were found between COVID-19 and DFU. Functional analyses indicated that pathways of apoptotic and Wnt signaling may contribute to progression of COVID-19. Gene co-expression network implied the shared pathways of immune regulation and cytokine response participated collectively in the development of DFU and COVID-19. A multifactor regulatory network was constructed integrating the corresponding microRNAs (miRNAs) and transcription factors. Additionally, we proposed potential drug objects for the combined therapy. Conclusion Our study revealed the shared molecular mechanisms underlying COVID-19 and DFU. The identified pivotal targets and common pathways can provide new perspectives for further research and assist the development of management strategies in patients of DFU complicated with COVID-19.
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Affiliation(s)
- Xueyao Cai
- Department of Burn and Plastic SurgeryDongguan Tungwah HospitalDongguanChina
| | - Ruijin Yang
- Department of Burn and Plastic SurgeryDongguan Tungwah HospitalDongguanChina
| | - Wenjun Shi
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yuchen Cai
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Zhengzheng Ma
- Department of Burn and Plastic SurgeryDongguan Tungwah HospitalDongguanChina
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Zhou M, Li Y, Cheng Z, Zheng X, Cai C, Wang H, Lu K, Zhu C, Ding Y. Important Factors Controlling Gibberellin Homeostasis in Plant Height Regulation. J Agric Food Chem 2023; 71:15895-15907. [PMID: 37862148 DOI: 10.1021/acs.jafc.3c03560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2023]
Abstract
Plant height is an important agronomic trait that is closely associated with crop yield and quality. Gibberellins (GAs), a class of highly efficient plant growth regulators, play key roles in regulating plant height. Increasing reports indicate that transcriptional regulation is a major point of regulation of the GA pathways. Although substantial knowledge has been gained regarding GA biosynthetic and signaling pathways, important factors contributing to the regulatory mechanisms homeostatically controlling GA levels remain to be elucidated. Here, we provide an overview of current knowledge regarding the regulatory network involving transcription factors, noncoding RNAs, and histone modifications involved in GA pathways. We also discuss the mechanisms of interaction between GAs and other hormones in plant height development. Finally, future directions for applying knowledge of the GA hormone in crop breeding are described.
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Affiliation(s)
- Mei Zhou
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Yakun Li
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Zhuowei Cheng
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Xinyu Zheng
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Chong Cai
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Huizhen Wang
- Huangshan Institute of Product Quality Inspection, Huangshan 242700, China
| | - Kaixing Lu
- Ningbo Key Laboratory of Agricultural Germplasm Resources Mining and Environmental Regulation, College of Science and Technology, Ningbo University, Ningbo 315000, China
| | - Cheng Zhu
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Yanfei Ding
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
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Gao Z, Zhai X, Yan G, Tian Y, Huang X, Wu Q, Yuan L, Su L. Bioinformatics analyses of gene expression profile to identify pathogenic mechanisms for COVID-19 infection and cutaneous lupus erythematosus. Front Immunol 2023; 14:1268912. [PMID: 38022551 PMCID: PMC10644101 DOI: 10.3389/fimmu.2023.1268912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Objective The global mortality rates have surged due to the ongoing coronavirus disease 2019 (COVID-19), leading to a worldwide catastrophe. Increasing incidents of patients suffering from cutaneous lupus erythematosus (CLE) exacerbations after either contracting COVID-19 or getting immunized against it, have been observed in recent research. However, the precise intricacies that prompt this unexpected complication are yet to be fully elucidated. This investigation seeks to probe into the molecular events inciting this adverse outcome. Method Gene expression patterns from the Gene Expression Omnibus (GEO) database, specifically GSE171110 and GSE109248, were extracted. We then discovered common differentially expressed genes (DEGs) in both COVID-19 and CLE. This led to the creation of functional annotations, formation of a protein-protein interaction (PPI) network, and identification of key genes. Furthermore, regulatory networks relating to these shared DEGs and significant genes were constructed. Result We identified 214 overlapping DEGs in both COVID-19 and CLE datasets. The following functional enrichment analysis of these DEGs highlighted a significant enrichment in pathways related to virus response and infectious disease in both conditions. Next, a PPI network was constructed using bioinformatics tools, resulting in the identification of 5 hub genes. Finally, essential regulatory networks including transcription factor-gene and miRNA-gene interactions were determined. Conclusion Our findings demonstrate shared pathogenesis between COVID-19 and CLE, offering potential insights for future mechanistic investigations. And the identification of common pathways and key genes in these conditions may provide novel avenues for research.
