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Wang Y, Zhang X, Biverstål H, Bazan NG, Tan S, Li N, Ohshima M, Schultzberg M, Li X. Pro-resolving lipid mediator reduces amyloid-β42-induced gene expression in human monocyte-derived microglia. Neural Regen Res 2025; 20:873-886. [PMID: 38886959 DOI: 10.4103/nrr.nrr-d-23-01688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 05/06/2024] [Indexed: 06/20/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202503000-00031/figure1/v/2024-06-17T092413Z/r/image-tiff Specialized pro-resolving lipid mediators including maresin 1 mediate resolution but the levels of these are reduced in Alzheimer's disease brain, suggesting that they constitute a novel target for the treatment of Alzheimer's disease to prevent/stop inflammation and combat disease pathology. Therefore, it is important to clarify whether they counteract the expression of genes and proteins induced by amyloid-β. With this objective, we analyzed the relevance of human monocyte-derived microglia for in vitro modeling of neuroinflammation and its resolution in the context of Alzheimer's disease and investigated the pro-resolving bioactivity of maresin 1 on amyloid-β42-induced Alzheimer's disease-like inflammation. Analysis of RNA-sequencing data and secreted proteins in supernatants from the monocyte-derived microglia showed that the monocyte-derived microglia resembled Alzheimer's disease-like neuroinflammation in human brain microglia after incubation with amyloid-β42. Maresin 1 restored homeostasis by down-regulating inflammatory pathway related gene expression induced by amyloid-β42 in monocyte-derived microglia, protection of maresin 1 against the effects of amyloid-β42 is mediated by a re-balancing of inflammatory transcriptional networks in which modulation of gene transcription in the nuclear factor-kappa B pathway plays a major part. We pinpointed molecular targets that are associated with both neuroinflammation in Alzheimer's disease and therapeutic targets by maresin 1. In conclusion, monocyte-derived microglia represent a relevant in vitro microglial model for studies on Alzheimer's disease-like inflammation and drug response for individual patients. Maresin 1 ameliorates amyloid-β42-induced changes in several genes of importance in Alzheimer's disease, highlighting its potential as a therapeutic target for Alzheimer's disease.
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Affiliation(s)
- Ying Wang
- Department of Neurobiology, Care Sciences & Society, Division of Neurogeriatrics, Karolinska Institutet, Stockholm, Sweden
- Department of Neurology, Neuroscience Center, The First Hospital of Jilin University, Changchun, Jilin Province, China
| | - Xiang Zhang
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Henrik Biverstål
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Nicolas G Bazan
- Neuroscience Center of Excellence, Louisiana State University, New Orleans, LA, USA
| | - Shuai Tan
- Department of Medicine, Solna, Clinical Pharmacology Group, Karolinska University Hospital, Stockholm, Sweden
| | - Nailin Li
- Department of Medicine, Solna, Clinical Pharmacology Group, Karolinska University Hospital, Stockholm, Sweden
| | - Makiko Ohshima
- Department of Neurobiology, Care Sciences & Society, Division of Neurogeriatrics, Karolinska Institutet, Stockholm, Sweden
| | - Marianne Schultzberg
- Department of Neurobiology, Care Sciences & Society, Division of Neurogeriatrics, Karolinska Institutet, Stockholm, Sweden
| | - Xiaofei Li
- Department of Neurobiology, Care Sciences & Society, Division of Neurogeriatrics, Karolinska Institutet, Stockholm, Sweden
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Yang Y, Shen J, Deng P, Chen P. Mechanism investigation of Forsythoside A against esophageal squamous cell carcinoma in vitro and in vivo. Cancer Biol Ther 2024; 25:2380023. [PMID: 39046082 PMCID: PMC11271126 DOI: 10.1080/15384047.2024.2380023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 06/21/2024] [Accepted: 07/10/2024] [Indexed: 07/25/2024] Open
Abstract
CONTEXT Forsythoside A (FSA) was extracted from Forsythia suspensa, a traditional Chinese medicine, which has been demonstrated to exert anti-inflammatory, antibacterial, and other pharmacological effects. However, the anticancer effect of FSA in esophageal squamous cell carcinoma (ESCC) has not been documented. OBJECTIVE The present study aimed to elucidate the mechanism of FSA against ESCC. MATERIALS AND METHODS Network pharmacology and molecular docking were employed to predict the mechanism. FSA was utilized to treat ESCC cell lines KYSE450 and KYSE30, followed by CCK-8 assay, cell cloning formation assay, flow cytometry, Western blot, RNA-seq analysis, and subsequent in vivo experiments. RESULTS Network pharmacology and molecular docking predicted that the therapeutic effect of FSA in ESCC is mediated through proteins such as BCL2 and BAX, influencing KEGG pathways associated with apoptosis. In vitro experiments showed that FSA inhibited cell proliferation and plate clone formation, promoted cell apoptosis and impacted the cell cycle distribution of G2/M phase by regulating BCL2, BAX, and p21. Further RNA-seq in KYSE450 cells showed that FSA regulated the expression of 223 genes, specifically affecting the biological process of epidermal development. In vivo experiments showed that gastric administration of FSA resulted in notable reductions in both tumor volume and weight by regulating BCL2, BAX, and p21. 16S rRNA sequencing showed that FSA led to significant changes of beta diversity. Abundance of 11 specific bacterial taxa were considerably changed following administration of FSA. CONCLUSIONS This study presents a novel candidate drug against ESCC and establishes a foundation for future clinical application.
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Affiliation(s)
- Yingying Yang
- School of Life Sciences, Zhengzhou Normal University, Zhengzhou, People’s Republic of China
| | - Junru Shen
- School of Life Sciences, Zhengzhou Normal University, Zhengzhou, People’s Republic of China
| | - Peiyuan Deng
- School of Life Sciences, Zhengzhou Normal University, Zhengzhou, People’s Republic of China
| | - Ping Chen
- Academy of Medical Sciences, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, People’s Republic of China
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Liao W, Liu T, Li Y, Liang H, Deng J, Shen F. The bioinfomatics analysis of the M1 macrophage-related gene CXCL9 signature in cervical cancer. J OBSTET GYNAECOL 2024; 44:2373951. [PMID: 38963237 DOI: 10.1080/01443615.2024.2373951] [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: 07/05/2023] [Accepted: 06/24/2024] [Indexed: 07/05/2024]
Abstract
BACKGROUND The expression and function of coexpression genes of M1 macrophage in cervical cancer have not been identified. And the CXCL9-expressing tumour-associated macrophage has been poorly reported in cervical cancer. METHODS To clarify the regulatory gene network of M1 macrophage in cervical cancer, we downloaded gene expression profiles of cervical cancer patients in TCGA database to identify M1 macrophage coexpression genes. Then we constructed the protein-protein interaction networks by STRING database and performed functional enrichment analysis to investigate the biological effects of the coexpression genes. Next, we used multiple bioinformatics databases and experiments to overall investigate coexpression gene CXCL9, including western blot assay and immunohistochemistry assay, GeneMANIA, Kaplan-Meier Plotter, Xenashiny, TISCH2, ACLBI, HPA, TISIDB, GSCA and cBioPortal databases. RESULTS There were 77 positive coexpression genes and 5 negative coexpression genes in M1 macrophage. The coexpression genes in M1 macrophage participated in the production and function of chemokines and chemokine receptors. Especially, CXCL9 was positively correlated with M1 macrophage infiltration levels in cervical cancer. CXCL9 expression would significantly decrease and high CXCL9 levels were linked to good prognosis in the cervical cancer tumour patients, it manifestly expressed in blood immune cells, and was positively related to immune checkpoints. CXCL9 amplification was the most common type of mutation. The CXCL9 gene interaction network could regulate immune-related signalling pathways, and CXCL9 amplification was the most common mutation type in cervical cancer. Meanwhile, CXCL9 may had clinical significance for the drug response in cervical cancer, possibly mediating resistance to chemotherapy and targeted drug therapy. CONCLUSION Our findings may provide new insight into the M1 macrophage coexpression gene network and molecular mechanisms in cervical cancer, and indicated that M1 macrophage association gene CXCL9 may serve as a good prognostic gene and a potential therapeutic target for cervical cancer therapies.
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Affiliation(s)
- Wenxin Liao
- Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China
| | - Tingting Liu
- Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China
| | - Yang Li
- Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China
| | - Hua Liang
- Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China
| | - Juexiao Deng
- Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China
| | - Fujin Shen
- Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China
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Ji Y, Xiao Y, Li S, Fan Y, Cai Y, Yang B, Chen H, Hu S. Protective effect and mechanism of Xiaoyu Xiezhuo decoction on ischemia-reperfusion induced acute kidney injury based on gut-kidney crosstalk. Ren Fail 2024; 46:2365982. [PMID: 39010816 DOI: 10.1080/0886022x.2024.2365982] [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: 02/07/2024] [Accepted: 06/04/2024] [Indexed: 07/17/2024] Open
Abstract
This study aimed to explore the mechanism of Xiaoyu Xiezhuo decoction (XXD) on ischemia-reperfusion-induced acute kidney injury (IRI-AKI) using network pharmacology methods and gut microbiota analysis. A total of 1778 AKI-related targets were obtained, including 140 targets possibly regulated by AKI in XXD, indicating that the core targets were mainly enriched in inflammatory-related pathways, such as the IL-17 signaling pathway and TNF signaling pathway. The unilateral IRI-AKI animal model was established and randomly divided into four groups: the sham group, the AKI group, the sham + XXD group, and the AKI + XXD group. Compared with the rats in the AKI group, XXD improved not only renal function, urinary enzymes, and biomarkers of renal damage such as Kim-1, cystatin C, and serum inflammatory factors such as IL-17, TNF-α, IL-6, and IL 1-β, but also intestinal metabolites including lipopolysaccharides, d-lactic acid, indoxyl sulfate, p-cresyl sulfate, and short-chain fatty acids. XXD ameliorated renal and colonic pathological injury as well as inflammation and chemokine gene abundance, such as IL-17, TNF-α, IL-6, IL-1β, ICAM-1, and MCP-1, in AKI rats via the TLR4/NF-κB/NLRP3 pathway, reducing the AKI score, renal pathological damage, and improving the intestinal mucosa's inflammatory infiltration. It also repaired markers of the mucosal barrier, including claudin-1, occludin, and ZO-1. Compared with the rats in the AKI group, the α diversity was significantly increased, and the Chao1 index was significantly enhanced after XXD treatment in both the sham group and the AKI group. The treatment group significantly reversed this change in microbiota.
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Affiliation(s)
- Yue Ji
- Department of Nephrology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, PR China
- Institute of Nephrology & Beijing Key Laboratory, Dongzhimen Hospital, Beijing University of Traditional Chinese Medicine, Beijing, PR China
- Department of Nephrology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, PR China
| | - Yunming Xiao
- Department of Nephrology, Medical School of Chinese PLA, First Medical Center of Chinese PLA General Hospital, Nephrology Institute of the Chinese People's Liberation Army, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing, PR China
| | - Shipian Li
- Department of Nephrology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, PR China
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, PR China
| | - Yihua Fan
- Department of Rheumatism and Immunity, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, PR China
| | - Yuzi Cai
- Institute of Nephrology & Beijing Key Laboratory, Dongzhimen Hospital, Beijing University of Traditional Chinese Medicine, Beijing, PR China
| | - Bo Yang
- Department of Nephrology, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, PR China
| | - Hongbo Chen
- Department of Nephrology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, PR China
| | - Shouci Hu
- Department of Nephrology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, PR China
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Nayar G, Altman RB. Heterogeneous network approaches to protein pathway prediction. Comput Struct Biotechnol J 2024; 23:2727-2739. [PMID: 39035835 PMCID: PMC11260399 DOI: 10.1016/j.csbj.2024.06.022] [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: 03/01/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 07/23/2024] Open
Abstract
Understanding protein-protein interactions (PPIs) and the pathways they comprise is essential for comprehending cellular functions and their links to specific phenotypes. Despite the prevalence of molecular data generated by high-throughput sequencing technologies, a significant gap remains in translating this data into functional information regarding the series of interactions that underlie phenotypic differences. In this review, we present an in-depth analysis of heterogeneous network methodologies for modeling protein pathways, highlighting the critical role of integrating multifaceted biological data. It outlines the process of constructing these networks, from data representation to machine learning-driven predictions and evaluations. The work underscores the potential of heterogeneous networks in capturing the complexity of proteomic interactions, thereby offering enhanced accuracy in pathway prediction. This approach not only deepens our understanding of cellular processes but also opens up new possibilities in disease treatment and drug discovery by leveraging the predictive power of comprehensive proteomic data analysis.
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Affiliation(s)
- Gowri Nayar
- Department of Biomedical Data Science, Stanford University, United States
| | - Russ B. Altman
- Department of Biomedical Data Science, Stanford University, United States
- Department of Genetics, Stanford University, United States
- Department of Medicine, Stanford University, United States
- Department of Bioengineering, Stanford University, United States
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Podgrajsek R, Hodzic A, Stimpfel M, Kunej T, Peterlin B. Insight into the complexity of male infertility: a multi-omics review. Syst Biol Reprod Med 2024; 70:73-90. [PMID: 38517373 DOI: 10.1080/19396368.2024.2317804] [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: 07/20/2023] [Accepted: 02/06/2024] [Indexed: 03/23/2024]
Abstract
Male infertility is a reproductive disorder, accounting for 40-50% of infertility. Currently, in about 70% of infertile men, the cause remains unknown. With the introduction of novel omics and advancement in high-throughput technology, potential biomarkers are emerging. The main purpose of our work was to overview different aspects of omics approaches in association with idiopathic male infertility and highlight potential genes, transcripts, non-coding RNA, proteins, and metabolites worth further exploring. Using the Gene Ontology (GO) analysis, we aimed to compare enriched GO terms from each omics approach and determine their overlapping. A PubMed database screening for the literature published between February 2014 and June 2022 was performed using the keywords: male infertility in association with different omics approaches: genomics, epigenomics, transcriptomics, ncRNAomics, proteomics, and metabolomics. A GO enrichment analysis was performed using the Enrichr tool. We retrieved 281 global studies: 171 genomics (DNA level), 21 epigenomics (19 of methylation and two histone residue modifications), 15 transcriptomics, 31 non-coding RNA, 29 proteomics, two protein posttranslational modification, and 19 metabolomics studies. Gene ontology comparison showed that different omics approaches lead to the identification of different molecular factors and that the corresponding GO terms, obtained from different omics approaches, do not overlap to a larger extent. With the integration of novel omics levels into the research of idiopathic causes of male infertility, using multi-omic systems biology approaches, we will be closer to finding the potential biomarkers and consequently becoming aware of the entire spectrum of male infertility, their cause, prognosis, and potential treatment.
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Affiliation(s)
- Rebeka Podgrajsek
- Department of Human Reproduction, University Medical Center Ljubljana, Ljubljana, Slovenia
| | - Alenka Hodzic
- Clinical Institute of Genomic Medicine, University Medical Center Ljubljana, Ljubljana, Slovenia
- Faculty of Health Sciences, University of Novo mesto, Novo Mesto, Slovenia
| | - Martin Stimpfel
- Department of Human Reproduction, University Medical Center Ljubljana, Ljubljana, Slovenia
- Medical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Center Ljubljana, Ljubljana, Slovenia
- Medical Faculty, University of Ljubljana, Ljubljana, Slovenia
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Bai S, Cheng H, Li H, Bo P. Integrated bioinformatics analysis identifies autophagy-associated genes as candidate biomarkers and reveals the immune infiltration landscape in psoriasis. Autoimmunity 2024; 57:2259137. [PMID: 38439147 DOI: 10.1080/08916934.2023.2259137] [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: 02/01/2023] [Accepted: 09/10/2023] [Indexed: 03/06/2024]
Abstract
Autophagy is implicated in the pathogenesis of psoriasis. We aimed to identify autophagy-related biomarkers in psoriasis via an integrated bioinformatics approach. We downloaded the gene expression profiles of GSE30999 dataset, and the "limma" package was applied to identify differentially expressed genes (DEGs). Then, differentially expressed autophagy-related genes (DEARGs) were identified via integrating autophagy-related genes with DEGs. CytoHubba plugin was used for the identification of hub genes and verified by the GSE41662 dataset. Subsequently, a series of bioinformatics analyses were employed, including protein-protein interaction network, functional enrichment, spearman correlation, receiver operating characteristic, and immune infiltration analyses. One hundred and one DEARGs were identified, and seven DEARGs were identified as hub genes and verified using the GSE41662 dataset. These validated genes had good diagnostic value in distinguishing psoriasis lesions. Immune infiltration analysis indicated that ATG5, SQSTM1, EGFR, MAPK8, MAPK3, MYC, and PIK3C3 were correlated with infiltration of immune cells. Seven DEARGs, namely ATG5, SQSTM1, EGFR, MAPK8, MAPK3, MYC, and PIK3C3, may be involved in the pathogenesis of psoriasis, which expanded the understanding of the development of psoriasis and provided important clinical significance for treatment of this disease.
