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Wang Q, Liu Y, Zhang Y, Zhang S, Zhao M, Peng Z, Xu H, Huang H. Characterization of macrophages in ischemia-reperfusion injury-induced acute kidney injury based on single-cell RNA-Seq and bulk RNA-Seq analysis. Int Immunopharmacol 2024; 130:111754. [PMID: 38428147 DOI: 10.1016/j.intimp.2024.111754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/13/2024] [Accepted: 02/21/2024] [Indexed: 03/03/2024]
Abstract
Acute kidney injury (AKI) is a complex disease, with macrophages playing a vital role in its progression. However, the mechanism of macrophage function remains unclear and strategies targeting macrophages in AKI are controversial. To address this issue, we used single-cell RNA-seq analysis to identify macrophage sub-types involved in ischemia-reperfusion-induced AKI, and then screened for associated hub genes using intersecting bulk RNA-seq data. The single-cell and bulk RNA-seq datasets were obtained from the Gene Expression Omnibus (GEO) database. Screening of differentially-expressed genes (DEGs) and pseudo-bulk DEG analyses were used to identify common hub genes. Pseudotime and trajectory analyses were performed to investigate the progression of cell differentiation. CellChat analysis was performed to reveal the crosstalk between cell clusters. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were used to identify enriched pathways in the cell clusters. Immunofluorescence and RT-PCR were preformed to validate the expression of the identified hub genes. Four hub genes, Vim, S100a6, Ier3, and Ccr1, were identified in the infiltrated macrophages between normal samples and those 3 days after ischemia-reperfusion renal injury (IRI); all were associated with the progression of IRI-induced AKI. Increased expression of Vim, S100a6, Ier3, and Ccr1 in infiltrated macrophages may be associated with inflammatory responses and may mediate crosstalk between macrophages and renal tubular epithelial cells under IRI conditions. Our results reveal that Ier3 may be critical in AKI, and that Vim, S100a6, Ier3, and Ccr1 may act as novel biomarkers and potential therapeutic targets for IRI-induced AKI.
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Affiliation(s)
- Qin Wang
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yuxing Liu
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China; Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Yan Zhang
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China; Hunan Key Laboratory of Organ Fibrosis, Central South University, Changsha, China
| | - Siyuan Zhang
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Meifang Zhao
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China; Hunan Key Laboratory of Organ Fibrosis, Central South University, Changsha, China
| | - Zhangzhe Peng
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China; Hunan Key Laboratory of Organ Fibrosis, Central South University, Changsha, China.
| | - Hui Xu
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China; Hunan Key Laboratory of Organ Fibrosis, Central South University, Changsha, China.
| | - Hao Huang
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China; Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China; Hunan Key Laboratory of Organ Fibrosis, Central South University, Changsha, China.
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Zhu Y, Peng B, Luo X, Sun W, Liu D, Li N, Qiu P, Long G. High-Resolution Profiling of Head and Neck Squamous Cells Carcinoma Identifies Specific Biomarkers and Expression Subtypes of Clinically Relevant Vulnerabilities. Curr Med Chem 2024; 31:2431-2448. [PMID: 37936459 DOI: 10.2174/0109298673276128231031112655] [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: 08/07/2023] [Revised: 10/18/2023] [Accepted: 10/24/2023] [Indexed: 11/09/2023]
Abstract
BACKGROUND Head and neck squamous cell carcinoma (HNSC) is the seventh most common cancer worldwide. Although there are several options for the treatment of HNSC, there is still a lack of better biomarkers to accurately predict the response to treatment and thus be more able to correctly treat the therapeutic modality. METHODS First, we typed cases from the TCGA-HNSC cohort into subtypes by a Bayesian non-negative matrix factorization (BayesNMF)-based consensus clustering approach. Subsequently, genomic and proteomic data from HNSC cell lines were integrated to identify biomarkers of response to targeted therapies and immunotherapies. Finally, associations between HNSC subtypes and CD8 T-cell-associated effector molecules, common immune checkpoint genes, were compared to assess the potential of HNSC subtypes as clinically predictive immune checkpoint blockade therapy. RESULTS The 500 HNSC cases from TCGA were put through a consensus clustering approach to identify six HNSC expression subtypes. In addition, subtypes with unique proteomics and dependency profiles were defined based on HNSC cell line histology and proteomics data. Subtype 4 (S4) exhibits hyperproliferative and hyperimmune properties, and S4-associated cell lines show specific vulnerability to ADAT2, EIF5AL1, and PAK2. PD-L1 and CASP1 inhibitors have therapeutic potential in S4, and we have also demonstrated that S4 is more responsive to immune checkpoint blockade therapy. CONCLUSION Overall, our HNSC typing approach identified robust tumor-expressing subtypes, and data from multiple screens also revealed subtype-specific biology and vulnerabilities. These HNSC expression subtypes and their biomarkers will help develop more effective therapeutic strategies.