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Affiliation(s)
- Zhenyu Gao
- Hubei Provincial Key Laboratory of Occurrence and Intervention of Rheumatic Disease, Minda Hospital of Hubei Minzu University, Enshi, China
- Department of Rheumatology and Immunology, Minda Hospital of Hubei Minzu University, Enshi, China
| | - Xinchao Zhai
- Hubei Provincial Key Laboratory of Occurrence and Intervention of Rheumatic Disease, Minda Hospital of Hubei Minzu University, Enshi, China
- Department of Rheumatology and Immunology, Minda Hospital of Hubei Minzu University, Enshi, China
| | - Guoqing Yan
- Hubei Provincial Key Laboratory of Occurrence and Intervention of Rheumatic Disease, Minda Hospital of Hubei Minzu University, Enshi, China
- Department of Rheumatology and Immunology, Minda Hospital of Hubei Minzu University, Enshi, China
| | - Yao Tian
- Hubei Provincial Key Laboratory of Occurrence and Intervention of Rheumatic Disease, Minda Hospital of Hubei Minzu University, Enshi, China
- Department of Rheumatology and Immunology, Minda Hospital of Hubei Minzu University, Enshi, China
| | - Xia Huang
- Hubei Provincial Key Laboratory of Occurrence and Intervention of Rheumatic Disease, Minda Hospital of Hubei Minzu University, Enshi, China
- Department of Rheumatology and Immunology, Minda Hospital of Hubei Minzu University, Enshi, China
| | - Qingchao Wu
- Hubei Provincial Key Laboratory of Occurrence and Intervention of Rheumatic Disease, Minda Hospital of Hubei Minzu University, Enshi, China
- Department of Rheumatology and Immunology, Minda Hospital of Hubei Minzu University, Enshi, China
| | - Lin Yuan
- Hubei Provincial Key Laboratory of Occurrence and Intervention of Rheumatic Disease, Minda Hospital of Hubei Minzu University, Enshi, China
| | - Linchong Su
- Hubei Provincial Key Laboratory of Occurrence and Intervention of Rheumatic Disease, Minda Hospital of Hubei Minzu University, Enshi, China
- Department of Rheumatology and Immunology, Minda Hospital of Hubei Minzu University, Enshi, China
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Wang X, Zhou R, Zhao S, Niu S. An Integrated Analysis of microRNAs and the Transcriptome Reveals the Molecular Mechanisms Underlying the Regulation of Leaf Development in Xinyang Maojian Green Tea ( Camellia sinensis). Plants (Basel) 2023; 12:3665. [PMID: 37960023 PMCID: PMC10649745 DOI: 10.3390/plants12213665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 10/03/2023] [Accepted: 10/22/2023] [Indexed: 11/15/2023]
Abstract
Xinyang Maojian (XYMJ) tea is one of the world's most popular green teas; the development of new sprouts directly affects the yield and quality of tea products, especially for XYMJ, which has hairy tips. Here, we used transcriptome and small RNA sequencing to identify mRNAs and miRNAs, respectively, involved in regulating leaf development in different plant tissues (bud, leaf, and stem). We identified a total of 381 conserved miRNAs. Given that no genomic data for XYMJ green tea are available, we compared the sequencing data for XYMJ green tea with genomic data from a closely related species (Tieguanyin) and the Camellia sinensis var. sinensis database; we identified a total of 506 and 485 novel miRNAs, respectively. We also identified 11 sequence-identical novel miRNAs in the tissues of XYMJ tea plants. Correlation analyses revealed 97 miRNA-mRNA pairs involved in leaf growth and development; the csn-miR319-2/csnTCP2 and miR159-csnMYB modules were found to be involved in leaf development in XYMJ green tea. Quantitative real-time PCR was used to validate the expression levels of the miRNAs and mRNAs. The miRNAs and target genes identified in this study might shed new light on the molecular mechanisms underlying the regulation of leaf development in tea plants.
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Affiliation(s)
- Xianyou Wang
- School of Horticulture Landscape Architecture, Henan Institute of Science and Technology, Xinxiang 453003, China
- Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang 453003, China
| | - Ruijin Zhou
- School of Horticulture Landscape Architecture, Henan Institute of Science and Technology, Xinxiang 453003, China
- Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang 453003, China
| | - Shanshan Zhao
- School of Food Science, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Shengyang Niu
- School of Food Science, Henan Institute of Science and Technology, Xinxiang 453003, China
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Yan Y, Zhao J, Lin S, Li M, Liu J, Raymond O, Vergne P, Kong W, Wu Q, Zhang X, Bao M, Bendahmane M, Fu X. Light-mediated anthocyanin biosynthesis in rose petals involves a balanced regulatory module comprising transcription factors RhHY5, RhMYB114a, and RhMYB3b. J Exp Bot 2023; 74:5783-5804. [PMID: 37392434 DOI: 10.1093/jxb/erad253] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 06/28/2023] [Indexed: 07/03/2023]
Abstract
Roses are significant botanical species with both ornamental and economic value, displaying diverse floral traits, particularly an extensive array of petal colors. The red pigmentation of rose petals is predominantly attributed to anthocyanin accumulation. However, the underlying regulatory mechanism of anthocyanin biosynthesis in roses remains elusive. This study presents a novel light-responsive regulatory module governing anthocyanin biosynthesis in rose petals, which involves the transcription factors RhHY5, RhMYB114a, and RhMYB3b. Under light conditions (1000-1500 μmol m-2 s-1), RhHY5 represses RhMYB3b expression and induces RhMYB114a expression, positively regulating anthocyanin biosynthesis in rose petals. Notably, activation of anthocyanin structural genes probably involves an interaction and synergy between RhHY5 and the MYB114a-bHLH3-WD40 complex. Additionally, RhMYB3b is activated by RhMYB114a to prevent excessive accumulation of anthocyanin. Conversely, under low light conditions (<10 μmol m-2 s-1), the degradation of RhHY5 leads to down-regulation of RhMYB114a and up-regulation of RhMYB3b, which in turn inhibits the expression of both RhMYB114a and anthocyanin structural genes. Additionally, RhMYB3b competes with RhMYB114a for binding to RhbHLH3 and the promoters of anthocyanin-related structural genes. Overall, our study uncovers a complex light-mediated regulatory network that governs anthocyanin biosynthesis in rose petals, providing new insights into the molecular mechanisms underlying petal color formation in rose.
