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Wang Y, Fu X, Shang Z, Qiao Y, Liu Y, Zhou L, Liu D. In vivo and in vitro study on the regulatory mechanism of XiaoChaiHu decoction on PANoptosis in sepsis-induced cardiomyopathy. JOURNAL OF ETHNOPHARMACOLOGY 2025; 336:118740. [PMID: 39197800 DOI: 10.1016/j.jep.2024.118740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 08/20/2024] [Accepted: 08/23/2024] [Indexed: 09/01/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE In accordance with the tenets of traditional Chinese medicine, sepsis is categorized into three distinct syndromes: heat syndrome, blood stasis syndrome, and deficiency syndrome. Xiaochaihu decoction (XCHD) has many functions, including the capacity to protect the liver, cholagogue, antipyretic, anti-inflammatory, and anti-pathogenic microorganisms. XCHD exerts the effect of clearing heat and reconciling Shaoyang. The XCHD contains many efficacious active ingredients, yet the mechanism of sepsis-induced cardiomyopathy (SIC) remains elusive. AIM OF THE STUDY To investigate the molecular mechanisms underlying the protective effects of XCHD against SIC using an integrated approach combining network pharmacology and molecular biology techniques. MATERIALS AND METHODS Network pharmacology methods identified the active ingredients, target proteins, and pathways affected by XCHD in the context of SIC. We conducted in vivo experiments using mice with lipopolysaccharide-induced SIC, evaluating cardiac function through echocardiography and histology. XCHD-containing serum was analyzed to determine its principal active components using ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). The effects of XCHD-containing serum on SIC were further tested in vitro in LPS-treated H9c2 cardiac cells. Protein expression levels were quantified via Western blotting and enzyme-linked immunosorbent assay (ELISA). Additionally, molecular docking was performed between the active components and ZBP1, a potential target protein. Overexpression of ZBP1 in H9c2 cells allowed for a deeper exploration of its role in modulating SIC-associated gene expression. RESULTS UPLC-MS/MS identified 31 shared XCHD and XCHD-containing serum components. These included organic acids, terpenoids, and flavonoids, which have been identified as the active components of XCHD. Our findings revealed that XCHD alleviated LPS-induced myocardial injury, improved cardiac function, and preserved cardiomyocyte morphology in mice. In vitro studies, we demonstrated that XCHD-containing serum significantly suppressed the expression of inflammatory cytokines (IL-6, IL-1β, and TNF-α) in LPS-induced H9c2 cells. Mechanistic investigations showed that XCHD downregulated genes associated with PANoptosis, a novel cell death pathway, suggesting its protective role in sepsis-damaged hearts. Conversely, overexpression of ZBP1 abolished the protective effects of XCHD and amplified PANoptosis-related gene expression. CONCLUSIONS Our study provides the first evidence supporting the protective effects of XCHD against SIC, both in vitro and in vivo. The underlying mechanism involves the inhibition of ZBP1-initiated PANoptosis, offering new insights into treating SIC using XCHD.
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Affiliation(s)
- Yaru Wang
- School of Pharmacy, Jiangxi Medical College, Nanchang University, Nanchang, 330006, PR China
| | - Xingxing Fu
- School of Pharmacy, Jiangxi Medical College, Nanchang University, Nanchang, 330006, PR China
| | - Zhao Shang
- School of Pharmacy, Jiangxi Medical College, Nanchang University, Nanchang, 330006, PR China
| | - Yamei Qiao
- School of Pharmacy, Jiangxi Medical College, Nanchang University, Nanchang, 330006, PR China
| | - Yue Liu
- School of Pharmacy, Jiangxi Medical College, Nanchang University, Nanchang, 330006, PR China
| | - Li Zhou
- School of Pharmacy, Jiangxi Medical College, Nanchang University, Nanchang, 330006, PR China
| | - Dan Liu
- School of Pharmacy, Jiangxi Medical College, Nanchang University, Nanchang, 330006, PR China.
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Huang L, Zhou Z, Deng T, Sun Y, Wang R, Wu R, Liu Y, Ye Y, Wang K, Yao C. A nomoscore of four genes for predicting the rupture risk in abdominal aortic aneurysm patients with osteoarthritis. Gene 2024; 931:148877. [PMID: 39173977 DOI: 10.1016/j.gene.2024.148877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Revised: 08/11/2024] [Accepted: 08/19/2024] [Indexed: 08/24/2024]
Abstract
BACKGROUND Abdominal aortic aneurysm (AAA) represents one of the most life-threatening cardiovascular diseases and is increasingly becoming a significant global public health concern. The aneurysms-osteoarthritis syndrome (AOS) has gained recognition, as patients with this syndrome often exhibit early-stage osteoarthritis (OA) and have a substantially increased risk of rupture, even with mild dilation of the aneurysm. The aim of this study was to discover potential biomarkers that can predict the occurrence of AAA rupture in patients with OA. METHODS Two gene expression profile datasets (GSE98278, GSE51588) and two single-cell RNA-seq datasets (GSE164678, GSE152583) were obtained from the GEO database. Functional enrichment analysis, PPI network construction, and machine learning algorithms, including LASSO, Random Forest, and SVM-RFE, were utilized to identify hub genes. In addition, a nomogram and ROC curves were generated to predict the risk of rupture in patients with AAA. Moreover, we analyzed the immune cell infiltration in the AAA tissue microenvironment by CIBERSORT and validated key gene expression in different macrophage subtypes through single-cell analysis. RESULTS A total of 105 intersecting DEGs that showed consistent changes between rAAA and OA dataset were identified. From these DEGs, four hub genes (PAK1, FCGR1B, LOX and PDPN) were selected by machine learning. High predictive performance was observed for the nomogram based on these hub genes, with an AUC of 0.975 (95 % CI: 0.942-1.000). Abnormal immune cell infiltration was detected in rAAA and correlated significantly with the hub genes. Ruptured AAA cases exhibited higher nomoscore values and lower M2 macrophage infiltration compared to stable AAA. Validation in animal models (PPE+BAPN-induced rAAA) confirmed the significant role of these biomarkers in AAA pathology. CONCLUSION The present study successfully identified four potential hub genes (PAK1, FCGR1B, LOX and PDPN) and developed a robust predictive nomogram to assess the risk of AAA rupture. The findings also shed light on the connection between hub genes and immune cell components in the microenvironment of rAAA. These findings support future research on key genes in AAA patients with OA, providing insights for novel management strategies for AAA.
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Affiliation(s)
- Lin Huang
- Division of Vascular Surgery, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510800, China; National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Disease, First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Zhihao Zhou
- Division of Vascular Surgery, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510800, China; National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Disease, First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Tang Deng
- Division of Vascular Surgery, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510800, China; National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Disease, First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Yunhao Sun
- Division of Vascular Surgery, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510800, China; National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Disease, First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Rui Wang
- Division of Vascular Surgery, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510800, China; National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Disease, First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Ridong Wu
- Division of Vascular Surgery, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510800, China; National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Disease, First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Yunyan Liu
- Division of Vascular Surgery, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510800, China; National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Disease, First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Yanchen Ye
- Division of Vascular Surgery, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510800, China; National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Disease, First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China.
| | - Kangjie Wang
- Division of Vascular Surgery, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510800, China; National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Disease, First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China.
| | - Chen Yao
- Division of Vascular Surgery, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510800, China; National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Disease, First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China.
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Chen H, Wu H, Wang Q, Zhang H. IFIT2 mediates iron retention and cholesterol efflux in atherosclerosis. Int Immunopharmacol 2024; 142:113131. [PMID: 39276454 DOI: 10.1016/j.intimp.2024.113131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 08/30/2024] [Accepted: 09/06/2024] [Indexed: 09/17/2024]
Abstract
BACKGROUND Abnormalities in iron and lipid metabolism are recognized as key contributors to atherosclerosis (AS). Therefore, this study proposes to characterize the biomarker related to iron and lipid metabolism in AS using bioinformatics, animal, and cell experiments. METHODS The limma package was utilized to identify differentially expressed genes (DEGs) in GSE70126 and GSE70619 datasets, and biomarkers were screened using enrichment analysis and PPI networks. IFIT2 was knocked down using shRNA lentivirus in a high fat diet (HFD)-induced APOE-/- AS model to investigate its effects of IFIT2 on the pathology, iron retention, and lipid accumulation. Iron storage-related and cholesterol efflux-related proteins were evaluated following exogenous modulation of IFIT2 expression in ox-LDL-induced foamy macrophages. RESULTS Compared to non-foamy macrophages from the aorta, 189 and 4152 DEGs were identified in foamy macrophages within the GSE70126 and GSE70619 datasets, respectively. Moreover, intersecting DEGs may modulate immune responses, cell adhesion, vascular permeability, and oxidative stress through NF-kappa B, Wnt, TNF and HIF-1 signaling pathways. Notably, IFIT2 was significantly upregulated in foamy macrophages and AS models. In vivo, IFIT2 co-localized with foamy macrophages, and its knockdown led to reductions in plasma lipid levels, plaque area, immune infiltration, iron retention, and lipid accumulation. In vitro, IFIT2 knockdown alleviated the ox-LDL-induced increase in iron storage-related proteins (Ferritin-L and Ferritin-H) and iron (Fe2+ and Fe3+) in foamy macrophages. Furthermore, IFIT2 knockdown reduced lipid accumulation and upregulated cholesterol efflux-related proteins (PPARγ, LXRα, ABCA1, and ABCG1) in foamy macrophages. CONCLUSION IFIT2 knockdown attenuates iron retention and lipid accumulation in AS plaques, and facilitated cholesterol efflux from foamy macrophages via the PPARγ/LXRα/ABCA1-ABCG1 pathway.
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Affiliation(s)
- Haoqiang Chen
- Department of Cardiovascular Medicine, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, No. 157 Jinbi Road, Kunming, Yunnan 650032, P.R.China
| | - Haiyan Wu
- Department of Cardiovascular Medicine, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, No. 157 Jinbi Road, Kunming, Yunnan 650032, P.R.China; Faculty of Life Science and Technology, Kunming University of Science and Technology, No.727 Jingming South Road, Kunming 650500, P.R.China
| | - Qian Wang
- Department of Cardiovascular Medicine, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, No. 157 Jinbi Road, Kunming, Yunnan 650032, P.R.China.
| | - Hong Zhang
- Department of Cardiovascular Medicine, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, No. 157 Jinbi Road, Kunming, Yunnan 650032, P.R.China.
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Rosati D, Palmieri M, Brunelli G, Morrione A, Iannelli F, Frullanti E, Giordano A. Differential gene expression analysis pipelines and bioinformatic tools for the identification of specific biomarkers: A review. Comput Struct Biotechnol J 2024; 23:1154-1168. [PMID: 38510977 PMCID: PMC10951429 DOI: 10.1016/j.csbj.2024.02.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/20/2024] [Accepted: 02/20/2024] [Indexed: 03/22/2024] Open
Abstract
In recent years, the role of bioinformatics and computational biology together with omics techniques and transcriptomics has gained tremendous importance in biomedicine and healthcare, particularly for the identification of biomarkers for precision medicine and drug discovery. Differential gene expression (DGE) analysis is one of the most used techniques for RNA-sequencing (RNA-seq) data analysis. This tool, which is typically used in various RNA-seq data processing applications, allows the identification of differentially expressed genes across two or more sample sets. Functional enrichment analyses can then be performed to annotate and contextualize the resulting gene lists. These studies provide valuable information about disease-causing biological processes and can help in identifying molecular targets for novel therapies. This review focuses on differential gene expression (DGE) analysis pipelines and bioinformatic techniques commonly used to identify specific biomarkers and discuss the advantages and disadvantages of these techniques.
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Affiliation(s)
- Diletta Rosati
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
- Cancer Genomics & Systems Biology Lab, Dept. of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy
| | - Maria Palmieri
- Cancer Genomics & Systems Biology Lab, Dept. of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy
| | - Giulia Brunelli
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy
| | - Andrea Morrione
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA
| | - Francesco Iannelli
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Elisa Frullanti
- Cancer Genomics & Systems Biology Lab, Dept. of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy
| | - Antonio Giordano
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA
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Rezatofighi SE. Exogenous interactome analysis of bovine viral diarrhea virus-host using network based-approach and identification of hub genes and important pathways involved in virus pathogenesis. Biochem Biophys Rep 2024; 40:101825. [PMID: 39318471 PMCID: PMC11421936 DOI: 10.1016/j.bbrep.2024.101825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 09/08/2024] [Accepted: 09/11/2024] [Indexed: 09/26/2024] Open
Abstract
Bovine viral diarrhea (BVD) is one of the most important diseases in livestock, caused by BVD virus (BVDV). During the pathogenesis of the virus, many interactions occur between host and viral proteins. Studying these interactions can help better understand the pathogenesis of the virus, identify putative functional proteins, and find new treatment and prevention strategies. To this aim, a BVDV-host protein-protein interaction (PPI) network map was constructed using Cytoscape and analyzed with cytoHubba, Kyoto Encyclopedia of Genes and Genomics (KEGG), Gene Ontology (GO), and Protein Analysis Through Evolutionary Relationships (PANTHER). Npro with 125 connections had the greatest number of interactions with host proteins. CD46, EEF-2, and TXN genes were detected as hub genes using different ranking algorithms in cytoHubba. BVDV interactions with its host mainly focus on targeting translation, protein synthesis, and cellular metabolism pathways. Different classes of proteins including translational proteins, nucleic acid metabolism proteins, metabolite interconversion enzymes, and protein-modifying enzymes are affected by BVDV. These findings improve our understanding of the effects of the virus on the cell. Hub genes and key pathways identified in the present study can serve as targets for novel BVDV prevention or treatment strategies.
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Xie R, Yun J, Li C, Zhang S, Zhong A, Wu J, Cen Y, Li Z, Chen J. Identification of potential therapeutic target SPP1 and related RNA regulatory pathway in keloid based on bioinformatics analysis. Ann Med 2024; 56:2382949. [PMID: 39041063 PMCID: PMC11268233 DOI: 10.1080/07853890.2024.2382949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 06/05/2024] [Indexed: 07/24/2024] Open
Abstract
OBJECTIVE To explore the complex mechanisms of keloid, new approaches have been developed by different strategies. However, conventional treatment did not significantly reduce the recurrence rate. This study aimed to identify new biomarkers and mechanisms for keloid progression through bioinformatics analyses. METHODS In our study, microarray datasets for keloid were downloaded from the GEO database. Differentially expressed genes (DEGs) were identified by R software. Multiple bioinformatics tools were used to identify hub genes, and reverse predict upstream miRNAs and lncRNA molecules of target hub genes. Finally, the total RNA-sequencing technique and miRNA microarray were combined to validate the identified genes. RESULTS Thirty-one DEGs were screened out and the upregulated hub gene SPP1 was finally identified, which was consistent with our RNA-sequencing analysis results and validation dataset. In addition, a ceRNA network of mRNA (SPP1)-miRNA (miR-181a-5p)-lncRNA (NEAT1, MALAT1, LINC00667, NORAD, XIST and MIR4458HG) was identified by the bioinformatics databases. The results of our miRNA microarray showed that miR-181a-5p was upregulated in keloid, also we found that the lncRNA NEAT1 could affect keloid progression by retrieving the relevant literature. CONCLUSIONS We speculate that SPP1 is a potential candidate biomarker and therapeutic target for patients with keloid, and NEAT1/miR-181a-5p/SPP1 might be the RNA regulatory pathway that regulates keloid formation.
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Affiliation(s)
- Ruxin Xie
- Department of Burn and Plastic Surgery, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Jiao Yun
- Department of Burn and Plastic Surgery, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Chenyu Li
- Department of Burn and Plastic Surgery, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Shiwei Zhang
- Department of Burn and Plastic Surgery, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Ai Zhong
- Department of Burn and Plastic Surgery, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Junliang Wu
- Department of Burn and Plastic Surgery, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Ying Cen
- Department of Burn and Plastic Surgery, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Zhengyong Li
- Department of Burn and Plastic Surgery, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Junjie Chen
- Department of Burn and Plastic Surgery, West China Hospital of Sichuan University, Chengdu, Sichuan, China
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Lan S, Zhai T, Zhang X, Xu L, Gao J, Lai C, Chen Y, Lai Z, Lin Y. Genome-wide identification and expression analysis of the GAD family reveal their involved in embryogenesis and hormones responses in Dimocarpus longan Lour. Gene 2024; 927:148698. [PMID: 38908456 DOI: 10.1016/j.gene.2024.148698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 06/06/2024] [Accepted: 06/13/2024] [Indexed: 06/24/2024]
Abstract
Glutamate decarboxylase (GAD) is involved in GABA metabolism and plays an essential regulatory role in plant growth, abiotic stresses, and hormone response. This study investigated the expression mechanism of the GAD family during longan early somatic embryogenesis (SE) and identified 6 GAD genes based on the longan genome. Homology analysis indicated that DlGAD genes had a closer relationship with dicotyledonous plants. The analysis of cis-acting elements in the promoter region suggests that the GAD genes were associated with various stress responses and hormones. RNA sequencing (RNA-Seq) and the qRT-PCR data indicated that most DlGAD genes were highly expressed in the incomplete compact pro-embryogenic cultures (ICpEC) and upregulated in longan embryogenic callus (EC) after treatments with 2,4-D, high temperature (35 °C), IAA, and ABA. Moreover, the RNA-Seq analysis also revealed that DlGADs exhibit different expression patterns in various tissues and organs. The subcellular localization results showed that DlGAD5 was localized in the cytoplasm, suggesting that it played a role in the cytoplasm. Transient overexpression of DlGAD5 enhanced the expression levels of DlGADs and increased the activity of glutamate decarboxylase in longan embryogenic callus (EC), while the content of glutamic acid decreased. Thus, the DlGAD gene can play an important role in the early somatic embryogenesis of longan by responding to hormones such as IAA and ABA. DlGAD5 can affect the growth and development of longan by stimulating the expression of the DlGAD gene family, thereby increasing the GAD activity in the early SE of longan, participating in hormone synthesis and signaling pathways.