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Affiliation(s)
- Sixian Bai
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Hongyu Cheng
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Hao Li
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Peng Bo
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
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Qi X, Yang Q, Cai J, Wu J, Gao Y, Ruan Q, Shao L, Liu J, Zhou X, Zhang W, Jiang N, Wang S. Transcriptional profiling of human peripheral blood mononuclear cells in household contacts of pulmonary tuberculosis patients provides insights into mechanisms of Mycobacterium tuberculosis control and elimination. Emerg Microbes Infect 2024; 13:2295387. [PMID: 38088554 PMCID: PMC10763880 DOI: 10.1080/22221751.2023.2295387] [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: 07/16/2023] [Accepted: 12/12/2023] [Indexed: 12/31/2023]
Abstract
Household contacts (HHCs) of patients with active tuberculosis (ATB) are at higher risk of Mycobacterium tuberculosis (M. tuberculosis) infection. However, the immune factors responsible for different defense responses in HHCs are unknown. Hence, we aimed to evaluate transcriptome signatures in human peripheral blood mononuclear cells (PBMCs) of HHCs to aid risk stratification. We recruited 112 HHCs of ATB patients and followed them for 6 years. Among the HHCs, only 2 developed ATB, while the remaining HHCs were classified into three groups: (1) HHC-1 group (n = 23): HHCs with consistently positive T-SPOT.TB test, negative chest radiograph, and no clinical symptoms or evidence of ATB during the 6-year follow-up period; (2) HHC-2 group (n = 15): HHCs with an initial positive T-SPOT result that later became negative without evidence of ATB; (3) HHC-3 group (n = 14): HHCs with a consistently negative T-SPOT.TB test and no clinical or radiological evidence of ATB. HHC-2 and HHC-3 were combined as HHC-23 group for analysis. RNA sequencing (RNA-seq) in PBMCs, with and without purified protein derivative (PPD) stimulation, identified significant differences in gene signatures between HHC-1 and HHC-23. Gene ontology analysis revealed functions related to bacterial pathogens, leukocyte chemotaxis, and inflammatory and cytokine responses. Modules associated with clinical features in the HHC-23 group were linked to the IL-17 signaling pathway, ferroptosis, complement and coagulation cascades, and the TNF signaling pathway. Validation using real-time PCR confirmed key genes like ATG-7, CXCL-3, and TNFRSF1B associated with infection outcomes in HHCs. Our research enhances understanding of disease mechanisms in HHCs. HHCs with persistent latent tuberculosis infection (HHC-1) showed significantly different gene expression compared to HHCs with no M. tuberculosis infection (HHC-23). These findings can help identify HHCs at risk of developing ATB and guide targeted public health interventions.
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Affiliation(s)
- Xiao Qi
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, People’s Republic of China
| | - Qingluan Yang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, People’s Republic of China
| | - Jianpeng Cai
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, People’s Republic of China
- Department of Infectious Diseases, Jing'an District Central Hospital, Shanghai, People’s Republic of China
| | - Jing Wu
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, People’s Republic of China
| | - Yan Gao
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, People’s Republic of China
| | - Qiaoling Ruan
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, People’s Republic of China
| | - Lingyun Shao
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, People’s Republic of China
| | - Jun Liu
- Department of Laboratory medicine, Department of Infectious Diseases, Wuxi Fifth People’s Hospital Affiliated to Nanjing Medical University, Wuxi, People’s Republic of China
| | - Xueshi Zhou
- Department of Laboratory medicine, Department of Infectious Diseases, Wuxi Fifth People’s Hospital Affiliated to Nanjing Medical University, Wuxi, People’s Republic of China
| | - Wenhong Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, People’s Republic of China
- Shanghai Sci-Tech InnoCenter for Infection and Immunity, Shanghai, People’s Republic of China
| | - Ning Jiang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, People’s Republic of China
| | - Sen Wang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, People’s Republic of China
- Department of Laboratory medicine, Department of Infectious Diseases, Wuxi Fifth People’s Hospital Affiliated to Nanjing Medical University, Wuxi, People’s Republic of China
- Shanghai Sci-Tech InnoCenter for Infection and Immunity, Shanghai, People’s Republic of China
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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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10
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Sun Y, Zhu C, Huang L, Luo C, Ju P, Chen J. Identification of key modules in metabolic syndrome induced by second-generation antipsychotics based on co-expression network analysis. Comput Struct Biotechnol J 2024; 23:723-731. [PMID: 38292473 PMCID: PMC10826125 DOI: 10.1016/j.csbj.2024.01.003] [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: 10/08/2023] [Revised: 12/28/2023] [Accepted: 01/03/2024] [Indexed: 02/01/2024] Open
Abstract
Background Second-generation antipsychotics (SGAs) frequently cause metabolic syndrome (MetS), which raises the risk of heart disease, type 2 diabetes, morbid obesity, atherosclerosis, and hypertension. MetS also impairs cognitive function in patients with schizophrenia. However, the fundamental reasons of MetS caused by SGAs are not yet fully understood. Thus, we aimed to identify potential therapeutic targets for MetS induced by SGAs. Methods The serum biochemical parameters and the RNA-sequencing of peripheral blood mononuclear cells were measured in three groups (healthy controls and patients with schizophrenia with and without MetS taking SGAs). The study of the weighted gene co-expression network was utilized to pinpoint modules that were significantly connected to clinical markers. Results Statistical analysis showed significant differences in triglyceride and high-density lipoprotein among the three groups. The TNF signaling pathway, TGF-β signaling pathway, fatty acid metabolism, NF-kappa B signaling pathway, MAPK signaling pathway, and Toll-like receptor signaling pathway were the pathways that were primarily enriched in the two unique co-expression network modules that were found. Finally, five specific genes (TNF, CXCL8, IL1B, TIMP1, and ESR1) associated with metabolism and immunity pathways were identified. Conclusions This study indicated that SGAs differentially induced MetS of patients with schizophrenia through metabolic and inflammation-related pathways. Therefore, the potential side effects of drugs on inflammatory processes need to be considered when using SGAs for the treatment of schizophrenia.
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Affiliation(s)
- Ying Sun
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
| | - Cuizhen Zhu
- Affiliated Psychological Hospital of Anhui Medical University, Hefei, China
- Anhui Clinical Center for Mental and Psychological Diseases, Hefei Fourth People's Hospital, Hefei, Anhui, China
- Anhui Mental Health Center, Hefei, Anhui, China
| | - Lixuan Huang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chao Luo
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Peijun Ju
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
- Shanghai Institute of Traditional Chinese Medicine for Mental Health, Shanghai, China
| | - Jianhua Chen
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
- Shanghai Institute of Traditional Chinese Medicine for Mental Health, Shanghai, China
- Yueyang Hospital of Integrated Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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11
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Pan G, Chai L, Chen R, Yuan Q, Song Z, Feng W, Wei J, Yang Z, Zhang Y, Xie G, Yan A, Lv Q, Wang C, Zhao Y, Wang Y. Potential mechanism of Qinggong Shoutao pill alleviating age-associated memory decline based on integration strategy. PHARMACEUTICAL BIOLOGY 2024; 62:105-119. [PMID: 38145345 PMCID: PMC10763866 DOI: 10.1080/13880209.2023.2291689] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 11/30/2023] [Indexed: 12/26/2023]
Abstract
CONTEXT Qinggong Shoutao Wan (QGSTW) is a pill used as a traditional medicine to treat age-associated memory decline (AAMI). However, its potential mechanisms are unclear. OBJECTIVE This study elucidates the possible mechanisms of QGSTW in treating AAMI. MATERIALS AND METHODS Network pharmacology and molecular docking approaches were utilized to identify the potential pathway by which QGSTW alleviates AAMI. C57BL/6J mice were divided randomly into control, model, and QGSTW groups. A mouse model of AAMI was established by d-galactose, and the pathways that QGSTW acts on to ameliorate AAMI were determined by ELISA, immunofluorescence staining and Western blotting after treatment with d-gal (100 mg/kg) and QGSTW (20 mL/kg) for 12 weeks. RESULTS Network pharmacology demonstrated that the targets of the active components were significantly enriched in the cAMP signaling pathway. AKT1, FOS, GRIN2B, and GRIN1 were the core target proteins. QGSTW treatment increased the discrimination index from -16.92 ± 7.06 to 23.88 ± 15.94% in the novel location test and from -19.54 ± 5.71 to 17.55 ± 6.73% in the novel object recognition test. ELISA showed that QGSTW could increase the levels of cAMP. Western blot analysis revealed that QGSTW could upregulate the expression of PKA, CREB, c-Fos, GluN1, GluA1, CaMKII-α, and SYN. Immunostaining revealed that the expression of SYN was decreased in the CA1 and DG. DISCUSSION AND CONCLUSIONS This study not only provides new insights into the mechanism of QGSTW in the treatment of AAMI but also provides important information and new research ideas for the discovery of traditional Chinese medicine compounds that can treat AAMI.
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Affiliation(s)
- Guiyun Pan
- Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Second Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Lijuan Chai
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Rui Chen
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Qing Yuan
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Zhihui Song
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Wanying Feng
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Jinna Wei
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Zhihua Yang
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yuhang Zhang
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Guinan Xie
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - An Yan
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Qingbo Lv
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Caijun Wang
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yingqiang Zhao
- Second Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yi Wang
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
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12
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Wurentuya, Han S, Mei S, Lai M, Sirigunqiqige, Luoricuo, Yang M, Feng Y, Zhong G, Zhu J, Li M. The effect of ethanol extracts of loulu flower on LPS-induced acute lung injury in mice. JOURNAL OF ETHNOPHARMACOLOGY 2024; 334:118515. [PMID: 38972530 DOI: 10.1016/j.jep.2024.118515] [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: 04/09/2024] [Revised: 06/26/2024] [Accepted: 06/30/2024] [Indexed: 07/09/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE In Mongolian medicine, Loulu flower (LLF), the dried inflorescence of Rhaponticum uniflorum (L.) DC. from the Compositae family, has been used to clear heat and relieve toxicity for millennia, particularly in the treatment of pneumonia. AIM OF THIS STUDY To reveal the effects of LLF on mice with lipopolysaccharide (LPS)-stimulated acute lung injury (ALI) and elucidate the underlying mechanisms. MATERIALS AND METHODS ALI was established in BALB/c mice via nasal drops administration of LPS (5 mg/kg). The mice were then orally administrated with various doses of LLF extracts and the positive drug dexamethasone (DEX, 5 mg/kg), once daily for seven consecutive days. Last day, after being stimulated with LPS for 6h, the mice were closed dislocation of cervical vertebra, the serum, bronchus alveolar lavage fluid (BALF) and lung tissue were put into the EP tube and stored at -80 °C for further analysis. The changes of histopathology were tested by hematoxylin and eosin stain (H&E), the levels of, IL-1β, IL-18, TNF-α and IL-4 in BALF and serum were measured by ELISA. The pathways related to the treatment of ALI were predicted by network pharmacology. The expression levels of TLR4/NF-κB and NLRP3 signaling pathway-associated proteins, COX-2 and ERK were tested by western blotting. The levels of P65 and NLRP3 in lung tissues were determined by immunofluorescence analysis. RESULTS LLF total extract and the extract parts could alleviate the inflammatory cell infiltration, thicken the alveolar walls in lung tissues, reduce the levels of IL-18, IL-1β in BALF, the TNF-α in both BALF and serum, meantime enhance the level of IL-4 in BALF and serum in mice with LPS-induced ALI. Our network pharmacology and comprehensive gene ontology analyses revealed the active constituents of LLF and the pathways, including TLR4/NF-κB, NLRP3 and MAPK signaling pathways, which play significant roles in ALI. Furthermore, both the total extract and its extraction portions suppressed the expressions of proteins related with the COX-2, p-ERK and TLR4/NF-κB signaling pathway (TLR4, p-IκB, p-p65), as well as the NLRP3 signaling pathway (NLRP3, cleaved caspase-1, caspase-1, IL-1β). CONCLUSION LLF could improve the pathological changes and reducing inflammatory reactions in mice induced by LPS. The mechanism may be related to the modulation of the TLR4/NLRP3 signaling pathways.
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Affiliation(s)
- Wurentuya
- Research Center of Natural Resources of Chinese Medicinal Materials and Ethnic Medicine, Jiangxi University of Chinese Medicine, Nanchang, 330004, China.
| | - Shan Han
- Research Center of Natural Resources of Chinese Medicinal Materials and Ethnic Medicine, Jiangxi University of Chinese Medicine, Nanchang, 330004, China
| | - Shengtao Mei
- Research Center of Natural Resources of Chinese Medicinal Materials and Ethnic Medicine, Jiangxi University of Chinese Medicine, Nanchang, 330004, China
| | - Mulin Lai
- Research Center of Natural Resources of Chinese Medicinal Materials and Ethnic Medicine, Jiangxi University of Chinese Medicine, Nanchang, 330004, China
| | | | - Luoricuo
- Research Center of Natural Resources of Chinese Medicinal Materials and Ethnic Medicine, Jiangxi University of Chinese Medicine, Nanchang, 330004, China
| | - Miaohong Yang
- Research Center of Natural Resources of Chinese Medicinal Materials and Ethnic Medicine, Jiangxi University of Chinese Medicine, Nanchang, 330004, China
| | - Yulin Feng
- Research Center of Natural Resources of Chinese Medicinal Materials and Ethnic Medicine, Jiangxi University of Chinese Medicine, Nanchang, 330004, China
| | - Guoyue Zhong
- Research Center of Natural Resources of Chinese Medicinal Materials and Ethnic Medicine, Jiangxi University of Chinese Medicine, Nanchang, 330004, China
| | - Jixiao Zhu
- Research Center of Natural Resources of Chinese Medicinal Materials and Ethnic Medicine, Jiangxi University of Chinese Medicine, Nanchang, 330004, China
| | - Min Li
- Research Center of Natural Resources of Chinese Medicinal Materials and Ethnic Medicine, Jiangxi University of Chinese Medicine, Nanchang, 330004, China.
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13
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Guo Y, Yuan C, Huang T, Cheng Z. Integrating UHPLC-Q-TOF-MS/MS, network pharmacology, bioinformatics and experimental validation to uncover the anti-cancer mechanisms of TiaoPi AnChang decoction in colorectal cancer. JOURNAL OF ETHNOPHARMACOLOGY 2024; 334:118576. [PMID: 39002822 DOI: 10.1016/j.jep.2024.118576] [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: 05/14/2024] [Revised: 06/27/2024] [Accepted: 07/10/2024] [Indexed: 07/15/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The TiaoPi AnChang Decoction (TPACD), a Traditional Chinese Medicine (TCM) prescription based on Xiangsha Liujunzi Decoction, has demonstrated clinical efficacy as an adjuvant therapy for colorectal cancer (CRC) patients. However, its specific ingredients and potential mechanisms of action remain unclear. AIM OF THE STUDY To identify the primary active ingredients of TPACD, their molecular targets, and potential mechanisms underlying the efficacy of TPACD in CRC treatment. MATERIALS AND METHODS This study investigated the clinically validated TCM formula TPACD. In vitro and in vivo experiments were used to demonstrate TPACD's regulatory effects on various malignant phenotypes of tumors, providing basic research support for its anti-cancer activity. To understand its pharmacodynamic basis, we utilized ultra-high performance liquid chromatography-quadrupole-time-of-flight-mass spectrometry/mass spectrometry (UHPLC-Q-TOF-MS/MS) to analyze TPACD constituents present in the bloodstream. Network pharmacology and bioinformatics analyses were used to identify potential active components and their molecular targets for TPACD's therapeutic effects in CRC. Subsequent experiments further elucidated its pharmacological mechanism. RESULTS TPACD inhibits various malignant cellular processes, such as cell proliferation, apoptosis, migration, and invasion, and has shown potential anti-CRC activities both in vitro and in vivo. Following the identification of 109 constituents absorbed into the blood from TPACD, network pharmacology analysis predicted 42 potential anti-CRC targets. Clinical analyses highlighted three genes as prognostic key genes of TPACD's therapeutic action: C-X-C motif chemokine ligand 8 (CXCL8), fatty acid binding protein 4 (FABP4), and matrix metallopeptidase 3 (MMP3). Drug sensitivity analyses, molecular docking simulations and reverse transcription-quantitative polymerase chain reaction (RT-qPCR) identified MMP3 as the most promising target for TPACD's anti-CRC action. Enzyme activity assays confirmed that TPACD inhibits MMP3 enzyme activity. Surface plasmon resonance (SPR) characterized the binding affinity between MMP3 and effective active components of TPACD, including luteolin, quercetin, kaempferol, and liensinine. CONCLUSIONS TPACD exhibits anti-CRC activity in vitro and in vivo, with MMP3 identified as a critical target. The active compounds, including luteolin, quercetin, kaempferol, and liensinine, absorbed into the bloodstream, contribute to TPACD's efficacy by targeting MMP3.
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Affiliation(s)
- Yantong Guo
- School of Clinical Medicine, Beijing University of Chinese Medicine, Beijing, 100029, China; Oncology Department of Integrated Traditional Chinese and Western Medicine, China-Japan Friendship Hospital, Beijing, 100029, China.
| | - Chunsheng Yuan
- School of Clinical Medicine, Beijing University of Chinese Medicine, Beijing, 100029, China; Oncology Department of Integrated Traditional Chinese and Western Medicine, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Ting Huang
- Department of Traditional Chinese Medicine, The People's Hospital of Ningxia Hui Autonomous Region, Ningxia, 750000, China
| | - Zhiqiang Cheng
- Oncology Department of Integrated Traditional Chinese and Western Medicine, China-Japan Friendship Hospital, Beijing, 100029, China.