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Affiliation(s)
- Yuhang Yan
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Jiaxing Zhao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Shengnan Lin
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Mouliang Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Jiayi Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Olivier Raymond
- Laboratoire Reproduction et Development des Plantes, INRA-CNRS-Lyon1-ENS, Ecole Normale Superieure de Lyon, Lyon, France
| | - Philippe Vergne
- Laboratoire Reproduction et Development des Plantes, INRA-CNRS-Lyon1-ENS, Ecole Normale Superieure de Lyon, Lyon, France
| | - Weilong Kong
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Quanshu Wu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Xiaoni Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Manzhu Bao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Mohammed Bendahmane
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
- Laboratoire Reproduction et Development des Plantes, INRA-CNRS-Lyon1-ENS, Ecole Normale Superieure de Lyon, Lyon, France
| | - Xiaopeng Fu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
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Xu D, Forbes AN, Cohen S, Palladino A, Karadimitriou T, Khurana E. Recapitulation of patient-specific 3D chromatin conformation using machine learning. Cell Rep Methods 2023; 3:100578. [PMID: 37673071 PMCID: PMC10545938 DOI: 10.1016/j.crmeth.2023.100578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 04/05/2023] [Accepted: 08/10/2023] [Indexed: 09/08/2023]
Abstract
Regulatory networks containing enhancer-gene edges define cellular states. Multiple efforts have revealed these networks for reference tissues and cell lines by integrating multi-omics data. However, the methods developed cannot be applied for large patient cohorts due to the infeasibility of chromatin immunoprecipitation sequencing (ChIP-seq) for limited biopsy material. We trained machine-learning models using chromatin interaction analysis with paired-end tag sequencing (ChIA-PET) and high-throughput chromosome conformation capture combined with chromatin immunoprecipitation (HiChIP) data that can predict connections using only assay for transposase-accessible chromatin using sequencing (ATAC-seq) and RNA-seq data as input, which can be generated from biopsies. Our method overcomes limitations of correlation-based approaches that cannot distinguish between distinct target genes of given enhancers or between active vs. poised states in different samples, a hallmark of network rewiring in cancer. Application of our model on 371 samples across 22 cancer types revealed 1,780 enhancer-gene connections for 602 cancer genes. Using CRISPR interference (CRISPRi), we validated enhancers predicted to regulate ESR1 in estrogen receptor (ER)+ breast cancer and A1CF in liver hepatocellular carcinoma.
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Affiliation(s)
- Duo Xu
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY, USA; Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Andre Neil Forbes
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY, USA; Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Sandra Cohen
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Ann Palladino
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY, USA
| | | | - Ekta Khurana
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY, USA; Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA.
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Xue X, Zhao A, Wang Y, Ren H, Su W, Li Y, Shi M, Liu L, Li D. Metabolomics and transcriptomics analyses for characterizing the alkaloid metabolism of Chinese jujube and sour jujube fruits. Front Plant Sci 2023; 14:1267758. [PMID: 37790781 PMCID: PMC10544937 DOI: 10.3389/fpls.2023.1267758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 08/24/2023] [Indexed: 10/05/2023]
Abstract
Introduction Jujube is an important economic forest tree whose fruit is rich in alkaloids. Chinese jujube (Ziziphus jujuba Mill.) and sour jujube (Ziziphus spinosa Hu.) are the two most important species of the jujube genus. However, the mechanisms underlying the synthesis and metabolism of alkaloids in jujube fruits remain poorly understood. Methods In this study, the fruits of Ziziphus jujuba 'Hupingzao' and Ziziphus spinosa 'Taigusuanzao' in different harvest stages were used as test materials, we first integrated widely targeted metabolomics and transcriptomics analyses to elucidate the metabolism of alkaloids of jujube fruits. Results In the metabolomics analysis, 44 alkaloid metabolites were identified in 4 samples, 3 of which were unique to sour jujube fruit. The differential alkaloid metabolites (DAMs) were more accumulated in sour jujube than in Chinese jujube; further, they were more accumulated in the white ripening stage than in the red stage. DAMs were annotated to 12 metabolic pathways. Additionally, transcriptomics data revealed 259 differentially expressed genes (DEGs) involved in alkaloid synthesis and metabolism. By mapping the regulatory networks of DAMs and DEGs, we screened out important metabolites and 11 candidate genes. Discussion This study preliminarily elucidated the molecular mechanism of jujube alkaloid synthesis. The candidate genes regulated the synthesis of key alkaloid metabolites, but the specific regulation mechanism is unclear. Taken together, our results provide insights into the metabolic networks of alkaloid synthesis in Chinese jujube and sour jujube fruits at different harvest stages, thereby providing a theoretical reference for further research on the regulatory mechanism of jujube alkaloids and their development and utilization.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Dengke Li
- Pomology Institute, Shanxi Agricultural University, Shanxi Key Laboratory of Germplasm Improvement and Utilization in Pomology, Taiyuan, China
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Kim JY, Lee Y, Dho SH, Park HJ, Kim DM, Lim JC, Kim SM, Kim LK. Integrative analysis of circular RNA regulatory network in papillary thyroid carcinoma. Am J Cancer Res 2023; 13:4446-4465. [PMID: 37818060 PMCID: PMC10560948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/21/2023] [Indexed: 10/12/2023] Open
Abstract
Papillary thyroid cancer (PTC) is the most common type of endocrine cancer worldwide. Generally, PTC has an excellent prognosis; however, lymph node metastases and recurrences occur frequently. Over the last decade, circular RNAs (circRNAs), a large class of noncoding RNAs (ncRNAs), have emerged as key regulators of various tumor progression pathways. Here, we aimed to identify novel circRNAs as PTC biomarkers. Differentially expressed circRNAs and mRNAs were analyzed using public datasets from the Gene Expression Omnibus and Cancer Genome Atlas. In addition, we screened for target miRNAs using online prediction databases. Based on these results, we established a circRNA-miRNA-mRNA regulatory network associated with PTC, in which protein-protein interaction networks led to the identification of hub genes. Functional enrichment and survival analyses were performed to gain insights into the biological mechanisms of circRNA involvement. As a result, we found that two circRNAs (hsa_circ_0041829 and has_circ_0092299), four miRNAs (miR-369, miR-486, miR-574, and miR-665), and nine hub genes (BBC3, E2F1, FYN, MAG, SDC1, SDC3, SNAP25, TK1, and TYMS) play significant roles in PTC progression. This study provides a novel framework for understanding the roles of circRNA-miRNA-mediated gene regulation in PTC. It also introduces potential therapeutic targets and prognostic biomarkers, which may serve as a basis for developing targeted therapeutic interventions for PTC.