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Affiliation(s)
- Shuoxian Lan
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Tingkai Zhai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xueying Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Luzhen Xu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Jie Gao
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Chunwang Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Yan Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
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Feng B, Yu H, Dong X, Díaz-Holguín A, Antolin AA, Hu H. Combining Data-Driven and Structure-Based Approaches in Designing Dual PARP1-BRD4 Inhibitors for Breast Cancer Treatment. J Chem Inf Model 2024; 64:7725-7742. [PMID: 39292752 DOI: 10.1021/acs.jcim.4c01421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2024]
Abstract
Poly(ADP-ribose) polymerase 1 (PARP1) inhibitors have revolutionized the treatment of many cancers with DNA-repairing deficiencies via synthetic lethality. Advocated by the polypharmacology concept, recent evidence discovered that a significantly synergistic effect in increasing the death of cancer cells was observed by simultaneously perturbating the enzymatic activities of bromodomain-containing protein 4 (BRD4) and PARP1. Here, we developed a novel cheminformatics approach combined with a structure-based method aiming to facilitate the design of dual PARP1-BRD4 inhibitors. Instead of linking pharmacophores, the developed approach first identified merged pharmacophores (a pool of amide-containing ring systems), from which phenanthridin-6(5H)-one was further prioritized. Based on this starting point, several small molecules were rationally designed, among which HF4 exhibited low micromolar inhibitory activity against BRD4 and PARP1, particularly exhibiting strong inhibition of BRD4 BD1 with an IC50 value of 204 nM. Furthermore, it demonstrated potent antiproliferative effects against breast cancer gene-deficient and proficient breast cancer cell lines by arresting cell cycle progression and impeding DNA damage repair. Collectively, our systematic efforts to design lead-like molecules have the potential to open doors for the exploration of dual PARP1-BRD4 inhibitors as a promising avenue for breast cancer treatment. Furthermore, the developed approach can be extended to systematically design inhibitors targeting PARP1 and other related targets.
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Affiliation(s)
- Bo Feng
- Department of Pharmacy, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, 225000, P. R. China
| | - Hui Yu
- Information School, University of Sheffield, 211 Portobello, Sheffield, S1 4DP, U.K
| | - Xu Dong
- Department of Pharmacy, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, 225000, P. R. China
| | - Alejandro Díaz-Holguín
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC, Box 596, SE-751 24, Uppsala, Sweden
| | - Albert A Antolin
- Centre for Cancer Drug Discovery, Division of Cancer Therapeutics, The Institute of Cancer Research, London SW7 3RP, U.K
- ProCURE, Catalan Institute of Oncology, Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Catalonia 08907, Spain
| | - Huabin Hu
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC, Box 596, SE-751 24, Uppsala, Sweden
- Centre for Cancer Drug Discovery, Division of Cancer Therapeutics, The Institute of Cancer Research, London SW7 3RP, U.K
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Li X, Zheng Y, Liu M, Wang K, Chen H. Weighted gene co-expression network analysis and identification of ginsenoside biosynthesis candidate genes for ginseng adventitious roots under MeJA treatment. Genes Genomics 2024:10.1007/s13258-024-01577-9. [PMID: 39373827 DOI: 10.1007/s13258-024-01577-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Accepted: 09/26/2024] [Indexed: 10/08/2024]
Abstract
BACKGROUND Ginseng (Panax ginseng) is an herb with a long history and a wide range of applications. Ginsenoside is one of the most representative and active ginseng compounds, with various pharmacological effects. Therefore, the development of bioreactors using methyl jasmonate (MeJA) as an inducer for targeted ginsenoside production is of great commercial value. Combined with transcriptomic research tools, screenings to obtain candidate genes involved in ginsenoside biosynthesis are crucial for future discoveries about the molecular mechanism of MeJA-regulated ginsenoside biosynthesis. OBJECTIVE AND METHODS In our study, the ginsenoside content of ginseng adventitious roots treated with MeJA at different times was analyzed. Transcriptome analysis was performed to investigate the effects of MeJA on changes in ginsenoside content in ginseng adventitious roots. RESULTS The MeJA could significantly increase changes in the content of pro-ginsenodiol ginsenosides as well as pro-triol ginsenosides Rg3, Re, and Rf in ginseng adventitious roots. Differential gene expression analysis showed that a total of 14,009 differentially expressed genes were obtained from the screening of the present study. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that differentially expressed genes were mainly enriched under GO terms in response to stimuli, metabolic processes, and the regulation of biological processes, with significant annotation to the metabolic terms of terpenoids and polyketides. Two expression modules of genes highly related to ginsenoside biosynthesis were obtained via WGCNA. CONCLUSIONS Our study provides a reference system for the targeted ginsenoside production using MeJA as an inducer, and also provides genetic and gene resources for subsequently validating genes related to the regulation of ginsenoside biosynthesis using weighted gene co-expression network analysis (WGCNA).
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Affiliation(s)
- Xiangzhu Li
- Tonghua Herbal Biotechnology Co., Ltd., Tonghua, 134100, China
| | - Yongjun Zheng
- Tonghua Herbal Biotechnology Co., Ltd., Tonghua, 134100, China
| | - Mingming Liu
- College of Life Science, Jilin Agricultural University, Changchun, 130118, China
| | - Kangyu Wang
- College of Life Science, Jilin Agricultural University, Changchun, 130118, China.
| | - Hong Chen
- Tonghua Herbal Biotechnology Co., Ltd., Tonghua, 134100, China.
- Shanghai Jiao Tong University, Shanghai, 200240, China.
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Chen JK, Merrick KA, Kong YW, Izrael-Tomasevic A, Eng G, Handly ED, Patterson JC, Cannell IG, Suarez-Lopez L, Hosios AM, Dinh A, Kirkpatrick DS, Yu K, Rose CM, Hernandez JM, Hwangbo H, Palmer AC, Vander Heiden MG, Yilmaz ÖH, Yaffe MB. An RNA damage response network mediates the lethality of 5-FU in colorectal cancer. Cell Rep Med 2024:101778. [PMID: 39378883 DOI: 10.1016/j.xcrm.2024.101778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/15/2024] [Accepted: 09/16/2024] [Indexed: 10/10/2024]
Abstract
5-fluorouracil (5-FU), a major anti-cancer therapeutic, is believed to function primarily by inhibiting thymidylate synthase, depleting deoxythymidine triphosphate (dTTP), and causing DNA damage. Here, we show that clinical combinations of 5-FU with oxaliplatin or irinotecan show no synergy in human colorectal cancer (CRC) trials and sub-additive killing in CRC cell lines. Using selective 5-FU metabolites, phospho- and ubiquitin proteomics, and primary human CRC organoids, we demonstrate that 5-FU-mediated CRC cell killing primarily involves an RNA damage response during ribosome biogenesis, causing lysosomal degradation of damaged rRNAs and proteasomal degradation of ubiquitinated ribosomal proteins. Tumor types clinically responsive to 5-FU treatment show upregulated rRNA biogenesis while 5-FU clinically non-responsive tumor types do not, instead showing greater sensitivity to 5-FU's DNA damage effects. Finally, we show that treatments upregulating ribosome biogenesis, including KDM2A inhibition, promote RNA-dependent cell killing by 5-FU, demonstrating the potential for combinatorial targeting of this ribosomal RNA damage response for improved cancer therapy.
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Affiliation(s)
- Jung-Kuei Chen
- Center for Precision Cancer Medicine, David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Karl A Merrick
- Center for Precision Cancer Medicine, David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yi Wen Kong
- Center for Precision Cancer Medicine, David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - George Eng
- Center for Precision Cancer Medicine, David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Erika D Handly
- Center for Precision Cancer Medicine, David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jesse C Patterson
- Center for Precision Cancer Medicine, David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ian G Cannell
- Center for Precision Cancer Medicine, David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lucia Suarez-Lopez
- Center for Precision Cancer Medicine, David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Aaron M Hosios
- Center for Precision Cancer Medicine, David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Anh Dinh
- Center for Precision Cancer Medicine, David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Kebing Yu
- Genentech Biotechnology company, South San Francisco, CA 94080, USA
| | | | - Jonathan M Hernandez
- Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Haeun Hwangbo
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Pharmacology, Computational Medicine Program, UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Adam C Palmer
- Department of Pharmacology, Computational Medicine Program, UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Matthew G Vander Heiden
- Center for Precision Cancer Medicine, David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Ömer H Yilmaz
- Center for Precision Cancer Medicine, David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael B Yaffe
- Center for Precision Cancer Medicine, David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Surgery, Beth Israel Medical Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
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Sequeira JC, Pereira V, Alves MM, Pereira MA, Rocha M, Salvador AF. MOSCA 2.0: A bioinformatics framework for metagenomics, metatranscriptomics and metaproteomics data analysis and visualization. Mol Ecol Resour 2024; 24:e13996. [PMID: 39099161 DOI: 10.1111/1755-0998.13996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 06/14/2024] [Accepted: 07/15/2024] [Indexed: 08/06/2024]
Abstract
The analysis of meta-omics data requires the utilization of several bioinformatics tools and proficiency in informatics. The integration of multiple meta-omics data is even more challenging, and the outputs of existing bioinformatics solutions are not always easy to interpret. Here, we present a meta-omics bioinformatics pipeline, Meta-Omics Software for Community Analysis (MOSCA), which aims to overcome these limitations. MOSCA was initially developed for analysing metagenomics (MG) and metatranscriptomics (MT) data. Now, it also performs MG and metaproteomics (MP) integrated analysis, and MG/MT analysis was upgraded with an additional iterative binning step, metabolic pathways mapping, and several improvements regarding functional annotation and data visualization. MOSCA handles raw sequencing data and mass spectra and performs pre-processing, assembly, annotation, binning and differential gene/protein expression analysis. MOSCA shows taxonomic and functional analysis in large tables, performs metabolic pathways mapping, generates Krona plots and shows gene/protein expression results in heatmaps, improving omics data visualization. MOSCA is easily run from a single command while also providing a web interface (MOSGUITO). Relevant features include an extensive set of customization options, allowing tailored analyses to suit specific research objectives, and the ability to restart the pipeline from intermediary checkpoints using alternative configurations. Two case studies showcased MOSCA results, giving a complete view of the anaerobic microbial communities from anaerobic digesters and insights on the role of specific microorganisms. MOSCA represents a pivotal advancement in meta-omics research, offering an intuitive, comprehensive, and versatile solution for researchers seeking to unravel the intricate tapestry of microbial communities.
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Affiliation(s)
- João C Sequeira
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Vítor Pereira
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - M Madalena Alves
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - M Alcina Pereira
- Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Miguel Rocha
- Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Andreia F Salvador
- Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
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Yi Z, Sharif R, Gulzar S, Huang Y, Ning T, Zhan H, Meng Y, Xu C. Changes in hemicellulose metabolism in banana peel during fruit development and ripening. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 215:109025. [PMID: 39142014 DOI: 10.1016/j.plaphy.2024.109025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 07/19/2024] [Accepted: 08/06/2024] [Indexed: 08/16/2024]
Abstract
Hemicellulose is key in determining the fate of plant cell wall in almost all growth and developmental stages. Nevertheless, there is limited knowledge regarding its involvement in the development and ripening of banana fruit. This study investigated changes in the temporal-spatial distribution of various hemicellulose components, hemicellulose content, activities of the main hydrolysis enzymes, and transcription level of the main hemicellulose-related gene families in banana peels. Both hemicellulose and xylan contents were positively correlated to the fruit firmness observed in our previous study. On the contrary, the xylanase activity was negatively correlated to xylan content and the fruit firmness. The vascular bundle cells, phloem, and cortex of bananas are abundant in xyloglucan, xylan, and mannan contents. Interestingly, the changes in the signal intensity of the CCRC-M104 antibody recognizing non-XXXG type xyloglucan are positively correlated to hemicellulose content. According to RNA-Seq analysis, xyloglucan and xylan-related genes were highly active in the early stages of growth, and the expression of MaMANs and MaXYNs increased as the fruit ripened. The abundance of plant hormonal and growth-responsive cis-acting elements was detected in the 2 kb upstream region of hemicellulose-related gene families. Interaction between hemicellulose and cell wall-specific proteins and MaKCBP1/2, MaCKG1, and MaHKL1 was found. The findings shed light on cell wall hemicellulose's role in banana fruit development and ripening, which could improve nutrition, flavor, and reduce postharvest fruit losses.
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Affiliation(s)
- Zan Yi
- Department of Horticulture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Rahat Sharif
- Department of Horticulture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Shazma Gulzar
- Department of Horticulture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Yongxin Huang
- Department of Horticulture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Tong Ning
- Department of Horticulture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Huiling Zhan
- Department of Horticulture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Yue Meng
- Department of Horticulture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Chunxiang Xu
- Department of Horticulture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China.
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Li Y, Yang Y, Zhu L, Xie S, Guo L, Zhang Z, Zhe C, Li W, Liu F. Angelica sinensis polysaccharide facilitates chondrogenic differentiation of adipose-derived stem cells via MDK-PI3K/AKT signaling cascade. Biomed Pharmacother 2024; 179:117349. [PMID: 39191028 DOI: 10.1016/j.biopha.2024.117349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 08/21/2024] [Accepted: 08/22/2024] [Indexed: 08/29/2024] Open
Abstract
OBJECT Adipose-derived mesenchymal stem cells (ADSCs) have received significant attention in the field of cartilage tissue repair. Angelica sinensis polysaccharide (ASP) can enhance both the proliferation and differentiation of mesenchymal stem cells. Therefore, we intend to explore the effect of ASP on chondrogenic differentiation of ADSCs in vitro, and elucidate the underlying mechanisms. METHOD ADSCs were treated with different concentrations of ASP to determine the optimal concentration. The chondrogenic differentiation of ADSCs was evaluated using Alcian blue staining, qRT-PCR, western blot, and IF staining. Transcriptome sequencing was performed to identify the expression profiles of ADSCs before and after ASP treatment, followed by bioinformatic analyses including differential expression analysis, enrichment analysis, and construction of PPI networks to identify differentially expressed genes (DEGs) associated with ASP and chondrogenic differentiation. RESULT Surface markers of isolated rat-derived ADSCs were identified by CD44+CD90+CD45-CD106-, and exhibited the capacity for lipogenic, osteogenic, and chondrogenic differentiation. With increasing concentration of ASP treatment, there was an upregulation in the activity and acidic mucosubstance of ADSCs. The levels of Aggrecan, COL2A1, and Sox9 showed an increase in ADSCs after 28 days of 80 µg/ml ASP treatment. Transcriptome sequencing revealed that ASP-associated DEGs regulate extracellular matrix synthesis, immune response, inflammatory response, and cell cycle, and are involved in the NF-κB, AGE-RAGE, and calcium pathways. Moreover, Edn1, Frzb, Mdk, Nog, and Sulf1 are hub genes in DEGs. Notably, ASP upregulated MDK levels in ADSCs, while knockdown of MDK mitigated ASP-induced elevations in acidic mucosubstance, chondrogenic differentiation-related markers (Aggrecan, COL2A1, and Sox9), and the activity of the PI3K/AKT pathway. CONCLUSION ASP enhances the proliferation and chondrogenic differentiation of ADSCs by activating the MDK-mediated PI3K/AKT pathway.
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Affiliation(s)
- Yangjie Li
- Qujing No.1 Hospital, Affiliated Qujing Hospital of Kunming Medical University, No. 1 Yuanlin Road, Qujing City, Yunnan Province, China
| | - Yongqiang Yang
- Qujing No.1 Hospital, Affiliated Qujing Hospital of Kunming Medical University, No. 1 Yuanlin Road, Qujing City, Yunnan Province, China
| | - Lina Zhu
- Qujing No.1 Hospital, Affiliated Qujing Hospital of Kunming Medical University, No. 1 Yuanlin Road, Qujing City, Yunnan Province, China
| | - Shukang Xie
- Qujing No.1 Hospital, Affiliated Qujing Hospital of Kunming Medical University, No. 1 Yuanlin Road, Qujing City, Yunnan Province, China
| | - Ling Guo
- Qujing No.1 Hospital, Affiliated Qujing Hospital of Kunming Medical University, No. 1 Yuanlin Road, Qujing City, Yunnan Province, China
| | - Zhiming Zhang
- Qujing No.1 Hospital, Affiliated Qujing Hospital of Kunming Medical University, No. 1 Yuanlin Road, Qujing City, Yunnan Province, China
| | - Chunyang Zhe
- Qujing No.1 Hospital, Affiliated Qujing Hospital of Kunming Medical University, No. 1 Yuanlin Road, Qujing City, Yunnan Province, China
| | - Wenhui Li
- Kunming Institute of Zoology, Chinese Academy of Sciences, No.17 Longxin Road, Kunming City, Yunnan Province, China
| | - Feng Liu
- Qujing No.1 Hospital, Affiliated Qujing Hospital of Kunming Medical University, No. 1 Yuanlin Road, Qujing City, Yunnan Province, China.