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14
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Özay B, Tükel EY, Ayna Duran G, Kiraz Y. Identification of potential inhibitors for drug resistance in acute lymphoblastic leukemia through differentially expressed gene analysis and in silico screening. Anal Biochem 2024; 694:115619. [PMID: 39025197 DOI: 10.1016/j.ab.2024.115619] [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: 05/13/2024] [Revised: 07/11/2024] [Accepted: 07/13/2024] [Indexed: 07/20/2024]
Abstract
Acute lymphoblastic leukemia (ALL) is a disease of lymphocyte origin predominantly diagnosed in children. While its 5-year survival rate is high, resistance to chemotherapy drugs is still an obstacle. Our aim is to determine differentially expressed genes (DEGs) related to Asparaginase, Daunorubicin, Prednisolone, and Vincristine resistance and identify potential inhibitors via docking. Three datasets were accessed from the Gene Expression Omnibus database; GSE635, GSE19143, and GSE22529. The microarray data was analyzed using R4.2.0 and Bioconductor packages, and pathway and protein-protein interaction analysis were performed. We identified 1294 upregulated DEGs, with 12 genes consistently upregulated in all four resistant groups. KEGG analysis revealed an association with the PI3K-Akt pathway. Among DEGs, 33 hub genes including MDM2 and USP7 were pinpointed. Within common genes, CLDN9 and HS3ST3A1 were subjected to molecular docking against 3556 molecules. Following ADMET analysis, three drugs emerged as potential inhibitors: Flunarizine, Talniflumate, and Eltrombopag. Molecular dynamics analysis for HS3ST3A1 indicated all candidates had the potential to overcome drug resistance, Eltrombopag displaying particularly promising results. This study promotes a further understanding of drug resistance in ALL, introducing novel genes for consideration in diagnostic screening. It also presents potential inhibitor candidates to tackle drug resistance through repurposing.
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Affiliation(s)
- Başak Özay
- İzmir University of Economics, Faculty of Engineering, Department of Genetics and Bioengineering, 35330, Balçova, Izmir, Turkey
| | - Ezgi Yağmur Tükel
- İzmir University of Economics, Faculty of Engineering, Department of Genetics and Bioengineering, 35330, Balçova, Izmir, Turkey
| | - Gizem Ayna Duran
- İzmir University of Economics, Faculty of Engineering, Department of Biomedical Engineering, 35330, Balçova, Izmir, Turkey
| | - Yağmur Kiraz
- İzmir University of Economics, Faculty of Engineering, Department of Genetics and Bioengineering, 35330, Balçova, Izmir, Turkey.
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15
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Leclercq J, Torres-Paz J, Policarpo M, Agnès F, Rétaux S. Evolution of the regulation of developmental gene expression in blind Mexican cavefish. Development 2024; 151:dev202610. [PMID: 39007346 DOI: 10.1242/dev.202610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 07/08/2024] [Indexed: 07/16/2024]
Abstract
Developmental evolution and diversification of morphology can arise through changes in the regulation of gene expression or protein-coding sequence. To unravel mechanisms underlying early developmental evolution in cavefish of the species Astyanax mexicanus, we compared transcriptomes of surface-dwelling and blind cave-adapted morphs at the end of gastrulation. Twenty percent of the transcriptome was differentially expressed. Allelic expression ratios in cave X surface hybrids showed that cis-regulatory changes are the quasi-exclusive contributors to inter-morph variations in gene expression. Among a list of 108 genes with change at the cis-regulatory level, we explored the control of expression of rx3, which is a master eye gene. We discovered that cellular rx3 levels are cis-regulated in a cell-autonomous manner, whereas rx3 domain size depends on non-autonomous Wnt and Bmp signalling. These results highlight how uncoupled mechanisms and regulatory modules control developmental gene expression and shape morphological changes. Finally, a transcriptome-wide search for fixed coding mutations and differential exon use suggested that variations in coding sequence have a minor contribution. Thus, during early embryogenesis, changes in gene expression regulation are the main drivers of cavefish developmental evolution.
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Affiliation(s)
- Julien Leclercq
- Paris-Saclay Institute of Neuroscience, CNRS and University Paris-Saclay, 91400 Saclay, France
| | - Jorge Torres-Paz
- Paris-Saclay Institute of Neuroscience, CNRS and University Paris-Saclay, 91400 Saclay, France
| | - Maxime Policarpo
- Paris-Saclay Institute of Neuroscience, CNRS and University Paris-Saclay, 91400 Saclay, France
| | - François Agnès
- Paris-Saclay Institute of Neuroscience, CNRS and University Paris-Saclay, 91400 Saclay, France
| | - Sylvie Rétaux
- Paris-Saclay Institute of Neuroscience, CNRS and University Paris-Saclay, 91400 Saclay, France
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16
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Bonnefous H, Teulière J, Lapointe FJ, Lopez P, Bapteste E. Most genetic roots of fungal and animal aging are hundreds of millions of years old according to phylostratigraphy analyses of aging networks. GeroScience 2024; 46:5037-5059. [PMID: 38862758 PMCID: PMC11335996 DOI: 10.1007/s11357-024-01234-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 05/30/2024] [Indexed: 06/13/2024] Open
Abstract
Few studies have systematically analyzed how old aging is. Gaining a more accurate knowledge about the natural history of aging could however have several payoffs. This knowledge could unveil lineages with dated genetic hardware, possibly maladapted to current environmental challenges, and also uncover "phylogenetic modules of aging," i.e., naturally evolved pathways associated with aging or longevity from a single ancestry, with translational interest for anti-aging therapies. Here, we approximated the natural history of the genetic hardware of aging for five model fungal and animal species. We propose a lower-bound estimate of the phylogenetic age of origination for their protein-encoding gene families and protein-protein interactions. Most aging-associated gene families are hundreds of million years old, older than the other gene families from these genomes. Moreover, we observed a form of punctuated evolution of the aging hardware in all species, as aging-associated families born at specific phylogenetic times accumulate preferentially in genomes. Most protein-protein interactions between aging genes are also old, and old aging-associated proteins showed a reduced potential to contribute to novel interactions associated with aging, suggesting that aging networks are at risk of losing in evolvability over long evolutionary periods. Finally, due to reshuffling events, aging networks presented a very limited phylogenetic structure that challenges the detection of "maladaptive" or "adaptative" phylogenetic modules of aging in present-day genomes.
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Affiliation(s)
- Hugo Bonnefous
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université Des Antilles, Paris, France
| | - Jérôme Teulière
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université Des Antilles, Paris, France
| | - François-Joseph Lapointe
- Département de Sciences Biologiques, Complexe Des Sciences, Université de Montréal, Montréal, QC, Canada
| | - Philippe Lopez
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université Des Antilles, Paris, France
| | - Eric Bapteste
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université Des Antilles, Paris, France.
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17
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Fekry M, Stenberg G, Dobritzsch D, Danielson UH. Production of stable and pure ZC3H11A - An extensively disordered RNA binding protein. Protein Expr Purif 2024; 222:106542. [PMID: 38969281 DOI: 10.1016/j.pep.2024.106542] [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: 05/21/2024] [Revised: 07/02/2024] [Accepted: 07/03/2024] [Indexed: 07/07/2024]
Abstract
Human ZC3H11A is an RNA-binding zinc finger protein involved in mRNA export and required for the efficient growth of human nuclear replicating viruses. Its biochemical properties are largely unknown so our goal has been to produce the protein in a pure and stable form suitable for its characterization. This has been challenging since the protein is large (810 amino acids) and with only the N-terminal zinc finger domain (amino acids 1-86) being well structured, the remainder is intrinsically disordered. Our production strategies have encompassed recombinant expression of full-length, truncated and mutated ZC3H11A variants with varying purification tags and fusion proteins in several expression systems, with or without co-expression of chaperones and putative interaction partners. A range of purification schemes have been explored. Initially, only truncated ZC3H11A encompassing the zinc finger domain could successfully be produced in a stable form. It required recombinant expression in insect cells since expression in E. coli gave a protein that aggregated. To reduce problematic nucleic acid contaminations, Cys8, located in one of the zinc fingers, was substituted by Ala and Ser. Interestingly, this did not affect nucleic acid binding, but the full-length protein was stabilised while the truncated version was insoluble. Ultimately, we discovered that when using alkaline buffers (pH 9) for purification, full-length ZC3H11A expressed in Sf9 insect cells was obtained in a stable and >90 % pure form, and as a mixture of monomers, dimers, tetramers and hexamers. Many of the challenges experienced are consistent with its predicted structure and unusual charge distribution.
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Affiliation(s)
- Mostafa Fekry
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden; Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Gun Stenberg
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | | | - U Helena Danielson
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden; Science for Life Laboratory, Drug Discovery & Development Platform, Uppsala University, SE 751 23 Uppsala, Sweden.
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18
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Hu J, Li Z, Rao B, Thafar MA, Arif M. Improving protein-protein interaction prediction using protein language model and protein network features. Anal Biochem 2024; 693:115550. [PMID: 38679191 DOI: 10.1016/j.ab.2024.115550] [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: 01/24/2024] [Revised: 04/12/2024] [Accepted: 04/25/2024] [Indexed: 05/01/2024]
Abstract
Interactions between proteins are ubiquitous in a wide variety of biological processes. Accurately identifying the protein-protein interaction (PPI) is of significant importance for understanding the mechanisms of protein functions and facilitating drug discovery. Although the wet-lab technological methods are the best way to identify PPI, their major constraints are their time-consuming nature, high cost, and labor-intensiveness. Hence, lots of efforts have been made towards developing computational methods to improve the performance of PPI prediction. In this study, we propose a novel hybrid computational method (called KSGPPI) that aims at improving the prediction performance of PPI via extracting the discriminative information from protein sequences and interaction networks. The KSGPPI model comprises two feature extraction modules. In the first feature extraction module, a large protein language model, ESM-2, is employed to exploit the global complex patterns concealed within protein sequences. Subsequently, feature representations are further extracted through CKSAAP, and a two-dimensional convolutional neural network (CNN) is utilized to capture local information. In the second feature extraction module, the query protein acquires its similar protein from the STRING database via the sequence alignment tool NW-align and then captures the graph embedding feature for the query protein in the protein interaction network of the similar protein using the algorithm of Node2vec. Finally, the features of these two feature extraction modules are efficiently fused; the fused features are then fed into the multilayer perceptron to predict PPI. The results of five-fold cross-validation on the used benchmarked datasets demonstrate that KSGPPI achieves an average prediction accuracy of 88.96 %. Additionally, the average Matthews correlation coefficient value (0.781) of KSGPPI is significantly higher than that of those state-of-the-art PPI prediction methods. The standalone package of KSGPPI is freely downloaded at https://github.com/rickleezhe/KSGPPI.
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Affiliation(s)
- Jun Hu
- College of Information Engineering, Zhejiang University of Technology, Hangzhou, 310023, China.
| | - Zhe Li
- College of Information Engineering, Zhejiang University of Technology, Hangzhou, 310023, China
| | - Bing Rao
- Engineering Research Center of Integration and Application of Digital Learning Technology, Ministry of Education, Beijing, 100039, China.
| | - Maha A Thafar
- Computer Science Department, College of Computers and Information Technology, Taif University, Taif, Saudi Arabia
| | - Muhammad Arif
- College of Science and Engineering, Hamad Bin Khalifa University, Doha 34110, Qatar.
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Li Y, Yan F, Xiang J, Wang W, Xie K, Luo L. Identification and experimental validation of immune-related gene PPARG is involved in ulcerative colitis. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167300. [PMID: 38880160 DOI: 10.1016/j.bbadis.2024.167300] [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: 02/23/2024] [Revised: 04/30/2024] [Accepted: 06/06/2024] [Indexed: 06/18/2024]
Abstract
BACKGROUND The pathophysiology of ulcerative colitis (UC) is believed to be heavily influenced by immunology, which presents challenges for both diagnosis and treatment. The main aims of this study are to deepen our understanding of the immunological characteristics associated with the disease and to identify valuable biomarkers for diagnosis and treatment. METHODS The UC datasets were sourced from the GEO database and were analyzed using unsupervised clustering to identify different subtypes of UC. Twelve machine learning algorithms and Deep learning model DNN were developed to identify potential UC biomarkers, with the LIME and SHAP methods used to explain the models' findings. PPI network is used to verify the identified key biomarkers, and then a network connecting super enhancers, transcription factors and genes is constructed. Single-cell sequencing technology was utilized to investigate the role of Peroxisome Proliferator Activated Receptor Gamma (PPARG) in UC and its correlation with macrophage infiltration. Furthermore, alterations in PPARG expression were validated through Western blot (WB) and immunohistochemistry (IHC) in both in vitro and in vivo experiments. RESULT By utilizing bioinformatics techniques, we were able to pinpoint PPARG as a key biomarker for UC. The expression of PPARG was significantly reduced in cell models, UC animal models, and colitis models induced by dextran sodium sulfate (DSS). Interestingly, overexpression of PPARG was able to restore intestinal barrier function in H2O2-induced IEC-6 cells. Additionally, immune-related differentially expressed genes (DEGs) allowed for efficient classification of UC samples into neutrophil and mitochondrial metabolic subtypes. A diagnostic model incorporating the three disease-specific genes PPARG, PLA2G2A, and IDO1 demonstrated high accuracy in distinguishing between the UC group and the control group. Furthermore, single-cell analysis revealed that decreased PPARG expression in colon tissue may contribute to the polarization of M1 macrophages through activation of inflammatory pathways. CONCLUSION In conclusion, PPARG, a gene related to immunity, has been established as a reliable potential biomarker for the diagnosis and treatment of UC. The immune response it controls plays a key role in the progression and development of UC by enabling interaction between characteristic biomarkers and immune infiltrating cells.
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Affiliation(s)
- Yang Li
- The First Clinical College, Guangdong Medical University, Zhanjiang, 524023, Guangdong, China
| | - Fangfang Yan
- The First Clinical College, Guangdong Medical University, Zhanjiang, 524023, 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
| | - Wenjian Wang
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, School of Ocean and Tropical Medicine, Guangdong Medical University, Zhanjiang, Guangdong 524023, China
| | - Kangping Xie
- The First Clinical College, Guangdong Medical University, Zhanjiang, 524023, Guangdong, 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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20
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Yan W, Hu W, Song Y, Liu X, Zhou Z, Li W, Cao Z, Pei W, Zhou G, Hu G. Differential network analysis reveals the key role of the ECM-receptor pathway in α-particle-induced malignant transformation. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102260. [PMID: 39049874 PMCID: PMC11268105 DOI: 10.1016/j.omtn.2024.102260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 06/14/2024] [Indexed: 07/27/2024]
Abstract
Space particle radiation is a major environmental factor in spaceflight, and it is known to cause body damage and even trigger cancer, but with unknown molecular etiologies. To examine these causes, we developed a systems biology approach by focusing on the co-expression network analysis of transcriptomics profiles obtained from single high-dose (SE) and multiple low-dose (ME) α-particle radiation exposures of BEAS-2B human bronchial epithelial cells. First, the differential network and pathway analysis based on the global network and the core modules showed that genes in the ME group had higher enrichment for the extracellular matrix (ECM)-receptor interaction pathway. Then, collagen gene COL1A1 was screened as an important gene in the ME group assessed by network parameters and an expression study of lung adenocarcinoma samples. COL1A1 was found to promote the emergence of the neoplastic characteristics of BEAS-2B cells by both in vitro experimental analyses and in vivo immunohistochemical staining. These findings suggested that the degree of malignant transformation of cells in the ME group was greater than that of the SE, which may be caused by the dysregulation of the ECM-receptor pathway.
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Affiliation(s)
- Wenying Yan
- MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Key Laboratory of Pathogen Bioscience and Anti-infective Medicine, Department of Bioinformatics, Center for Systems Biology, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou 215213, China
- Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Soochow University, Suzhou 215123, China
| | - Wentao Hu
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Yidan Song
- MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Key Laboratory of Pathogen Bioscience and Anti-infective Medicine, Department of Bioinformatics, Center for Systems Biology, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou 215213, China
| | - Xingyi Liu
- MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Key Laboratory of Pathogen Bioscience and Anti-infective Medicine, Department of Bioinformatics, Center for Systems Biology, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou 215213, China
| | - Ziyun Zhou
- MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Key Laboratory of Pathogen Bioscience and Anti-infective Medicine, Department of Bioinformatics, Center for Systems Biology, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou 215213, China
- Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Soochow University, Suzhou 215123, China
| | - Wanshi Li
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Zhifei Cao
- Department of Pathology, the Second Affiliated Hospital of Soochow University, Suzhou 215004, China
| | - Weiwei Pei
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Guangming Zhou
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Guang Hu
- MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Key Laboratory of Pathogen Bioscience and Anti-infective Medicine, Department of Bioinformatics, Center for Systems Biology, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou 215213, China
- Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Soochow University, Suzhou 215123, China
- Key Laboratory of Alkene-carbon Fibres-based Technology & Application for Detection of Major Infectious Diseases, Soochow University, Suzhou 215123, China
- Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou 215123, China
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21
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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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22
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Ball NJ, Ghimire S, Follain G, Pajari AO, Wurzinger D, Vaitkevičiūtė M, Cowell AR, Berki B, Ivaska J, Paatero I, Goult BT, Jacquemet G. TLNRD1 is a CCM complex component and regulates endothelial barrier integrity. J Cell Biol 2024; 223:e202310030. [PMID: 39013281 PMCID: PMC11252447 DOI: 10.1083/jcb.202310030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 04/08/2024] [Accepted: 05/23/2024] [Indexed: 07/18/2024] Open
Abstract
We previously identified talin rod domain-containing protein 1 (TLNRD1) as a potent actin-bundling protein in vitro. Here, we report that TLNRD1 is expressed in the vasculature in vivo. Its depletion leads to vascular abnormalities in vivo and modulation of endothelial cell monolayer integrity in vitro. We demonstrate that TLNRD1 is a component of the cerebral cavernous malformations (CCM) complex through its direct interaction with CCM2, which is mediated by a hydrophobic C-terminal helix in CCM2 that attaches to a hydrophobic groove on the four-helix domain of TLNRD1. Disruption of this binding interface leads to CCM2 and TLNRD1 accumulation in the nucleus and actin fibers. Our findings indicate that CCM2 controls TLNRD1 localization to the cytoplasm and inhibits its actin-bundling activity and that the CCM2-TLNRD1 interaction impacts endothelial actin stress fiber and focal adhesion formation. Based on these results, we propose a new pathway by which the CCM complex modulates the actin cytoskeleton and vascular integrity.