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Affiliation(s)
- Ji Young Kim
- Department of Biomedical Sciences, Graduate School of Medical Science, Brain Korea 21 Project, Gangnam Severance Hospital, Yonsei University College of MedicineSeoul, Republic of Korea
| | - Yeongun Lee
- Department of Biomedical Sciences, Graduate School of Medical Science, Brain Korea 21 Project, Gangnam Severance Hospital, Yonsei University College of MedicineSeoul, Republic of Korea
| | - So Hee Dho
- Department of Biomedical Sciences, Graduate School of Medical Science, Brain Korea 21 Project, Gangnam Severance Hospital, Yonsei University College of MedicineSeoul, Republic of Korea
| | - Hyo Jin Park
- Department of Biomedical Sciences, Graduate School of Medical Science, Brain Korea 21 Project, Gangnam Severance Hospital, Yonsei University College of MedicineSeoul, Republic of Korea
| | - Da-Mi Kim
- Radioisotope Research Division, Korea Atomic Energy Research InstituteDaejeon, Republic of Korea
| | - Jae Cheong Lim
- Radioisotope Research Division, Korea Atomic Energy Research InstituteDaejeon, Republic of Korea
| | - Seok-Mo Kim
- Department of Surgery, Thyroid Cancer Center, Gangnam Severance Hospital, Institute of Refractory Thyroid Cancer, Yonsei University College of MedicineSeoul, Republic of Korea
| | - Lark Kyun Kim
- Department of Biomedical Sciences, Graduate School of Medical Science, Brain Korea 21 Project, Gangnam Severance Hospital, Yonsei University College of MedicineSeoul, Republic of Korea
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Jiang C, Storey KB, Yang H, Sun L. Aestivation in Nature: Physiological Strategies and Evolutionary Adaptations in Hypometabolic States. Int J Mol Sci 2023; 24:14093. [PMID: 37762394 PMCID: PMC10531719 DOI: 10.3390/ijms241814093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/14/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
Aestivation is considered to be one of the "purest" hypometabolic states in nature, as it involves aerobic dormancy that can be induced and sustained without complex factors. Animals that undergo aestivation to protect themselves from environmental stressors such as high temperatures, droughts, and food shortages. However, this shift in body metabolism presents new challenges for survival, including oxidative stress upon awakening from aestivation, accumulation of toxic metabolites, changes in energy sources, adjustments to immune status, muscle atrophy due to prolonged immobility, and degeneration of internal organs due to prolonged food deprivation. In this review, we summarize the physiological and metabolic strategies, key regulatory factors, and networks utilized by aestivating animals to address the aforementioned components of aestivation. Furthermore, we present a comprehensive overview of the advancements made in aestivation research across major species, including amphibians, fish, reptiles, annelids, mollusks, and echinoderms, categorized according to their respective evolutionary positions. This approach offers a distinct perspective for comparative analysis, facilitating an understanding of the shared traits and unique features of aestivation across different groups of organisms.
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Affiliation(s)
- Chunxi Jiang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences & Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (C.J.); (H.Y.)
- Laboratory for Marine Ecology and Environmental Science & Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kenneth B. Storey
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada;
| | - Hongsheng Yang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences & Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (C.J.); (H.Y.)
- Laboratory for Marine Ecology and Environmental Science & Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lina Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences & Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (C.J.); (H.Y.)
- Laboratory for Marine Ecology and Environmental Science & Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Abstract
Fruit ripening is a crucial stage in quality development, influenced by a diverse array of internal and external factors. Among these factors, epigenetic regulation holds significant importance and has garnered substantial research attention in recent years. Here, this review aims to discuss the breakthrough in epigenetic regulation of tomato (Solanum lycopersicum) fruit ripening, including DNA methylation, N6-Methyladenosine mRNA modification, histone demethylation/deacetylation, and non-coding RNA. Through this brief review, we seek to enhance our understanding of the regulatory mechanisms governing tomato fruit ripening, while providing fresh insights for the precise modulation of these mechanisms.
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Affiliation(s)
| | - Libo Jiang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
| | - Dongchao Ji
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
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Wu G, Tian X, Qiu Q, Zhang Y, Fan X, Yuan D. Dynamic cytological and transcriptomic analyses provide novel insights into the mechanisms of sex determination in Castanea henryi. Front Plant Sci 2023; 14:1257541. [PMID: 37771497 PMCID: PMC10523332 DOI: 10.3389/fpls.2023.1257541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 08/25/2023] [Indexed: 09/30/2023]
Abstract
Castanea henryi is a monoecious woody food tree species whose yield and industrialization potential are limited by its low female-to-male flower ratio. Here, the male flowers on the male inflorescence of C. henryi were converted to female flowers by triple applications of exogenous cytokinin (CK) (N-(2-chloro-4-pyridyl)-N'-phenylurea, CPPU). To study the role of exogenous CK in flower sex determination, cytological and transcriptomic analyses were performed on samples from the five stages after CK treatment. Cytological analysis showed that stage 3 (nine days after the last CK treatment) was the critical stage in the differential development of the pistil primordium and stamen primordium. On this basis, one key module and two modules with significant positive correlations with stage 3 were identified by weighted gene co-expression network analysis (WGCNA), combined with transcriptome data. The CK and GA biosynthesis- and signaling-related genes, three transcription factor (TF) families, and 11 floral organ identity genes were identified in the related modules. In particular, the TFs WRKY47, ERF021, and MYB4, and floral organ identity genes AGL11/15, DEF, and SEP1 with large differences are considered to be critical regulators of sex determination in C. henryi. Based on these results, a genetic regulatory network for exogenous CK in the sex determination of flowers in C. henryi is proposed. This study contributes to the understanding of the role of CK in the sex regulation of flowers and provides new insights into the regulatory network of sex determination in C. henryi.