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Wu H, Chen H, Ding X, Kuang X, Pang M, Liu S, Zhang Y, Wang Q, Li K, Zhang H. Identification of autophagy-related signatures in doxorubicin-induced cardiotoxicity. Toxicol Appl Pharmacol 2024; 491:117082. [PMID: 39218162 DOI: 10.1016/j.taap.2024.117082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 08/12/2024] [Accepted: 08/29/2024] [Indexed: 09/04/2024]
Abstract
PURPOSE Doxorubicin is an antibiotic drug used clinically to treat infectious diseases and tumors. Unfortunately, it is cardiotoxic. Autophagy is a cellular self-decomposition process that is essential for maintaining homeostasis in the internal environment. Accordingly, the present study was proposed to characterize the autophagy-related signatures of doxorubicin-induced cardiotoxicity. METHODS Datasets related to doxorubicin-induced cardiotoxicity were retrieved by searching the GEO database and differentially expressed genes (DEGs) were identified. DEGs were taken to intersect with autophagy-related genes to obtain autophagy-related signatures, and Gene Ontology (GO)/Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and protein-protein interaction (PPI) network were performed on them. Further, construction of miRNA-hub gene networks and identification of target drugs to reveal potential molecular mechanisms and therapeutic strategies. Animal models of doxorubicin-induced cardiotoxicity were constructed to validate differences in gene expression for autophagy-related signatures. RESULTS PBMC and heart samples from the GSE37260 dataset were selected for analysis. There were 995 and 2357 DEGs in PBMC and heart samples, respectively, and they had 23 intersecting genes with autophagy-related genes. RT-qPCR confirmed the differential expression of 23 intersecting genes in doxorubicin-induced cardiotoxicity animal models in general agreement with the bioinformatics results. An autophagy-related signatures consisting of 23 intersecting genes is involved in mediating processes and pathways such as autophagy, oxidative stress, apoptosis, protein ubiquitination and phosphorylation. Moreover, Akt1, Hif1a and Mapk3 are hub genes in autophagy-associated signatures and their upstream miRNAs are mainly rno-miR-1188-5p, rno-miR-150-3p and rno-miR-326-3p, and their drugs are mainly CHEMBL55802, Carboxyamidotriazole and 3-methyladenine. CONCLUSION This study identifies for the first-time autophagy-related signatures in doxorubicin's cardiotoxicity, which could provide potential molecular mechanisms and therapeutic strategies for doxorubicin-induced cardiotoxicity.
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Affiliation(s)
- Haiyan Wu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, No. 727 Jingming South Road, Kunming 650500, P.R.China; Department of Cardiovascular Medicine, The First People's Hospital of Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, No. 157 Jinbi Road, Kunming 650032, P.R.China
| | - Haoqiang Chen
- Department of Cardiovascular Medicine, The First People's Hospital of Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, No. 157 Jinbi Road, Kunming 650032, P.R.China
| | - Xiaoxue Ding
- Department of Cardiovascular Medicine, The First People's Hospital of Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, No. 157 Jinbi Road, Kunming 650032, P.R.China
| | - Xiaohui Kuang
- Department of Cardiovascular Medicine, The First People's Hospital of Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, No. 157 Jinbi Road, Kunming 650032, P.R.China
| | - Mingjie Pang
- Department of Cardiovascular Medicine, The First People's Hospital of Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, No. 157 Jinbi Road, Kunming 650032, P.R.China
| | - Suijuan Liu
- Department of Cardiovascular Medicine, The First People's Hospital of Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, No. 157 Jinbi Road, Kunming 650032, P.R.China
| | - Yan Zhang
- Department of Magnetic Resonance lmaging, The First People's Hospital of Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, No. 157 Jinbi Road, Kunming, 650032, P.R. China
| | - Qian Wang
- Department of Cardiovascular Medicine, The First People's Hospital of Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, No. 157 Jinbi Road, Kunming 650032, P.R.China
| | - Kunzhi Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, No. 727 Jingming South Road, Kunming 650500, P.R.China.
| | - Hong Zhang
- Department of Cardiovascular Medicine, The First People's Hospital of Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, No. 157 Jinbi Road, Kunming 650032, P.R.China.
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Dean LE, Wang H, Bullert AJ, Wang H, Adamcakova-Dodd A, Mangalam AK, Thorne PS, Ankrum JA, Klingelhutz AJ, Lehmler HJ. Inhalation of 2,2',5,5'-tetrachlorobiphenyl (PCB52) causes changes to the gut microbiome throughout the gastrointestinal tract. JOURNAL OF HAZARDOUS MATERIALS 2024; 480:135999. [PMID: 39369679 DOI: 10.1016/j.jhazmat.2024.135999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 09/16/2024] [Accepted: 09/27/2024] [Indexed: 10/08/2024]
Abstract
Polychlorinated biphenyls (PCBs), such as PCB52, are hazardous environmental contaminants present in indoor and outdoor environments. Oral PCB exposure affects the colon microbiome; however, it is unknown if inhalation of PCBs alters the intestinal microbiome. We hypothesize that sub-acute inhalation of PCB52 affects microbial communities depending on the location in the (GI) gastrointestinal tract and the local profiles of PCB52 and its metabolites present in the GI tract following mucociliary clearance and biliary or intestinal excretion. Sprague-Dawley rats were exposed via nose-only inhalation 4 h per day, 7 days per week, for 4 weeks to either filtered air or PCB52. After 28 days, differences in the microbiome and levels of PCB52 and its metabolites were characterized throughout the GI tract. PCB52 inhalation altered taxa abundances and predicted functions altered throughout the gut, with most alterations occurring in the large intestine. PCB52 and metabolite levels varied across the GI tract, resulting in differing PCB × microbiome networks. Thus, the presence of different levels of PCB52 and its metabolites in different parts of the GI tract has varying effects on the composition and predicted function of microbial communities. Future studies need to investigate whether these changes lead to adverse outcomes.
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Affiliation(s)
- Laura E Dean
- Department of Occupational and Environmental Health, University of Iowa, Iowa City, IA, United States.
| | - Hui Wang
- Department of Occupational and Environmental Health, University of Iowa, Iowa City, IA, United States.
| | - Amanda J Bullert
- Department of Occupational and Environmental Health, University of Iowa, Iowa City, IA, United States; Interdisciplinary Graduate Program in Neuroscience, University of Iowa, Iowa City, IA, United States.
| | - Hui Wang
- Department of Occupational and Environmental Health, University of Iowa, Iowa City, IA, United States.
| | - Andrea Adamcakova-Dodd
- Department of Occupational and Environmental Health, University of Iowa, Iowa City, IA, United States.
| | | | - Peter S Thorne
- Department of Occupational and Environmental Health, University of Iowa, Iowa City, IA, United States; Interdisciplinary Graduate Program in Neuroscience, University of Iowa, Iowa City, IA, United States.
| | - James A Ankrum
- Department of Biomedical Engineering, University of Iowa, Iowa City, IA, United States.
| | - Aloysius J Klingelhutz
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, United States.
| | - Hans-Joachim Lehmler
- Department of Occupational and Environmental Health, University of Iowa, Iowa City, IA, United States; Interdisciplinary Graduate Program in Neuroscience, University of Iowa, Iowa City, IA, United States.
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Bhanukiran K, Priya V. Exploring multitarget potential of Piper nigrum fruit constituents for Alzheimer's disease: An AI-driven strategy. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 135:156108. [PMID: 39383634 DOI: 10.1016/j.phymed.2024.156108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 09/13/2024] [Accepted: 09/28/2024] [Indexed: 10/11/2024]
Abstract
BACKGROUND Alzheimer's disease (AD) is a neurodegenerative disease that leads to development of cognition and memory dysfunctions. Currently, there is no known cure for AD, although limited medications are approved for the management of disease condition. Various plant-based leads give new hope for considering phytoconstituents as anti-AD drugs. The Piper nigrum L. fruit extract was reported to have anti-Alzheimer's activity. It creates an interest in the finding of active moieties that may be accountable for anti-AD activity. HYPOTHESIS/PURPOSE Identification of multitarget directed ligands isolated from Piper nigrum fruits through AI based studies. STUDY DESIGN The phytochemical analysis of alkaloid fraction was carried out by LCMS, followed by the evaluation of constituents through in silico studies. METHODS The fruits methanolic extract was prepared by cold maceration technique. The chemical profiling of the alkaloidal fraction was carried out using LCMS/MS analysis. The obtained compound's target hit genes were identified through network pharmacology studies using String, Metascape, and Cytoscape tools. Further, docking studies and MD simulations were carried out using AutoDock4 and Desmond-Maestro software. Then, electrochemical properties of hit compound P4 were determined using Gaussview6 software. RESULTS From LCMS/MS analysis data, 29 compounds were considered based on compound intensity and accuracy (>95 %). Then, 41 common gene targets were identified from AD genes and compound-targeted genes. The 41 common genes in the PPI network suggested that AChE and BACE1 were the most abundant proteins. Further, docking studies revealed the hit compound P4 binding interaction and energies when compared to other 28 ligands. The molecular dynamics studies showed that P4-AChE and P4-BACE1 complexes were stable, and there were no RMSD and RMSF fluctuations were observed up to 100 ns. Further, PCA and MM-GBSA analysis data supported that complexes (P4-AChE and P4-BACE1) were stable. The DFT and surface properties indicated that compound P4 was ideal candidate for AD treatment and must be considered for further biological activity studies. CONCLUSION The study identified compound P4 (dehydropipernonaline) from alkaloidal fraction of Piper nigrum fruits, suggesting it may be hit candidate for AD treatment.
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Affiliation(s)
- Kancharla Bhanukiran
- Shobhaben Pratapbhai Patel School of Pharmacy & Technology Management, SVKM's NMIMS (Deemed to be University), Mumbai 400056, India; Department of Pharmacognosy, GITAM School of Pharmacy, GITAM (Deemed to be University), Visakhapatnam 530045, India.
| | - Vishnu Priya
- Shobhaben Pratapbhai Patel School of Pharmacy & Technology Management, SVKM's NMIMS (Deemed to be University), Mumbai 400056, India
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Qasmi M, Fareed MM, Ali H, Khan Z, Shityakov S. Integrative multi-target analysis of Urtica dioica for gout arthritis treatment: a network pharmacology and clustering approach. In Silico Pharmacol 2024; 12:88. [PMID: 39351010 PMCID: PMC11438756 DOI: 10.1007/s40203-024-00254-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 08/13/2024] [Indexed: 10/04/2024] Open
Abstract
Urtica dioica (stinging nettle) has been traditionally used in Chinese medicine for the treatment of joint pain and rheumatoid arthritis. This study aims to elucidate the active compounds and mechanisms by which it acts against gout arthritis (GA). Gout-related genes were identified from the DisGeNet, GeneCards, and OMIM databases. These genes may play a role in inhibiting corresponding proteins targeted by the active compounds identified from the literature, which have an oral bioavailability of ≥ 30% and a drug-likeness score of ≥ 0.18. A human protein-protein interaction network was constructed, resulting in sixteen clusters containing plant-targeted genes, including ABCG2, SLC22A12, MAP2K7, ADCY10, RELA, and TP53. The key bioactive compounds, apigenin-7-O-glucoside and kaempferol, demonstrated significant binding to SLC22A12 and ABCG2, suggesting their potential to reduce uric acid levels and inflammation. Pathway enrichment analysis further identified key metabolic pathways involved, highlighting a dual mechanism of anti-inflammatory and urate-lowering effects. These findings underscore the potential of U. dioica in targeting multiple pathways involved in GA, combining traditional medicine with modern pharmacology. This integrated approach provides a foundation for future research and the development of multi-target therapeutic strategies for managing gout arthritis. Graphical Abstract Supplementary Information The online version contains supplementary material available at 10.1007/s40203-024-00254-9.
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Affiliation(s)
- Maryam Qasmi
- Faculty of Life Sciences, Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Muhammad Mazhar Fareed
- Department of Computer Science, School of Science and Engineering, Università degli Studi di Verona, Verona, Italy
- Department of Biotechnology, Applied Bioinformatics Group, Università degli Studi di Verona, Verona, Italy
- Department of Computer Science, Systems, and Communications, Università degli Studi di Milano-Bicocca, Milan, Italy
| | - Haider Ali
- Department of Meat Science and Technology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Zarmina Khan
- Faculty of Life Sciences, Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Sergey Shityakov
- Laboratory of Chemoinformatics, Infochemistry Scientific Center, ITMO University, Saint-Petersburg, Russian Federation
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Liu A, Lu J, Song H, Wang X, Wang M, Lei Z, Liu H, Lei H, Niu T. Comparative genomics and transcriptomics analysis of the bHLH gene family indicate their roles in regulating flavonoid biosynthesis in Sophora flavescens. FRONTIERS IN PLANT SCIENCE 2024; 15:1445488. [PMID: 39381512 PMCID: PMC11458398 DOI: 10.3389/fpls.2024.1445488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 09/05/2024] [Indexed: 10/10/2024]
Abstract
The basic helix-loop-helix (bHLH) transcription factors play crucial roles in various processes, such as plant development, secondary metabolism, and response to biotic/abiotic stresses. Sophora flavescens is a widely used traditional herbal medicine in clinical practice, known for its abundant flavonoids as the main active compounds. However, there has been no comprehensive analysis of S. flavescens bHLH (SfbHLH) gene family reported currently. In this study, we identified 167 SfbHLH genes and classified them into 23 subfamilies based on comparative genomics and phylogenetic analysis. Furthermore, widespread duplications significantly contributed to the expansion of SfbHLH family. Notably, SfbHLH042 was found to occupy a central position in the bHLH protein-protein interaction network. Transcriptome analysis of four tissues (leaf, stem, root and flower) revealed that most SfbHLH genes exhibited high expression levels exclusively in specific tissues of S. flavescens. The integrated analysis of transcriptomics and metabolomics during pod development stages revealed that SfbHLH042 may play a central role in connecting SfbHLH genes, flavonoids, and key enzymes involved in the biosynthesis pathway. Moreover, we also checked the expression of 8 SfbHLH genes using RT-qPCR analysis to realize the expression profiles of these genes among various tissues at different cultivated periods and root development. Our study would aid to understand the phylogeny and expression profile of SfbHLH family genes, and provide a promising candidate gene, SfbHLH042, for regulating the biosynthesis of flavonoids in S. flavescens.
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Affiliation(s)
- Ake Liu
- Department of Life Sciences, Changzhi University, Changzhi, China
| | - Junjie Lu
- Department of Life Sciences, Changzhi University, Changzhi, China
| | - Huifang Song
- Department of Life Sciences, Changzhi University, Changzhi, China
| | - Xi Wang
- Department of Life Sciences, Changzhi University, Changzhi, China
| | - Mingyang Wang
- School of Life Science, Shanxi Normal University, Taiyuan, China
| | - Zhenhong Lei
- Shanxi Zhendong Pharmaceutical Co., Ltd., Changzhi, China
| | - Huixuan Liu
- Department of Life Sciences, Changzhi University, Changzhi, China
| | - Haiying Lei
- Department of Life Sciences, Changzhi University, Changzhi, China
| | - Tianzeng Niu
- Department of Life Sciences, Changzhi University, Changzhi, China
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Guo Y, Sun F, Wang J, Wang Z, Yang H, Wu F. Application of Synchronous Evaluation-Diagnosis Model with Quantitative Stressor-Response Analysis (SED-QSR) to Urban Lake Ecological Status: A Proposed Multiple-Level System. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:16028-16039. [PMID: 39207301 DOI: 10.1021/acs.est.4c04901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Ecological integrity assessment and degradation diagnosis are used globally to evaluate the health of water bodies and pinpoint critical stressors. However, current studies mainly focus on separate evaluation or diagnosis, leading to an inadequate exploration of the relationship between stressors and responses. Here, based on multiple data sets in an urban lake system, a synchronous evaluation-diagnosis model with quantitative stressor-response analysis was advanced, aiming to improve the accuracy of evaluation and diagnosis. The weights for key physicochemical stressors were quantitatively determined in the sequence of NDAVIadj > CODMn > TP > NH4+-N by the combination of generalized additive model and structural equation modeling, clarifying the most significant effects of aquatic vegetation on the degradation of fish assemblages. Then, sensitive biological metrics were screened by considering the distinct contributions of four key stressors to alleviate the possible deviation caused by common methods. Finally, ecological integrity was evaluated by summing the key physicochemical stressors and sensitive biological metrics according to the model-deduced weights instead of empirical weights. Our system's diagnosis and evaluation results achieved an accuracy of over 80% when predicting anthropogenic stress and biological status, which highlights the great potential of our multiple-level system for ecosystem management.
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Affiliation(s)
- Yiding Guo
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
- School of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Fuhong Sun
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
| | - Jie Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
| | - Ziteng Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
| | - Hao Yang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
| | - Fengchang Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
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20
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Zheng K, Li M, Yang Z, He C, Wu Z, Tong Z, Zhang J, Zhang Y, Cao S. The Vital Role of the CAMTA Gene Family in Phoebe bournei in Response to Drought, Heat, and Light Stress. Int J Mol Sci 2024; 25:9767. [PMID: 39337256 PMCID: PMC11432206 DOI: 10.3390/ijms25189767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Revised: 09/07/2024] [Accepted: 09/08/2024] [Indexed: 09/30/2024] Open
Abstract
The calmodulin-binding transcriptional activator (CAMTA) is a small, conserved gene family in plants that plays a crucial role in regulating growth, development, and responses to various abiotic stress. Given the significance of the CAMTA gene family, various studies have been dedicated to uncovering its functional characteristics. In this study, genome-wide identification and bioinformatics analysis were conducted to explore CAMTAs in Phoebe bournei. A total of 17 CAMTA genes, each containing at least one domain from CG-1, TIG, ANK, or IQ, were identified in the P. bournei genome. The diversity of PbCAMTAs could be varied depending on their subcellular localization. An analysis of protein motifs, domains, and gene structure revealed that members within the same subgroup exhibited similar organization, supporting the results of the phylogenetic analysis. Gene duplications occurred among members of the PbCAMTA gene family. According to the cis-regulatory element prediction and protein-protein interaction network analysis, eight genes were subjected to qRT-PCR under drought, heat, and light stresses. The expression profiles indicated that PbCAMTAs, particularly PbCAMTA2, PbCAMTA12, and PbCAMTA16, were induced by abiotic stress. This study provides profound insights into the functions of CAMTAs in P. bournei.