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Affiliation(s)
- Neil J. Ball
- School of Biosciences, University of Kent, Canterbury, UK
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Sujan Ghimire
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
| | - Gautier Follain
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Ada O. Pajari
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
| | - Diana Wurzinger
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
| | - Monika Vaitkevičiūtė
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
| | | | - Bence Berki
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Johanna Ivaska
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Department of Life Technologies, University of Turku, Turku, Finland
- Western Finnish Cancer Center (FICAN West), University of Turku, Turku, Finland
- Foundation for the Finnish Cancer Institute, Helsinki, Finland
- InFLAMES Research Flagship Center, University of Turku and Åbo Akademi University, Turku, Finland
| | - Ilkka Paatero
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Benjamin T. Goult
- School of Biosciences, University of Kent, Canterbury, UK
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Guillaume Jacquemet
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku and Åbo Akademi University, Turku, Finland
- Turku Bioimaging, University of Turku and Åbo Akademi University, Turku, Finland
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23
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Dai F, Yuan Y, Hao J, Cheng X, Zhou X, Zhou L, Tian R, Zhao Y, Xiang T. PDCD2 as a prognostic biomarker in glioma correlates with malignant phenotype. Genes Dis 2024; 11:101106. [PMID: 39022129 PMCID: PMC11252777 DOI: 10.1016/j.gendis.2023.101106] [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: 03/28/2023] [Accepted: 08/04/2023] [Indexed: 07/20/2024] Open
Abstract
Programmed cell death 2 (PDCD2) is related to cancer progression and chemotherapy sensitivity. The role of PDCD2 in solid cancers (excluding hematopoietic malignancies) and their diagnosis and prognosis remains unclear. The TCGA, CGGA, GEPIA, cBioPortal, and GTEx databases were analyzed for expression, prognostic value, and genetic modifications of PDCD2 in cancer patients. Functional enrichment analysis, CCK8, colony formation assay, transwell assay, and xenograft tumor model were undertaken to study the PDCD2's biological function in glioma (GBMLGG). The PDCD2 gene was associated with solid cancer progression. In the functional enrichment analysis results, PDCD2 was shown to participate in several important GBMLGG biological processes. GBMLGG cells may be inhibited in their proliferation, migration, invasion, and xenograft tumor growth by knocking down PDCD2. Our research can provide new insights into solid cancer prognostic biomarkers of PDCD2.
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Affiliation(s)
- Fengsheng Dai
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Yixiao Yuan
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Jiaqi Hao
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Xing Cheng
- Department of Neuro-Oncology, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Xiangyi Zhou
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Li Zhou
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Rui Tian
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Yi Zhao
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Tingxiu Xiang
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing 400030, China
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24
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Yan Z, Xia J, Cao Z, Zhang H, Wang J, Feng T, Shu Y, Zou L. Multi-omics integration reveals potential stage-specific druggable targets in T-cell acute lymphoblastic leukemia. Genes Dis 2024; 11:100949. [PMID: 39071111 PMCID: PMC11282411 DOI: 10.1016/j.gendis.2023.03.022] [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: 10/20/2022] [Accepted: 03/11/2023] [Indexed: 07/30/2024] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL), a heterogeneous hematological malignancy, is caused by the developmental arrest of normal T-cell progenitors. The development of targeted therapeutic regimens is impeded by poor knowledge of the stage-specific aberrances in this disease. In this study, we performed multi-omics integration analysis, which included mRNA expression, chromatin accessibility, and gene-dependency database analyses, to identify potential stage-specific druggable targets and repositioned drugs for this disease. This multi-omics integration helped identify 29 potential pathological genes for T-ALL. These genes exhibited tissue-specific expression profiles and were enriched in the cell cycle, hematopoietic stem cell differentiation, and the AMPK signaling pathway. Of these, four known druggable targets (CDK6, TUBA1A, TUBB, and TYMS) showed dysregulated and stage-specific expression in malignant T cells and may serve as stage-specific targets in T-ALL. The TUBA1A expression level was higher in the early T cell precursor (ETP)-ALL cells, while TUBB and TYMS were mainly highly expressed in malignant T cells arrested at the CD4 and CD8 double-positive or single-positive stage. CDK6 exhibited a U-shaped expression pattern in malignant T cells along the naïve to maturation stages. Furthermore, mebendazole and gemcitabine, which target TUBA1A and TYMS, respectively, exerted stage-specific inhibitory effects on T-ALL cell lines, indicating their potential stage-specific antileukemic role in T-ALL. Collectively, our findings might aid in identifying potential stage-specific druggable targets and are promising for achieving more precise therapeutic strategies for T-ALL.
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Affiliation(s)
- Zijun Yan
- Clinical Research Unit, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200062, China
| | - Jie Xia
- Bioinformatics and BioMedical Bigdata Mining Laboratory, School of Big Health, Guizhou Medical University, Guiyang, Guizhou 554300, China
| | - Ziyang Cao
- Clinical Research Unit, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200062, China
| | - Hongyang Zhang
- Clinical Research Unit, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200062, China
| | - Jinxia Wang
- Clinical Research Unit, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200062, China
| | - Tienan Feng
- Clinical Research Unit, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
- Clinical Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yi Shu
- Center for Clinical Molecular Laboratory Medicine of Children's Hospital of Chongqing Medical University, Chongqing 400014, China
| | - Lin Zou
- Clinical Research Unit, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200062, China
- Center for Clinical Molecular Laboratory Medicine of Children's Hospital of Chongqing Medical University, Chongqing 400014, China
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25
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Chen J, Sun Q, Wang Y, Yin W. Revealing the key role of cuproptosis in osteoporosis via the bioinformatic analysis and experimental validation of cuproptosis-related genes. Mamm Genome 2024; 35:414-431. [PMID: 38904833 DOI: 10.1007/s00335-024-10049-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 06/14/2024] [Indexed: 06/22/2024]
Abstract
The incidence of osteoporosis has rapidly increased owing to the ageing population. Cuproptosis, a novel mechanism that regulates cell death, may be a new therapeutic approach. However, the relevance of cuproptosis in the immune microenvironment and osteoporosis immunotherapy is still unknown. We intersected the differentially expressed genes from osteoporotic samples with 75 cuproptosis-related genes to identify 16 significantly expressed cuproptosis genes. We further explored the connection between the cuproptosis pattern, immune microenvironment, and immunotherapy. The weighted gene co-expression network analysis algorithm was used to identify cuproptosis phenotype-associated genes, and we used quantitative real-time PCR and immunohistochemistry in mouse femur tissues to verify hub gene (MAP2K2, FDX1, COX19, VEGFA, CDKN2A, and NFE2L2) expression. Six hub genes and 59 cuproptosis phenotype-associated genes involved in immunisation were identified among the osteoporosis and control groups, and the majority of these 59 genes were enriched in the inflammatory response, as well as in signal transducers, Janus kinase, and transcription pathway activators. In addition, two different clusters of cuproptosis were found, and immune infiltration analysis showed that gene Cluster 1 had a greater immune score and immune infiltration level. Further analysis revealed that three key genes (COX19, MAP2K2, and FDX1) were highly correlated with immune cell infiltration, and external experiments validated the association of these three genes with the prognosis of osteoporosis. We used the three key mRNAs COX19, MAP2K2, and FDX1 as a classification model that may systematically elucidate the complex connection between cuproptosis and the immune microenvironment of osteoporosis. New insights into osteoporosis pathogenesis and immunotherapy prospects may be gained from this study.
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Affiliation(s)
- Jianxing Chen
- Department of Joint Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150000, China
| | - Qifeng Sun
- Department of Joint Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150000, China
| | - Yi Wang
- Department of Joint Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150000, China
| | - Wenzhe Yin
- Department of Joint Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150000, China.
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Wang Y, Wang J, Zhou T, Chen Z, Wang W, Liu B, Li Y. Investigating the potential mechanism and therapeutic effects of SLXG for cholesterol gallstone treatment. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 132:155886. [PMID: 39059092 DOI: 10.1016/j.phymed.2024.155886] [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: 01/15/2024] [Revised: 06/30/2024] [Accepted: 07/14/2024] [Indexed: 07/28/2024]
Abstract
BACKGROUND Shugan Lidan Xiaoshi Granules (SLXG) is a traditional Chinese medicine (TCM) formulation frequently employed to prevent and treat cholesterol gallstones. SLXG is formulated based on the Chaihu Shugan Formula found in an ancient Chinese medical book, a traditional remedy in China for centuries, and has demonstrated successful treatment of numerous patients with gallbladder stones. PURPOSE This research sought to clarify the therapeutic impact and molecular mechanisms of SLXG and its active components in the treatment of cholesterol gallbladder stones. METHODS The study employed network pharmacology, UPLC-HRMS transcriptome sequencing, animal model experiments, molecular docking, and Surface Plasmon Resonance (SPR) to explore the molecular mechanisms of SLXG and its relationship with Traditional Chinese Medicines (TCMs) and potential targets. Furthermore, PPI network analysis, along with GO and KEGG enrichment analyses, were performed to explore the potential mechanisms through which SLXG and its active ingredient, naringenin, prevent and treat cholesterol gallstones. The mechanism of action was further elucidated using an animal model for gallbladder stone formation. RESULTS The study employed a network pharmacology and UPLC-HRMS to investigate the active compounds of SLXG for the treatment of cholesterol gallbladder stones, and subsequently constructed a network of therapeutic targets of SLXG. The results from gene enrichment analyses indicated that SLXG targets the metabolic pathway of bile secretion and the cholesterol metabolism pathway in addressing cholesterol gallbladder stones. The molecular docking results confirmed the interaction between the genes enriched in the pathways and the active ingredients in SLXG. Transcriptome sequencing results demonstrated that SLXG exerts its therapeutic effect on gallstones by regulating cholesterol and bile acid synthesis and metabolism. Furthermore, animal model experiments and SPR provided evidence that SLXG and its active ingredient, naringenin, exert therapeutic effects on cholesterol gallbladder stones by targeting the genes HMGCR, SOAT2, and UGT1A1, and influencing substances associated with cholesterol synthesis and metabolism. CONCLUSIONS Using systematic network pharmacology methods combined with in vivo validation experiments, we uncovered the fundamental pharmacological effects and potential mechanisms of SLXG and its active ingredient, naringenin, in the treatment of cholesterol gallstones. This research underscores the valuable role that traditional remedies can play in addressing medical challenges and suggests a promising direction for further exploration of natural treatments for the disease.
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Affiliation(s)
- Yang Wang
- Department of Intervention Medicine and Microinvasive Oncology, The Second Hospital of Shandong University, Jinan, PR China; Institute of Interventional Oncology, Shandong University, Jinan, PR China
| | - Jiaxing Wang
- Department of Intervention Medicine and Microinvasive Oncology, The Second Hospital of Shandong University, Jinan, PR China; Institute of Interventional Oncology, Shandong University, Jinan, PR China
| | - Tong Zhou
- Department of Intervention Medicine and Microinvasive Oncology, The Second Hospital of Shandong University, Jinan, PR China; Institute of Interventional Oncology, Shandong University, Jinan, PR China
| | - Zitong Chen
- Department of Intervention Medicine and Microinvasive Oncology, The Second Hospital of Shandong University, Jinan, PR China; Institute of Interventional Oncology, Shandong University, Jinan, PR China
| | - Wujie Wang
- Department of Intervention Medicine and Microinvasive Oncology, The Second Hospital of Shandong University, Jinan, PR China; Institute of Interventional Oncology, Shandong University, Jinan, PR China
| | - Bin Liu
- Department of Intervention Medicine and Microinvasive Oncology, The Second Hospital of Shandong University, Jinan, PR China; Institute of Interventional Oncology, Shandong University, Jinan, PR China
| | - Yuliang Li
- Department of Intervention Medicine and Microinvasive Oncology, The Second Hospital of Shandong University, Jinan, PR China; Institute of Interventional Oncology, Shandong University, Jinan, PR China.
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Caglar HO, Aytatli A, Barlak N, Aydin Karatas E, Tatar A, Sahin A, Karatas OF. Bioinformatics approach combined with experimental verification reveals OAS3 gene implicated in paclitaxel resistance in head and neck cancer. Head Neck 2024; 46:2178-2196. [PMID: 38752376 DOI: 10.1002/hed.27803] [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: 10/26/2023] [Revised: 04/18/2024] [Accepted: 05/05/2024] [Indexed: 08/09/2024] Open
Abstract
BACKGROUND This study aimed to identify a candidate gene associated with paclitaxel (PTX) resistance and to evaluate functionally its biological role in the PTX-resistant head and neck squamous cell carcinoma (HNSCC) cell lines and clinical specimens. METHODS Microarray data series containing samples of different types of cancers resistant to PTX were analyzed and then a candidate gene associated with PTX resistance was identified using various bioinformatics tools. After the suppression of the target gene expression, changes in cell viability and colony-forming ability were evaluated in PTX-resistant FaDu and SCC-9 cell lines. RESULTS Bioinformatics analyses of upregulated genes in PTX-resistant cancer cells indicated that OAS3 was associated with PTX resistance. The downregulation of OAS3 expression significantly reduced the viability and colony-forming capacity of PTX-resistant SCC-9 cells by inducing apoptosis and cell cycle arrest at G0/G1 phase. CONCLUSIONS The therapeutic targeting of OAS3 may resensitize PTX-resistant HNSCC cells with high OAS3 expression to PTX treatment.
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Affiliation(s)
- Hasan Onur Caglar
- Department of Molecular Biology and Genetics, Faculty of Science, Erzurum Technical University, Erzurum, Turkey
| | - Abdulmelik Aytatli
- Department of Molecular Biology and Genetics, Faculty of Science, Erzurum Technical University, Erzurum, Turkey
- Molecular Cancer Biology Laboratory, High Technology Application and Research Center, Erzurum Technical University, Erzurum, Turkey
| | - Neslisah Barlak
- Department of Molecular Biology and Genetics, Faculty of Science, Erzurum Technical University, Erzurum, Turkey
- Molecular Cancer Biology Laboratory, High Technology Application and Research Center, Erzurum Technical University, Erzurum, Turkey
| | - Elanur Aydin Karatas
- Department of Molecular Biology and Genetics, Faculty of Science, Erzurum Technical University, Erzurum, Turkey
- Molecular Cancer Biology Laboratory, High Technology Application and Research Center, Erzurum Technical University, Erzurum, Turkey
| | - Arzu Tatar
- Department of Otorhinolaryngology Diseases, Faculty of Medicine, Ataturk University, Erzurum, Turkey
| | - Abdulkadir Sahin
- Department of Otorhinolaryngology Diseases, Faculty of Medicine, Ataturk University, Erzurum, Turkey
| | - Omer Faruk Karatas
- Department of Molecular Biology and Genetics, Faculty of Science, Erzurum Technical University, Erzurum, Turkey
- Molecular Cancer Biology Laboratory, High Technology Application and Research Center, Erzurum Technical University, Erzurum, Turkey
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Li C, Hu J, Jiang X, Tan H, Mao Y. Identification and validation of an immune-derived multiple programmed cell death index for predicting clinical outcomes, molecular subtyping, and drug sensitivity in lung adenocarcinoma. Clin Transl Oncol 2024; 26:2274-2295. [PMID: 38563847 DOI: 10.1007/s12094-024-03439-y] [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: 01/23/2024] [Accepted: 03/01/2024] [Indexed: 04/04/2024]
Abstract
OBJECTIVES Comprehensive cross-interaction of multiple programmed cell death (PCD) patterns in the patients with lung adenocarcinoma (LUAD) have not yet been thoroughly investigated. METHODS Here, we collected 19 different PCD patterns, including 1911 PCD-related genes, and developed an immune-derived multiple programmed cell death index (MPCDI) based on machine learning methods. RESULTS Using the median MPCDI scores, we categorized the LUAD patients into two groups: low-MPCDI and high-MPCDI. Our analysis of the TCGA-LUAD training cohort and three external GEO cohorts (GSE37745, GSE30219, and GSE68465) revealed that patients with high-MPCDI experienced a more unfavorable prognosis, whereas those with low-MPCDI had a better prognosis. Furthermore, the results of both univariate and multivariate Cox regression analyses further confirmed that MPCDI serves as a novel independent risk factor. By combining clinical characteristics with the MPCDI, we constructed a nomogram that provides an accurate and reliable quantitative tool for personalized clinical management of LUAD patients. The findings obtained from the analysis of C-index and the decision curve revealed that the nomogram outperformed various clinical variables in terms of net clinical benefit. Encouragingly, the low-MPCDI patients are more sensitive to commonly used chemotherapy drugs, which suggests that MPCDI scores have a guiding role in chemotherapy for LUAD patients. CONCLUSION Therefore, MPCDI can be used as a novel clinical diagnostic classifier, providing valuable insights into the clinical management and clinical decision-making for LUAD patients.