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Affiliation(s)
- Guolong Wu
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China
- Key Laboratory of Non-Wood Forest Products of State Forestry Administration, Central South University of Forestry and Technology, Changsha, China
| | | | - Qi Qiu
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China
- Key Laboratory of Non-Wood Forest Products of State Forestry Administration, Central South University of Forestry and Technology, Changsha, China
| | - Yue Zhang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China
- Key Laboratory of Non-Wood Forest Products of State Forestry Administration, Central South University of Forestry and Technology, Changsha, China
| | - Xiaoming Fan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China
- Key Laboratory of Non-Wood Forest Products of State Forestry Administration, Central South University of Forestry and Technology, Changsha, China
| | - Deyi Yuan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China
- Key Laboratory of Non-Wood Forest Products of State Forestry Administration, Central South University of Forestry and Technology, Changsha, China
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Peng X, Zhu Y, Wang T, Wang S, Sun J. Integrative analysis links autophagy to intrauterine adhesion and establishes autophagy-related circRNA-miRNA-mRNA regulatory network. Aging (Albany NY) 2023; 15:8275-8297. [PMID: 37616056 PMCID: PMC10497020 DOI: 10.18632/aging.204969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/06/2023] [Indexed: 08/25/2023]
Abstract
BACKGROUND Intrauterine adhesion (IUA) is a troublesome complication characterized with endometrial fibrosis after endometrial trauma. Increasing number of investigations focused on autophagy and non-coding RNA in the pathogenesis of uterine adhesion, but the underlying mechanism needs to be further studied. METHODS mRNA expression profile and miRNA expression profile were obtained from Gene Expression Omnibus database. The autophagy related genes were low. Venn diagram was used to set the intersection of autophagy genes and DEGs to obtain ARDEGs. Circbank was used to select hub autophagy-related circRNAs based on ARDEMs. Then, the differentially expressed autophagy-related genes, miRNAs and circRNAs were analyzed by functional enrichment analysis, and protein-protein interaction network analysis. Finally, the expression levels of hub circRNAs and hub miRNAs were validated through RT-PCR of clinical intrauterine adhesion samples. In vitro experiments were investigated to explore the effect of hub ARCs on cell autophagy, myofibroblast transformation and collagen deposition. RESULTS 11 autophagy-related differentially expressed genes (ARDEGs) and 41 differentially expressed miRNA (ARDEMs) compared between normal tissues and IUA were identified. Subsequently, the autophagy-related miRNA-mRNA network was constructed and hub ARDEMs were selected. Furthermore, the autophagy-related circRNA-miRNA-mRNA network was established. According to the ranking of number of regulated ARDEMs, hsa-circ-0047959, hsa-circ-0032438, hsa-circ-0047301 were regarded as the hub ARCs. In comparison of normal endometrial tissue, all three hub ARCs were upregulated in IUA tissue. All hub ARDEMs were downregulated except has-miR-320c. CONCLUSIONS In the current study, we firstly constructed autophagy-related circRNA-miRNA-mRNA regulatory network and identified hub ARCs and ARDEMs had not been reported in IUA.
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Affiliation(s)
- Xiaotong Peng
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 200092, China
- Department of Gynaecology and Obstetrics, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Yiping Zhu
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Tao Wang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Shuo Wang
- Department of Orthopedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
| | - Jing Sun
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 200092, China
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Cao F, Wang X, Ye Q, Yan F, Lu W, Xie J, Bi B, Wang X. Identifying circRNA-miRNA-mRNA Regulatory Networks in Chemotherapy-Induced Peripheral Neuropathy. Curr Issues Mol Biol 2023; 45:6804-6822. [PMID: 37623249 PMCID: PMC10453290 DOI: 10.3390/cimb45080430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/13/2023] [Accepted: 08/15/2023] [Indexed: 08/26/2023] Open
Abstract
Chemotherapy-induced peripheral neuropathy (CIPN) is a frequent and severe side effect of first-line chemotherapeutic agents. The association between circular RNAs (circRNAs) and CIPN remains unclear. In this study, CIPN models were constructed with Taxol, while 134 differentially expressed circRNAs, 353 differentially expressed long non-coding RNAs, and 86 differentially expressed messenger RNAs (mRNAs) were identified utilizing RNA sequencing. CircRNA-targeted microRNAs (miRNAs) were predicted using miRanda, and miRNA-targeted mRNAs were predicted using TargetScan and miRDB. The intersection of sequencing and mRNA prediction results was selected to establish the circRNA-miRNA-mRNA networks, which include 15 circRNAs, 18 miRNAs, and 11 mRNAs. Functional enrichment pathway analyses and immune infiltration analyses revealed that differentially expressed mRNAs were enriched in the immune system, especially in T cells, monocytes, and macrophages. Cdh1, Satb2, Fas, P2ry2, and Zfhx2 were further identified as hub genes and validated by RT-qPCR, correlating with macrophages, plasmacytoid dendritic cells, and central memory CD4 T cells in CIPN. Additionally, we predicted the associated diseases, 36 potential transcription factors (TFs), and 30 putative drugs for hub genes using the DisGeNET, TRRUST, and DGIdb databases, respectively. Our results indicated the crucial role of circRNAs, and the immune microenvironment played in CIPN, providing novel insights for further research.
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Affiliation(s)
- Fei Cao
- Department of Anesthesiology, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou 510060, China; (F.C.); (X.W.); (Q.Y.); (F.Y.); (W.L.); (J.X.)
| | - Xintong Wang
- Department of Anesthesiology, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou 510060, China; (F.C.); (X.W.); (Q.Y.); (F.Y.); (W.L.); (J.X.)
| | - Qingqing Ye
- Department of Anesthesiology, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou 510060, China; (F.C.); (X.W.); (Q.Y.); (F.Y.); (W.L.); (J.X.)
| | - Fang Yan
- Department of Anesthesiology, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou 510060, China; (F.C.); (X.W.); (Q.Y.); (F.Y.); (W.L.); (J.X.)
| | - Weicheng Lu
- Department of Anesthesiology, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou 510060, China; (F.C.); (X.W.); (Q.Y.); (F.Y.); (W.L.); (J.X.)
| | - Jingdun Xie
- Department of Anesthesiology, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou 510060, China; (F.C.); (X.W.); (Q.Y.); (F.Y.); (W.L.); (J.X.)
| | - Bingtian Bi
- Department of Clinical Trial Center, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Xudong Wang
- Department of Anesthesiology, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou 510060, China; (F.C.); (X.W.); (Q.Y.); (F.Y.); (W.L.); (J.X.)