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Affiliation(s)
- Kehui Zheng
- College of Computer and Information Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Min Li
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhicheng Yang
- College of Future Technologiesm, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chenyue He
- College of Computer and Information Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zekai Wu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zaikang Tong
- State Key Laboratory of Subtropical Silviculture, School of Forestry & Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Junhong Zhang
- State Key Laboratory of Subtropical Silviculture, School of Forestry & Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou 311300, China
| | - Yanzi Zhang
- Center for Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shijiang Cao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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21
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Liu M, Wang Y, Deng W, Xie J, He Y, Wang L, Zhang J, Cui M. Combining network pharmacology, machine learning, molecular docking and molecular dynamic to explore the mechanism of Chufeng Qingpi decoction in treating schistosomiasis. Front Cell Infect Microbiol 2024; 14:1453529. [PMID: 39310787 PMCID: PMC11413488 DOI: 10.3389/fcimb.2024.1453529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Accepted: 08/05/2024] [Indexed: 09/25/2024] Open
Abstract
Background Although the Chufeng Qingpi Decoction (CQD) has demonstrated clinical effectiveness in the treatment of schistosomiasis, the precise active components and the underlying mechanisms of its therapeutic action remain elusive. To achieve a profound comprehension, we incorporate network pharmacology, bioinformatics analysis, molecular docking, and molecular dynamics simulations as investigative methodologies within our research framework. Method Utilizing TCMSP and UniProt, we identified formula components and targets. Cytoscape 3.10.0 was used to construct an herb-target interaction network. Genecards, DisGeNET, and OMIM databases were examined for disease-related objectives. A Venn diagram identified the intersection of compound and disease targets. Using Draw Venn, overlapping targets populated STRING for PPI network. CytoNCA identified schistosomiasis treatment targets. GO & KEGG enrichment analysis followed High-scoring genes in PPI were analyzed by LASSO, RF, SVM-RFE. Molecular docking & simulations investigated target-compound interactions. Result The component's target network encompassed 379 nodes, 1629 edges, highlighting compounds such as wogonin, kaempferol, luteolin, and quercetin. Amongst the proteins within the PPI network, PTGS2, TNF, TGFB1, BCL2, TP53, IL10, JUN, MMP2, IL1B, and MYC stood out as the most prevalent entities. GO and KEGG revealed that mainly involved the responses to UV, positive regulation of cell migration and motility. The signal pathways encompassed Pathways in cancer, Lipid and atherosclerosis, Fluid shear stress and atherosclerosis, as well as the AGE-RAGE. Bioinformatics analysis indicated TP53 was the core gene. Ultimately, the molecular docking revealed that wogonin, kaempferol, luteolin, and quercetin each exhibited significant affinity in their respective interactions with TP53. Notably, kaempferol exhibited the lowest binding energy, indicating a highly stable interaction with TP53. Lastly, we validated the stability of the binding interaction between the four small molecules and the TP53 through molecular dynamics simulations. The molecular dynamics simulation further validated the strongest binding between TP53 and kaempferol. In essence, our research groundbreaking in its nature elucidates for the first time the underlying molecular mechanism of CQD in the therapeutic management of schistosomiasis, thereby providing valuable insights and guidance for the treatment of this disease. Conclusion This study uncovered the efficacious components and underlying molecular mechanisms of the Chufeng Qingpi Decoction in the management of schistosomiasis, thereby offering valuable insights for future fundamental research endeavors.
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Affiliation(s)
- Minglu Liu
- Emergency Department, The Second Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Yuxin Wang
- Research and Teaching Department of Comparative Medicine, Dalian Medical University, Dalian, Liaoning, China
| | - Wen Deng
- College of Pharmacy, Dalian Medical University, Dalian, Liaoning, China
| | - Jiahao Xie
- Emergency Department, The Second Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Yanyao He
- Research and Teaching Department of Comparative Medicine, Dalian Medical University, Dalian, Liaoning, China
| | - Liang Wang
- Research and Teaching Department of Comparative Medicine, Dalian Medical University, Dalian, Liaoning, China
| | - Jianbin Zhang
- College of Pharmacy, Dalian Medical University, Dalian, Liaoning, China
| | - Ming Cui
- Emergency Department, The Second Hospital of Dalian Medical University, Dalian, Liaoning, China
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22
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Wang Y, Zhang L, Xu J, Ma J. The Proteomic Landscape of Monocytes in Response to Colorectal Cancer Cells. J Proteome Res 2024; 23:4067-4081. [PMID: 39106312 PMCID: PMC11385372 DOI: 10.1021/acs.jproteome.4c00400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2024]
Abstract
Colorectal cancer (CRC) involves a complex interaction between tumor cells and immune cells, notably monocytes, leading to immunosuppression. This study explored these interactions using in vitro coculture systems of THP-1 cells and CRC cell lines, employing quantitative proteomics to analyze protein changes in monocytes. Multiple analytical methods were utilized to delineate the altered proteomic landscape, identify key proteins, and their associated functional pathways for comprehensive data analysis. Differentially expressed proteins (DEPs) were selected and validated by cross-referencing them with publicly available TCGA and GEO data sets to explore their potential clinical significance. Our analysis identified 161 up-regulated and 130 down-regulated DEPs. The enrichment results revealed impairments in adhesion and innate immune functions in monocytes, potentially facilitating cancer progression. The down-regulation of FN1, THSB1, and JUN may contribute to these impairments. Furthermore, the overexpression of ADAMTSL4, PRAM1, GPNMB, and NPC2 on monocytes was associated with unfavorable prognostic outcomes in CRC patients, suggesting potential biomarkers or therapeutic targets. This study illustrated the proteomic landscape of monocytes in response to CRC cells, providing clues for future investigations of the crosstalk between cancer cells and monocytes within the tumor microenvironment.
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Affiliation(s)
- Yiran Wang
- Peking University Fifth School of Clinical Medicine, Beijing 100730, China
- Center of Biotherapy, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Luyao Zhang
- Center of Biotherapy, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Jing Xu
- Center of Biotherapy, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Jie Ma
- Peking University Fifth School of Clinical Medicine, Beijing 100730, China
- Center of Biotherapy, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing 100730, China
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Zeng Z, Hu Y, Xiang J, Su J, Tan H, Lai T, Chen X, Fang G, Li L, Luo L. Cucurbitacin B targets STAT3 to induce ferroptosis in non-small cell lung cancer. Eur J Pharmacol 2024; 978:176805. [PMID: 38950838 DOI: 10.1016/j.ejphar.2024.176805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 06/28/2024] [Accepted: 06/29/2024] [Indexed: 07/03/2024]
Abstract
Cucurbitacin B (CuB) is a compound found in plants like Cucurbitaceae that has shown promise in fighting cancer, particularly in lung cancer. However, the specific impact of CuB on ferroptosis and how it works in lung cancer cells has not been fully understood. Our research has discovered that CuB can effectively slow down the growth of non-small cell lung cancer (NSCLC) cells. Even in small amounts, it was able to inhibit the growth of various NSCLC cell lines. This inhibitory effect was reversed when ferroptosis inhibitors DFO, Lip-1 and Fer-1 were introduced. CuB was found to increase the levels of reactive oxygen species (ROS), lipid ROS, MDA, and ferrous ions within H358 lung cancer cells, leading to a decrease in GSH, mitochondrial membrane potential (MMP) and changes in ferroptosis-related proteins in a dose-dependent manner. These findings were also confirmed in A549 lung cancer cells. In A549 cells, different concentrations of CuB induced the accumulation of intracellular lipid ROS, ferrous ions and changes in ferroptosis-related indicators in a concentration-dependent manner. Meanwhile, the cytotoxic effect induced by CuB in A549 cells was counteracted by ferroptosis inhibitors DFO and Fer-1. Through network pharmacology, we identified potential targets related to ferroptosis in NSCLC cells treated with CuB, with STAT3 targets showing high scores. Further experiments using molecular docking and cell thermal shift assay (CETSA) revealed that CuB interacts with the STAT3 protein. Western blot and immunofluorescence staining demonstrated that CuB inhibits the phosphorylation of STAT3 (P-STAT3) in H358 cells. Silencing STAT3 enhanced CuB-induced accumulation of lipid ROS and iron ions, as well as the expression of ferroptosis-related proteins. On the other hand, overexpression of STAT3 reversed the effects of CuB-induced ferroptosis. The results indicate that CuB has the capability to suppress STAT3 activation, resulting in ferroptosis, and could be a promising treatment choice for NSCLC.
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Affiliation(s)
- Zeyao Zeng
- The First Clinical College, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Yingying Hu
- Department of Pathophysiology, Guangdong Medical University, Zhanjiang, 524002, Guangdong, China
| | - Jing Xiang
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, School of Ocean and Tropical Medicine. Guangdong Medical University, Zhanjiang, Guangdong, 524023, China
| | - Jiating Su
- The First Clinical College, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Huiting Tan
- The First Clinical College, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Tianli Lai
- The First Clinical College, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Xinming Chen
- The First Clinical College, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Guixuan Fang
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, School of Ocean and Tropical Medicine. Guangdong Medical University, Zhanjiang, Guangdong, 524023, China
| | - Li Li
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, School of Ocean and Tropical Medicine. Guangdong Medical University, Zhanjiang, Guangdong, 524023, China.
| | - Lianxiang Luo
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, School of Ocean and Tropical Medicine. Guangdong Medical University, Zhanjiang, Guangdong, 524023, China.
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Gregoris F, Minervini G, Tosatto SCE. In Silico Exploration of AHR-HIF Pathway Interplay: Implications for Therapeutic Targeting in ccRCC. Genes (Basel) 2024; 15:1167. [PMID: 39336758 PMCID: PMC11431742 DOI: 10.3390/genes15091167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Revised: 08/28/2024] [Accepted: 08/30/2024] [Indexed: 09/30/2024] Open
Abstract
The oxygen-sensing pathway is a crucial regulatory circuit that defines cellular conditions and is extensively exploited in cancer development. Pathogenic mutations in the von Hippel-Lindau (VHL) tumour suppressor impair its role as a master regulator of hypoxia-inducible factors (HIFs), leading to constitutive HIF activation and uncontrolled angiogenesis, increasing the risk of developing clear cell renal cell carcinoma (ccRCC). HIF hyperactivation can sequester HIF-1β, preventing the aryl hydrocarbon receptor (AHR) from correctly activating gene expression in response to endogenous and exogenous ligands such as TCDD (dioxins). In this study, we used protein-protein interaction networks and gene expression profiling to characterize the impact of VHL loss on AHR activity. Our findings reveal specific expression patterns of AHR interactors following exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and in ccRCC. We identified several AHR interactors significantly associated with poor survival rates in ccRCC patients. Notably, the upregulation of the androgen receptor (AR) and retinoblastoma-associated protein (RB1) by TCDD, coupled with their respective downregulation in ccRCC and association with poor survival rates, suggests novel therapeutic targets. The strategic activation of the AHR via selective AHR modulators (SAhRMs) could stimulate its anticancer activity, specifically targeting RB1 and AR to reduce cell cycle progression and metastasis formation in ccRCC. Our study provides comprehensive insights into the complex interplay between the AHR and HIF pathways in ccRCC pathogenesis, offering novel strategies for targeted therapeutic interventions.
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Affiliation(s)
- Francesco Gregoris
- Department of Biomedical Sciences, University of Padova, Viale G. Colombo 3, 35121 Padova, Italy
| | - Giovanni Minervini
- Department of Biomedical Sciences, University of Padova, Viale G. Colombo 3, 35121 Padova, Italy
| | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padova, Viale G. Colombo 3, 35121 Padova, Italy
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Bai X, Qiao P, Liu H, Shang Y, Guo J, Dai K. Genome-wide identification of the E-class gene family in wheat: evolution, expression, and interaction. FRONTIERS IN PLANT SCIENCE 2024; 15:1419437. [PMID: 39290745 PMCID: PMC11405201 DOI: 10.3389/fpls.2024.1419437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 08/14/2024] [Indexed: 09/19/2024]
Abstract
Introduction Wheat (Triticum aestivum L.) is among themost important crop worldwide. Given a growing population and changing climate, enhancing wheat yield is of great importance. Yield is closely associated with flower and spike development, and E-class genes play important roles in the flower and kernel development of plants. Currently, the absence of systematic analysis on the E gene family hinders our comprehension of their roles in plant growth and development. Methods Identify E-class genes based on homologous sequence searches. Analyze the identified E-class genes through a series of gene family analyses. Determine the expression levels of wheat E-class genes by searching public databases. Validate the functions of these genes by transforming them into Arabidopsis. Finally, determine the interactions between the genes through yeast two-hybrid experiments. Results Fifteen E-class genes (TaEs) were identified in common wheat. Nine E-class genes were detected in five ancestral/closely related species, including one in Aegilops tauschii (AtE), one in T. Urartu (TuEs), two in T. turgidum (TtEs), two in T. dicoccoides (TdEs), and three in T. spelta (TsEs). The 24 E-class genes were classified into three subgroups using a phylogenetic approach. All genes were highly expressed in spikes, and most were only highly expressed at the floret meristem stage. The effects of TaSEP5-A on flowering and growth cycles were confirmed in homologous mutants and transgenic Arabidopsis thaliana. The E-class genes were able to regulate the growth cycle of Arabidopsis. Finally, we confirmed the interactions between TaSEP5-A and other wheat E-class genes based on yeast two-hybrid assays. Discussion Our findings provide information regarding the E-class genes in wheat and will potentially promote the application of these genes in wheat improvement.
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Affiliation(s)
- Xionghui Bai
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, China
| | - Pengfei Qiao
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, China
| | - Hanxiao Liu
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, China
| | - Yuping Shang
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, China
| | - Jie Guo
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, China
| | - Keli Dai
- College of Agronomy, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shanxi Agricultural University, Jinzhong, China
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26
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Bao L, Zhu Z, Ismail A, Zhu B, Anandan V, Whiteley M, Kitten T, Xu P. Experimental evolution of gene essentiality in bacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.16.600122. [PMID: 39071448 PMCID: PMC11275930 DOI: 10.1101/2024.07.16.600122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Essential gene products carry out fundamental cellular activities in interaction with other components. However, the lack of essential gene mutants and appropriate methodologies to link essential gene functions with their partners poses significant challenges. Here, we have generated deletion mutants in 32 genes previously identified as essential, with 23 mutants showing extremely slow growth in the SK36 strain of Streptococcus sanguinis. The 23 genes corresponding to these mutants encode components of diverse pathways, are widely conserved among bacteria, and are essential in many other bacterial species. Whole-genome sequencing of 243 independently evolved populations of these mutants has identified >1000 spontaneous suppressor mutations in experimental evolution. Many of these mutations define new gene and pathway relationships, such as F1Fo-ATPase/V1Vo-ATPase/TrkA1-H1 that were demonstrated across multiple Streptococcus species. Patterns of spontaneous mutations occurring in essential gene mutants differed from those found in wildtype. While gene duplications occurred rarely and appeared most often at later stages of evolution, substitutions, deletions, and insertions were prevalent in evolved populations. These essential gene deletion mutants and spontaneous mutations fixed in the mutant populations during evolution establish a foundation for understanding gene essentiality and the interaction of essential genes in networks.
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Affiliation(s)
- Liang Bao
- Department of Oral and Craniofacial Molecular Biology, Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Virginia, USA
| | - Zan Zhu
- Department of Oral and Craniofacial Molecular Biology, Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Virginia, USA
| | - Ahmed Ismail
- Department of Oral and Craniofacial Molecular Biology, Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Virginia, USA
| | - Bin Zhu
- Massey Cancer Center, Virginia Commonwealth University, Virginia, USA
| | - Vysakh Anandan
- Department of Oral and Craniofacial Molecular Biology, Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Virginia, USA
| | - Marvin Whiteley
- School of Biological Sciences, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Georgia, USA
| | - Todd Kitten
- Department of Oral and Craniofacial Molecular Biology, Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Virginia, USA
| | - Ping Xu
- Department of Oral and Craniofacial Molecular Biology, Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Virginia, USA
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Jiang P, Zhang Z, Yu Q, Wang Z, Diao L, Li D. ToxDAR: A Workflow Software for Analyzing Toxicologically Relevant Proteomic and Transcriptomic Data, from Data Preparation to Toxicological Mechanism Elucidation. Int J Mol Sci 2024; 25:9544. [PMID: 39273492 PMCID: PMC11394870 DOI: 10.3390/ijms25179544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2024] [Revised: 08/26/2024] [Accepted: 08/30/2024] [Indexed: 09/15/2024] Open
Abstract
Exploration of toxicological mechanisms is imperative for the assessment of potential adverse reactions to chemicals and pharmaceutical agents, the engineering of safer compounds, and the preservation of public health. It forms the foundation of drug development and disease treatment. High-throughput proteomics and transcriptomics can accurately capture the body's response to toxins and have become key tools for revealing complex toxicological mechanisms. Recently, a vast amount of omics data related to toxicological mechanisms have been accumulated. However, analyzing and utilizing these data remains a major challenge for researchers, especially as there is a lack of a knowledge-based analysis system to identify relevant biological pathways associated with toxicity from the data and to establish connections between omics data and existing toxicological knowledge. To address this, we have developed ToxDAR, a workflow-oriented R package for preprocessing and analyzing toxicological multi-omics data. ToxDAR integrates packages like NormExpression, DESeq2, and igraph, and utilizes R functions such as prcomp and phyper. It supports data preparation, quality control, differential expression analysis, functional analysis, and network analysis. ToxDAR's architecture also includes a knowledge graph with five major categories of mechanism-related biological entities and details fifteen types of interactions among them, providing comprehensive knowledge annotation for omics data analysis results. As a case study, we used ToxDAR to analyze a transcriptomic dataset on the toxicology of triphenyl phosphate (TPP). The results indicate that TPP may impair thyroid function by activating thyroid hormone receptor β (THRB), impacting pathways related to programmed cell death and inflammation. As a workflow-oriented data analysis tool, ToxDAR is expected to be crucial for understanding toxic mechanisms from omics data, discovering new therapeutic targets, and evaluating chemical safety.
