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Ke D, Ni J, Yuan Y, Cao M, Chen S, Zhou H. Identification and Validation of Hub Genes Related to Neutrophil Extracellular Traps-Mediated Cell Damage During Myocardial Infarction. J Inflamm Res 2024; 17:617-637. [PMID: 38323113 PMCID: PMC10844013 DOI: 10.2147/jir.s444975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 01/23/2024] [Indexed: 02/08/2024] Open
Abstract
Purpose Studies have shown that neutrophil-mediated formation of neutrophil extracellular traps (NETs) leads to increased inflammatory response and cellular tissue damage during myocardial infarction (MI). We aimed to identify and validate possible hub genes in the process of NETs-mediated cell damage. Methods We performed an immune cell infiltration analysis of the MI transcriptome dataset based on CIBERSORT and ssGSEA algorithms. Gene expression profiles of NETs formation (GSE178883) were used to analyze the physiological processes of peripheral blood neutrophils after phorbol myristate acetate (PMA) stimulation. Bioinformatics and machine learning algorithms were utilized to find candidate hub genes based on NETs-related genes and transcriptome datasets (GSE66360 and GSE179828). We generated the receiver operating curve (ROC) to evaluate the diagnostic value of hub genes. Next, the correlation between hub genes and immune cells was analyzed using CIBERSORT, ssGSEA and xCell algorithms. Finally, we used quantitative real-time PCR (qRT-PCR) and immunohistochemistry to verify gene expression. Results Immune cell infiltration analysis revealed that inflammatory cells such as neutrophils were highly expressed in the peripheral blood of patients with MI. Functional analysis of differentially expressed genes (DEGs) in GSE178883 indicated that the potential pathogenesis lies in immune terms. Using weighted gene co-expression network analysis (WGCNA) and machine learning algorithms, we finally identified the seven hub genes (FCAR, IL1B, MMP9, NFIL3, CXCL2, ICAM1, and ZFP36). The qRT-PCR results showed that IL-1B, MMP9, and NFIL3 mRNA expression was up-regulated in the MI group compared to the control. Immunohistochemical results showed high MMP9, IL-1B, and NFIL3 expression in the infarcted area compared to the non-infarcted area and sham-operated groups. Conclusion We identified seven hub genes associated with NETs-mediated cellular damage during MI. Our results may provide insights into the mechanisms of neutrophil-mediated cell injury during MI.
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Affiliation(s)
- Da Ke
- Department of Cardiology, Renmin Hospital of Wuhan University, Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, 430060, People’s Republic of China
| | - Jian Ni
- Department of Cardiology, Renmin Hospital of Wuhan University, Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, 430060, People’s Republic of China
| | - Yuan Yuan
- Department of Cardiology, Renmin Hospital of Wuhan University, Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, 430060, People’s Republic of China
| | - Mingzhen Cao
- Department of Cardiology, Renmin Hospital of Wuhan University, Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, 430060, People’s Republic of China
| | - Si Chen
- Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, 430060, People’s Republic of China
| | - Heng Zhou
- Department of Cardiology, Renmin Hospital of Wuhan University, Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan, 430060, People’s Republic of China
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Fei Q, Zhang X, Wang S, Shu G, Yin G. A pan-cancer characterization of immune-related NFIL3 identifies potential predictive biomarker. J Cancer 2024; 15:1271-1286. [PMID: 38356719 PMCID: PMC10861811 DOI: 10.7150/jca.88765] [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: 08/02/2023] [Accepted: 10/09/2023] [Indexed: 02/16/2024] Open
Abstract
Background: Nuclear factor interleukin 3 (NFIL3) mainly focuses on the regulation of the circadian rhythm and immune system. However, the potential role of NFIL3 in human cancers has not been studied extensively. Methods: We retrieved original data from the TCGA, TARGET, and GTEx datasets via the UCSC Xena browser (http://genome.ucsc.edu/) and integrated them using R version 3.6.4. NFIL3 expression was assessed using resources such as UCSC, GEPIA (http://gepia.cancer-pku.cn/), Kaplan-Meier Plotter (KM Plotter; https://kmplot.com/), and the Human Protein Atlas (HPA; https://www.proteinatlas.org/) databases. To investigate the prognostic implications of NFIL3, we utilized GEPIA, Kaplan-Meier Plotter, and PrognoScan (http://www.abren.net/PrognoScan/) datasets. For a comprehensive analysis across multiple cancer types, we employed pan-cancer data from UCSC, examining associations between NFIL3 expression and genomic heterogeneity, tumor mutational burden (TMB), microsatellite instability (MSI), tumor purity, and neoantigens. Furthermore, we explored the relationships between NFIL3 expression and the infiltration of immune cells and the expression of immune checkpoint genes. In the context of ovarian cancer, we validated the expression and functional relevance of NFIL3. Cell Counting Kit 8 (CCK8) assays were conducted to assess cell proliferation, while scratch and transwell assays were employed to evaluate cell migration capabilities. We further examined the interaction between NFIL3 and the p53 signaling pathway through quantitative real-time polymerase chain reaction (qRT-PCR), Western blot analysis, immunofluorescence confocal, and Coimmunoprecipitation (Co-IP) assays. Results: In general, NFIL3 expression in cancerous tissues exhibited diminished levels when compared to normal tissue samples. Notably, NFIL3 expression demonstrated a robust correlation with several pivotal aspects, including prognosis, immune cell infiltration, immune checkpoint-related genes, TMB, MSI, tumor purity, and the presence of neoantigens. Experimental investigations involving scratch assays, transwell assays, and assessments of cell proliferation in ovarian cancer cells have provided indications that NFIL3 may exert influence over cell migration and proliferation processes. Moreover, a substantial association between NFIL3 and the p53 signaling pathway was discerned through Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, with subsequent validation through qRT-PCR, Western blot analysis, immunofluorescence confocal, and co-immunoprecipitation (Co-IP) assays. Conclusions: Therefore, we concluded NFIL3 may serve as a possible prognostic and immunological pan-cancer biomarker.
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Affiliation(s)
- Qin Fei
- Department of Pathology, Xiangya Hospital, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Xiaojun Zhang
- Department of Pathology, Xiangya Hospital, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Shutong Wang
- Department of Xiangya School of Medicine, Central South University, Changsha, China
| | - Guang Shu
- Department of Pathology, Xiangya Hospital, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Gang Yin
- Department of Pathology, Xiangya Hospital, School of Basic Medical Sciences, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- China-Africa Research Center of Infectious Diseases, School of Basic Medical Sciences, Central South University, Changsha, Hunan Province, China
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Chen L, Shangguan Z, Dong Z, Deng Q, Ding Y, Yang S. NFIL3 aggravates human coronary artery endothelial cell injury by promoting ITGAM transcription in Kawasaki disease. Hematology 2023; 28:2277502. [PMID: 37933872 DOI: 10.1080/16078454.2023.2277502] [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: 07/12/2023] [Accepted: 10/25/2023] [Indexed: 11/08/2023] Open
Abstract
OBJECTIVE High expression of nuclear factor interleukin-3 (NFIL3) and integrin Alpha M (ITGAM) was found in serum samples from Kawasaki disease (KD) patients through bioinformatics analysis. Hence, this study aimed to explore the biological functions of NFIL3 and ITGAM in KD serum-stimulated human coronary artery endothelial cells (HCAECs). METHODS The differentially-expressed genes in KD were analyzed through bioinformatics analysis. Serum samples were obtained from 18 KD patients and 18 healthy volunteers, followed by detection of NFIL3 and ITGAM levels in KD serum. After HCAECs were transfected with sh-NFIL3, sh-ITGAM, or sh-NFIL3 + oe-ITGAM and underwent 24-h KD serum stimulation, cell viability and apoptosis and the levels of inflammation-related factors were measured. The binding between NFIL3 and ITGAM was validated by dual-luciferase and chromatin immunoprecipitation (ChIP) assays. RESULTS NFIL3 and ITGAM were up-regulated in serum from KD patients and KD serum-stimulated HCAECs. Down-regulation of NFIL3 or ITGAM inhibited KD serum-induced cell apoptosis and inflammatory response of HCAECs and promoted cell viability. Mechanistically, NFIL3 promoted ITGAM transcription level. Up-regulation of ITGAM reversed the improvement of NFIL3 down-regulation on KD serum-induced HCAEC injury. CONCLUSION NFIL3 aggravated KD serum-induced HCAEC injury by promoting ITGAM transcription, which provided new insights into the treatment of KD.