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Wan Z, Zuo X, Wang S, Zhou L, Wen X, Yao Y, Song J, Gu J, Wang Z, Liu R, Luo C. Identification of angiogenesis-related genes signature for predicting survival and its regulatory network in glioblastoma. Cancer Med 2023; 12:17445-17467. [PMID: 37434432 PMCID: PMC10501277 DOI: 10.1002/cam4.6316] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/26/2023] [Accepted: 06/24/2023] [Indexed: 07/13/2023] Open
Abstract
Glioblastoma (GBM) is notorious for malignant neovascularization that contributes to undesirable outcome. However, its mechanisms remain unclear. This study aimed to identify prognostic angiogenesis-related genes and the potential regulatory mechanisms in GBM. RNA-sequencing data of 173 GBM patients were obtained from the Cancer Genome Atlas (TCGA) database for screening differentially expressed genes (DEGs), differentially transcription factors (DETFs), and reverse phase protein array (RPPA) chips. Differentially expressed genes from angiogenesis-related gene set were extracted for univariate Cox regression analysis to identify prognostic differentially expressed angiogenesis-related genes (PDEARGs). A risk predicting model was constructed based on 9 PDEARGs, namely MARK1, ITGA5, NMD3, HEY1, COL6A1, DKK3, SERPINA5, NRP1, PLK2, ANXA1, SLIT2, and PDPN. Glioblastoma patients were stratified into high-risk and low-risk groups according to their risk scores. GSEA and GSVA were applied to explore the possible underlying GBM angiogenesis-related pathways. CIBERSORT was employed to identify immune infiltrates in GBM. The Pearson's correlation analysis was performed to evaluate the correlations among DETFs, PDEARGs, immune cells/functions, RPPA chips, and pathways. A regulatory network centered by three PDEARGs (ANXA1, COL6A1, and PDPN) was constructed to show the potential regulatory mechanisms. External cohort of 95 GBM patients by immunohistochemistry (IHC) assay demonstrated that ANXA1, COL6A1, and PDPN were significantly upregulated in tumor tissues of high-risk GBM patients. Single-cell RNA sequencing also validated malignant cells expressed high levels of the ANXA1, COL6A1, PDPN, and key DETF (WWTR1). Our PDEARG-based risk prediction model and regulatory network identified prognostic biomarkers and provided valuable insight into future studies on angiogenesis in GBM.
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Affiliation(s)
- Zhiping Wan
- Department of Neurosurgery, Tongji Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Xiaokun Zuo
- Department of Neurosurgery, Tongji Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Siqiao Wang
- Division of Spine, Department of Orthopedics, Tongji Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Lei Zhou
- Department of OrthopedicsJinxian County People's HospitalNanchangChina
| | - Xiaojing Wen
- Department of InfectionJinxian County People's HospitalNanchangChina
| | - Ying Yao
- Department of Operating Room, Tongji Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Jiefang Song
- Department of Neurosurgery, Tongji Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Juan Gu
- Department of Operating Room, Tongji Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Zhimin Wang
- Department of Emergency, Ruijin Hospital Luwan BranchShanghai Jiaotong University School of MedicineShanghaiChina
| | - Ran Liu
- The Medical School of Zhengzhou UniversityZhengzhou CityPeople's Republic of China
| | - Chun Luo
- Department of Neurosurgery, Tongji Hospital, School of MedicineTongji UniversityShanghaiChina
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Yang S, Xie BL, Dong XP, Wang LX, Zhu GH, Wang T, Wu WJ, Lai RS, Tao R, Guan MX, Chen FY, Tan DH, Deng Z, Xie HP, Zeng Y, Xiao ZA, Xie DH. cdh23 affects congenital hearing loss through regulating purine metabolism. Front Mol Neurosci 2023; 16:1079529. [PMID: 37575969 PMCID: PMC10416109 DOI: 10.3389/fnmol.2023.1079529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 02/13/2023] [Indexed: 08/15/2023] Open
Abstract
Introduction The pathogenic gene CDH23 plays a pivotal role in tip links, which is indispensable for mechanoelectrical transduction in the hair cells. However, the underlying molecular mechanism and signal regulatory networks that influence deafness is still largely unknown. Methods In this study, a congenital deafness family, whole exome sequencing revealed a new mutation in the pathogenic gene CDH23, subsequently; the mutation has been validated using Sanger sequencing method. Then CRISPR/Cas9 technology was employed to knockout zebrafish cdh23 gene. Startle response experiment was used to compare with wide-type, the response to sound stimulation between wide-type and cdh23-/-. To further illustrate the molecular mechanisms underlying congenital deafness, comparative transcriptomic profiling and multiple bioinformatics analyses were performed. Results The YO-PRO-1 assay result showed that in cdh23 deficient embryos, the YO-PRO-1 signal in inner ear and lateral line neuromast hair cells were completely lost. Startle response experiment showed that compared with wide-type, the response to sound stimulation decreased significantly in cdh23 mutant larvae. Comparative transcriptomic showed that the candidate genes such as atp1b2b and myof could affect hearing by regulating ATP production and purine metabolism in a synergetic way with cdh23. RT-qPCR results further confirmed the transcriptomics results. Further compensatory experiment showed that ATP treated cdh23-/- embryos can partially recover the mutant phenotype. Conclusion In conclusion, our study may shed light on deciphering the principal mechanism and provide a potential therapeutic method for congenital hearing loss under the condition of CDH23 mutation.