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Affiliation(s)
- Peng Jiang
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Zuzhen Zhang
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Qing Yu
- College of Life Sciences, Hebei University, Baoding 071002, China
| | - Ze Wang
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Lihong Diao
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Dong Li
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
- College of Life Sciences, Hebei University, Baoding 071002, China
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
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Liu F, Zhong M, Yang L, Song C, Chen C, Xu Z, Zhang C, Li Z, Wu X, Jiang C, Chen F, Yan Q. Experimental confirmation and bioinformatics reveal biomarkers of immune system infiltration and hypertrophy ligamentum flavum. JOR Spine 2024; 7:e1354. [PMID: 39071860 PMCID: PMC11272949 DOI: 10.1002/jsp2.1354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 06/23/2024] [Accepted: 06/29/2024] [Indexed: 07/30/2024] Open
Abstract
Background Hypertrophy ligamentum flavum is a prevalent chronic spinal condition that affects middle-aged and older adults. However, the molecular pathways behind this disease are not well comprehended. Objective The objective of this work is to implement bioinformatics techniques in order to identify crucial biological markers and immune infiltration that are linked to hypertrophy ligamentum flavum. Further, the study aims to experimentally confirm the molecular mechanisms that underlie the hypertrophy ligamentum flavum. Methods The corresponding gene expression profiles (GSE113212) were selected from a comprehensive gene expression database. The gene dataset for hypertrophy ligamentum flavum was acquired from GeneCards. A network of interactions between proteins was created, and an analysis of functional enrichment was conducted using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) databases. An study of hub genes was performed to evaluate the infiltration of immune cells in patient samples compared to tissues from the control group. Finally, samples of the ligamentum flavum were taken with the purpose of validating the expression of important genes in a clinical setting. Results Overall, 27 hub genes that were differently expressed were found through molecular biology. The hub genes were found to be enriched in immune response, chemokine-mediated signaling pathways, inflammation, ossification, and fibrosis processes, as demonstrated by GO and KEGG studies. The main signaling pathways involved include the TNF signaling pathway, cytokine-cytokine receptor interaction, and TGF-β signaling pathway. An examination of immunocell infiltration showed notable disparities in B cells (naïve and memory) and activated T cells (CD4 memory) between patients with hypertrophic ligamentum flavum and the control group of healthy individuals. The in vitro validation revealed markedly elevated levels of ossification and fibrosis-related components in the hypertrophy ligamentum flavum group, as compared to the normal group. Conclusion The TGF-β signaling pathway, TNF signaling pathway, and related hub genes play crucial roles in the progression of ligamentum flavum hypertrophic. Our study may guide future research on fibrosis of the ligamentum flavum.
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Affiliation(s)
- Fei Liu
- Department of OrthopedicsRuiKang Hospital affiliated to Guangxi University of Chinese MedicineNanningChina
- Department of OrthopedicsThe Affiliated Hospital of Traditional Chinese Medicine of Southwest Medical UniversityLuzhouChina
| | - Min Zhong
- Department of ElectrocardiographyThe Affiliated Hospital of Southwest Medical UniversityLuzhouChina
| | - Lei Yang
- Department of OrthopedicsRuiKang Hospital affiliated to Guangxi University of Chinese MedicineNanningChina
| | - Chao Song
- Department of OrthopedicsRuiKang Hospital affiliated to Guangxi University of Chinese MedicineNanningChina
- Department of OrthopedicsThe Affiliated Hospital of Traditional Chinese Medicine of Southwest Medical UniversityLuzhouChina
| | - Chaoqi Chen
- Department of OrthopedicsRuiKang Hospital affiliated to Guangxi University of Chinese MedicineNanningChina
| | - Zhiwei Xu
- Department of OrthopedicsRuiKang Hospital affiliated to Guangxi University of Chinese MedicineNanningChina
| | - Chi Zhang
- Department of OrthopedicsRuiKang Hospital affiliated to Guangxi University of Chinese MedicineNanningChina
| | - Zhifa Li
- Department of OrthopedicsRuiKang Hospital affiliated to Guangxi University of Chinese MedicineNanningChina
| | - Xiaofei Wu
- Department of OrthopedicsRuiKang Hospital affiliated to Guangxi University of Chinese MedicineNanningChina
| | - Chen Jiang
- Department of OrthopedicsRuiKang Hospital affiliated to Guangxi University of Chinese MedicineNanningChina
| | - Feng Chen
- Department of OrthopedicsRuiKang Hospital affiliated to Guangxi University of Chinese MedicineNanningChina
| | - Qian Yan
- Department of OrthopedicsRuiKang Hospital affiliated to Guangxi University of Chinese MedicineNanningChina
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Yu R, Yang X, Xiao D, Bao H, Wang Y. MiRNAs profiles among three poplar varieties provide insights into different molecular responses in resistance to newly emerging bacterial pathogen. PHYSIOLOGIA PLANTARUM 2024; 176:e14498. [PMID: 39223906 DOI: 10.1111/ppl.14498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 07/31/2024] [Accepted: 08/09/2024] [Indexed: 09/04/2024]
Abstract
Canker caused by Lonsdalea populi has seriously reduced the economic and ecological benefits of poplar. MicroRNAs play vital roles in the response of plants to biotic stress. However, there is little research about the regulatory mechanism of miRNAs among different tree varieties upon pathogen infection. To dissect miRNAs involved in L. populi resistance, three poplar varieties, 2025 (susceptible), 107 (moderately resistant) and Populus. tomentosa cv 'henan' (resistant) were selected to elucidate the expression profiles of miRNAs using small RNA-seq. A total of 227 miRNAs were identified from all varieties. Intriguingly, miR160, miR169, miR171 and miR482b-5p were only identified in the resistant variety P. tomentosa upon pathogen infection, and these miRNAs might be important candidates for future investigation to improve the tolerance of poplar to L. populi. Among all identified miRNAs, 174 were differentially expressed in all varieties. Functional annotation analysis indicated that an array of miRNAs, including miR482, miR472, miR169, miR481, and miR172, should be involved in disease resistance and phytohormone signal transduction. Furthermore, correlation analysis of small RNA-seq and RNA-seq identified a handful of L. populi-responsive miRNAs and target genes, which exhibited that miR159 and miR172 played key roles in resistant variety P. tomentosa by targeting MYB and ERF, while miR6462c-5p and miR828 were related to the susceptibility of 2025 by targeting MYB. The comprehensive integration analysis in this research provides new insights into the regulatory pathways involved in the defence response of poplar to L. populi and offers crucial candidate miRNAs-target genes modules for poplar resistance improvement.
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Affiliation(s)
- Ruen Yu
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Xiaoqian Yang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Dandan Xiao
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Hai Bao
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Yanwei Wang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
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Guo P, Liu A, Qi Y, Wang X, Fan X, Guo X, Yu C, Tian C. Genome-wide identification of cold shock proteins (CSPs) in sweet cherry (Prunus avium L.) and exploring the differential responses of PavCSP1 and PavCSP3 to low temperature and salt stress. Genes Genomics 2024; 46:1023-1036. [PMID: 38997611 DOI: 10.1007/s13258-024-01542-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 07/01/2024] [Indexed: 07/14/2024]
Abstract
BACKGROUND Cold shock proteins (CSPs) are ubiquitous nucleic acid-binding proteins involved in growth, development, and stress response across various organisms. While extensively studied in many species, their regulatory roles in sweet cherry (Prunus avium L.) remain unclear. OBJECTIVE To identify and analyze CSP genes (PavCSPs) in sweet cherry genome, and explore the differential responses of PavCSP1 and PavCSP3 to low temperature and salt stress. METHODS Three methods were employed to identify and characterize CSP in sweet cherry genomes. To explore the potential functions and evolutionary relationships of sweet cherry CSP proteins, sequence alignment and phylogenetic tree incorporating genes from five species were conducted and constructed, respectively. To investigate the responses to abiotic stresses, cis-acting elements analysis and gene expression patterns to low-temperature and salt stress were examined. Moreover, transgenic yeasts overexpressing PavCSP1 or PavCSP3 were generated and their growth under stress conditions were observed. RESULTS In this study, three CSP genes (PavCSPs) were identified and comprehensively analyzed. The quantitative real-time PCR revealed diverse expression patterns, with PavCSP1-3 demonstrating a particular activity in the upper stem and all members were responsive to low-temperature and salt stress. Further investigation demonstrated that transgenic yeasts overexpressing PavCSP1 or PavCSP3 exhibited improved growth states following high-salt and low-temperature stress. CONCLUSION These findings elucidated the responses of PavCSP1 and PavCSP3 to salt and low-temperature stresses, laying the groundwork for further functional studies of PavCSPs in response to abiotic stresses.
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Affiliation(s)
- Pan Guo
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong, 264025, China
- Yantai Academy of Agricultural Sciences, Yantai, Shandong, 265500, China
| | - Ao Liu
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong, 264025, China
- Yantai Academy of Agricultural Sciences, Yantai, Shandong, 265500, China
| | - Yueting Qi
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong, 264025, China
| | - Xueting Wang
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong, 264025, China
| | - Xiaole Fan
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong, 264025, China
| | - Xiaotong Guo
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong, 264025, China
| | - Chunyan Yu
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, 186 Hongqizhong Road, Yantai, Shandong, 264025, China.
| | - Changping Tian
- Yantai Academy of Agricultural Sciences, Yantai, Shandong, 265500, China.
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Wang Y, Zhang H, Zhang Z, Hua B, Liu J, Miao M. Source leaves are regulated by sink strengths through non-coding RNAs and alternative polyadenylation in cucumber (Cucumis sativus L.). BMC PLANT BIOLOGY 2024; 24:812. [PMID: 39198785 PMCID: PMC11360537 DOI: 10.1186/s12870-024-05416-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 07/12/2024] [Indexed: 09/01/2024]
Abstract
BACKGROUND The yield of major crops is generally limited by sink capacity and source strength. Cucumber is a typical raffinose family oligosaccharides (RFOs)-transporting crop. Non-coding RNAs and alternative polyadenylation (APA) play important roles in the regulation of growth process in plants. However, their roles on the sink‒source regulation have not been demonstrated in RFOs-translocating species. RESULTS Here, whole-transcriptome sequencing was applied to compare the leaves of cucumber under different sink strength, that is, no fruit-carrying leaves (NFNLs) and fruit-carrying leaves (FNLs) at 12th node from the bottom. The results show that 1101 differentially expressed (DE) mRNAs, 79 DE long non-coding RNAs (lncRNAs) and 23 DE miRNAs were identified, which were enriched in photosynthesis, energy production and conversion, plant hormone signal transduction, starch and carbohydrate metabolism and protein synthesis pathways. Potential co-expression networks like, DE lncRNAs-DE mRNAs/ DE miRNAs-DE mRNAs, and competing endogenous RNA (ceRNA) regulation models (DE lncRNAs-DE miRNAs-DE mRNAs) associated with sink‒source allocation, were constructed. Furthermore, 37 and 48 DE genes, which enriched in MAPK signaling and plant hormone signal transduction pathway, exist differentially APA, and SPS (CsaV3_2G033300), GBSS1 (CsaV3_5G001560), ERS1 (CsaV3_7G029600), PNO1 (CsaV3_3G003950) and Myb (CsaV3_3G022290) may be regulated by both ncRNAs and APA between FNLs and NFNLs, speculating that ncRNAs and APA are involved in the regulation of gene expression of cucumber sink‒source carbon partitioning. CONCLUSIONS These results reveal a comprehensive network among mRNAs, ncRNAs, and APA in cucumber sink-source relationships. Our findings also provide valuable information for further research on the molecular mechanism of ncRNA and APA to enhance cucumber yield.
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Affiliation(s)
- Yudan Wang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China
| | - Huimin Zhang
- Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong, 226541, China
| | - Zhiping Zhang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China
| | - Bing Hua
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China
| | - Jiexia Liu
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China
| | - Minmin Miao
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China.
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, 225009, China.
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Sukumaran SY, Herrscher C, Rasol NE, Othman MA, Liew SY, Ismail NH, Séron K, Litaudon M, Awang K, El Kalamouni C, Apel C, Zahari A. Targeted Isolation of Antiviral Labdane Diterpenes from the Bark of Neo-uvaria foetida (Annonaceae) using LC-MS/MS-Based Molecular Networking. JOURNAL OF NATURAL PRODUCTS 2024; 87:1941-1951. [PMID: 39028935 DOI: 10.1021/acs.jnatprod.4c00342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/21/2024]
Abstract
In the search of new inhibitors for human coronavirus (HCoV), we screened extracts of endemic Annonaceae plants on an assay using a cellular model of Huh-7 cells infected with the human alphacoronavirus HCoV-229E. The EtOAc bark extract of the rare Southeast Asian plant Neo-uvaria foetida exhibited inhibition of HCoV-229E and SARS-CoV-2 viruses with IC50 values of 3.8 and 7.8 μg/mL, respectively. Using LC-MS/MS and molecular networking analysis guided isolation, we discovered two new labdane-type diterpenoids, 8-epi-acuminolide (1) and foetidalabdane A (4), and three known labdane diterpenoids, acuminolide (2), 17-O-acetylacuminolide (3), and spiroacuminolide (5). A new norlabdane diterpene, 16-foetinorlabdoic acid (6), was also isolated and identified. Excluding compounds 5 and 6, all other metabolites were active against the virus HCoV-229E. Terpenoids 1 and 4 presented antiviral activity against SARS-CoV-2 with IC50 values of 63.3 and 93.5 μM, respectively, indicating lower potency. Additionally, virological assays demonstrated that compounds 1, 2, and 3 exert antiviral effects against Zika virus by specifically interfering with the late stage of its infectious cycle with IC50 values of 76.0, 31.9, and 14.9 μM, respectively.
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Affiliation(s)
- S Yaallini Sukumaran
- Department of Chemistry, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Charline Herrscher
- Unité Mixte Processus Infectieux en Milieu Insulaire Tropical, Université de la Réunion, INSERM U1187, CNRS UMR 9192, IRD UMR 249, Plateforme Technologique CYROI, Sainte Clotilde 94791, France
| | - Nurulfazlina Edayah Rasol
- Atta-ur-Rahman Institute for Natural Product Discovery, Level 9 FF3, Universiti Teknologi MARA Puncak Alam Campus, Bandar Puncak Alam 42300, Malaysia
| | - Muhamad Aqmal Othman
- Department of Chemistry, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Sook Yee Liew
- Chemistry Division, Centre for Foundation Studies in Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Nor Hadiani Ismail
- Atta-ur-Rahman Institute for Natural Product Discovery, Level 9 FF3, Universiti Teknologi MARA Puncak Alam Campus, Bandar Puncak Alam 42300, Malaysia
| | - Karin Séron
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017-Center for Infection and Immunity of Lille (CIIL), Lille F-59000, France
| | - Marc Litaudon
- Institut de Chimie des Substances Naturelles, CNRS, UPR 2301, Université Paris-Saclay, Gif-sur-Yvette 91198, France
| | - Khalijah Awang
- Department of Chemistry, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Chaker El Kalamouni
- Unité Mixte Processus Infectieux en Milieu Insulaire Tropical, Université de la Réunion, INSERM U1187, CNRS UMR 9192, IRD UMR 249, Plateforme Technologique CYROI, Sainte Clotilde 94791, France
| | - Cécile Apel
- Institut de Chimie des Substances Naturelles, CNRS, UPR 2301, Université Paris-Saclay, Gif-sur-Yvette 91198, France
| | - Azeana Zahari
- Department of Chemistry, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
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Zhang J, Peng C, Lv M, Yang S, Xie L, Feng J, Wei Y, Hu T, He J, Xie Z, Yu M. Polygonum hydropiper Compound Extract Inhibits Clostridium perfringens-Induced Intestinal Inflammatory Response and Injury in Broiler Chickens by Modulating NLRP3 Inflammasome Signaling. Antibiotics (Basel) 2024; 13:793. [PMID: 39334968 PMCID: PMC11428944 DOI: 10.3390/antibiotics13090793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Revised: 08/19/2024] [Accepted: 08/20/2024] [Indexed: 09/30/2024] Open
Abstract
Necrotic enteritis (NE) is a critical disease affecting broiler health, with Clostridium perfringens as its primary pathogen. Polygonum hydropiper compound extract (PHCE), formulated based on traditional Chinese veterinary principles, contains primarily flavonoids with antibacterial, anti-inflammatory, and antioxidant properties. However, PHCE's efficacy against Clostridium perfringens-induced NE and its underlying mechanism remain unclear. This study employed network pharmacology and molecular docking to predict PHCE's potential mechanisms in treating NE, followed by determining its minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) against Clostridium perfringens (C. perf). Subsequently, the effects of various PHCE doses on intestinal damage, antioxidant capacity, and inflammatory factors in C. perf-infected broilers were assessed. Network pharmacology and molecular docking suggested that PHCE's therapeutic mechanism for NE involves the NOD-like receptor thermal protein domain associated protein 3 (NLRP3) inflammasome signaling pathway, with flavonoids such as quercetin, kaempferol, and isorhamnetin as key active components. PHCE exhibited an MIC of 3.13 mg/mL and an MBC of 12.5 mg/mL against C. perf. High PHCE doses effectively reduced intestinal damage scores in both the jejunum and ileum, accompanied by attenuated intestinal pathological changes. Additionally, the high dose significantly increased superoxide dismutase (SOD) levels while decreasing malondialdehyde (MDA), hydrogen peroxide (H2O2), tumor necrosis factor-alpha (TNF-α), interleukin-1 beta (IL-1β), and interleukin-6 (IL-6) in the jejunum and ileum (p < 0.01 or p < 0.05). PHCE also modulated the expression of caspase-1, IL-1β, gasdermin D (GSDMD), and NLRP3 mRNA, key components of the NLRP3 inflammasome signaling pathway, in both intestinal segments. These findings collectively indicate that PHCE protects against C. perf-induced oxidative stress and inflammatory damage in NE. By enhancing antioxidant capacity, PHCE likely reduces oxidative stress and inflammatory responses, subsequently modulating NLRP3 inflammasome signaling pathway key factor expression. Overall, this research provides valuable insights into the protective mechanism of the herbal compound PHCE and its potential benefits for avian health.