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Affiliation(s)
- Yingying Zhu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Bi Peng
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiaoxiao Luo
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Wei Sun
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Dongbo Liu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Na Li
- Department of Medical, Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and Therapy, Shenzhen, 518038, China
| | - Ping Qiu
- Department of Medical, Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and Therapy, Shenzhen, 518038, China
| | - Guoxian Long
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
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Xiong M, Hu JJ, Yao ML, Song TT, Zhao L, Mou BQ, Qian YX, Zheng MJ, Dong YJ, Wang HY, Zou J, Yang H. Single-cell sequencing of head and neck carcinoma: Transcriptional landscape and prognostic model based on malignant epithelial cell features. FASEB J 2024; 38:e23354. [PMID: 38085162 DOI: 10.1096/fj.202301287rr] [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: 06/27/2023] [Revised: 11/07/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023]
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the sixth most common malignancy worldwide, and the development of novel therapeutic strategies for HNSCC requires a profound understanding of tumor cells and the tumor microenvironment (TME). Additionally, HNSCC has a poor prognosis, necessitating the use of genetic markers for predicting clinical outcomes in HNSCC. In this study, we performed single-cell sequencing analysis on tumor tissues from seven HNSCC patients, along with one adjacent normal tissue. Firstly, the analysis of epithelial cell clusters revealed two clusters of malignant epithelial cells, characterized by unique gene expression patterns and dysregulated signaling pathways compared to normal epithelial cells. Secondly, the examination of the TME unveiled extensive crosstalk between fibroblasts and malignant epithelial cells, potentially mediated through ligand-receptor interactions such as COL1A1-SDC1, COL1A1-CD44, and COL1A2-SDC1. Furthermore, transcriptional heterogeneity was observed in immune cells present in the TME, including macrophages and dendritic cells. Finally, leveraging the gene expression profiles of malignant epithelial cells, we developed a prognostic model comprising six genes, which we validated using two independent datasets. These findings shed light on the heterogeneity within HNSCC tumors and the intricate interplay between malignant cells and the TME. Importantly, the developed prognostic model demonstrates high efficacy in predicting the survival outcomes of HNSCC patients.
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Affiliation(s)
- Ming Xiong
- Department of Otorhinolaryngology-Head & Neck Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Juan-Juan Hu
- Department of Otorhinolaryngology-Head & Neck Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Meng-Lin Yao
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center for Geriatrics, Center of Precision Medicine, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Ting-Ting Song
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center for Geriatrics, Center of Precision Medicine, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Lei Zhao
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Bi-Qin Mou
- Precision Medicine Key Laboratory of Sichuan Province, Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ying-Xue Qian
- Department of Otorhinolaryngology-Head & Neck Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Mei-Jun Zheng
- Department of Otorhinolaryngology-Head & Neck Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Yi-Jun Dong
- Department of Otorhinolaryngology-Head & Neck Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Hai-Yang Wang
- Department of Otorhinolaryngology-Head & Neck Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Jian Zou
- Department of Otorhinolaryngology-Head & Neck Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Hui Yang
- Department of Otorhinolaryngology-Head & Neck Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
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Wei X, Tian Z, Zhao F, Sun A, Zhao S, Jamil M, Yan W. Unveiling pathogenic mutations in BRCA1 and BRCA2 genes across head and neck squamous cell carcinoma patients via next generation sequencing. Am J Cancer Res 2023; 13:6099-6112. [PMID: 38187047 PMCID: PMC10767334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/09/2023] [Indexed: 01/09/2024] Open
Abstract
Head and Neck Squamous Cell Carcinoma (HNSC) presents a formidable challenge in the field of oncology due to its aggressive nature and the limited therapeutic options available. In this study, our primary focus was on the Pakistani HNSC patient population, aiming to investigate germline oncogenic mutations within the BRCA1 and BRCA2 genes via Next Generation Sequencing (NGS) and explore their clinical implications. We sought to understand the functional consequences of these mutations via RT-qPCR and Immunohistochemistry (IHC) techniques. The key discovery of our research lies in the identification of three pathogenic mutations, including two within BRCA1 (p.Cys274Ter and p.Glu272Ter) and one within BRCA2 (p.Met1Val), among Pakistani HNSC patients. These mutations previously associated with an increased risk of various cancers. What sets our study apart is the uniqueness of these pathogenic mutations, absent in HNSC patients from other populations. This suggests a distinct genetic profile in Pakistani HNSC patients, possibly contributing to their susceptibility to this malignancy. Furthermore, our research revealed elevated expression levels of BRCA1 and BRCA2 genes in HNSC samples harboring pathogenic mutations, offering insights into mechanisms driving tumor progression in HNSC. Importantly, we identified significant enrichment of BRCA1/2 genes in pathways related to cancer development within the KEGG database. Finally, in our quest to explore therapeutic avenues, we systematically analyzed drugs targeting up-regulated and mutated BRCA1/2 genes, identifying promising candidates for tailored treatment modalities in HNSC. In conclusion, our study reveals the unique genetic profile of HNSC in Pakistani patients, featuring unique pathogenic mutations in BRCA1 and BRCA2 genes. These mutations offer promise as valuable diagnostic markers and potential therapeutic targets.