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Affiliation(s)
- Chunhong Li
- Central Laboratory, The Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, Guangxi, China.
- Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, The Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, Guangxi, China.
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, The Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, Guangxi, China.
| | - Jiahua Hu
- Central Laboratory, The Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, Guangxi, China
- Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, The Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, Guangxi, China
| | - Xiling Jiang
- School of Medical Laboratory Medicine, Guilin Medical University, Guilin, 541004, Guangxi, China
| | - Haiyin Tan
- School of Medical Laboratory Medicine, Guilin Medical University, Guilin, 541004, Guangxi, China
| | - Yiming Mao
- Department of Thoracic Surgery, Suzhou Kowloon Hospital, Shanghai Jiao Tong University School of Medicine, Suzhou, 215028, China.
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Yu AT, Hanna DN, Li TM, Sarfaty E, Khajoueinejad N, Li J, Golas B, Hiotis S, Labow D, Sarpel U, Magge DR, Cohen NA. Genetic Clustering of Cytoreductive Surgery and Hyperthermic Intraperitoneal Chemotherapy Patients of Colorectal Origin: KRAS and Not TP53 Cluster Alterations are Associated with Poor Outcomes. Ann Surg Oncol 2024; 31:6252-6261. [PMID: 39003380 DOI: 10.1245/s10434-024-15786-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 06/27/2024] [Indexed: 07/15/2024]
Abstract
BACKGROUND The prognostic impact of genetic mutations for patients who undergo cytoreductive surgery (CRS) with hyperthermic intraperitoneal chemotherapy (HIPEC) of colorectal origin (CRC) is not well defined. OBJECTIVE We aimed to describe the genetic classifications in an unsupervised fashion, and the outcomes of this patient population. METHODS A retrospective, bi-institutional study was performed on patients who underwent CRS-HIPEC with targeted mutation data with a median follow-up time of 61 months. Functional link analysis was performed using STRING v11.5. Genes with similar functional significance were clustered using unsupervised k-means clustering. Chi-square, Kaplan-Meier, and the log-rank test were used for comparative statistics. RESULTS Sixty-four patients with peritoneal carcinomatosis from CRC origin underwent CRS-HIPEC between 2007 and 2022 and genetic mutation data were extracted. We identified 19 unique altered genes, with KRAS (56%), TP53 (33%), and APC (22%) being the most commonly altered; 12.5% had co-altered KRAS/TP53. After creating an interactome map, k-means clustering revealed three functional clusters. Reactome Pathway analysis on three clusters showed unique pathways (1): Ras/FGFR3 signaling; (2) p53 signaling; and (3): NOTCH signaling. Seventy-one percent of patients in cluster 1 had KRAS mutations and a median overall survival of 52.3 months (p < 0.05). CONCLUSIONS Patients with peritoneal carcinomatosis (PC) of CRC origin who underwent CRS-HIPEC and with tumors that harbored mutations in cluster 1 (Ras/FGFR3 signaling) had worse outcomes. Pathway disruption and a cluster-centric perspective may affect prognosis more than individual genetic alterations in patients with PC of CRC origin.
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Affiliation(s)
- Allen T Yu
- Division of Surgical Oncology, Department of Surgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - David N Hanna
- Division of Surgical Oncology, Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Thomas M Li
- Division of Surgical Oncology, Department of Surgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elad Sarfaty
- Division of Surgical Oncology, Department of Surgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nazanin Khajoueinejad
- Division of Surgical Oncology, Department of Surgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Judy Li
- Division of Surgical Oncology, Department of Surgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Benjamin Golas
- Division of Surgical Oncology, Department of Surgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Spiros Hiotis
- Division of Surgical Oncology, Department of Surgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniel Labow
- Division of Surgical Oncology, Department of Surgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Umut Sarpel
- Division of Surgical Oncology, Department of Surgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Deepa R Magge
- Division of Surgical Oncology, Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Noah A Cohen
- Division of Surgical Oncology, Department of Surgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Panzenhagen AC, Petry FDS, Alves-Teixeira A, Santos L, Carazza-Kessler FG, Gelain DP, Moreira JCF. Biomarkers of methylmercury neurotoxicity and neurodevelopmental features: A systematic review. Food Chem Toxicol 2024; 191:114851. [PMID: 38986832 DOI: 10.1016/j.fct.2024.114851] [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: 06/03/2023] [Revised: 07/02/2024] [Accepted: 07/04/2024] [Indexed: 07/12/2024]
Abstract
The issue of MeHg contamination is a significant concern due to its detrimental impact on the environment. This study aimed to thoroughly investigate the effects of MeHg on neurodevelopmental biomarkers, as there is a lack of systematic reviews in this area. We conducted a comprehensive search of three databases (PubMed, Scopus, and Web of Science) and found 522 records, which were then meticulously reviewed by two independent reviewers. A total of 66 studies were included, with biomarkers related to oxidative stress, neurotransmission, inflammation, epigenetics, and apoptosis being the most prominent. The results of both in vitro and in vivo models indicate that antioxidant enzymes and other oxidative stress-related markers are indeed, altered following MeHg exposure. Moreover, MeHg exposure causes significant disruptions to neurotransmitter levels, activities of neurotransmitter synthesis enzymes, receptor densities, and proteins involved in synaptic function. Proinflammatory biomarkers are consistently overexpressed in both MeHg-treated cells and the brains of exposed rats. Furthermore, studies on DNA methylation and biomarker activity suggest that MeHg exposure may lead to neurotoxicity and neurodevelopmental issues via perturbations to epigenetic markers and the apoptosis pathway.
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Affiliation(s)
- Alana Castro Panzenhagen
- Centro de Estudos Em Estresse Oxidativo, Programa de Pós-Graduação Em Ciências Biológicas: Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil.
| | - Fernanda Dos Santos Petry
- Centro de Estudos Em Estresse Oxidativo, Programa de Pós-Graduação Em Ciências Biológicas: Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
| | - Alexsander Alves-Teixeira
- Centro de Estudos Em Estresse Oxidativo, Programa de Pós-Graduação Em Ciências Biológicas: Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
| | - Lucas Santos
- Centro de Estudos Em Estresse Oxidativo, Programa de Pós-Graduação Em Ciências Biológicas: Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
| | - Flávio Gabriel Carazza-Kessler
- Centro de Estudos Em Estresse Oxidativo, Programa de Pós-Graduação Em Ciências Biológicas: Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
| | - Daniel Pens Gelain
- Centro de Estudos Em Estresse Oxidativo, Programa de Pós-Graduação Em Ciências Biológicas: Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
| | - José Cláudio Fonseca Moreira
- Centro de Estudos Em Estresse Oxidativo, Programa de Pós-Graduação Em Ciências Biológicas: Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
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31
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Surati U, Niranjan SK, Pundir RK, Koul Y, Vohra V, Gandham RK, Kumar A. Genome-wide comparative analyses highlight selection signatures underlying saline adaptation in Chilika buffalo. Physiol Genomics 2024; 56:609-620. [PMID: 38949516 DOI: 10.1152/physiolgenomics.00028.2024] [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: 03/06/2024] [Revised: 05/30/2024] [Accepted: 06/25/2024] [Indexed: 07/02/2024] Open
Abstract
Chilika, a native buffalo breed of the Eastern coast of India, is mainly distributed around the Chilika brackish water lake connected with the Bay of Bengal Sea. This breed possesses a unique ability to delve deep into the salty water of the lake and stay there to feed on local vegetation of saline nature. Adaptation to salinity is a genetic phenomenon; however, the genetic basis underlying salinity tolerance is still limited in animals, specifically in livestock. The present study explores the genetic evolution that unveils the Chilika buffalo's adaptation to the harsh saline habitat, including both water and food systems. For this study, whole genome resequencing data on 18 Chilika buffalo and for comparison 10 Murrah buffalo of normal habitat were generated. For identification of selection sweeps, intrapopulation and interpopulation statistics were used. A total of 709, 309, 468, and 354 genes were detected to possess selection sweeps in Chilika buffalo using the nucleotide diversity (θπ), Tajima's D, nucleotide diversity ratio (θπ-ratio), and FST methods, respectively. Further analysis revealed a total of 23 genes including EXOC6B, VPS8, LYPD1, VPS35, CAMKMT, NCKAP5, COMMD1, myosin light chain kinase 3 (MYLK3), and B3GNT2 were found to be common by all the methods. Furthermore, functional annotation study of identified genes provided pathways such as MAPK signaling, renin secretion, endocytosis, oxytocin signaling pathway, etc. Gene network analysis enlists that hub genes provide insights into their interactions with each other. In conclusion, this study has highlighted the genetic basis underlying the local adaptive function of Chilika buffalo under saline environment.NEW & NOTEWORTHY Indian Chilika buffaloes are being maintained on extensive grazing system and have a unique ability to convert local salty vegetation into valuable human food. However, adaptability to saline habitat of Chilika buffalo has not been explored to date. Here, we identified genes and biological pathways involved, such as MAPK signaling, renin secretion, endocytosis, and oxytocin signaling pathway, underlying adaptability of Chilika buffalo to saline environment. This investigation shed light on the mechanisms underlying the buffalo's resilience in its native surroundings.
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Affiliation(s)
- Utsav Surati
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
- ICAR-National Dairy Research Institute, Karnal, India
| | | | | | - Ymberzal Koul
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
- ICAR-National Dairy Research Institute, Karnal, India
| | - Vikas Vohra
- ICAR-National Dairy Research Institute, Karnal, India
| | | | - Amod Kumar
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
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Sokouti B. The identification of biomarkers for Alzheimer's disease using a systems biology approach based on lncRNA-circRNA-miRNA-mRNA ceRNA networks. Comput Biol Med 2024; 179:108860. [PMID: 38996555 DOI: 10.1016/j.compbiomed.2024.108860] [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: 03/13/2024] [Revised: 06/16/2024] [Accepted: 07/06/2024] [Indexed: 07/14/2024]
Abstract
In addition to being the most prevalent form of neurodegeneration among the elderly, AD is a devastating multifactorial disease. Currently, treatments address only its symptoms. Several clinical studies have shown that the disease begins to manifest decades before the first symptoms appear, indicating that studying early changes is crucial to improving early diagnosis and discovering novel treatments. Our study used bioinformatics and systems biology to identify biomarkers in AD that could be used for diagnosis and prognosis. The procedure was performed on data from the GEO database, and GO and KEGG enrichment analysis were performed. Then, we set up a network of interactions between proteins. Several miRNA prediction tools including miRDB, miRWalk, and TargetScan were used. The ceRNA network led to the identification of eight mRNAs, four circRNAs, seven miRNAs, and seven lncRNAs. Multiple mechanisms, including the cell cycle and DNA replication, have been linked to the promotion of AD development by the ceRNA network. By using the ceRNA network, it should be possible to extract prospective biomarkers and therapeutic targets for the treatment of AD. It is possible that the processes involved in DNA cell cycle and the replication of DNA contribute to the development of Alzheimer's disease.
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Affiliation(s)
- Babak Sokouti
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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Li M, Muhammad JS, Zhao QL, Zakki SA, Hiraku Y, Hatta H, Tong X, Cui ZG, Wu C. Protective effects of baicalin against phenylarsine oxide-induced cytotoxicity in human skin keratinocytes. Bioorg Chem 2024; 150:107535. [PMID: 38865859 DOI: 10.1016/j.bioorg.2024.107535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 06/02/2024] [Accepted: 06/03/2024] [Indexed: 06/14/2024]
Abstract
Phenylarsine oxide (PAO) is a known environmental pollutant and skin keratinocytes are most seriously affected. Baicalin (BCN) was reported to have antioxidant and anti-inflammatory effects, but its protective effect against PAO toxicity is unknown. This study aimed at exploring whether baicalin can reverse the toxicity of human epidermal keratinocytes that are subjected to PAO exposure and underlying mechanisms. In silico analysis from a publicly accessible HaCaT cell transcriptome dataset exposed to chronic Arsenic showed significant differential expression of several genes, including the genes related to DNA replication. Later, we performed in vitro experiments, in which HaCaT cells were exposed to PAO (500 nM) in the existence of BCN (10-50 µM). Treatment of PAO alone induces the JNK, p38 and caspase-3 activation, which were engaged in the apoptosis induction, while the activity of AKT was significantly inhibited, which was engaged in the suppression of apoptosis. PAO suppressed SIRT3 expression and induced intracellular reactive oxygen species (ROS), causing a marked reduce in cell viability and apoptosis. However, BCN treatment restored the PAO-induced suppression of SIRT3 and AKT expression, reduced intracellular ROS generation, and markedly suppressed both caspase-3 activation and apoptosis induction. However, the protective effect of BCN was significantly attenuated after pretreatment with nicotinamide, an inhibitor of SIRT3. These findings indicate that BCN protects against cell death induced by PAO via inhibiting excessive intracellular ROS generation via restoring SIRT3 activity and reactivating downstream AKT pathway. In this study, we firstly shown that BCN is an efficient drug to prevent PAO-induced skin cytotoxicity, and these findings need to be confirmed by in vivo and clinical investigations.
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Affiliation(s)
- Mengling Li
- School of Medicine, Xizang Minzu University, No. 6 Wenhui East Road, Weicheng District, Xianyang, Shaanxi, 712082, China; Department of Environmental Health, University of Fukui School of Medical Sciences, University of Fukui, Fukui 910-1193, Japan
| | - Jibran Sualeh Muhammad
- Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Qing-Li Zhao
- Department of Radiology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 910-0194, Japan
| | - Shahbaz Ahmad Zakki
- Department of Public Health & Nutrition, The University of Haripur, Haripur, Khyber Pakhtunkhwa, Pakistan
| | - Yusuke Hiraku
- Department of Environmental Health, University of Fukui School of Medical Sciences, University of Fukui, Fukui 910-1193, Japan
| | - Hideki Hatta
- Department of Diagnostic Pathology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Xiaopeng Tong
- School of Medicine, Xizang Minzu University, No. 6 Wenhui East Road, Weicheng District, Xianyang, Shaanxi, 712082, China
| | - Zheng-Guo Cui
- Department of Environmental Health, University of Fukui School of Medical Sciences, University of Fukui, Fukui 910-1193, Japan.
| | - Chengai Wu
- National Center for Orthopaedics, Department of Molecular Orthopaedics, Beijing Research Institute of Traumatology and Orthopaedics, Beijing Jishuitan Hospital, Capital Medical University, Beijing, 100035, China.
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Liu H, Guan L, Su X, Zhao L, Shu Q, Zhang J. A broken network of susceptibility genes in the monocytes of Crohn's disease patients. Life Sci Alliance 2024; 7:e202302394. [PMID: 38925865 PMCID: PMC11208737 DOI: 10.26508/lsa.202302394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 06/15/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
Genome-wide association studies have identified over 200 genetic loci associated with inflammatory bowel disease; however, the mechanism of such a large amount of susceptibility genes remains uncertain. In this study, we integrated bioinformatics analysis and two independent single-cell transcriptome datasets to investigate the expression network of 232 susceptibility genes in Crohn's disease (CD) patients and healthy controls. The study revealed that most of the susceptibility genes are specifically and strictly expressed in the monocytes of the human intestinal tract. The susceptibility genes established a network within the monocytes of health control. The robustness of a gene network may prevent disease onset that is influenced by the genetic and environmental alteration in the expression of susceptibility genes. In contrast, we showed a sparse network in pediatric/adult CD patients, suggesting the broken network contributed to the CD etiology. The network status of susceptibility genes at the single-cell level of monocytes provided novel insight into the etiology.