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Affiliation(s)
- Jinwu Zhang
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Chunzi Peng
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Maojie Lv
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Shisen Yang
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Liji Xie
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning 530001, China
| | - Jiaxun Feng
- College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Yingyi Wei
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Tingjun Hu
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Jiakang He
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Zhixun Xie
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning 530001, China
| | - Meiling Yu
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning 530001, China
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Wei L, Xie Y, Yu P, Zhu Q, Lan X, Xiao J. Bioinformatics analysis and validation of RNA methylation-related genes in osteogenic and adipogenic differentiation of rat bone marrow mesenchymal stem cells. Biochem Biophys Res Commun 2024; 739:150570. [PMID: 39181069 DOI: 10.1016/j.bbrc.2024.150570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/29/2024] [Accepted: 08/19/2024] [Indexed: 08/27/2024]
Abstract
BACKGROUND The regulatory mechanisms of RNA methylation during the processes of osteogenic and adipogenic differentiation of bone marrow mesenchymal stem cells (BMSCs) have yet to be fully understood. The objective of our study was to analyze and validate the contribution of RNA methylation regulators to the mechanisms underlying the osteogenic and adipogenic differentiation of rat BMSCs. METHODS We downloaded the GSE186026 from the Gene Expression Omnibus (GEO). Differentially expressed genes (DEGs) were screened using the DESeq2 package in R software (version 3.6.3). A total of 50 RNA methylation genes obtained from literature review and summary were intersected with the previous DEGs to obtain RNA methylation genes, which have different expressions (RM-DEGs). Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were utilized to reveal the functional enrichment. Quantitative real-time polymerase chain reaction (qRT-PCR) was performed to validate RM-DEGs. Protein-protein interaction network (PPI) analysis and visual analysis were performed using STRING and Cytoscape. RM-DEGs regulatory network was constructed to analyze the top 10 hub genes. The relationship between RM-DEGs, some enriched GO and pathways was also been analyzed. The miRNAs and RM-DEGs regulatory networks were established by using miRWalk and TargetScan. RESULTS As part of our research, we detected varying levels of expression for m6A regulators Mettl3 and Rbm15, as well as m7G regulators Mettl1 and Wdr4, in relation to osteogenic differentiation, along with m6A regulator Fmr1 in adipogenic differentiation. The protein-protein interaction (PPI) networks were constructed for 49 differentially expressed genes (DEGs) related to RNA methylation during the process of osteogenic differentiation, and 13 DEGs for adipogenic differentiation. Moreover, top10 hub genes were calculated. In osteogenic differentiation, Mettl3 regulated the Wnt pathway and Hippo pathway by regulating Smad3, Rbm15 regulated the Notch pathway by Notch1, Mettl1 regulated the PI3K-Akt pathway by Gnb4. In adipogenic differentiation, Fmr1 regulated the PI3K-Akt pathway by Egfr. M6A methylation sites of Smad3, Notch1 and Gnb4 were predicted, and the results showed that all three genes were possibly methylated by m6A, and more than 9 sites per gene were possibly methylated. Finally, we constructed the regulatory networks of Mettl3, Rbm15, Mettl1, and Wdr4 and 109 miRNAs in osteogenic differentiation, Fmr1 and 118 miRNAs in adipogenic differentiation. CONCLUSIONS Mettl3(m6A), Rbm15(m6A), Wdr4 and Mettl1(m7G) were differentially expressed in osteogenic differentiation, while Fmr1(m6A) was differentially expressed in adipogenic differentiation. These findings offered potential candidates for further research on the involvement of RNA methylation in the osteogenic and adipogenic differentiation of BMSCs.
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Affiliation(s)
- Li Wei
- Department of Oral Implantology, The Affiliated Stomatological Hospital of Southwest Medical University, Luzhou, China; Luzhou Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, The Affiliated Stomatological Hospital of Southwest Medical University, Luzhou, China
| | - Yuping Xie
- Department of Oral Implantology, The Affiliated Stomatological Hospital of Southwest Medical University, Luzhou, China
| | - Peiyang Yu
- Department of Oral Implantology, The Affiliated Stomatological Hospital of Southwest Medical University, Luzhou, China
| | - Qiang Zhu
- Luzhou Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, The Affiliated Stomatological Hospital of Southwest Medical University, Luzhou, China; Department of Oral and Maxillofacial Surgery, The Affiliated Stomatological Hospital of Southwest Medical University, Luzhou, China
| | - Xiaorong Lan
- Luzhou Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, The Affiliated Stomatological Hospital of Southwest Medical University, Luzhou, China
| | - Jingang Xiao
- Department of Oral Implantology, The Affiliated Stomatological Hospital of Southwest Medical University, Luzhou, China; Luzhou Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, The Affiliated Stomatological Hospital of Southwest Medical University, Luzhou, China; Department of Oral and Maxillofacial Surgery, The Affiliated Stomatological Hospital of Southwest Medical University, Luzhou, China.
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Huang L, Sun J, Guo Q, Jiang Y, Hao B, Chang G. Effect of Early Ciprofloxacin Administration on Growth Performance, Meat Quality, Food Safety, and Metabolomic Profiles in Xueshan Chickens. Animals (Basel) 2024; 14:2395. [PMID: 39199929 PMCID: PMC11350917 DOI: 10.3390/ani14162395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 08/06/2024] [Accepted: 08/14/2024] [Indexed: 09/01/2024] Open
Abstract
To investigate the effects of early administration of ciprofloxacin (CIP) on Xueshan chickens, in this study Xueshan chickens were measured for growth performance, tested for drug residues, evaluated for meat quality, and muscle metabolism changes were explored using a non-target metabolomics approach. Experimental findings revealed that early CIP use did not significantly impact the overall growth rate of Xueshan chickens (p > 0.05). However, notable alterations in meat quality were observed: the CIP-treated group exhibited a significant decrease in muscle pH (pH1 and pH24) and a marked increase in drip loss and moisture content (p > 0.05). No CIP residues were detected in muscle tissue. Untargeted metabolomics analyses unveiled significant alterations in the metabolic profile of market-age chickens following CIP treatment. Both functional enrichment and metabolic network analyses indicated significant effects on the ko01120 (microbial metabolism in diverse environments) and ko00350 (tyrosine metabolism) pathways, implying that CIP treatment may influence chicken meat quality by modulating microbial communities and amino acid metabolism. This study provides a crucial foundation for understanding the impact of antibiotics on meat quality and metabolism in poultry production, offering scientific insights for optimizing antibiotic-use strategies and safeguarding poultry product quality.
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Affiliation(s)
- Lan Huang
- Key Laboratory for Animal Genetics & Molecular Breeding of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (L.H.); (J.S.); (Q.G.); (Y.J.)
| | - Jialuo Sun
- Key Laboratory for Animal Genetics & Molecular Breeding of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (L.H.); (J.S.); (Q.G.); (Y.J.)
| | - Qixin Guo
- Key Laboratory for Animal Genetics & Molecular Breeding of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (L.H.); (J.S.); (Q.G.); (Y.J.)
| | - Yong Jiang
- Key Laboratory for Animal Genetics & Molecular Breeding of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (L.H.); (J.S.); (Q.G.); (Y.J.)
| | - Bai Hao
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China
| | - Guobin Chang
- Key Laboratory for Animal Genetics & Molecular Breeding of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (L.H.); (J.S.); (Q.G.); (Y.J.)
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Jin B, Han Y, Xu F, Wang J, Zhao Y, Liu H, Wang F, Wang Z, Lu W, Wang M, Cui L, Zhao Y, Hao J, Chai G. Translatome analysis in acute ischemic stroke: Astrocytes and microglia exhibit differences in poststroke alternative splicing of expressed transcripts. FASEB J 2024; 38:e23855. [PMID: 39096134 DOI: 10.1096/fj.202400341r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 06/28/2024] [Accepted: 07/21/2024] [Indexed: 08/04/2024]
Abstract
Astrocytes and microglia undergo dynamic and complex morphological and functional changes following ischemic stroke, which are instrumental in both inflammatory responses and neural repair. While gene expression alterations poststroke have been extensively studied, investigations into posttranscriptional regulatory mechanisms, specifically alternative splicing (AS), remain limited. Utilizing previously reported Ribo-Tag-seq data, this study analyzed AS alterations in poststroke astrocytes and microglia from young adult male and female mice. Our findings reveal that in astrocytes, compared to the sham group, 109 differential alternative splicing (DAS) events were observed at 4 h poststroke, which increased to 320 at day 3. In microglia, these numbers were 316 and 266, respectively. Interestingly, the disparity between DAS genes and differentially expressed genes is substantial, with fewer than 10 genes shared at both poststroke time points in astrocytes and microglia. Gene ontology enrichment analysis revealed the involvement of these DAS genes in diverse functions, encompassing immune response (Adam8, Ccr1), metabolism (Acsl6, Pcyt2, Myo5a), and developmental cell growth (App), among others. Selective DAS events were further validated by semiquantitative RT-PCR. Overall, this study comprehensively describes the AS alterations in astrocytes and microglia during the hyperacute and acute phases of ischemic stroke and underscores the significance of certain hub DAS events in neuroinflammatory processes.
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Affiliation(s)
- Bingxue Jin
- Department of Neurology, National Center for Neurological Disorders, Xuanwu Hospital Capital Medical University, Beijing, China
- Beijing Municipal Geriatric Medical Research Center, Beijing, China
| | - Yilai Han
- Department of Neurology, National Center for Neurological Disorders, Xuanwu Hospital Capital Medical University, Beijing, China
- Beijing Municipal Geriatric Medical Research Center, Beijing, China
| | - Fang Xu
- Department of Neurology, National Center for Neurological Disorders, Xuanwu Hospital Capital Medical University, Beijing, China
- Beijing Municipal Geriatric Medical Research Center, Beijing, China
| | - Junjie Wang
- Department of Neurology, National Center for Neurological Disorders, Xuanwu Hospital Capital Medical University, Beijing, China
- Beijing Municipal Geriatric Medical Research Center, Beijing, China
| | - Yunzhi Zhao
- Department of Neurology, National Center for Neurological Disorders, Xuanwu Hospital Capital Medical University, Beijing, China
- Beijing Municipal Geriatric Medical Research Center, Beijing, China
| | - Haijie Liu
- Department of Neurology, National Center for Neurological Disorders, Xuanwu Hospital Capital Medical University, Beijing, China
- Beijing Municipal Geriatric Medical Research Center, Beijing, China
| | - Fei Wang
- Department of Neurology, National Center for Neurological Disorders, Xuanwu Hospital Capital Medical University, Beijing, China
- Beijing Municipal Geriatric Medical Research Center, Beijing, China
| | - Ze Wang
- Department of Neurology, National Center for Neurological Disorders, Xuanwu Hospital Capital Medical University, Beijing, China
- Beijing Municipal Geriatric Medical Research Center, Beijing, China
| | - Wanting Lu
- Department of Neurology, National Center for Neurological Disorders, Xuanwu Hospital Capital Medical University, Beijing, China
- Beijing Municipal Geriatric Medical Research Center, Beijing, China
| | - Mingyang Wang
- Department of Neurology, National Center for Neurological Disorders, Xuanwu Hospital Capital Medical University, Beijing, China
- Beijing Municipal Geriatric Medical Research Center, Beijing, China
| | - Lili Cui
- Department of Neurology, National Center for Neurological Disorders, Xuanwu Hospital Capital Medical University, Beijing, China
- Beijing Municipal Geriatric Medical Research Center, Beijing, China
| | - Yinan Zhao
- Department of Neurology, National Center for Neurological Disorders, Xuanwu Hospital Capital Medical University, Beijing, China
- Beijing Municipal Geriatric Medical Research Center, Beijing, China
| | - Junwei Hao
- Department of Neurology, National Center for Neurological Disorders, Xuanwu Hospital Capital Medical University, Beijing, China
- Beijing Municipal Geriatric Medical Research Center, Beijing, China
- Key Laboratory for Neurodegenerative Diseases of Ministry of Education, Beijing, China
| | - Guoliang Chai
- Department of Neurology, National Center for Neurological Disorders, Xuanwu Hospital Capital Medical University, Beijing, China
- Beijing Municipal Geriatric Medical Research Center, Beijing, China
- Key Laboratory for Neurodegenerative Diseases of Ministry of Education, Beijing, China
- Chinese Institutes for Medical Research, Beijing, China
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Zeng Z, Hu J, Xiao G, Liu Y, Jia D, Wu G, Xie C, Li S, Bi X. Integrating network toxicology and molecular docking to explore the toxicity of the environmental pollutant butyl hydroxyanisole: An example of induction of chronic urticaria. Heliyon 2024; 10:e35409. [PMID: 39170477 PMCID: PMC11336633 DOI: 10.1016/j.heliyon.2024.e35409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 07/08/2024] [Accepted: 07/29/2024] [Indexed: 08/23/2024] Open
Abstract
The study aimed to comprehensively investigate environmental pollutants' potential toxicity and underlying molecular mechanisms, focusing on chronic urticaria (CU) induced by butylated hydroxyanisole (BHA) exposure, further drawing public awareness regarding the potential risks of environmental pollutants, applying ChEMBL, STITCH, and SwissTargetPrediction databases to predict the targets of BHA, CTD, GeneCards, and OMIM databases to collect the relevant targets of CU. Ultimately, we identified 81 potential targets of BHA-induced CU and extracted 31 core targets, including TNF, SRC, CASP3, BCL2, IL2, and MMP9. GO and KEGG enrichment analyses revealed that these core targets were predominantly involved in cancer signaling, estrogen and endocrine resistance pathways. Furthermore, molecular docking confirmed the ability of BHA to bind with core targets. The onset and development of CU may result from BHA by affecting multiple immune signaling pathways. Our study elucidated the molecular mechanisms of BHA toxicity and its role in CU induction, providing the basis for preventing and treating chronic urticaria associated with environmental BHA exposure.
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Affiliation(s)
- Zhihao Zeng
- School of the Fifth Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Jiaoting Hu
- Artemisinin Research Center, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Guanlin Xiao
- Guangdong Provincial Engineering and Technology Research Institute of Traditional Chinese Medicine/Guangdong Provincial Key Laboratory of Research and Development in Traditional Chinese Medicine, Guangzhou, 510095, China
| | - Yanchang Liu
- School of the Fifth Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Dezheng Jia
- School of the Fifth Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Guangying Wu
- School of the Fifth Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Canhui Xie
- School of the Fifth Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Sumei Li
- Guangdong Provincial Engineering and Technology Research Institute of Traditional Chinese Medicine/Guangdong Provincial Key Laboratory of Research and Development in Traditional Chinese Medicine, Guangzhou, 510095, China
| | - Xiaoli Bi
- Guangdong Provincial Engineering and Technology Research Institute of Traditional Chinese Medicine/Guangdong Provincial Key Laboratory of Research and Development in Traditional Chinese Medicine, Guangzhou, 510095, China
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Olanrewaju JA, Arietarhire LO, Soremekun OE, Olugbogi EA, Aribisala PO, Alege PE, Adeleke SO, Afolabi TO, Sodipo AO. Reporting the anti-neuroinflammatory potential of selected spondias mombin flavonoids through network pharmacology and molecular dynamics simulations. In Silico Pharmacol 2024; 12:74. [PMID: 39155973 PMCID: PMC11324643 DOI: 10.1007/s40203-024-00243-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 07/14/2024] [Indexed: 08/20/2024] Open
Abstract
Neuroinflammation plays a pivotal role in the development and progression of neurodegenerative diseases, with a complex interplay between immune responses and brain activity. Understanding this interaction is crucial for identifying therapeutic targets and developing effective treatments. This study aimed to explore the neuroprotective properties of flavonoid compounds from Spondias mombin via the modulation of neuroinflammatory pathway using a comprehensive in-silico approach, including network pharmacology, molecular docking, and dynamic simulations. Active flavonoid ingredients from S. mombin were identified, and their potential protein targets were predicted through Network Pharmacology. Molecular docking was conducted to determine the binding affinities of these compounds against targets obtained from network pharmacology, prioritizing docking scores ≥ - 8.0 kcal/mol. Molecular dynamic simulations (MDS) assessed the stability and interaction profiles of these ligand-protein complexes. The docking study highlighted ≥ - 8.0 kcal/mol for the ligands (catechin and epicatechin) against FYN kinase as a significant target. However, these compounds failed the blood-brain barrier (BBB) permeability test. MDS confirmed the stability of catechin and the reference ligand at the FYN kinase active site, with notable interactions involving hydrogen bonds, hydrophobic contacts, and water bridges. GLU54 emerged as a key residue in the catechin-FYN complex stability due to its prolonged hydrogen bond interaction. The findings underscore the potential of S. mombin flavonoids as therapeutic agents against neuroinflammation, though optimization and nanotechnology-based delivery methods are suggested to enhance drug efficacy and overcome BBB limitations. Graphical abstract
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Affiliation(s)
- John A. Olanrewaju
- Department of Biocomputing, Eureka Research Laboratory, Faculty of Basic Medical Science, Benjamin Carson (Snr.) School of Medical Science, BABCOCK University, Ilishan-Remo, Ogun State Nigeria
| | - Leviticus O. Arietarhire
- Department of Biocomputing, Eureka Research Laboratory, Faculty of Basic Medical Science, Benjamin Carson (Snr.) School of Medical Science, BABCOCK University, Ilishan-Remo, Ogun State Nigeria
| | - Oladimeji E. Soremekun
- Department of Biocomputing, Eureka Research Laboratory, Faculty of Basic Medical Science, Benjamin Carson (Snr.) School of Medical Science, BABCOCK University, Ilishan-Remo, Ogun State Nigeria
| | - Ezekiel A. Olugbogi
- Department of Biocomputing, Eureka Research Laboratory, Faculty of Basic Medical Science, Benjamin Carson (Snr.) School of Medical Science, BABCOCK University, Ilishan-Remo, Ogun State Nigeria
| | - Precious O. Aribisala
- Department of Biocomputing, Eureka Research Laboratory, Faculty of Basic Medical Science, Benjamin Carson (Snr.) School of Medical Science, BABCOCK University, Ilishan-Remo, Ogun State Nigeria
| | - Pelumi E. Alege
- Department of Biocomputing, Eureka Research Laboratory, Faculty of Basic Medical Science, Benjamin Carson (Snr.) School of Medical Science, BABCOCK University, Ilishan-Remo, Ogun State Nigeria
| | - Stephen O. Adeleke
- Department of Biocomputing, Eureka Research Laboratory, Faculty of Basic Medical Science, Benjamin Carson (Snr.) School of Medical Science, BABCOCK University, Ilishan-Remo, Ogun State Nigeria
| | - Toluwanimi O. Afolabi
- Department of Biocomputing, Eureka Research Laboratory, Faculty of Basic Medical Science, Benjamin Carson (Snr.) School of Medical Science, BABCOCK University, Ilishan-Remo, Ogun State Nigeria
| | - Abayomi O. Sodipo
- Department of Biocomputing, Eureka Research Laboratory, Faculty of Basic Medical Science, Benjamin Carson (Snr.) School of Medical Science, BABCOCK University, Ilishan-Remo, Ogun State Nigeria
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Wu JW, Gao W, Shen LP, Chen YL, Du SQ, Du ZY, Zhao XD, Lu XJ. Leonurus japonicus Houtt. modulates neuronal apoptosis in intracerebral hemorrhage: Insights from network pharmacology and molecular docking. JOURNAL OF ETHNOPHARMACOLOGY 2024; 330:118223. [PMID: 38642624 DOI: 10.1016/j.jep.2024.118223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/09/2024] [Accepted: 04/17/2024] [Indexed: 04/22/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Leonurus japonicus Houtt. (Labiatae), commonly known as Chinese motherwort, is a herbaceous flowering plant that is native to Asia. It is widely acknowledged in traditional medicine for its diuretic, hypoglycemic, antiepileptic properties and neuroprotection. Currently, Leonurus japonicus (Leo) is included in the Pharmacopoeia of the People's Republic of China. Traditional Chinese Medicine (TCM) recognizes Leo for its myriad pharmacological attributes, but its efficacy against ICH-induced neuronal apoptosis is unclear. AIMS OF THE STUDY This study aimed to identify the potential targets and regulatory mechanisms of Leo in alleviating neuronal apoptosis after ICH. MATERIALS AND METHODS The study employed network pharmacology, UPLC-Q-TOF-MS technique, molecular docking, pharmacodynamic studies, western blotting, and immunofluorescence techniques to explore its potential mechanisms. RESULTS Leo was found to assist hematoma absorption, thus improving the neurological outlook in an ICH mouse model. Importantly, molecular docking highlighted JAK as Leo's potential therapeutic target in ICH scenarios. Further experimental evidence demonstrated that Leo adjusts JAK1 and STAT1 phosphorylation, curbing Bax while augmenting Bcl-2 expression. CONCLUSION Leo showcases potential in mitigating neuronal apoptosis post-ICH, predominantly via the JAK/STAT mechanism.
