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Wu Y, Bashir MA, Shao C, Wang H, Zhu J, Huang Q. Astaxanthin targets IL-6 and alleviates the LPS-induced adverse inflammatory response of macrophages. Food Funct 2024; 15:4207-4222. [PMID: 38512055 DOI: 10.1039/d4fo00610k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Numerous natural compounds are recognized for their anti-inflammatory properties attributed to antioxidant effects and the modulation of key inflammatory factors. Among them, astaxanthin (AST), a potent carotenoid antioxidant, remains relatively underexplored regarding its anti-inflammatory mechanisms and specific molecular targets. In this study, human monocytic leukemia cell-derived macrophages (THP-1) were selected as experimental cells, and lipopolysaccharides (LPS) served as inflammatory stimuli. Upon LPS treatment, the oxidative stress was significantly increased, accompanied by remarkable cellular damage. Moreover, LPSs escalated the expression of inflammation-related molecules. Our results demonstrate that AST intervention could effectively alleviate LPS-induced oxidative stress, facilitate cellular repair, and significantly attenuate inflammation. Further exploration of the anti-inflammatory mechanism revealed AST could substantially inhibit NF-κB translocation and activation, and mitigate inflammatory factor production by hindering NF-κB through the antioxidant mechanism. We further confirmed that AST exhibited protective effects against cell damage and reduced the injury from inflammatory cytokines by activating p53 and inhibiting STAT3. In addition, utilizing network pharmacology and in silico calculations based on molecular docking, molecular dynamics simulation, we identified interleukin-6 (IL-6) as a prominent core target of AST anti-inflammation, which was further validated by the RNA interference experiment. This IL-6 binding capacity actually enabled AST to curb the positive feedback loop of inflammatory factors, averting the onset of possible inflammatory storms. Therefore, this study offers a new possibility for the application and development of astaxanthin as a popular dietary supplement of anti-inflammatory or immunomodulatory function.
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Affiliation(s)
- Yahui Wu
- CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Anhui Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institute of Intelligent Agriculture, Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China.
- Science Island Branch of Graduate School, University of Science & Technology of China, Hefei 230026, China
| | - Mona A Bashir
- CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Anhui Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institute of Intelligent Agriculture, Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China.
- Science Island Branch of Graduate School, University of Science & Technology of China, Hefei 230026, China
| | - Changsheng Shao
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - Han Wang
- CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Anhui Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institute of Intelligent Agriculture, Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China.
- Science Island Branch of Graduate School, University of Science & Technology of China, Hefei 230026, China
| | - Jianxia Zhu
- CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Anhui Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institute of Intelligent Agriculture, Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China.
- School of Nursing, Anhui Medical University, Hefei, Anhui 230032, China
| | - Qing Huang
- CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Anhui Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institute of Intelligent Agriculture, Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China.
- Science Island Branch of Graduate School, University of Science & Technology of China, Hefei 230026, China
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Elsborg J, Salvatore M. Using LLMs and Explainable ML to Analyze Biomarkers at Single-Cell Level for Improved Understanding of Diseases. Biomolecules 2023; 13:1516. [PMID: 37892198 PMCID: PMC10605495 DOI: 10.3390/biom13101516] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/07/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) technology has significantly advanced our understanding of the diversity of cells and how this diversity is implicated in diseases. Yet, translating these findings across various scRNA-seq datasets poses challenges due to technical variability and dataset-specific biases. To overcome this, we present a novel approach that employs both an LLM-based framework and explainable machine learning to facilitate generalization across single-cell datasets and identify gene signatures to capture disease-driven transcriptional changes. Our approach uses scBERT, which harnesses shared transcriptomic features among cell types to establish consistent cell-type annotations across multiple scRNA-seq datasets. Additionally, we employed a symbolic regression algorithm to pinpoint highly relevant, yet minimally redundant models and features for inferring a cell type's disease state based on its transcriptomic profile. We ascertained the versatility of these cell-specific gene signatures across datasets, showcasing their resilience as molecular markers to pinpoint and characterize disease-associated cell types. The validation was carried out using four publicly available scRNA-seq datasets from both healthy individuals and those suffering from ulcerative colitis (UC). This demonstrates our approach's efficacy in bridging disparities specific to different datasets, fostering comparative analyses. Notably, the simplicity and symbolic nature of the retrieved gene signatures facilitate their interpretability, allowing us to elucidate underlying molecular disease mechanisms using these models.