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Affiliation(s)
- Hankui Liu
- Hebei Industrial Technology Research Institute of Genomics in Maternal & Child Health, Clin Lab, BGI Genomics, Shijiazhuang, China
- BGI Genomics, Shenzhen, China
| | - Liping Guan
- Hebei Industrial Technology Research Institute of Genomics in Maternal & Child Health, Clin Lab, BGI Genomics, Shijiazhuang, China
- BGI Genomics, Shenzhen, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xi Su
- BGI Genomics, Shenzhen, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lijian Zhao
- Hebei Industrial Technology Research Institute of Genomics in Maternal & Child Health, Clin Lab, BGI Genomics, Shijiazhuang, China
- BGI Genomics, Shenzhen, China
- Hebei Medical University, Shijiazhuang, China
| | - Qing Shu
- Department of Gastroenterology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China
| | - Jianguo Zhang
- Hebei Industrial Technology Research Institute of Genomics in Maternal & Child Health, Clin Lab, BGI Genomics, Shijiazhuang, China
- BGI Research, Shenzhen, China
- Hebei Medical University, Shijiazhuang, China
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Karczewska M, Wang AY, Narajczyk M, Słomiński B, Szalewska-Pałasz A, Nowicki D. Antibacterial activity of t-cinnamaldehyde: An approach to its mechanistic principle towards enterohemorrhagic Escherichia coli (EHEC). PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 132:155845. [PMID: 38964154 DOI: 10.1016/j.phymed.2024.155845] [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: 02/07/2024] [Revised: 06/14/2024] [Accepted: 06/25/2024] [Indexed: 07/06/2024]
Abstract
BACKGROUND Compounds of natural origin are potent source of drugs with unique mechanisms of action. Among phytochemicals, trans-cinnamaldehyde (t-CA) exhibits a wide range of biological activity, thus has been used for centuries to fight bacterial and fungal infections. However, the molecular basis of these properties has not been fully covered. Considering that difficult-to-control infections are becoming a rising global problem, there is a need to elucidate the molecular potential of t-CA. PURPOSE To evaluate the antibacterial activity of t-CA against Shiga-toxigenic E. coli strains and elucidate its mechanism of action based on the inhibition of the virulence factor expression. METHODS The antimicrobial potential of t-CA was assessed with two-fold microdilution and time-kill assays. Further evaluation included bioluminescence suppression assays, quantification of reactive oxygen species (ROS) and assessment of NAD+/NADH ratios. Morphological changes post t-CA exposure were examined using transmission electron microscopy. RNA sequencing and radiolabeling of nucleotides elucidated the metabolic alterations induced by t-CA. Toxin expression level was monitored through the application of fusion proteins, monitoring of bacteriophage development, and fluorescence microscopy studies. Lastly, the therapeutic efficacy in vivo was assessed using Galleria mellonella infection model. RESULTS A comprehensive study of t-CA's bioactivity showed unique properties affecting bacterial metabolism and morphology, resulting in significant bacterial cell deformation and effective virulence inhibition. Elucidation of the underlying mechanisms indicated that t-CA activates the global regulatory system, the stringent response, manifested by its alarmone, (p)ppGpp, overproduction mediated by the RelA enzyme, thereby inhibiting bacterial proliferation. Intriguingly, t-CA effectively downregulates Shiga toxin gene expression via alarmone molecules, indicating its potential for therapeutic effect. In vivo validation demonstrated a significant improvement in larval survival rates post- t-CA treatment with 50 mg/kg (p < 0.05), akin to the efficacy observed with azithromycin, thus indicating its effectiveness against EHEC infections (p < 0.05). CONCLUSIONS Collectively, these results reveal the robust antibacterial capabilities of t-CA, warranting its further exploration as a viable anti-infective agent.
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Affiliation(s)
- Monika Karczewska
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Ai Yan Wang
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Magdalena Narajczyk
- Bioimaging Laboratory, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Bartosz Słomiński
- Department of Medical Immunology, Faculty of Medicine, Medical University of Gdańsk, Gdańsk, Poland
| | - Agnieszka Szalewska-Pałasz
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Dariusz Nowicki
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland.
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López-Cerdán A, Andreu Z, Hidalgo MR, Soler-Sáez I, de la Iglesia-Vayá M, Mikozami A, Guerini FR, García-García F. An integrated approach to identifying sex-specific genes, transcription factors, and pathways relevant to Alzheimer's disease. Neurobiol Dis 2024; 199:106605. [PMID: 39009097 DOI: 10.1016/j.nbd.2024.106605] [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: 01/24/2024] [Revised: 06/06/2024] [Accepted: 07/11/2024] [Indexed: 07/17/2024] Open
Abstract
BACKGROUND Age represents a significant risk factor for the development of Alzheimer's disease (AD); however, recent research has documented an influencing role of sex in several features of AD. Understanding the impact of sex on specific molecular mechanisms associated with AD remains a critical challenge to creating tailored therapeutic interventions. METHODS The exploration of the sex-based differential impact on disease (SDID) in AD used a systematic review to first select transcriptomic studies of AD with data regarding sex in the period covering 2002 to 2021 with a focus on the primary brain regions affected by AD - the cortex (CT) and the hippocampus (HP). A differential expression analysis for each study and two tissue-specific meta-analyses were then performed. Focusing on the CT due to the presence of significant SDID-related alterations, a comprehensive functional characterization was conducted: protein-protein network interaction and over-representation analyses to explore biological processes and pathways and a VIPER analysis to estimate transcription factor activity. RESULTS We selected 8 CT and 5 HP studies from the Gene Expression Omnibus (GEO) repository for tissue-specific meta-analyses. We detected 389 significantly altered genes in the SDID comparison in the CT. Generally, female AD patients displayed more affected genes than males; we grouped said genes into six subsets according to their expression profile in female and male AD patients. Only subset I (repressed genes in female AD patients) displayed significant results during functional profiling. Female AD patients demonstrated more significant impairments in biological processes related to the regulation and organization of synapsis and pathways linked to neurotransmitters (glutamate and GABA) and protein folding, Aβ aggregation, and accumulation compared to male AD patients. These findings could partly explain why we observe more pronounced cognitive decline in female AD patients. Finally, we detected 23 transcription factors with different activation patterns according to sex, with some associated with AD for the first time. All results generated during this study are readily available through an open web resource Metafun-AD (https://bioinfo.cipf.es/metafun-ad/). CONCLUSION Our meta-analyses indicate the existence of differences in AD-related mechanisms in female and male patients. These sex-based differences will represent the basis for new hypotheses and could significantly impact precision medicine and improve diagnosis and clinical outcomes in AD patients.
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Affiliation(s)
- Adolfo López-Cerdán
- Computational Biomedicine Laboratory, Principe Felipe Research Center (CIPF), 46012, Valencia, Spain; Biomedical Imaging Unit FISABIO-CIPF, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana, 46012, Valencia, Spain
| | - Zoraida Andreu
- Foundation Valencian Institute of Oncology (FIVO), 46009, Valencia, Spain
| | - Marta R Hidalgo
- Computational Biomedicine Laboratory, Principe Felipe Research Center (CIPF), 46012, Valencia, Spain
| | - Irene Soler-Sáez
- Computational Biomedicine Laboratory, Principe Felipe Research Center (CIPF), 46012, Valencia, Spain
| | - María de la Iglesia-Vayá
- Biomedical Imaging Unit FISABIO-CIPF, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana, 46012, Valencia, Spain
| | - Akiko Mikozami
- Oral Health/Brain Health/Total health (OBT) Research Center, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | | | - Francisco García-García
- Computational Biomedicine Laboratory, Principe Felipe Research Center (CIPF), 46012, Valencia, Spain.
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Wang Z, Zhou W, Zhang Z, Zhang L, Li M. Metformin alleviates spinal cord injury by inhibiting nerve cell ferroptosis through upregulation of heme oxygenase-1 expression. Neural Regen Res 2024; 19:2041-2049. [PMID: 38227534 DOI: 10.4103/1673-5374.390960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 10/18/2023] [Indexed: 01/17/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202409000-00037/figure1/v/2024-01-16T170235Z/r/image-tiff Previous studies have reported upregulation of heme oxygenase-1 in different central nervous system injury models. Heme oxygenase-1 plays a critical anti-inflammatory role and is essential for regulating cellular redox homeostasis. Metformin is a classic drug used to treat type 2 diabetes that can inhibit ferroptosis. Previous studies have shown that, when used to treat cardiovascular and digestive system diseases, metformin can also upregulate heme oxygenase-1 expression. Therefore, we hypothesized that heme oxygenase-1 plays a significant role in mediating the beneficial effects of metformin on neuronal ferroptosis after spinal cord injury. To test this, we first performed a bioinformatics analysis based on the GEO database and found that heme oxygenase-1 was upregulated in the lesion of rats with spinal cord injury. Next, we confirmed this finding in a rat model of T9 spinal cord compression injury that exhibited spinal cord nerve cell ferroptosis. Continuous intraperitoneal injection of metformin for 14 days was found to both upregulate heme oxygenase-1 expression and reduce neuronal ferroptosis in rats with spinal cord injury. Subsequently, we used a lentivirus vector to knock down heme oxygenase-1 expression in the spinal cord, and found that this significantly reduced the effect of metformin on ferroptosis after spinal cord injury. Taken together, these findings suggest that metformin inhibits neuronal ferroptosis after spinal cord injury, and that this effect is partially dependent on upregulation of heme oxygenase-1.
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Affiliation(s)
- Zhihua Wang
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China
- Postdoctoral Innovation Practice Base, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China
| | - Wu Zhou
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China
| | - Zhixiong Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China
| | - Lulu Zhang
- Department of Nephrology, Nanchang People's Hospital Affiliated to Nanchang Medical College, Nanchang, Jiangxi Province, China
| | - Meihua Li
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China
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Yu JE, Jeon SH, Kim MJ, Kim DH, Koo JK, Kim TH, Kim B, Yoon JY, Lim YS, Park SR, Yeo IJ, Yun J, Son DJ, Han SB, Lee YS, Hong JT. Anti-chitinase-3-like 1 antibody attenuated atopic dermatitis-like skin inflammation through inhibition of STAT3-dependent CXCL8 expression. Br J Pharmacol 2024; 181:3232-3245. [PMID: 38745399 DOI: 10.1111/bph.16365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 01/27/2024] [Accepted: 02/02/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND AND PURPOSE Chitinase-3-like 1 (CHI3L1) causes skin inflammation in the progression of atopic dermatitis. We investigated if anti-CHI3L1 antibody could prevent the development of atopic dermatitis and its mechanisms of action. EXPERIMENTAL APPROACH The effect of CHI3L1 antibody on phthalic anhydride-induced atopic dermatitis animal model and in vitro reconstructed human skin (RHS) model were investigated. Expression and release of atopic dermatitis-related cytokines were determined using an enzyme-linked immunosorbent assay, and RT-qPCR, STAT3 and CXCL8 signalling were measured by western blotting. KEY RESULTS Anti-CHI3L1 antibody suppressed phthalic anhydride-induced epidermal thickening, clinical score, IgE level and infiltration of inflammatory cells, and reduced phthalic anhydride-induced inflammatory cytokines concentration. In addition, CHI3L1 antibody treatment inhibited the expression of STAT3 activity in phthalic anhydride-treated skin. It was also confirmed that CHI3L1 antibody treatment alleviated atopic dermatitis-related inflammation in the RHS model. The inhibitory effects of CHI3L1 antibody was similar or more effective compared with that of the IL-4 antibody. We further found that CHI3L1 is associated with CXCL8 by protein-association network analysis. siRNA of CHI3L1 blocked the mRNA levels of CHI3L1, IL-1β, IL-4, CXCL8, TSLP, and the expression of CHI3L1 and p-STAT, and the level of CXCL8, whereas recombinant level of CXCL8 was elevated. Moreover, siRNA of STAT3 reduced the mRNA level of these cytokines. CHI3L1 and p-STAT3 expression correlated with the reduced CXCL8 level in the RHS in vitro model. CONCLUSION AND IMPLICATIONS Our data demonstrated that CHI3L1 antibody could be a promising effective therapeutic drug for atopic dermatitis.
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Affiliation(s)
- Ji Eun Yu
- College of Pharmacy and Medical Research Center, Chungbuk National University, Cheongju-si, Chungbuk, Republic of Korea
- College of Pharmacy, Mokpo National University, Muan-gun, Jeonnam, Republic of Korea
| | - Seong Hee Jeon
- College of Pharmacy and Medical Research Center, Chungbuk National University, Cheongju-si, Chungbuk, Republic of Korea
| | - Min Ji Kim
- College of Pharmacy and Medical Research Center, Chungbuk National University, Cheongju-si, Chungbuk, Republic of Korea
| | - Dae Hwan Kim
- College of Pharmacy and Medical Research Center, Chungbuk National University, Cheongju-si, Chungbuk, Republic of Korea
| | - Ja Keun Koo
- College of Pharmacy and Medical Research Center, Chungbuk National University, Cheongju-si, Chungbuk, Republic of Korea
| | - Tae Hun Kim
- Autotelic Bio Inc., Cheongju-si, Chungbuk, Republic of Korea
| | - Bongcheol Kim
- Senelix Co. Ltd., Songpa-gu, Seoul, Republic of Korea
| | - Ji Yong Yoon
- PRESTI GEBIOLOGICS Co. Ltd., Cheongju-si, Chungbuk, Republic of Korea
| | - Young-Soo Lim
- PRESTI GEBIOLOGICS Co. Ltd., Cheongju-si, Chungbuk, Republic of Korea
| | - So Ra Park
- New Drug Development Center, Osong Medical Innovation Foundation, Cheongju-si, Chungcheongbuk-do, Korea
| | - In Jun Yeo
- College of Pharmacy and Medical Research Center, Chungbuk National University, Cheongju-si, Chungbuk, Republic of Korea
- College of Pharmacy, Kyungpook National University, Buk-gu, Daegu, Republic of Korea
| | - Jaesuk Yun
- College of Pharmacy and Medical Research Center, Chungbuk National University, Cheongju-si, Chungbuk, Republic of Korea
| | - Dong Ju Son
- College of Pharmacy and Medical Research Center, Chungbuk National University, Cheongju-si, Chungbuk, Republic of Korea
| | - Sang-Bae Han
- College of Pharmacy and Medical Research Center, Chungbuk National University, Cheongju-si, Chungbuk, Republic of Korea
| | - Yong Sun Lee
- College of Pharmacy and Medical Research Center, Chungbuk National University, Cheongju-si, Chungbuk, Republic of Korea
| | - Jin Tae Hong
- College of Pharmacy and Medical Research Center, Chungbuk National University, Cheongju-si, Chungbuk, Republic of Korea
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Li J, Yao J. CD8 + T cell‑related KCTD5 contributes to malignant progression and unfavorable clinical outcome of patients with triple‑negative breast cancer. Mol Med Rep 2024; 30:166. [PMID: 39027992 PMCID: PMC11267436 DOI: 10.3892/mmr.2024.13290] [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: 03/14/2024] [Accepted: 06/06/2024] [Indexed: 07/20/2024] Open
Abstract
Triple‑negative breast cancer (TNBC) is a highly aggressive and heterogeneous subtype of breast cancer that lacks expression of estrogen receptor, progesterone receptor, and HER2, making it more challenging to treat with targeted therapies. The present study aimed to identify CD8+ T cell‑associated genes, which could provide insight into the mechanisms underlying TNBC to facilitate developing novel immunotherapies. TNBC datasets were downloaded from public databases including The Cancer Genome Atlas, Molecular Taxonomy of Breast Cancer International Consortium, and Gene Expression Omnibus. Candidate genes were identified integrating weighted gene co‑expression network analysis (WGCNA), differential gene expression, protein‑protein‑interaction network construction and univariate Cox regression analysis. Kaplan‑Meier survival, multivariate Cox regression and receiver operating characteristic analysis were performed to evaluate the prognostic value of hub genes. Knockdown experiments, alongside wound healing, Cell Counting Kit‑8 and Transwell migration and invasion assays were performed. In total, seven gene modules were associated with CD8+ T cells using WGCNA, among which potassium channel tetramerization domain 5 (KCTD5) was significantly upregulated in TNBC samples and was associated with poor prognosis. KCTD5 expression inversely associated with infiltration ratios of 'Macrophages M1', 'Plasma cells', and 'γδ T cells', but positively with 'activated Mast cells', 'Macrophages M0', and 'Macrophages M2'. As an independent prognostic indicator for TNBC, KCTD5 was also associated with drug sensitivity and the expression of programmed cell death protein 1, Cytotoxic T‑Lymphocyte‑Associated Protein 4 (CTLA4), CD274), Cluster of Differentiation 86 (CD86), Lymphocyte‑Activation Gene 3 (LAG3), T Cell Immunoreceptor with Ig and ITIM Domains (TIGIT). Knockdown of KCTD5 significantly inhibited viability, migration and invasion of TNBC cells in vitro. KCTD5 was suggested to impact the tumor immune microenvironment by influencing the infiltration of immune cells and may serve as a potential therapeutic target for TNBC.
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Affiliation(s)
- Jia Li
- Department of Breast Surgical Oncology, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, Shanxi 030013, P.R. China
| | - Jingchun Yao
- Department of Head and Neck, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, Shanxi 030013, P.R. China
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Yuan Z, Shu L, Fu J, Yang P, Wang Y, Sun J, Zheng M, Liu Z, Yang J, Song J, Song S, Cai Z. Single-Cell RNA Sequencing Deconstructs the Distribution of Immune Cells Within Abdominal Aortic Aneurysms in Mice. Arterioscler Thromb Vasc Biol 2024; 44:1986-2003. [PMID: 39051127 DOI: 10.1161/atvbaha.124.321129] [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: 04/20/2024] [Accepted: 07/15/2024] [Indexed: 07/27/2024]
Abstract
BACKGROUND Inflammation is a key component in the development of abdominal aortic aneurysm (AAA), yet insights into the roles of immune cells and their interactions in this process are limited. METHODS Using single-cell RNA transcriptomic analysis, we deconstructed the CD45+ cell population in elastase-induced murine AAA at the single-cell level. We isolated each group of immune cells from murine AAA tissue at different time points and divided them into several subtypes, listed the remarkable differentially expressed genes, explored the developmental trajectories of immune cells, and demonstrated the interactions among them. RESULTS Our findings reveal significant differences in several immune cell subsets, including macrophages, dendritic cells, and T cells, within the AAA microenvironment compared with the normal aorta. Especially, conventional dendritic cell type 1 exclusively existed in the AAA tissue rather than the normal aortas. Via CellChat analysis, we identified several intercellular communication pathways like visfatin, which targets monocyte differentiation and neutrophil extracellular trap-mediated interaction between neutrophils and dendritic cells, which might contribute to AAA development. Some of these pathways were validated in human AAA. CONCLUSIONS Despite the absence of external pathogenic stimuli, AAA tissues develop a complex inflammatory microenvironment involving numerous immune cells. In-depth studies of the inflammatory network shall provide new strategies for patients with AAA.