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Affiliation(s)
- Li Chen
- Clinical College, Fuzhou Medical College, Nanchang University, Fuzhou, People's Republic of China
| | - Zhiyang Shangguan
- Basic Medicine College, Fuzhou Medical College, Nanchang University, Fuzhou, People's Republic of China
| | - Zeya Dong
- Clinical College, Fuzhou Medical College, Nanchang University, Fuzhou, People's Republic of China
| | - Qunfan Deng
- Department of Pediatrics, First People's Hospital of Fuzhou, Fuzhou, People's Republic of China
| | - Yunyun Ding
- Department of Pediatrics, First People's Hospital of Fuzhou, Fuzhou, People's Republic of China
| | - Shulong Yang
- Department of Physiology, Fuzhou Medical College of Nanchang University, Fuzhou, People's Republic of China
- Key Laboratory of Chronic Diseases, Fuzhou Medical University, Fuzhou, People's Republic of China
- Technology Innovation Center of Chronic Disease Research in Fuzhou CityFuzhou, People's Republic of China
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Hippocampal Changes Elicited by Metabolic and Inflammatory Stressors following Prenatal Maternal Infection. Genes (Basel) 2022; 14:genes14010077. [PMID: 36672818 PMCID: PMC9859158 DOI: 10.3390/genes14010077] [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: 12/14/2022] [Revised: 12/23/2022] [Accepted: 12/24/2022] [Indexed: 12/28/2022] Open
Abstract
The hippocampus participates in spatial navigation and behavioral processes, displays molecular plasticity in response to environmental challenges, and can play a role in neuropsychiatric diseases. The combined effects of inflammatory prenatal and postnatal challenges can disrupt the hippocampal gene networks and regulatory mechanisms. Using a proven pig model of viral maternal immune activation (MIA) matched to controls and an RNA-sequencing approach, the hippocampal transcriptome was profiled on two-month-old female and male offspring assigned to fasting, mimetic viral, or saline treatments. More than 2600 genes presented single or combined effects (FDR-adjusted p-value < 0.05) of MIA, postnatal stress, or sex. Biological processes and pathways encompassing messenger cyclic adenosine 3',5'-monophosphate (cAMP) signaling were enriched with genes including gastric inhibitory polypeptide receptor (GIPR) predominantly over-expressed in the MIA-exposed fasting males relative to groups that differed in sex, prenatal or postnatal challenge. While this pattern was amplified in fasting offspring, the postnatal inflammatory challenge appeared to cancel out the effects of the prenatal challenge. The transcription factors C-terminal binding protein 2 (CTBP2), RE1 silencing transcription factor (REST), signal transducer and activator of transcription 1 (STAT1), and SUZ12 polycomb repressive complex 2 subunit were over-represented among the genes impacted by the prenatal and postnatal factors studied. Our results indicate that one environmental challenge can influence the effect of another challenge on the hippocampal transcriptome. These findings can assist in the identification of molecular targets to ameliorate the effects of pre-and post-natal stressors on hippocampal-associated physiology and behavior.
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Zhuo H, Liu J. Nuclear factor interleukin 3 (NFIL3) participates in regulation of the NF-κB-mediated inflammation and antioxidant system in Litopenaeus vannamei under ammonia-N stress. FISH & SHELLFISH IMMUNOLOGY 2022; 131:1192-1205. [PMID: 36403704 DOI: 10.1016/j.fsi.2022.11.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
Nuclear factor interleukin 3 (NFIL3) is a critical upstream regulator of the NF-κB pathway. Nevertheless, the detailed molecular mechanism of NFIL3 and its function in shrimp have not been well characterized. In the present study, NFIL3 was identified and characterized from Litopenaeus vannamei. Molecular feature analysis revealed that the open reading frame (ORF) of LvNFIL3 was 2963 bp, which codes for a polypeptide of 516 amino acids with a conserved basic region leucine zipper (bZIP) domain. Sequence alignments and phylogenetic tree analysis showed that the amino acid sequence of LvNFIL3 shared 18.82%-98.07% identity with that of NFIL3 in other species, and was closely related to Penaeus monodon NFIL3. A core promoter in the 5' flanking region of LvNFIL3 was essential for regulation of transcription. LvNFIL3 mRNA was highly expressed in gills and hepatopancreas. Subcellular localization of the protein was observed almost exclusively in the nucleus. Amplification of mRNA by RT-qPCR showed that LvNFIL3 was induced in shrimp gills, hepatopancreas, and muscle after ammonia-N stress. Moreover, silencing of LvNFIL3 increased the mortality of shrimp exposed to ammonia-N. Furthermore, dual-luciferase reporter assay data suggested that LvNFIL3 was capable of activating the NF-κB pathway. Conversely, knockdown of LvNFIL3 decreased NF-κB homolog (Dorsal and Relish) and IkB homolog (Cactus) expression, as well as expression of anti-inflammatory cytokine (IL-16) and five antioxidant-related genes (HO-1, Mn-SOD, CAT, GPx, and GST), whereas NF-κB repressing factor (NKRF) and inflammation-related genes (TNFα and Spz) were upregulated. More importantly, LvNFIL3 knockdown exacerbated the pathology in hepatopancreas exposed to ammonia-N, and the total antioxidant capacity (T-AOC) and superoxide dismutase (T-SOD) were significantly decreased, resulting in a significant increased lipid peroxidation and protein carbonization. Taken together, these data suggest that LvNFIL3 was involved in ammonia-N tolerance in L. vannamei by regulating the inflammation and antioxidant system through the NF-κB pathway.