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Affiliation(s)
- Jonas Elsborg
- Department of Energy Conversion and Storage, Technical University of Denmark, 2800 Kongens Lyngby, Denmark;
- Abzu ApS, 2150 København, Denmark
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Baker KJ, Brint E, Houston A. Transcriptomic and functional analyses reveal a tumour-promoting role for the IL-36 receptor in colon cancer and crosstalk between IL-36 signalling and the IL-17/ IL-23 axis. Br J Cancer 2023; 128:735-747. [PMID: 36482185 PMCID: PMC9977920 DOI: 10.1038/s41416-022-02083-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 11/15/2022] [Accepted: 11/18/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The interleukin (IL)-36 cytokines are a sub-family of the IL-1 family which are becoming increasingly implicated in the pathogenesis of inflammatory diseases and malignancies. Initial studies of IL-36 signalling in tumorigenesis identified an immune-mediated anti-tumorigenic function for these cytokines. However, more recent studies have shown IL-36 cytokines also contribute to the pathogenesis of lung and colorectal cancer (CRC). METHODS The aim of this study was to investigate IL-36 expression in CRC using transcriptomic datasets and software such as several R packages, Cytoscape, GEO2R and AnalyzeR. Validation of results was completed by qRT-PCR on both cell lines and a patient cohort. Cellular proliferation was assessed by flow cytometry and resazurin reduction. RESULTS We demonstrate that IL-36 gene expression increases with CRC development. Decreased tumoral IL-36 receptor expression was shown to be associated with improved patient outcome. Our differential gene expression analysis revealed a novel role for the IL-36/IL-17/IL-23 axis, with these findings validated using patient-derived samples and cell lines. IL-36γ, together with either IL-17a or IL-22, was able to synergistically induce different genes involved in the IL-17/IL-23 axis in CRC cells and additively induce colon cancer cell proliferation. CONCLUSIONS Collectively, this data support a pro-tumorigenic role for IL-36 signalling in colon cancer, with the IL-17/IL-23 axis influential in IL-36-mediated colon tumorigenesis.
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Affiliation(s)
- Kevin James Baker
- Department of Pathology, University College Cork, Cork, Ireland.,Department of Medicine, University College Cork, Cork, Ireland.,APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Elizabeth Brint
- Department of Pathology, University College Cork, Cork, Ireland. .,APC Microbiome Ireland, University College Cork, Cork, Ireland.
| | - Aileen Houston
- Department of Medicine, University College Cork, Cork, Ireland.,APC Microbiome Ireland, University College Cork, Cork, Ireland
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Zhang Z, Bahaji Azami NL, Liu N, Sun M. Research Progress of Intestinal Microecology in the Pathogenesis of Colorectal Adenoma and Carcinogenesis. Technol Cancer Res Treat 2023; 22:15330338221135938. [PMID: 36740990 PMCID: PMC9903042 DOI: 10.1177/15330338221135938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Colorectal adenoma is a precancerous lesion that may progress to colorectal cancer. Patients with colorectal adenoma had a 4-fold higher risk of developing colorectal malignancy than the rest of the population, with approximately 80% of colorectal cancer originating from colorectal adenoma. Therefore, preventing the occurrence and progression of colorectal adenoma is crucial in reducing the risk for colorectal cancer. The human intestinal microecology is a complex system consisting of numerous microbial communities with a sophisticated structure. Interactions among intestinal microorganisms play crucial roles in maintaining normal intestinal structure, digestion, absorption, metabolism, and other functions. The colorectal system is the largest microbial bank or fermentation system in the human body. Studies suggest that intestinal microecological imbalance, one of the most important environmental factors, may play an essential role in the occurrence and development of colorectal adenoma and colorectal cancer. Based on the complexity of studying the gut microbiota ecosystem, its specific role in the occurrence and development of colorectal adenoma is yet to be elucidated. In addition, further studies are expected to provide new insights regarding the prevention and treatment of colorectal adenoma. This article reviews the relationship and mechanism of the diversity of the gut microbiota, the relevant inflammatory response, immune regulation, and metabolic changes in the presence of colorectal adenomas.