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MESH Headings
- Aortic Aneurysm, Abdominal/immunology
- Aortic Aneurysm, Abdominal/genetics
- Aortic Aneurysm, Abdominal/chemically induced
- Aortic Aneurysm, Abdominal/pathology
- Aortic Aneurysm, Abdominal/metabolism
- Animals
- Single-Cell Analysis
- Disease Models, Animal
- Mice, Inbred C57BL
- Aorta, Abdominal/pathology
- Aorta, Abdominal/metabolism
- Aorta, Abdominal/immunology
- Mice
- Dendritic Cells/immunology
- Dendritic Cells/metabolism
- Humans
- Macrophages/metabolism
- Macrophages/immunology
- Male
- Transcriptome
- RNA-Seq
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- Gene Expression Profiling/methods
- Pancreatic Elastase
- Cell Communication
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Affiliation(s)
- Zhen Yuan
- Departments of Cardiology (Z.Y., L.S., Y.W., Z.C.), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- State Key Laboratory of Transvascular Implantation Devices, China (Z.Y., L.S., Y.W., Z.C.)
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, China (Z.Y., L.S., Y.W., Z.C.)
| | - Li Shu
- Departments of Cardiology (Z.Y., L.S., Y.W., Z.C.), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- State Key Laboratory of Transvascular Implantation Devices, China (Z.Y., L.S., Y.W., Z.C.)
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, China (Z.Y., L.S., Y.W., Z.C.)
| | - Jiantao Fu
- Institute of Hepatology and Metabolic Diseases, Hangzhou Normal University, China (J.F., P.Y., J.Y.)
| | - Peipei Yang
- Institute of Hepatology and Metabolic Diseases, Hangzhou Normal University, China (J.F., P.Y., J.Y.)
| | - Yidong Wang
- Departments of Cardiology (Z.Y., L.S., Y.W., Z.C.), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- State Key Laboratory of Transvascular Implantation Devices, China (Z.Y., L.S., Y.W., Z.C.)
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, China (Z.Y., L.S., Y.W., Z.C.)
| | - Jie Sun
- Pathology (J. Sun, M.Z.), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Mengsha Zheng
- Pathology (J. Sun, M.Z.), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhenjie Liu
- Vascular Surgery (Z.L.), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jin Yang
- Institute of Hepatology and Metabolic Diseases, Hangzhou Normal University, China (J.F., P.Y., J.Y.)
| | - Jiangping Song
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, China (J. Song, S.S.)
| | - Shen Song
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, China (J. Song, S.S.)
| | - Zhejun Cai
- Departments of Cardiology (Z.Y., L.S., Y.W., Z.C.), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- State Key Laboratory of Transvascular Implantation Devices, China (Z.Y., L.S., Y.W., Z.C.)
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, China (Z.Y., L.S., Y.W., Z.C.)
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Kırbaş OK, Bozkurt BT, Yıldırım MR, Taşlı PN, Abdik H, Şahin F, Avşar Abdik E. A Perspective on the Characterization of Early Neural Progenitor Cell-Derived Extracellular Vesicles for Targeted Delivery to Neuroblastoma Cells. Neurochem Res 2024; 49:2364-2378. [PMID: 38837091 PMCID: PMC11310242 DOI: 10.1007/s11064-024-04165-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 04/24/2024] [Accepted: 05/22/2024] [Indexed: 06/06/2024]
Abstract
As an element of the cellular signaling systems, extracellular vesicles (EVs) exhibit many desirable traits for usage as targeted delivery vehicles. When administered, EVs cause little to no toxic or immune response, stay in circulation for longer periods compared to synthetic carriers, preferentially accumulate in tissues that are the same or similar to their cell-of-origin and can pass through the blood-brain barrier. Combined, these traits make neural EVs a particularly promising tool for delivering drugs to the brain. This study aims to combine tissue and EVs engineering to prepare neural differentiated cells derived EVs that exhibit neural properties, to develop an effective, tissue-homing drug and gene delivery platform for the brain. Early neural differentiated cell-derived EVs were produced with neural characteristics from neural differentiated human neonatal dermal fibroblasts. The EVs carried key neural proteins such as Nestin, Sox2 and Doublecortin. The cellular uptake of early neural differentiated cell-derived EVs was higher compared to non-neural EVs during in vitro uptake assays on neuroblastoma cells. Moreover, eND-EVs were significantly decreased the viability of neuroblastoma cells. In conclusion, this study revealed that early neural differentiated cell-derived EVs have potential as a promising drug carrier for the treatment of various neural disorders.
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Affiliation(s)
- Oğuz Kaan Kırbaş
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Yeditepe University, Istanbul, 34755, Turkey
| | - Batuhan Turhan Bozkurt
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Yeditepe University, Istanbul, 34755, Turkey
| | - Melis Rahime Yıldırım
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Yeditepe University, Istanbul, 34755, Turkey
| | - Pakize Neslihan Taşlı
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Yeditepe University, Istanbul, 34755, Turkey
| | - Hüseyin Abdik
- Department of Molecular Biology and Genetics, Faculty of Engineering and Natural Sciences, İstanbul Sabahattin Zaim University, Istanbul, 34303, Turkey
| | - Fikrettin Şahin
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Yeditepe University, Istanbul, 34755, Turkey
| | - Ezgi Avşar Abdik
- Department of Genomics, Faculty of Aquatic Sciences, Istanbul University, Istanbul, 34134, Turkey.
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Lu T, Chen X, Zhang Q, Shang K, Yang X, Xiang W. Vitamin D Relieves Epilepsy Symptoms and Neuroinflammation in Juvenile Mice by Activating the mTOR Signaling Pathway via RAF1: Insights from Network Pharmacology and Molecular Docking Studies. Neurochem Res 2024; 49:2379-2392. [PMID: 38837094 DOI: 10.1007/s11064-024-04176-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 03/15/2024] [Accepted: 05/22/2024] [Indexed: 06/06/2024]
Abstract
Epilepsy is a common neurological disorder, and the exploration of potential therapeutic drugs for its treatment is still ongoing. Vitamin D has emerged as a promising treatment due to its potential neuroprotective effects and anti-epileptic properties. This study aimed to investigate the effects of vitamin D on epilepsy and neuroinflammation in juvenile mice using network pharmacology and molecular docking, with a focus on the mammalian target of rapamycin (mTOR) signaling pathway. Experimental mouse models of epilepsy were established through intraperitoneal injection of pilocarpine, and in vitro injury models of hippocampal neurons were induced by glutamate (Glu) stimulation. The anti-epileptic effects of vitamin D were evaluated both in vivo and in vitro. Network pharmacology and molecular docking analysis were used to identify potential targets and regulatory pathways of vitamin D in epilepsy. The involvement of the mTOR signaling pathway in the regulation of mouse epilepsy by vitamin D was validated using rapamycin (RAPA). The levels of inflammatory cytokines (TNF-α, IL-1β, and IL-6) were assessed by enzyme-linked immunosorbent assay (ELISA). Gene and protein expressions were detected by quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot, respectively. The terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate nick end-labeling (TUNEL) staining was used to analyze the apoptosis of hippocampal neurons. In in vivo experiments, vitamin D reduced the Racine scores of epileptic mice, prolonged the latency of epilepsy, and inhibited the production of TNF-α, IL-1β, and IL-6 in the hippocampus. Furthermore, network pharmacology analysis identified RAF1 as a potential target of vitamin D in epilepsy, which was further confirmed by molecular docking analysis. Additionally, the mTOR signaling pathway was found to be involved in the regulation of mouse epilepsy by vitamin D. In in vitro experiments, Glu stimulation upregulated the expressions of RAF1 and LC3II/LC3I, inhibited mTOR phosphorylation, and induced neuronal apoptosis. Mechanistically, vitamin D activated the mTOR signaling pathway and alleviated mouse epilepsy via RAF1, while the use of the pathway inhibitor RAPA reversed this effect. Vitamin D alleviated epilepsy symptoms and neuroinflammation in juvenile mice by activating the mTOR signaling pathway via RAF1. These findings provided new insights into the molecular mechanisms underlying the anti-epileptic effects of vitamin D and further supported its use as an adjunctive therapy for existing anti-epileptic drugs.
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Affiliation(s)
- Tiantian Lu
- School of Pediatrics, Hainan Medical University, Haikou, 571199, China
- Department of Neonatology, Haikou Maternal and Child Health Hospital, Haikou, 570203, China
| | - Xiuling Chen
- Department of Pediatric Medicine, Affiliated Haikou Hospital of Xiangya Medical School Central South University, Haikou, 570208, China
| | - Qin Zhang
- Department of Neurosurgery, Hainan Women and Children's Medical Center, Haikou, 570312, China
| | - Kun Shang
- Institute of Deep-sea Science and Engineering, Chinese Academy of Science, Sanya, 572000, China
| | - Xiaogui Yang
- Department of Neonatology, Haikou Maternal and Child Health Hospital, Haikou, 570203, China
| | - Wei Xiang
- School of Pediatrics, Hainan Medical University, Haikou, 571199, China.
- Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, 570312, China.
- National Health Commission (NHC) Key Laboratory of Tropical Disease Control, Hainan Medical University, Haikou, 570216, China.
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Agarwal P, Chittora A, Baraiya BM, Fatnani D, Patel K, Akhyani DD, Parida AK, Agarwal PK. Rab7 GTPase-Mediated stress signaling enhances salinity tolerance in AlRabring7 tobacco transgenics by modulating physio-biochemical parameters. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 214:108928. [PMID: 39033652 DOI: 10.1016/j.plaphy.2024.108928] [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: 04/11/2024] [Revised: 06/19/2024] [Accepted: 07/09/2024] [Indexed: 07/23/2024]
Abstract
The RING-type E3 ligases play a significant role in stress signaling, primarily through post-translational regulation. Ubiquitination is a crucial post-translational modification that regulates the turnover and activity of proteins. The overexpression of AlRabring7, RING-HC E3 Ub ligase in tobacco provides insights into the regulation of salinity and ABA signaling in transgenic tobacco. The seed germination potential of AlRabring7 transgenics was higher than WT, with NaCl and ABA treatments. The transgenics showed improved morpho-physio-biochemical parameters in response to salinity and ABA treatments. The photosynthetic pigments, soluble sugars, reducing sugars and proline increased in transgenics in response to NaCl and ABA treatments. The decreased ROS accumulation in transgenics on NaCl and ABA treatments can be co-related to improved activity of enzymatic and non-enzymatic antioxidants. The potential of transgenics to maintain ABA levels with ABA treatment, highlights the active participation of ABA feedback loop mechanism. Interestingly, the ability of AlRabring7 transgenics to upregulate Rab7 protein, suggests its role in facilitating vacuolar transport. Furthermore, the improved potassium accumulation and reduced sodium content indicate an efficient ion regulation mechanism in transgenic plants facilitating higher stomatal opening. The expression of downstream ion transporter (NbNHX1 and NbVHA1), ABA signaling (NbABI2 and NbABI5) and vesicle trafficking (NbMON1) responsive genes were upregulated with stress. The present study, reports that AlRabring7 participates in maintaining vacuolar transport, ion balance, ROS homeostasis, stomatal regulation through activation of Rab7 protein and regulation of downstream stress-responsive during stress. This emphasizes the potential of AlRabring7 gene for improved performance and resilience in challenging environments.
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Affiliation(s)
- Parinita Agarwal
- Plant Omics Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Gijubhai Badheka Marg, Bhavnagar, 364 002, Gujarat, India.
| | - Anjali Chittora
- Plant Omics Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Gijubhai Badheka Marg, Bhavnagar, 364 002, Gujarat, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Bhagirath M Baraiya
- Plant Omics Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Gijubhai Badheka Marg, Bhavnagar, 364 002, Gujarat, India
| | - Dhara Fatnani
- Plant Omics Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Gijubhai Badheka Marg, Bhavnagar, 364 002, Gujarat, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Khantika Patel
- Plant Omics Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Gijubhai Badheka Marg, Bhavnagar, 364 002, Gujarat, India
| | - Dhanvi D Akhyani
- Plant Omics Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Gijubhai Badheka Marg, Bhavnagar, 364 002, Gujarat, India
| | - Asish K Parida
- Plant Omics Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Gijubhai Badheka Marg, Bhavnagar, 364 002, Gujarat, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Pradeep K Agarwal
- Plant Omics Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Gijubhai Badheka Marg, Bhavnagar, 364 002, Gujarat, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Datta C, Das P, Dutta S, Prasad T, Banerjee A, Gehlot S, Ghosal A, Dhabal S, Biswas P, De D, Chaudhuri S, Bhattacharjee A. AMPK activation reduces cancer cell aggressiveness via inhibition of monoamine oxidase A (MAO-A) expression/activity. Life Sci 2024; 352:122857. [PMID: 38914305 DOI: 10.1016/j.lfs.2024.122857] [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: 03/01/2024] [Revised: 06/14/2024] [Accepted: 06/16/2024] [Indexed: 06/26/2024]
Abstract
AIM AMPK can be considered as an important target molecule for cancer for its unique ability to directly recognize cellular energy status. The main aim of this study is to explore the role of different AMPK activators in managing cancer cell aggressiveness and to understand the mechanistic details behind the process. MAIN METHODS First, we explored the AMPK expression pattern and its significance in different subtypes of lung cancer by accessing the TCGA data sets for LUNG, LUAD and LUSC patients and then established the correlation between AMPK expression pattern and overall survival of lung cancer patients using Kaplan-Meire plot. We further carried out several cell-based assays by employing different wet lab techniques including RT-PCR, Western Blot, proliferation, migration and invasion assays to fulfil the aim of the study. KEY FINDINGS SIGNIFICANCE: This study identifies the importance of AMPK activators as a repurposing agent for combating lung and colon cancer cell aggressiveness. It also suggests SRT-1720 as a potent repurposing agent for cancer treatment especially in NSCLC patients where a point mutation is present in LKB1.
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Affiliation(s)
- Chandreyee Datta
- Department of Biotechnology, National Institute of Technology, Durgapur, Mahatma Gandhi Avenue, 713209 Burdwan, West Bengal, India
| | - Payel Das
- Department of Biotechnology, National Institute of Technology, Durgapur, Mahatma Gandhi Avenue, 713209 Burdwan, West Bengal, India
| | - Subhajit Dutta
- Department of Biotechnology, National Institute of Technology, Durgapur, Mahatma Gandhi Avenue, 713209 Burdwan, West Bengal, India
| | - Tuhina Prasad
- Department of Biotechnology, National Institute of Technology, Durgapur, Mahatma Gandhi Avenue, 713209 Burdwan, West Bengal, India
| | - Abhineet Banerjee
- Department of Biotechnology, National Institute of Technology, Durgapur, Mahatma Gandhi Avenue, 713209 Burdwan, West Bengal, India
| | - Sameep Gehlot
- Department of Biotechnology, National Institute of Technology, Durgapur, Mahatma Gandhi Avenue, 713209 Burdwan, West Bengal, India
| | - Arpa Ghosal
- Department of Biotechnology, National Institute of Technology, Durgapur, Mahatma Gandhi Avenue, 713209 Burdwan, West Bengal, India
| | - Sukhamoy Dhabal
- Department of Biotechnology, National Institute of Technology, Durgapur, Mahatma Gandhi Avenue, 713209 Burdwan, West Bengal, India
| | - Pritam Biswas
- Department of Biotechnology, National Institute of Technology, Durgapur, Mahatma Gandhi Avenue, 713209 Burdwan, West Bengal, India
| | - Debojyoti De
- Department of Biotechnology, National Institute of Technology, Durgapur, Mahatma Gandhi Avenue, 713209 Burdwan, West Bengal, India
| | - Surabhi Chaudhuri
- Department of Biotechnology, National Institute of Technology, Durgapur, Mahatma Gandhi Avenue, 713209 Burdwan, West Bengal, India
| | - Ashish Bhattacharjee
- Department of Biotechnology, National Institute of Technology, Durgapur, Mahatma Gandhi Avenue, 713209 Burdwan, West Bengal, India.
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45
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Ghosh S, Ghatak D, Dutta R, Goswami D, De R. PINK1 insufficiency can be exploited as a specific target for drug combinations inducing mitochondrial pathology-mediated cell death in gastric adenocarcinoma. Arch Biochem Biophys 2024; 759:110110. [PMID: 39103009 DOI: 10.1016/j.abb.2024.110110] [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: 02/04/2024] [Revised: 07/23/2024] [Accepted: 08/02/2024] [Indexed: 08/07/2024]
Abstract
There exist very limited non-hazardous therapeutic strategies except for surgical resection and lymphadenectomy against gastric cancer (GC) despite being the third leading cause of cancer deaths worldwide. This study proposes an innovative treatment approach against GC using a drug combination strategy that manipulates mitochondrial dynamics in conjunction with the induction of mitochondrial pathology-mediated cell death. Comparative analysis was done with gastric adenocarcinoma and normal cells by qPCR, western blot, microscopic immunocytochemistry, and live cell imaging. In this study, impairment of dynamin-related protein 1 (Drp1)-mediated mitochondrial fission by Mdivi-1 created an imbalance in mitochondrial structural dynamics in indomethacin-treated AGS cells in which mitophagy-regulator protein PINK1 is downregulated. These drug combinations with the individual sub-lethal doses ultimately led to the activation of cell death machinery upregulating pro-apoptotic proteins like Bax, Puma, and Noxa. Interestingly, this combinatorial therapy did not affect normal gastric epithelial cells significantly and also no significant upregulation of death markers was observed. Moreover, the drug combination strategy also retarded cell migration and reduced stemness in GC cells. In summary, this study offers a pioneering specific therapeutic strategy for GC treatment, sparing normal cells providing opportunities for minimal drug-mediated toxicity utilizing mitochondria as a viable and specific target for anti-cancer therapy in gastric cancer.