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Affiliation(s)
- Shu Yang
- Department of Otorhinolaryngology—Head & Neck Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Bing-Lin Xie
- Laboratory of Animal Nutrition and Human Health, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, College of Life Science, Hunan Normal University, Changsha, Hunan, China
| | - Xiao-ping Dong
- The National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Science, Hunan Normal University, Changsha, Hunan, China
| | - Ling-xiang Wang
- The National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Science, Hunan Normal University, Changsha, Hunan, China
| | - Gang-hua Zhu
- Department of Otorhinolaryngology—Head & Neck Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Tian Wang
- Department of Otorhinolaryngology—Head & Neck Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Wei-jing Wu
- Department of Otorhinolaryngology—Head & Neck Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Ruo-sha Lai
- Department of Otorhinolaryngology—Head & Neck Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Rong Tao
- Department of Otorhinolaryngology—Head & Neck Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Min-xin Guan
- Institute of Genetics, Zhejiang University, Hangzhou, Zhejiang, China
- Department of Human Genetics, Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Hangzhou, Zhejiang, China
| | - Fang-yi Chen
- Shenzhen Key Laboratory of Smart Healthcare Engineering, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Dong-hui Tan
- Department of Otolaryngology—Head and Neck Surgery, The Affiliated Hospital of Xiang Nan College, Chenzhou, China
| | - Zhong Deng
- Department of Otolaryngology—Head and Neck Surgery, The Affiliated Hospital of Xiang Nan College, Chenzhou, China
| | - Hua-ping Xie
- Laboratory of Animal Nutrition and Human Health, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, College of Life Science, Hunan Normal University, Changsha, Hunan, China
| | - Yong Zeng
- The National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Science, Hunan Normal University, Changsha, Hunan, China
| | - Zi-an Xiao
- Department of Otorhinolaryngology—Head & Neck Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Ding-hua Xie
- Department of Otorhinolaryngology—Head & Neck Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
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Wang L, Wei C, Wang Y, Huang N, Zhang T, Dai Y, Xue L, Lin S, Wu ZB. Identification of the enhancer RNAs related to tumorgenesis of pituitary neuroendocrine tumors. Front Endocrinol (Lausanne) 2023; 14:1149997. [PMID: 37534217 PMCID: PMC10393250 DOI: 10.3389/fendo.2023.1149997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 06/27/2023] [Indexed: 08/04/2023] Open
Abstract
Background Pituitary neuroendocrine tumors (PitNETs), which originate from the pituitary gland, account for 10%-15% of all intracranial neoplasms. Recent studies have indicated that enhancer RNAs (eRNAs) exert regulatory effects on tumor growth. However, the mechanisms underlying the eRNA-mediated tumorigenesis of PitNETs have not been elucidated. Methods Normal pituitary and PitNETs tissues were used to identify the differentially expressed eRNAs (DEEs). Immune gene sets and hallmarks of cancer gene sets were quantified based on single sample gene set enrichment analysis (ssGSEA) algorithm using GSVA. The perspective of immune cells among all samples was calculated by the CIBERSORT algorithm. Moreover, the regulatory network composed of key DEEs, target genes of eRNAs, hallmarks of cancer gene sets, differentially expressed TF, immune cells and immune gene sets were constructed by Pearson correlation analysis. Small molecular anti-PitNETs drugs were explored by CMap analysis and the accuracy of the study was verified by in vitro and in vivo experiments, ATAC-seq and ChIP-seq. Results In this study, data of 134 PitNETs and 107 non-tumorous pituitary samples were retrieved from a public database to identify differentially expressed genes. In total, 1128 differentially expressed eRNAs (DEEs) (494 upregulated eRNAs and 634 downregulated eRNAs) were identified. Next, the correlation of DEEs with cancer-related and immune-related gene signatures was examined to establish a co-expression regulatory network comprising 18 DEEs, 50 potential target genes of DEEs, 5 cancer hallmark gene sets, 2 differentially expressed transcription factors, 4 immune cell types, and 4 immune gene sets. Based on this network, the following four therapeutics for PitNETs were identified using Connectivity Map analysis: ciclopirox, bepridil, clomipramine, and alexidine. The growth-inhibitory effects of these therapeutics were validated using in vitro experiments. Ciclopirox exerted potential growth-inhibitory effects on PitNETs. Among the DEEs, GNLY, HOXB7, MRPL33, PRDM16, TCF7, and ZNF26 were determined to be potential diagnostic and therapeutic biomarkers for PitNETs. Conclusion This study illustrated the significant influence of eRNAs on the occurrence and development of PitNETs. By constructing the co-expression regulation network, GNLY, HOXB6, MRPL33, PRDM16, TCF7, and ZNF26 were identified as relatively significant DEEs which were considered as the novel biomarkers of diagnosis and treatment of PitNETs. This study demonstrated the roles of eRNAs in the occurrence and development of PitNETs and revealed that ciclopirox was a potential therapeutic for pituitary adenomas.
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Affiliation(s)
- Liangbo Wang
- Department of Neurosurgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Department of Neurosurgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chenlu Wei
- Center for Reproductive Medicine, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yu Wang
- Department of Neurosurgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ning Huang
- Department of Neurosurgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Tao Zhang
- Department of Neurosurgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yuting Dai
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Xue
- Department of Neurosurgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shaojian Lin
- Department of Neurosurgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhe Bao Wu
- Department of Neurosurgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Department of Neurosurgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Feng Y, Yang M, Fan Z, Zhao W, Kim P, Zhou X. COVIDanno, COVID-19 annotation in human. Front Microbiol 2023; 14:1129103. [PMID: 37497545 PMCID: PMC10366449 DOI: 10.3389/fmicb.2023.1129103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 06/26/2023] [Indexed: 07/28/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiologic agent of coronavirus disease 19 (COVID-19), has caused a global health crisis. Despite ongoing efforts to treat patients, there is no universal prevention or cure available. One of the feasible approaches will be identifying the key genes from SARS-CoV-2-infected cells. SARS-CoV-2-infected in vitro model, allows easy control of the experimental conditions, obtaining reproducible results, and monitoring of infection progression. Currently, accumulating RNA-seq data from SARS-CoV-2 in vitro models urgently needs systematic translation and interpretation. To fill this gap, we built COVIDanno, COVID-19 annotation in humans, available at http://biomedbdc.wchscu.cn/COVIDanno/. The aim of this resource is to provide a reference resource of intensive functional annotations of differentially expressed genes (DEGs) among different time points of COVID-19 infection in human in vitro models. To do this, we performed differential expression analysis for 136 individual datasets across 13 tissue types. In total, we identified 4,935 DEGs. We performed multiple bioinformatics/computational biology studies for these DEGs. Furthermore, we developed a novel tool to help users predict the status of SARS-CoV-2 infection for a given sample. COVIDanno will be a valuable resource for identifying SARS-CoV-2-related genes and understanding their potential functional roles in different time points and multiple tissue types.