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Affiliation(s)
- Zhipeng Zhang
- Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Institute of Liver Diseases, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Nisma Lena Bahaji Azami
- Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Institute of Liver Diseases, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ningning Liu
- Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Medical Oncology and Cancer Institute, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Ningning Liu, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
Mingyu Sun, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
| | - Mingyu Sun
- Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Institute of Liver Diseases, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Shanghai University of Traditional Chinese Medicine, Shanghai, China
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Candido S, Tomasello B, Lavoro A, Falzone L, Gattuso G, Russo A, Paratore S, McCubrey JA, Libra M. Bioinformatic analysis of the LCN2–SLC22A17–MMP9 network in cancer: The role of DNA methylation in the modulation of tumor microenvironment. Front Cell Dev Biol 2022; 10:945586. [PMID: 36211450 PMCID: PMC9532607 DOI: 10.3389/fcell.2022.945586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/24/2022] [Indexed: 11/13/2022] Open
Abstract
Several features of cancer cells such as proliferation, invasion, metastatic spreading, and drug resistance are affected by their interaction with several tumor microenvironment (TME) components, including neutrophil gelatinase-associated lipocalin (NGAL), solute carrier family 22 member 17 (SLC22A17), and matrix metallopeptidase 9 (MMP9). These molecules play a key role in tumor growth, invasion, and iron-dependent metabolism of cancer cells. However, the precise epigenetic mechanisms underlying the gene regulation of Lipocalin 2 (LCN2), SLC22A17, and MMP9 in cancer still remain unclear. To this purpose, computational analysis was performed on TCGA and GTEx datasets to evaluate the expression and DNA methylation status of LCN2, SLC22A17, and MMP9 genes in different tumor types. Correlation analysis between gene/isoforms expression and DNA methylation levels of LCN2, SLC22A17, and MMP9 was performed to investigate the role of DNA methylation in the modulation of these genes. Protein network analysis was carried out using reverse phase protein arrays (RPPA) data to identify protein–protein interactions of the LCN2–SLC22A17–MMP9 network. Furthermore, survival analysis was performed according to gene expression and DNA methylation levels. Our results demonstrated that LCN2 and MMP9 were mainly upregulated in most tumor types, whereas SLC22A17 was largely downregulated, representing a specific hallmark signature for all gastrointestinal tumors. Notably, the expression of LCN2, SLC22A17, and MMP9 genes was negatively affected by promoter methylation. Conversely, intragenic hypermethylation was associated with the overexpression of SLC22A17 and MMP9 genes. Protein network analysis highlighted the role of the LCN2–SLC22A17–MMP9 network in TME by the interaction with fibronectin 1 and claudin 7, especially in rectal tumors. Moreover, the impact of expression and methylation status of LCN2, SLC22A17, and MMP9 on overall survival and progression free interval was tumor type–dependent. Overall, our analyses provide a detailed overview of the expression and methylation status of LCN2, SLC22A17, and MMP9 in all TCGA tumors, indicating that the LCN2–SLC22A17–MMP9 network was strictly regulated by DNA methylation within TME. Our findings pave the way for the identification of novel DNA methylation hotspots with diagnostic and prognostic values and suitable for epi-drug targeting.
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Affiliation(s)
- Saverio Candido
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
- Research Center for Prevention, Diagnosis and Treatment of Cancer, University of Catania, Catania, Italy
- *Correspondence: Saverio Candido,
| | - Barbara Tomasello
- Department of Drug and Health Sciences, University of Catania, Catania, Italy
| | - Alessandro Lavoro
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Luca Falzone
- Epidemiology Unit, IRCCS Istituto Nazionale Tumori “Fondazione G. Pascale”, Naples, Italy
| | - Giuseppe Gattuso
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Angela Russo
- Pathological Anatomy Unit, ARNAS Garibaldi Hospital, Catania, Italy
| | - Sabrina Paratore
- Pathological Anatomy Unit, ARNAS Garibaldi Hospital, Catania, Italy
| | - James A. McCubrey
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC, United States
| | - Massimo Libra
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
- Research Center for Prevention, Diagnosis and Treatment of Cancer, University of Catania, Catania, Italy
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Role of miRNAs in the regulation of cancer-associated signaling pathways. Noncoding RNA Res 2022. [DOI: 10.1016/j.ncrna.2022.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Abedi M, Rahgozar S. Puzzling Out Iron Complications in Cancer Drug Resistance. Crit Rev Oncol Hematol 2022; 178:103772. [PMID: 35914667 DOI: 10.1016/j.critrevonc.2022.103772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 07/23/2022] [Accepted: 07/28/2022] [Indexed: 12/09/2022] Open
Abstract
Iron metabolism are frequently disrupted in cancer. Patients with cancer are prone to anemia and receive transfusions frequently; the condition which results in iron overload, contributing to serious therapeutic complications. Iron is introduced as a carcinogen that may increase tumor growth. However, investigations regarding its impact on response to chemotherapy, particularly the induction of drug resistance are still limited. Here, iron contribution to cell signaling and various molecular mechanisms underlying iron-mediated drug resistance are described. A dual role of this vital element in cancer treatment is also addressed. On one hand, the need to administer iron chelators to surmount iron overload and improve the sensitivity of tumor cells to chemotherapy is discussed. On the other hand, the necessary application of iron as a therapeutic option by iron-oxide nanoparticles or ferroptosis inducers is explained. Authors hope that this paper can help unravel the clinical complications related to iron in cancer therapy.
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Affiliation(s)
- Marjan Abedi
- Department of Cell and Molecular biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - Soheila Rahgozar
- Department of Cell and Molecular biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
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