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Affiliation(s)
- Hongbiao Zhuo
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088, China; Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Jianyong Liu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088, China; Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Ocean University, Zhanjiang, 524088, China.
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Fang Y, Chen W, Li Z, Chen Y, Wu X, Zhu X, Wang H, Chen X, Liang Q, Huang J, Han X, Hong W, Wang X, Wei W, Yu Z, Tu J. The role of a key transcription factor PU.1 in autoimmune diseases. Front Immunol 2022; 13:1001201. [PMID: 36248862 PMCID: PMC9557192 DOI: 10.3389/fimmu.2022.1001201] [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: 07/23/2022] [Accepted: 09/12/2022] [Indexed: 12/03/2022] Open
Abstract
PU.1, a transcription factor member of the E26 transformation-specific family, affects the function of a variety of immune cells in several physiological and pathological conditions. Previous studies studying the role of PU.1 in pathological conditions have mainly focused on immune system-related cancers, and a series of articles have confirmed that PU.1 mutation can induce a variety of immune cell-related malignancies. The underlying mechanism has also been extensively validated. However, the role of PU.1 in other major immune system-related diseases, namely, systemic autoimmune diseases, is still unclear. It was only in recent years that researchers began to gradually realize that PU.1 also played an important role in a variety of autoimmune diseases, such as rheumatoid arthritis (RA), experimental autoimmune encephalomyelitis (EAE) and systemic lupus erythematosus (SLE). This review article summarizes the findings of recent studies that investigated the role of PU.1 in various autoimmune diseases and the related underlying mechanisms. Furthermore, it presents new ideas and provides insight into the role of PU.1 as a potential treatment target for autoimmune diseases and highlights existing research problems and future research directions in related fields.
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Affiliation(s)
- Yilong Fang
- Institute of Clinical Pharmacology, Anhui Medical University, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Hefei, China
| | - Weile Chen
- Institute of Clinical Pharmacology, Anhui Medical University, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Hefei, China
| | - Zhe Li
- The First Clinical Medical College, Southern Medical University, Guangzhou, China
| | - Yu Chen
- Department of Gynecology, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen Second People’s Hospital, Shenzhen, China
| | - Xuming Wu
- Institute of Clinical Pharmacology, Anhui Medical University, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Hefei, China
| | - Xiangling Zhu
- Institute of Clinical Pharmacology, Anhui Medical University, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Hefei, China
| | - Huihui Wang
- Institute of Clinical Pharmacology, Anhui Medical University, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Hefei, China
| | - Xiaochun Chen
- Department of Gynecology, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen Second People’s Hospital, Shenzhen, China
| | - Qiuni Liang
- Department of Gynecology, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen Second People’s Hospital, Shenzhen, China
| | - Jinghua Huang
- Department of Gynecology, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen Second People’s Hospital, Shenzhen, China
| | - Xintong Han
- Department of Gynecology, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen Second People’s Hospital, Shenzhen, China
| | - Wenming Hong
- The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xinming Wang
- The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Wei Wei
- Institute of Clinical Pharmacology, Anhui Medical University, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Hefei, China,*Correspondence: Jiajie Tu, ; Zhiying Yu, ; Wei Wei,
| | - Zhiying Yu
- Department of Gynecology, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen Second People’s Hospital, Shenzhen, China,*Correspondence: Jiajie Tu, ; Zhiying Yu, ; Wei Wei,
| | - Jiajie Tu
- Institute of Clinical Pharmacology, Anhui Medical University, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Hefei, China,*Correspondence: Jiajie Tu, ; Zhiying Yu, ; Wei Wei,
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