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Affiliation(s)
- Yuzhou Feng
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, China
- Med-X Center for Informatics, Sichuan University, Chengdu, China
| | - Mengyuan Yang
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Zhiwei Fan
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Weiling Zhao
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Pora Kim
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States
- McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
- School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, United States
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Sun S, Ye X, Zou Q. Editorial: Machine learning on understanding the epigenetic mechanisms underlying plant adaptation and domestication. Front Plant Sci 2023; 14:1236787. [PMID: 37469779 PMCID: PMC10352903 DOI: 10.3389/fpls.2023.1236787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 06/27/2023] [Indexed: 07/21/2023]
Affiliation(s)
- Shanwen Sun
- College of Life Science, Northeast Forestry University, Harbin, China
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Xiucai Ye
- Department of Computer Science, University of Tsukuba, Tsukuba, Japan
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
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Li X, Tian Y. STOP1 and STOP1-like proteins, key transcription factors to cope with acid soil syndrome. Front Plant Sci 2023; 14:1200139. [PMID: 37416880 PMCID: PMC10321353 DOI: 10.3389/fpls.2023.1200139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/25/2023] [Indexed: 07/08/2023]
Abstract
Acid soil syndrome leads to severe yield reductions in various crops worldwide. In addition to low pH and proton stress, this syndrome includes deficiencies of essential salt-based ions, enrichment of toxic metals such as manganese (Mn) and aluminum (Al), and consequent phosphorus (P) fixation. Plants have evolved mechanisms to cope with soil acidity. In particular, STOP1 (Sensitive to proton rhizotoxicity 1) and its homologs are master transcription factors that have been intensively studied in low pH and Al resistance. Recent studies have identified additional functions of STOP1 in coping with other acid soil barriers: STOP1 regulates plant growth under phosphate (Pi) or potassium (K) limitation, promotes nitrate (NO3 -) uptake, confers anoxic tolerance during flooding, and inhibits drought tolerance, suggesting that STOP1 functions as a node for multiple signaling pathways. STOP1 is evolutionarily conserved in a wide range of plant species. This review summarizes the central role of STOP1 and STOP1-like proteins in regulating coexisting stresses in acid soils, outlines the advances in the regulation of STOP1, and highlights the potential of STOP1 and STOP1-like proteins to improve crop production on acid soils.
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Affiliation(s)
- Xinbo Li
- Hainan Yazhou Bay Seed Lab, Sanya, Hainan, China
- Center for Advanced Bioindustry Technologies, and Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yifu Tian
- Hainan Yazhou Bay Seed Lab, Sanya, Hainan, China
- Center for Advanced Bioindustry Technologies, and Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Bian H, Zhou Q, Du Z, Zhang G, Han R, Chen L, Tian J, Li Y. Integrated Transcriptomics and Metabolomics Analysis of the Fructan Metabolism Response to Low-Temperature Stress in Garlic. Genes (Basel) 2023; 14:1290. [PMID: 37372470 DOI: 10.3390/genes14061290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 06/07/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
As the main reserve carbohydrate in garlic, fructan contributes to garlic's yield and quality formation. Numerous studies have shown that plant fructan metabolism induces a stress response to adverse environments. However, the transcriptional regulation mechanism of garlic fructan in low-temperature environments is still unknown. In this study, the fructan metabolism of garlic seedlings under low-temperature stress was revealed by transcriptome and metabolome approaches. With the extension of stress time, the number of differentially expressed genes and metabolites increased. Using weighted gene co-expression network analysis (WGCNA), three key enzyme genes related to fructan metabolism were screened (a total of 12 transcripts): sucrose: sucrose 1-fructosyltransferase (1-SST) gene; fructan: fructan 6G fructosyltransferase (6G-FFT) gene; and fructan 1-exohydrolase (1-FEH) gene. Finally, two hub genes were obtained, namely Cluster-4573.161559 (6G-FFT) and Cluster-4573.153574 (1-FEH). The correlation network and metabolic heat map analysis between fructan genes and carbohydrate metabolites indicate that the expression of key enzyme genes in fructan metabolism plays a positive promoting role in the fructan response to low temperatures in garlic. The number of genes associated with the key enzyme of fructan metabolism in trehalose 6-phosphate was the highest, and the accumulation of trehalose 6-phosphate content may mainly depend on the key enzyme genes of fructan metabolism rather than the enzyme genes in its own synthesis pathway. This study not only obtained the key genes of fructan metabolism in garlic seedlings responding to low temperatures but also preliminarily analyzed its regulatory mechanism, providing an important theoretical basis for further elucidating the cold resistance mechanism of garlic fructan metabolism.
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Affiliation(s)
- Haiyan Bian
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Academy of Agricultural and Forestry Sciences of Qinghai University, Xining 810016, China
| | - Qianyi Zhou
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Academy of Agricultural and Forestry Sciences of Qinghai University, Xining 810016, China
| | - Zhongping Du
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Academy of Agricultural and Forestry Sciences of Qinghai University, Xining 810016, China
| | - Guangnan Zhang
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Academy of Agricultural and Forestry Sciences of Qinghai University, Xining 810016, China
| | - Rui Han
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Academy of Agricultural and Forestry Sciences of Qinghai University, Xining 810016, China
| | - Laisheng Chen
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Academy of Agricultural and Forestry Sciences of Qinghai University, Xining 810016, China
| | - Jie Tian
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Academy of Agricultural and Forestry Sciences of Qinghai University, Xining 810016, China
| | - Yi Li
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agricultural and Forestry Sciences of Qinghai University, Xining 810016, China
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