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Affiliation(s)
- Jia-Wei Wu
- Neuroscience Center, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu Province, 214122, PR China; Department of Neurosurgery, Jiangnan University Medical Center, Wuxi, Jiangsu Province, 214122, PR China; Wuxi Neurosurgical Institute, Wuxi, Jiangsu Province, 214122, PR China
| | - Wei Gao
- Department of Neurology, Wuxi Ninth People's Hospital Affiliated to Soochow University, Wuxi, Jiangsu Province, 214122, PR China
| | - Li-Ping Shen
- Department of Neurosurgery, Jiangnan University Medical Center, Wuxi, Jiangsu Province, 214122, PR China; Wuxi Neurosurgical Institute, Wuxi, Jiangsu Province, 214122, PR China
| | - Yong-Lin Chen
- Neuroscience Center, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu Province, 214122, PR China; Department of Neurosurgery, Jiangnan University Medical Center, Wuxi, Jiangsu Province, 214122, PR China; Wuxi Neurosurgical Institute, Wuxi, Jiangsu Province, 214122, PR China
| | - Shi-Qing Du
- Neuroscience Center, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu Province, 214122, PR China; Department of Neurosurgery, Jiangnan University Medical Center, Wuxi, Jiangsu Province, 214122, PR China; Wuxi Neurosurgical Institute, Wuxi, Jiangsu Province, 214122, PR China
| | - Zhi-Yong Du
- Neuroscience Center, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu Province, 214122, PR China; Department of Neurosurgery, Jiangnan University Medical Center, Wuxi, Jiangsu Province, 214122, PR China; Wuxi Neurosurgical Institute, Wuxi, Jiangsu Province, 214122, PR China
| | - Xu-Dong Zhao
- Neuroscience Center, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu Province, 214122, PR China; Department of Neurosurgery, Jiangnan University Medical Center, Wuxi, Jiangsu Province, 214122, PR China; Wuxi Neurosurgical Institute, Wuxi, Jiangsu Province, 214122, PR China.
| | - Xiao-Jie Lu
- Neuroscience Center, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu Province, 214122, PR China; Department of Neurosurgery, Jiangnan University Medical Center, Wuxi, Jiangsu Province, 214122, PR China; Wuxi Neurosurgical Institute, Wuxi, Jiangsu Province, 214122, PR China.
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Wang L, Guo X, Qin J, Jin Z, Liu Q, Sun C, Sun K, Li L, Wei X, Zhang Y. Assessing the causal relationship between plasma proteins and osteoporosis: novel insights into pathological mechanisms and therapeutic implications. Osteoporos Int 2024:10.1007/s00198-024-07225-y. [PMID: 39120624 DOI: 10.1007/s00198-024-07225-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 08/02/2024] [Indexed: 08/10/2024]
Abstract
Identifying dysregulated plasma proteins in osteoporosis (OP) progression offers insights into prevention and treatment. This study found 8 such proteins associated with OP, suggesting them as therapy targets. This discovery may cut drug development costs and improve personalized treatments. PURPOSE This study aims to identify potential therapeutic targets for OP using summary data-based Mendelian randomization (SMR) and colocalization analysis methods. Furthermore, we seek to explore the biological significance and pharmacological value of these drug targets. METHODS To identify potential therapeutic targets for OP, we conducted SMR and colocalization analysis. Plasma protein (pQTL, exposure) data were sourced from the study by Ferkingstad et al. (n = 35,559). Summary statistics for bone mineral density (BMD, outcome) were obtained from the GWAS Catalog (n = 56,284). Additionally, we utilized enrichment analysis, protein-protein interaction (PPI) network analysis, drug prediction, and molecular docking to further analyze the biological significance and pharmacological value of these drug targets. RESULTS In the SMR analysis, while 20 proteins showed significance, only 8 potential drug targets (GCKR, ERBB3, CFHR1, GPN1, SDF2, VTN, BET1L, and SERPING1) received support from colocalization (PP.H4 > 0.8). These proteins are closely associated with immune function in terms of biological significance. Molecular docking also demonstrated favorable binding of drugs to proteins, consistent with existing structural data, further substantiating the pharmacological value of these targets. CONCLUSIONS The study identified 8 potential drug targets for OP. These prospective targets are believed to have a higher chance of success in clinical trials, thus aiding in prioritizing OP drug development and reducing development costs.
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Affiliation(s)
- Liang Wang
- School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China
| | - Xiangyun Guo
- School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China
| | - Jinran Qin
- School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China
| | - Zikai Jin
- Wangjing Hospital, China Academy of Chinese Medical Sciences, Beijing, 100102, China
| | - Qingqing Liu
- School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China
| | - Chuanrui Sun
- Wangjing Hospital, China Academy of Chinese Medical Sciences, Beijing, 100102, China
| | - Kai Sun
- Wangjing Hospital, China Academy of Chinese Medical Sciences, Beijing, 100102, China
| | - Linghui Li
- Wangjing Hospital, China Academy of Chinese Medical Sciences, Beijing, 100102, China
| | - Xu Wei
- Wangjing Hospital, China Academy of Chinese Medical Sciences, Beijing, 100102, China.
| | - Yili Zhang
- School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China.
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Tong YR, Chen K, Jiang ZQ, Tu LC, Luo YF, Zheng H, Zhao YQ, Shen SY, Hu YT, Gao W. Spatiotemporal expression analysis of jasmonic acid and saponin-related genes uncovers a potential biosynthetic regulation in Panax notoginseng. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024. [PMID: 39118479 DOI: 10.1002/jsfa.13800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 07/06/2024] [Accepted: 07/15/2024] [Indexed: 08/10/2024]
Abstract
BACKGROUND Sanqi, the root of Panax notoginseng, has long been recognized for its therapeutic effects on cardiovascular diseases. Saponins, including ginsenosides and notoginsenosides, are the main bioactive components of P. notoginseng. The biosynthesis of saponins is closely related to the defense responses orchestrated by endogenous hormones. RESULTS To provide new insights into the underlying role of phytohormone jasmonic acid (JA) in the synthesis and regulation of saponins, we performed an ultra-performance liquid chromatography analysis of different tissues of P. notoginseng aged 2-4 years. Moreover, by combined evaluation of saponin content and transcriptome profiling of each tissue, the spatial and temporal distribution of saponins was analyzed. N notoginsenoside R1, ginsenoside Rb1 and ginsenoside Rd accumulated in the underground tissues, including the root, tuqi, fibril and rhizome. In agreement with this data, the corresponding genes of the endogenous hormone JAs, especially coronatine insensitive 1 (COI1) and myelocytomatosis proteins 2 (MYC2), were predominantly expressed in the underground tissues. The tissue- and age-specific distribution of saponins was consistent with the expression of genes involved in JA biosynthetic, metabolic and signaling pathways. CONCLUSION The present study has revealed the temporal and spatial effects of endogenous phtohormones in the synthesis and regulation of notoginsenosides, which will provide a significant impact on improving the ecological planting technology, cultivating new high-quality varieties and protecting the rare resources of medicinal P. notoginseng. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Yu-Ru Tong
- School of Pharmaceutical Sciences, Capital Medical University, Beijing, China
| | - Kang Chen
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijng, China
| | - Zhou-Qian Jiang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Li-Chan Tu
- School of Medicine, Zhejiang University City College, Hangzhou, China
| | - Yun-Feng Luo
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Han Zheng
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijng, China
| | - Ya-Qiu Zhao
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijng, China
| | - Si-Yu Shen
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Ya-Ting Hu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijng, China
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Wei Gao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
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Mao G, Xu W, Wan L, Wang H, Xu S, Zhang L, Li S, Zhang J, Lai Z, Lan Y, Liu J. Unveiling the bioinformatic genes and their involved regulatory mechanisms in type 2 diabetes combined with osteoarthritis. Front Immunol 2024; 15:1353915. [PMID: 39176085 PMCID: PMC11338775 DOI: 10.3389/fimmu.2024.1353915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 07/24/2024] [Indexed: 08/24/2024] Open
Abstract
Background Type 2 Diabetes Mellitus (T2D) and Osteoarthritis (OA) are both prevalent diseases that significantly impact the health of patients. Increasing evidence suggests that there is a big correlation between T2D and OA, but the molecular mechanisms remain elusive. The aims of this study are to investigate the shared biomarkers and potential molecular mechanisms in T2D combined with OA. Methods T2D and OA-related differentially expressed genes (DEGs) were identified via bioinformatic analysis on Gene Expression Omnibus (GEO) datasets GSE26168 and GSE114007 respectively. Subsequently, extensive target prediction and network analysis were finished with Gene Ontology (GO), protein-protein interaction (PPI), and pathway enrichment with DEGs. The transcription factors (TFs) and miRNAs coupled in co-expressed DEGs involved in T2D and OA were predicted as well. The key genes expressed both in the clinical tissues of T2D and OA were detected with western blot and qRT-PCR assay. Finally, the most promising candidate compounds were predicted with the Drug-Gene Interaction Database (DGIdb) and molecular docking. Results In this study, 209 shared DEGs between T2D and OA were identified. Functional analysis disclosed that these DEGs are predominantly related to ossification, regulation of leukocyte migration, extracellular matrix (ECM) structural constituents, PI3K/AKT, and Wnt signaling pathways. Further analysis via Protein-Protein Interaction (PPI) analysis and validation with external datasets emphasized MMP9 and ANGPTL4 as crucial genes in both T2D and OA. Our findings were validated through qRT-PCR and Western blot analyses, which indicated high expression levels of these pivotal genes in T2D, OA, and T2D combined with OA cases. Additionally, the analysis of Transcription Factors (TFs)-miRNA interactions identified 7 TFs and one miRNA that jointly regulate these important genes. The Receiver Operating characteristic (ROC) analysis demonstrated the significant diagnostic potential of MMP9 and ANGPTL4.Moreover, we identified raloxifene, ezetimibe, and S-3304 as promising agents for patients with both T2D and OA. Conclusion This study uncovers the shared signaling pathways, biomarkers, potential therapeutics, and diagnostic models for individuals suffering from both T2D and OA. These findings not only present novel perspectives on the complex interplay between T2D and OA but also hold significant promise for improving the clinical management and prognosis of patients with this concurrent condition.
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Affiliation(s)
- Guangming Mao
- Department of Pharmacy, Panzhihua Central Hospital, Panzhihua, China
| | - Wenhao Xu
- Department of Pharmacy, Panzhihua Central Hospital, Panzhihua, China
| | - Lingli Wan
- Department of Pharmacy, Panzhihua Central Hospital, Panzhihua, China
| | - Hongpin Wang
- Department of Pharmacy, Panzhihua Central Hospital, Panzhihua, China
| | - Shutao Xu
- Department of Pharmacy, Panzhihua Central Hospital, Panzhihua, China
| | - Liangming Zhang
- Department of Pharmacy, Panzhihua Central Hospital, Panzhihua, China
| | - Shiyang Li
- Department of Pharmacy, Panzhihua Central Hospital, Panzhihua, China
- Department of Pharmacy, Dali University, Dali, China
| | - Jifa Zhang
- Department of Pharmacy, Panzhihua Central Hospital, Panzhihua, China
| | - Zhongming Lai
- Department of Pharmacy, Panzhihua Central Hospital, Panzhihua, China
| | - Yuping Lan
- Department of Pharmacy, Panzhihua Central Hospital, Panzhihua, China
| | - Jianhui Liu
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
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Luo C, Li Z, Shi Y, Gao Y, Xu Y, Zhang Y, Chu H. Arbuscular mycorrhizal fungi enhance drought resistance in Bombax ceiba by regulating SOD family genes. PeerJ 2024; 12:e17849. [PMID: 39131625 PMCID: PMC11316461 DOI: 10.7717/peerj.17849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 07/10/2024] [Indexed: 08/13/2024] Open
Abstract
The physiological activity facilitated by arbuscular mycorrhizal fungi (AMF) contributes to plants' ability to tolerate drought. Nevertheless, it is unclear if AMF colonization affects the expression of genes in the host plant that encode antioxidant enzymes in the superoxide dismutase (SOD) family, which help alleviate drought stress in plants. Here, we conducted a pot trial to determine whether colonization by the AMF Rhizophagus irregularis improves drought resistance in Bombax ceiba. We comprehensively analyzed the SOD gene family and evaluated genome-wide expression patterns of SODs and SOD activity in AMF-colonized and non-mycorrhizal plants under simulated drought. We identified a total of 13 SODs in the genome of B. ceiba, including three FeSODs (BcFSDs), three MnSODs (BcMSDs), and seven Cu/ZnSODs (BcCSDs). Phylogenetic analysis based on binding domain revealed that SOD genes from B. ceiba and various other plant species can be divided into three separate groups, showing significant bootstrap values. Our examination of gene composition and patterns suggests that most BcSOD genes in these three subgroups are significantly conserved. Additionally, it was noted that hormones and stress-responsive cis-regulatory elements were found in all BcSOD promoters. Expression profiling by qRT-PCR demonstrated that AMF increased relative expression levels of Cu/Zn-SODs in both roots and shoots under drought stress, except for BcCSD3 in roots. Furthermore, AMF colonization increased the relative expression of BcMSD1a and BcMSD1b in roots, augmenting SOD activities and increasing ROS scavenging during drought. In general, this work offers molecular evidence in support of the beneficial effect of AMF colonization on drought tolerance in B. ceiba. It also elucidates the expression patterns of SOD genes, which will support efforts to optimize mycorrhizal seedling cultivation under stressful conditions.