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Affiliation(s)
- Sayak Ghosh
- Amity Institute of Biotechnology, Amity University Kolkata, Plot No: 36, 37 & 38, Major Arterial Road, Action Area II, Kadampukur Village, Newtown, Kolkata, 700135, West Bengal, India
| | - Debapriya Ghatak
- Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700032, West Bengal, India
| | - Rittick Dutta
- Swami Vivekananda University, Kolkata, 700121, West Bengal, India
| | - Devyani Goswami
- Amity Institute of Biotechnology, Amity University Kolkata, Plot No: 36, 37 & 38, Major Arterial Road, Action Area II, Kadampukur Village, Newtown, Kolkata, 700135, West Bengal, India
| | - Rudranil De
- Amity Institute of Biotechnology, Amity University Kolkata, Plot No: 36, 37 & 38, Major Arterial Road, Action Area II, Kadampukur Village, Newtown, Kolkata, 700135, West Bengal, India.
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46
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Shi X, Qi Z, Huang D, Zhu J, Shen X, Liu T. HuR facilitates miR-93-5p-induced activation of MAP3K2 translation via MAP3K2 3'UTR ARE2 in hepatocellular carcinoma. Biochem Biophys Res Commun 2024; 722:150152. [PMID: 38795452 DOI: 10.1016/j.bbrc.2024.150152] [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: 05/07/2024] [Revised: 05/09/2024] [Accepted: 05/20/2024] [Indexed: 05/28/2024]
Abstract
MicroRNAs (miRNAs) can positively regulate gene expression through an unconventional RNA activation mechanism involving direct targeting 3' untranslated regions (UTRs). Our prior study found miR-93-5p activates mitogen-activated protein kinase kinase kinase 2 (MAP3K2) in hepatocellular carcinoma (HCC) via its 3'UTR. However, the underlying mechanism remains elusive. Here, we identified two candidate AU-rich element (ARE) motifs (ARE1 and ARE2) adjacent to the miR-93-5p binding site located within the MAP3K2 3'UTR using AREsite2. Luciferase reporter and translation assays validated that only ARE2 participated in MAP3K2 activation. Integrative analysis revealed that human antigen R (HuR), an ARE2-associated RNA-binding protein (RBP), physically and functionally interacted with the MAP3K2 3'UTR. Consequently, an HuR-ARE2 complex was shown to facilitate miR-93-5p-mediated upregulation of MAP3K2 expression. Furthermore, bioinformatics analysis and studies of HCC cells and specimens highlighted an oncogenic role for HuR and positive HuR-MAP3K2 expression correlation. HuR is also an enhancing factor in the positive feedback circuit comprising miR-93-5p, MAP3K2, and c-Jun demonstrated in our prior study. The newly identified HuR-ARE2 involvement enriches the mechanism of miR-93-5p-driven MAP3K2 activation and suggests new therapeutic strategies warranted for exploration in HCC.
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Affiliation(s)
- Xuan Shi
- Department of Gastroenterology and Hepatology, and Shanghai Institute of Liver Diseases, Zhongshan Hospital of Fudan University, 180 Fenglin Rd., Shanghai, 200032, China
| | - Zhuoran Qi
- Department of Gastroenterology and Hepatology, and Shanghai Institute of Liver Diseases, Zhongshan Hospital of Fudan University, 180 Fenglin Rd., Shanghai, 200032, China
| | - Dongbo Huang
- Department of Gastroenterology and Hepatology, and Shanghai Institute of Liver Diseases, Zhongshan Hospital of Fudan University, 180 Fenglin Rd., Shanghai, 200032, China
| | - Jimin Zhu
- Department of Gastroenterology and Hepatology, and Shanghai Institute of Liver Diseases, Zhongshan Hospital of Fudan University, 180 Fenglin Rd., Shanghai, 200032, China
| | - Xizhong Shen
- Department of Gastroenterology and Hepatology, and Shanghai Institute of Liver Diseases, Zhongshan Hospital of Fudan University, 180 Fenglin Rd., Shanghai, 200032, China
| | - Taotao Liu
- Department of Gastroenterology and Hepatology, and Shanghai Institute of Liver Diseases, Zhongshan Hospital of Fudan University, 180 Fenglin Rd., Shanghai, 200032, China; Department of Gastroenterology and Hepatology, Shanghai Geriatric Medical Center, 2560 Chunshen Rd., Shanghai, 201104, China.
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47
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Moskalenko AM, Ikrin AN, Kozlova AV, Mukhamadeev RR, de Abreu MS, Riga V, Kolesnikova TO, Kalueff AV. Decoding Molecular Bases of Rodent Social Hetero-Grooming Behavior Using in Silico Analyses and Bioinformatics Tools. Neuroscience 2024; 554:146-155. [PMID: 38876356 DOI: 10.1016/j.neuroscience.2024.06.004] [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: 05/04/2024] [Revised: 06/03/2024] [Accepted: 06/06/2024] [Indexed: 06/16/2024]
Abstract
Highly prevalent in laboratory rodents, 'social' hetero-grooming behavior is translationally relevant to modeling a wide range of neuropsychiatric disorders. Here, we comprehensively evaluated all known to date mouse genes linked to aberrant hetero-grooming phenotype, and applied bioinformatics tools to construct a network of their established protein-protein interactions (PPI). We next identified several distinct molecular clusters within this complex network, including neuronal differentiation, cytoskeletal, WNT-signaling and synapsins-associated pathways. Using additional bioinformatics analyses, we further identified 'central' (hub) proteins within these molecular clusters, likely key for mouse hetero-grooming behavior. Overall, a more comprehensive characterization of intricate molecular pathways linked to aberrant rodent grooming may markedly advance our understanding of underlying cellular mechanisms and related neurological disorders, eventually helping discover novel targets for their pharmacological or gene therapy interventions.
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Affiliation(s)
- Anastasia M Moskalenko
- Graduate Program in Genetics and Genetic Technologies, Sirius University of Science and Technology, Sochi 354340, Russia; Neuroscience Department, Sirius University of Science and Technology, Sochi 354340, Russia
| | - Aleksey N Ikrin
- Graduate Program in Genetics and Genetic Technologies, Sirius University of Science and Technology, Sochi 354340, Russia; Neuroscience Department, Sirius University of Science and Technology, Sochi 354340, Russia
| | - Alena V Kozlova
- Graduate Program in Genetics and Genetic Technologies, Sirius University of Science and Technology, Sochi 354340, Russia
| | - Radmir R Mukhamadeev
- Graduate Program in Bioinformatics and Genomics, Sirius University of Science and Technology, Sochi 354340, Russia; Neuroscience Department, Sirius University of Science and Technology, Sochi 354340, Russia
| | - Murilo S de Abreu
- Graduate Program in Health Sciences, Federal University of Health Sciences of Porto Alegre, Porto Alegre 90050, Brazil.
| | - Vyacheslav Riga
- Neuroscience Department, Sirius University of Science and Technology, Sochi 354340, Russia
| | - Tatiana O Kolesnikova
- Neuroscience Department, Sirius University of Science and Technology, Sochi 354340, Russia
| | - Allan V Kalueff
- Neuroscience Department, Sirius University of Science and Technology, Sochi 354340, Russia; Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia; Institute of Experimental Medicine, Almazov National Medical Research Centre, Ministry of Healthcare of Russian Federation, St. Petersburg 194021, Russia; Suzhou Key Laboratory of Neurobiology and Cell Signaling, Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University (XJTLU), Suzhou 215123, China.
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48
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Zhong Y, Wen W, Luo Z, Cheng N. A multi-component, multi-target, and multi-pathway prediction method for Chinese medicine based on the combination of mass spectrometry analysis and network analysis: An example using Weifuchun. J Chromatogr A 2024; 1731:465164. [PMID: 39043100 DOI: 10.1016/j.chroma.2024.465164] [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: 04/02/2024] [Revised: 07/03/2024] [Accepted: 07/12/2024] [Indexed: 07/25/2024]
Abstract
Weifuchun, a Chinese medicinal prescription made from herbs of natural origin including Hongshen (Ginseng Radix et Rhizoma Rubra), Xiangchacai (Rabdosia Amethystoides), and Zhiqiao (Aurantii Fructus), has attracted increasing attention for clinically treating chronic atrophic gastritis, which is characterized by the chronic inflammation of the gastric mucosa leading to progressive loss of gastric glandular cells. To investigate the active ingredients and potential mechanisms of WFC, it was analyzed using a novel multi-component, multi-target, and multi-pathway prediction method. High/ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (HPLC/UPLC-Q-TOF-MS) was employed to separate and profile the chemical constituents of WFC with high precision and efficiency. Network analysis and molecular docking were used to predict bioactive compounds and their interactions with biological targets. The results highlight 42 significant compounds potentially contributing to the therapeutic effects of WFC by effecting on several key pathways, including proved PI3K/Akt, NF-κB, and JAK/STAT signaling pathways. This study showcases the efficacy of combining advanced chromatographic techniques with computational methods to elucidate the pharmacological mechanisms of complex botanical drugs.
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Affiliation(s)
- Yi Zhong
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, China
| | - Wu Wen
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, China
| | - Zhenyu Luo
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, China
| | - Ningtao Cheng
- School of Medicine, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, China.
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49
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Ferreira JC, Fadl S, Cardoso THS, Andrade BS, Melo TS, Silva EMDA, Agarwal A, Turville SJ, Saksena NK, Rabeh WM. Boosting immunity: synergistic antiviral effects of luteolin, vitamin C, magnesium and zinc against SARS-CoV-2 3CLpro. Biosci Rep 2024; 44:BSR20240617. [PMID: 39045772 PMCID: PMC11327220 DOI: 10.1042/bsr20240617] [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: 05/17/2024] [Revised: 07/10/2024] [Accepted: 07/23/2024] [Indexed: 07/25/2024] Open
Abstract
SARS-CoV-2 was first discovered in 2019 and has disseminated throughout the globe to pandemic levels, imposing significant health and economic burdens. Although vaccines against SARS-CoV-2 have been developed, their long-term efficacy and specificity have not been determined, and antiviral drugs remain necessary. Flavonoids, which are commonly found in plants, fruits, and vegetables and are part of the human diet, have attracted considerable attention as potential therapeutic agents due to their antiviral and antimicrobial activities and effects on other biological activities, such as inflammation. The present study uses a combination of biochemical, cellular, molecular dynamics, and molecular docking experiments to provide compelling evidence that the flavonoid luteolin (2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one) has antiviral activity against SARS-CoV-2 3-chymotrypsin-like protease (3CLpro) that is synergistically enhanced by magnesium, zinc, and vitamin C. The IC50 of luteolin against 2 µM 3CLpro is 78 µM and decreases 10-fold to 7.6 µM in the presence of zinc, magnesium, and vitamin C. Thermodynamic stability analyses revealed that luteolin has minimal effects on the structure of 3CLpro, whereas metal ions and vitamin C significantly alter the thermodynamic stability of the protease. Interactome analysis uncovered potential host-virus interactions and functional clusters associated with luteolin activity, supporting the relevance of this flavone for combating SARS-CoV-2 infection. This comprehensive investigation sheds light on luteolin's therapeutic potential and provides insights into its mechanisms of action against SARS-CoV-2. The novel formulation of luteolin, magnesium, zinc, and vitamin C may be an effective avenue for treating COVID-19 patients.
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Affiliation(s)
- Juliana C Ferreira
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Samar Fadl
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Thyago H S Cardoso
- G42 Healthcare Omics Excellence Center, Masdar City, Abu Dhabi, United Arabes Emirates
| | - Bruno Silva Andrade
- UESB - Universidade Estatudal Do Sudoeste da Bahia. Deparmento de Ciencias Biologicas
| | - Tarcisio S Melo
- UESB - Universidade Estatudal Do Sudoeste da Bahia. Deparmento de Ciencias Biologicas
| | | | | | | | - Nitin K Saksena
- Victoria University, Footscray Park Campus, Melbourne, VIC, 3134, Australia
- Aegros Therapeutics Pty Ltd, 5-6 Eden Park Drive, Macquarie Park, NSW 2113, Australia
| | - Wael M Rabeh
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
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50
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Andreu Z, Hidalgo MR, Masiá E, Romera-Giner S, Malmierca-Merlo P, López-Guerrero JA, García-García F, Vicent MJ. Comparative profiling of whole-cell and exosome samples reveals protein signatures that stratify breast cancer subtypes. Cell Mol Life Sci 2024; 81:363. [PMID: 39172142 DOI: 10.1007/s00018-024-05403-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 08/02/2024] [Accepted: 08/07/2024] [Indexed: 08/23/2024]
Abstract
Identifying novel breast cancer biomarkers will improve patient stratification, enhance therapeutic outcomes, and help develop non-invasive diagnostics. We compared the proteomic profiles of whole-cell and exosomal samples of representative breast cancer cell subtypes to evaluate the potential of extracellular vesicles as non-invasive disease biomarkers in liquid biopsies. Overall, differentially-expressed proteins in whole-cell and exosome samples (which included markers for invasion, metastasis, angiogenesis, and drug resistance) effectively discriminated subtypes; furthermore, our results confirmed that the proteomic profile of exosomes reflects breast cancer cell-of-origin, which underscores their potential as disease biomarkers. Our study will contribute to identifying biomarkers that support breast cancer patient stratification and developing novel therapeutic strategies. We include an open, interactive web tool to explore the data as a molecular resource that can explain the role of these protein signatures in breast cancer classification.
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Affiliation(s)
- Zoraida Andreu
- Polymer Therapeutics Laboratory and Screening Platform, Príncipe Felipe Research Center (CIPF), Av. Eduardo Primo Yúfera 3, Valencia, 46012, Spain.
- IVO-CIPF Joint Cancer Research Unit, Príncipe Felipe Research Center (CIPF), Av. Eduardo Primo Yúfera 3, Valencia, 46012, Spain.
- Computational Biomedicine Laboratory, Príncipe Felipe Research Center (CIPF), Av. Eduardo Primo Yúfera 3, Valencia, 46012, Spain.
- Laboratory of Molecular Biology, Foundation of the Valencian Institute of Oncology, Valencia, 46009, Spain.
| | - Marta R Hidalgo
- IVO-CIPF Joint Cancer Research Unit, Príncipe Felipe Research Center (CIPF), Av. Eduardo Primo Yúfera 3, Valencia, 46012, Spain
- Computational Biomedicine Laboratory, Príncipe Felipe Research Center (CIPF), Av. Eduardo Primo Yúfera 3, Valencia, 46012, Spain
- Department of Mathematics, School of Mathematics, University of Valencia, Valencia, 46010, Spain
| | - Esther Masiá
- Polymer Therapeutics Laboratory and Screening Platform, Príncipe Felipe Research Center (CIPF), Av. Eduardo Primo Yúfera 3, Valencia, 46012, Spain
- IVO-CIPF Joint Cancer Research Unit, Príncipe Felipe Research Center (CIPF), Av. Eduardo Primo Yúfera 3, Valencia, 46012, Spain
- CIBERONC, Carlos III Health Institute (IISCIII), Madrid, Spain
| | - Sergio Romera-Giner
- Computational Biomedicine Laboratory, Príncipe Felipe Research Center (CIPF), Av. Eduardo Primo Yúfera 3, Valencia, 46012, Spain
| | - Pablo Malmierca-Merlo
- Computational Biomedicine Laboratory, Príncipe Felipe Research Center (CIPF), Av. Eduardo Primo Yúfera 3, Valencia, 46012, Spain
| | - José A López-Guerrero
- IVO-CIPF Joint Cancer Research Unit, Príncipe Felipe Research Center (CIPF), Av. Eduardo Primo Yúfera 3, Valencia, 46012, Spain
- Laboratory of Molecular Biology, Foundation of the Valencian Institute of Oncology, Valencia, 46009, Spain
- Department of Pathology, Medical School, Catholic University of Valencia 'San Vicente Mártir', Valencia, 46001, Spain
| | - Francisco García-García
- IVO-CIPF Joint Cancer Research Unit, Príncipe Felipe Research Center (CIPF), Av. Eduardo Primo Yúfera 3, Valencia, 46012, Spain.
- Computational Biomedicine Laboratory, Príncipe Felipe Research Center (CIPF), Av. Eduardo Primo Yúfera 3, Valencia, 46012, Spain.
| | - María J Vicent
- Polymer Therapeutics Laboratory and Screening Platform, Príncipe Felipe Research Center (CIPF), Av. Eduardo Primo Yúfera 3, Valencia, 46012, Spain.
- IVO-CIPF Joint Cancer Research Unit, Príncipe Felipe Research Center (CIPF), Av. Eduardo Primo Yúfera 3, Valencia, 46012, Spain.
- CIBERONC, Carlos III Health Institute (IISCIII), Madrid, Spain.
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