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Affiliation(s)
- Changxin Luo
- College of Biological Resource and Food Engineering, Center for Yunnan Plateau Biological Resources Protection and Utilization, Qujing Normal University, Qujing, Yunnan, China
| | - Zhumei Li
- College of Biological Resource and Food Engineering, Center for Yunnan Plateau Biological Resources Protection and Utilization, Qujing Normal University, Qujing, Yunnan, China
| | - Yumei Shi
- College of Biological Resource and Food Engineering, Center for Yunnan Plateau Biological Resources Protection and Utilization, Qujing Normal University, Qujing, Yunnan, China
| | - Yong Gao
- College of Biological Resource and Food Engineering, Center for Yunnan Plateau Biological Resources Protection and Utilization, Qujing Normal University, Qujing, Yunnan, China
| | - Yanguo Xu
- College of Biological Resource and Food Engineering, Center for Yunnan Plateau Biological Resources Protection and Utilization, Qujing Normal University, Qujing, Yunnan, China
| | - Yanan Zhang
- College of Biological Resource and Food Engineering, Center for Yunnan Plateau Biological Resources Protection and Utilization, Qujing Normal University, Qujing, Yunnan, China
| | - Honglong Chu
- College of Biological Resource and Food Engineering, Center for Yunnan Plateau Biological Resources Protection and Utilization, Qujing Normal University, Qujing, Yunnan, China
- Qujing Normal University, Key Laboratory of Yunnan Provincial Department of Education of the Deep-Time Evolution on Biodiversity from the Origin of the Pearl River, Qujing, Yunnan, China
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Clark AJ, Lillard JW. A Comprehensive Review of Bioinformatics Tools for Genomic Biomarker Discovery Driving Precision Oncology. Genes (Basel) 2024; 15:1036. [PMID: 39202397 PMCID: PMC11353282 DOI: 10.3390/genes15081036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 07/25/2024] [Accepted: 07/30/2024] [Indexed: 09/03/2024] Open
Abstract
The rapid advancement of high-throughput technologies, particularly next-generation sequencing (NGS), has revolutionized cancer research by enabling the investigation of genetic variations such as SNPs, copy number variations, gene expression, and protein levels. These technologies have elevated the significance of precision oncology, creating a demand for biomarker identification and validation. This review explores the complex interplay of oncology, cancer biology, and bioinformatics tools, highlighting the challenges in statistical learning, experimental validation, data processing, and quality control that underpin this transformative field. This review outlines the methodologies and applications of bioinformatics tools in cancer genomics research, encompassing tools for data structuring, pathway analysis, network analysis, tools for analyzing biomarker signatures, somatic variant interpretation, genomic data analysis, and visualization tools. Open-source tools and repositories like The Cancer Genome Atlas (TCGA), Genomic Data Commons (GDC), cBioPortal, UCSC Genome Browser, Array Express, and Gene Expression Omnibus (GEO) have emerged to streamline cancer omics data analysis. Bioinformatics has significantly impacted cancer research, uncovering novel biomarkers, driver mutations, oncogenic pathways, and therapeutic targets. Integrating multi-omics data, network analysis, and advanced ML will be pivotal in future biomarker discovery and patient prognosis prediction.
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Affiliation(s)
| | - James W. Lillard
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA 30310, USA;
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Yu T, Chen JM, Liu W, Zhao JQ, Li P, Liu FJ, Jiang Y, Li HJ. In-depth characterization of cycloartane triterpenoids and discovery of species-specific markers from three Cimicifuga species guided by a strategy that integrates in-source fragment elimination, diagnostic ion recognition, and feature-based molecular networking. J Chromatogr A 2024; 1728:465015. [PMID: 38821032 DOI: 10.1016/j.chroma.2024.465015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/13/2024] [Accepted: 05/21/2024] [Indexed: 06/02/2024]
Abstract
Characterization studies of the plant metabolome are crucial for revealing plant physiology, developing functional foods, and controlling quality. Mass spectrometry-based metabolite profiling allows unprecedented qualitative coverage of complex biological extract composition. However, the electrospray ionization used in metabolite profiling generates multiple artifactual signals for a single analyte, which makes it challenging to filter out redundant signals and organize the signals corresponding to abundant constituents. This study proposed a strategy integrating in-source fragments elimination, diagnostic ions recognition, and feature-based molecular networking (ISFE-DIR-FBMN) to simultaneously characterize cycloartane triterpenoids (CTs) from three medicinal Cimicifuga species. The results showed that 63.1 % of the measured ions were redundant. A total of 184 CTs were annotated, with 27.1 % being reported for the first time. It presents a promising approach to assess the composition of natural extracts, thus facilitating new ingredient registrations or natural-extracts-based drug discovery campaigns. Besides, chemometrics analysis of the three Cimicifuga species identified 32 species-specific markers, highlighting significant differences among them. The valuable information can enhance the sustainable utilization and further development of Cimicifuga resources. The codes involved in ISFE-DIR-FBMN are freely available on GitHub (https://github.com/LHJ-Group/ISFE-DIR-FBMN.git).
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Affiliation(s)
- Ting Yu
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Jia-Min Chen
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Wei Liu
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Jin-Quan Zhao
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Ping Li
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Feng-Jie Liu
- Key Laboratory of Pharmaceutical Quality Control of Hebei Province, College of Pharmaceutical Science, Hebei University, Baoding 071002, China.
| | - Yan Jiang
- College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China.
| | - Hui-Jun Li
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China.
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Li J, Yang M, He D, Luo Z, Li B, Huang X, Wu F, Xie G, Fan C, Sun W, Yu S, Wang L. Genome-wide association study of stem structural characteristics that extracted by a high-throughput phenotypic analysis "LabelmeP rice" in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:2080-2095. [PMID: 38860937 DOI: 10.1111/tpj.16872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/12/2024] [Accepted: 05/27/2024] [Indexed: 06/12/2024]
Abstract
Stem is important for assimilating transport and plant strength; however, less is known about the genetic basis of its structural characteristics. In this study, a high-throughput method, "LabelmeP rice" was developed to generate 14 traits related to stem regions and vascular bundles, which allows the establishment of a stem cross-section phenotype dataset containing anatomical information of 1738 images from hand-cut transections of stems collected from 387 rice germplasm accessions grown over two successive seasons. Then, the phenotypic diversity of the rice accessions was evaluated. Genome-wide association studies identified 94, 83, and 66 significant single nucleotide polymorphisms (SNPs) for the assayed traits in 2 years and their best linear unbiased estimates, respectively. These SNPs can be integrated into 29 quantitative trait loci (QTL), and 11 of them were common in 2 years, while correlated traits shared 19. In addition, 173 candidate genes were identified, and six located at significant SNPs were repeatedly detected and annotated with a potential function in stem development. By using three introgression lines (chromosome segment substitution lines), four of the 29 QTLs were validated. LOC_Os01g70200, located on the QTL uq1.4, is detected for the area of small vascular bundles (SVB) and the rate of large vascular bundles number to SVB number. Besides, the CRISPR/Cas9 editing approach has elucidated the function of the candidate gene LOC_Os06g46340 in stem development. In conclusion, the results present a time- and cost-effective method that provides convenience for extracting rice stem anatomical traits and the candidate genes/QTL, which would help improve rice.
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Affiliation(s)
- Jianguo Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mingchong Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Dandan He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Zixuan Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Bo Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Xiaojin Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Fangxi Wu
- Fujian Academy of Agricultural Sciences, Fujian, China
| | - Guosheng Xie
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenqiang Sun
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Sibin Yu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lingqiang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
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Tao M, Chen J, Cui C, Xu Y, Xu J, Shi Z, Yun J, Zhang J, Ou GZ, Liu C, Chen Y, Zhu ZR, Pan R, Xu S, Chen XX, Rokas A, Zhao Y, Wang S, Huang J, Shen XX. Identification of a longevity gene through evolutionary rate covariation of insect mito-nuclear genomes. NATURE AGING 2024; 4:1076-1088. [PMID: 38834883 DOI: 10.1038/s43587-024-00641-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 05/02/2024] [Indexed: 06/06/2024]
Abstract
Oxidative phosphorylation, essential for energy metabolism and linked to the regulation of longevity, involves mitochondrial and nuclear genes. The functions of these genes and their evolutionary rate covariation (ERC) have been extensively studied, but little is known about whether other nuclear genes not targeted to mitochondria evolutionarily and functionally interact with mitochondrial genes. Here we systematically examined the ERC of mitochondrial and nuclear benchmarking universal single-copy ortholog (BUSCO) genes from 472 insects, identifying 75 non-mitochondria-targeted nuclear genes. We found that the uncharacterized gene CG11837-a putative ortholog of human DIMT1-regulates insect lifespan, as its knockdown reduces median lifespan in five diverse insect species and Caenorhabditis elegans, whereas its overexpression extends median lifespans in fruit flies and C. elegans and enhances oxidative phosphorylation gene activity. Additionally, DIMT1 overexpression protects human cells from cellular senescence. Together, these data provide insights into the ERC of mito-nuclear genes and suggest that CG11837 may regulate longevity across animals.
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Affiliation(s)
- Mei Tao
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, China
- Centre for Evolutionary and Organismal Biology, Zhejiang University, Hangzhou, China
| | - Jiani Chen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Chunlai Cui
- New Cornerstone Science Laboratory, CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yandong Xu
- Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Lab of Genetic and Developmental Disorders, Hangzhou, China
| | - Jingxiu Xu
- Zhejiang University School of Medicine, Hangzhou, China
| | - Zheyi Shi
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Jiaqi Yun
- New Cornerstone Science Laboratory, CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Junwei Zhang
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Guo-Zheng Ou
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Chao Liu
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yun Chen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zeng-Rong Zhu
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Ronghui Pan
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Suhong Xu
- Zhejiang University School of Medicine, Hangzhou, China
| | - Xue-Xin Chen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Antonis Rokas
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA
| | - Yang Zhao
- Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Lab of Genetic and Developmental Disorders, Hangzhou, China
| | - Sibao Wang
- New Cornerstone Science Laboratory, CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
| | - Jianhua Huang
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
| | - Xing-Xing Shen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, China.
- Centre for Evolutionary and Organismal Biology, Zhejiang University, Hangzhou, China.
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Hao H, Ren X, Ma Z, Chen Z, Yang K, Wang Q, Liu S. Comprehensive analysis of the differential expression of mRNAs, lncRNAs, and miRNAs in Zi goose testis with high and low sperm mobility. Poult Sci 2024; 103:103895. [PMID: 38917609 PMCID: PMC11255893 DOI: 10.1016/j.psj.2024.103895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/20/2024] [Accepted: 05/20/2024] [Indexed: 06/27/2024] Open
Abstract
Sperm mobility (SM) is an objective index for measuring sperm motility; however, the mechanisms underlying its regulation in geese remain unclear. The present study sought to elucidate the genetic mechanism underlying SM traits in Zi geese (Anser cygnoides L.). To this end, three successive experiments were performed. In Experiment I, SM was determined in 40 ganders; the 3 ganders with the highest mobility and three with the lowest mobility were assigned to the high and low sperm mobility rank (SMR) groups, respectively. In Experiment II, the differences in fertility between the two SMR groups were assessed within two breeding flocks comprising the selected six ganders from Experiment I and 30 females (each flock had 3 ganders and 15 females). In Experiment III, the testes of the 6 ganders were harvested for histological observation and whole-transcriptome sequencing. Results revealed better fertility, well-developed seminiferous tubules, and abundant mature sperm in the high-SMR-flock compared to those of the low-SMR-flock (89 vs. 81%) (P < 0.05). Differential expression (DE) analysis identified 76 mRNAs, 344 lncRNAs, and 17 miRNAs between the SMR groups, with LOC106049708, XPNPEP3, GNB3, ADCY8, PRKAG3, oha-miR-182-5p, and ocu-miR-10b-5p identified as key mRNAs and miRNAs contributing to SM. Enrichment analysis implicated these DE RNAs in pathways related to ATP binding, cell metabolism, apelin signaling, Wnt signaling, and Adherens junctions. Additionally, competing endogenous RNA (ceRNA) networks comprising 9 DE mRNAs, 17 DE miRNAs, and 169 DE lncRNAs were constructed. Two ceRNA network pathways (LOC106049708-oha-miR-182-5p-MSTRG.2479.6 and PRKAG3-ocu-miR-10b-5p-MSTRG.9047.14) were identified as key regulators of SM in geese. These findings offer crucial insights into the identification of key genes and ceRNA pathways influencing sperm mobility in geese.
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Affiliation(s)
- Hongrun Hao
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, PR China; Key Laboratory of Exploration and Innovative Utilization of White Goose Germplasm Resources in the Cold Region of Heilongjiang Province, Daqing 163319, PR China
| | - Xiaofang Ren
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, PR China; Key Laboratory of Exploration and Innovative Utilization of White Goose Germplasm Resources in the Cold Region of Heilongjiang Province, Daqing 163319, PR China
| | - Zhigang Ma
- Heilongjiang Academy of Agricultural Sciences, Animal Husbandry Research Institute, Qiqihar 161000, PR China
| | - Zhifeng Chen
- Heilongjiang Academy of Agricultural Sciences, Animal Husbandry Research Institute, Qiqihar 161000, PR China
| | - Kun Yang
- Heilongjiang Academy of Agricultural Sciences, Animal Husbandry Research Institute, Qiqihar 161000, PR China
| | - Qiuju Wang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, PR China; Key Laboratory of Exploration and Innovative Utilization of White Goose Germplasm Resources in the Cold Region of Heilongjiang Province, Daqing 163319, PR China
| | - Shengjun Liu
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, PR China; Key Laboratory of Exploration and Innovative Utilization of White Goose Germplasm Resources in the Cold Region of Heilongjiang Province, Daqing 163319, PR China.
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49
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Ravindranath BS, Ananya G, Hema Kumar C, Ramirez DC, Gomez Mejiba SE. Computational prediction of crucial genes involved in gonorrhea infection and neoplastic cell transformation: A multiomics approach. Microb Pathog 2024; 193:106770. [PMID: 38960215 DOI: 10.1016/j.micpath.2024.106770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 04/24/2024] [Accepted: 06/29/2024] [Indexed: 07/05/2024]
Abstract
Neisseria gonorrheae, the causative agent of genitourinary infections, has been associated with asymptomatic or recurrent infections and has the potential to form biofilms and induce inflammation and cell transformation. Herein, we aimed to use computational analysis to predict novel associations between chronic inflammation caused by gonorrhea infection and neoplastic transformation. Prioritization and gene enrichment strategies based on virulence and resistance genes utilizing essential genes from the DEG and PANTHER databases, respectively, were performed. Using the STRING database, protein‒protein interaction networks were constructed with 55 nodes of bacterial proteins and 72 nodes of proteins involved in the host immune response. MCODE and cytoHubba were used to identify 12 bacterial hub proteins (murA, murB, murC, murD, murE, purN, purL, thyA, uvrB, kdsB, lpxC, and ftsH) and 19 human hub proteins, of which TNF, STAT3 and AKT1 had high significance. The PPI networks are based on the connectivity degree (K), betweenness centrality (BC), and closeness centrality (CC) values. Hub genes are vital for cell survival and growth, and their significance as potential drug targets is discussed. This computational study provides a comprehensive understanding of inflammation and carcinogenesis pathways that are activated during gonorrhea infection.
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Affiliation(s)
- B S Ravindranath
- Manipal Institute of Technology, Manipal Academy of Higher Education (MAHE), Manipal, 576104, Karnataka, India.
| | - G Ananya
- Manipal School of Life Sciences, Manipal Academy of Higher Education (MAHE), Manipal, 576104, Karnataka, India
| | - C Hema Kumar
- Department of Biotechnology, Dayananda Sagar College of Engineering, Shavige Malleshwara Hills, Kumaraswamy Layout, Bangalore, 560111, Karnataka, India
| | - D C Ramirez
- Laboratory of Experimental and Translational Medicine, CCT-San Luis-National University of San Luis, San Luis, 5700, San Luis, Argentina.
| | - S E Gomez Mejiba
- Laboratory of Nutrition and Experimental Therapeutics, CCT-San Luis-National University of San Luis, San Luis, 5700, San Luis, Argentina.
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50
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Saranya G, Viswanathan P. Identification of renal protective gut microbiome derived-metabolites in diabetic chronic kidney disease: An integrated approach using network pharmacology and molecular docking. Saudi J Biol Sci 2024; 31:104028. [PMID: 38854894 PMCID: PMC11154206 DOI: 10.1016/j.sjbs.2024.104028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/14/2024] [Accepted: 05/19/2024] [Indexed: 06/11/2024] Open
Abstract
Metabolites from the gut microbiota define molecules in the gut-kidney cross talks. However, the mechanistic pathway by which the kidneys actively sense gut metabolites and their impact on diabetic chronic kidney disease (DCKD) remains unclear. This study is an attempt to investigate the gut microbiome metabolites, their host targeting genes, and their mechanistic action against DCKD. Gut microbiome, metabolites, and host targets were extracted from the gutMgene database and metabolites from the PubChem database. DCKD targets were identified from DisGeNET, GeneCard, NCBI, and OMIM databases. Computational examination such as protein-protein interaction networks, enrichment pathway, identification of metabolites for potential targets using molecular docking, hubgene-microbes-metabolite-samplesource-substrate (HMMSS) network architecture were executed using Network analyst, ShinyGo, GeneMania, Cytoscape, Autodock tools. There were 574 microbial metabolites, 2861 DCKD targets, and 222 microbes targeting host genes. After screening, we obtained 27 final targets, which are used for computational examination. From enrichment analysis, we found NF-ΚB1, AKT1, EGFR, JUN, and RELA as the main regulators in the DCKD development through mitogen activated protein kinase (MAPK) pathway signalling. The (HMMSS) network analysis found F.prausnitzi, B.adolescentis, and B.distasonis probiotic bacteria that are found in the intestinal epithelium, colonic region, metabolize the substrates like tryptophan, other unknown substrates might have direct interaction with the NF-kB1 and epidermal growth factor receptor (EGFR) targets. On docking of these target proteins with 3- Indole propionic acid (IPA) showed high binding energy affinity of -5.9 kcal/mol and -7.4kcal/mol. From this study we identified, the 3 IPA produced by F. prausnitzi A2-165 was found to have renal sensing properties inhibiting MAPK/NF-KB1 inflammatory pathway and would be useful in treating CKD in diabetics.
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Affiliation(s)
- G.R. Saranya
- Renal Research Lab, Pearl Research Park, School of Bioscience and Technology, Vellore Institute of Technology, Vellore 632 014, Tamil Nadu, India
| | - Pragasam Viswanathan
- Renal Research Lab, Pearl Research Park, School of Bioscience and Technology, Vellore Institute of Technology, Vellore 632 014, Tamil Nadu, India
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