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Affiliation(s)
- Xiaotong Wei
- Department of Oral and Maxillofacial Surgery, Cangzhou Central HospitalCangzhou 061000, Hebei, China
| | - Zhizhengrong Tian
- Department of Ultrasound, Cangzhou Central HospitalCangzhou 061000, Hebei, China
| | - Fengyun Zhao
- Department of Ultrasound, Cangzhou Maternal and Child Health Care HospitalCangzhou 061000, Hebei, China
| | - Anjun Sun
- Department of Oral and Maxillofacial Surgery, Cangzhou Central HospitalCangzhou 061000, Hebei, China
| | - Shujuan Zhao
- Department of Oral and Maxillofacial Surgery, Cangzhou Central HospitalCangzhou 061000, Hebei, China
| | - Muhammad Jamil
- PARC Arid Zone Research CenterDera Ismail Khan 29050, Pakistan
| | - Wei Yan
- Department of Oral and Maxillofacial Surgery, Cangzhou Central HospitalCangzhou 061000, Hebei, China
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Zhu C, Bai Y, Zhao X, Liu S, Xia X, Zhang S, Wang Y, Zhang H, Xu Y, Chen S, Jiang J, Wu Y, Wu X, Zhang G, Zhang X, Hu J, Wang L, Zhao Y, Bai Y. Antimicrobial Peptide MPX with Broad-Spectrum Bactericidal Activity Promotes Proper Abscess Formation and Relieves Skin Inflammation. Probiotics Antimicrob Proteins 2023; 15:1608-1625. [PMID: 36626016 DOI: 10.1007/s12602-022-10035-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2022] [Indexed: 01/11/2023]
Abstract
Bacteria have developed antibiotic resistance during the large-scale use of antibiotics, and multidrug-resistant strains are common. The development of new antibiotics or antibiotic substitutes has become an important challenge for humankind. MPX is a 14 amino acid peptide belonging to the MP antimicrobial peptide family. In this study, the antibacterial spectrum of the antimicrobial peptide MPX was first tested. The antimicrobial peptide MPX was tested for antimicrobial activity against the gram-positive bacterium S. aureus ATCC 25923, the gram-negative bacteria E. coli ATCC 25922 and Salmonella enterica serovar Typhimurium CVCC541, and the fungus Candida albicans ATCC 90029. The results showed that MPX had good antibacterial activity against the above four strains, especially against E. coli, for which the MIC was as low as 15.625 μg/mL. The study on the bactericidal mechanism of the antimicrobial peptide revealed that MPX can destroy the integrity of the cell membrane, increase membrane permeability, and change the electromotive force of the membrane, thereby allowing the contents to leak out and mediating bacterial death. A mouse acute infection model was used to evaluate the therapeutic effect of MPX after acute infection of subcutaneous tissue by S. aureus. The study showed that MPX could promote tissue repair in S. aureus infection and alleviate lung damage caused by S. aureus. In addition, skin H&E staining showed that MPX treatment facilitated the formation of appropriate abscesses at the subcutaneous infection site and facilitated the clearance of bacteria by the skin immune system. The above results show that MPX has good antibacterial activity and broad-spectrum antibacterial potential and can effectively prevent the invasion of subcutaneous tissue by S. aureus, providing new ideas and directions for the immunotherapy of bacterial infections.
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Affiliation(s)
- Chunling Zhu
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, 453003, China
- College of Veterinary Medicine, Jilin University, Changchun, 130000, China
| | - Yilin Bai
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China
| | - Xueqin Zhao
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Shanqin Liu
- School of Chemistry and Chemical Engineering, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Xiaojing Xia
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Shouping Zhang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Yimin Wang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Huihui Zhang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Yanzhao Xu
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Shijun Chen
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Jinqing Jiang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Yundi Wu
- School of Chemistry and Chemical Engineering, Henan Institute of Science and Technology, Xinxiang, 453003, China
- School of Biomedical Engineering, State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, 570228, China
| | - Xilong Wu
- School of Chemistry and Chemical Engineering, Henan Institute of Science and Technology, Xinxiang, 453003, China
- School of Biomedical Engineering, State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, 570228, China
| | - Gaiping Zhang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Xueming Zhang
- College of Veterinary Medicine, Jilin University, Changchun, 130000, China
| | - Jianhe Hu
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Lei Wang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, 453003, China.
- School of Biomedical Engineering, State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, 570228, China.
| | - Yaya Zhao
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, 453003, China.
| | - Yueyu Bai
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, 453003, China.
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Huang C, Zhu F, Zhang H, Wang N, Huang Q. Identification of S1PR4 as an immune modulator for favorable prognosis in HNSCC through machine learning. iScience 2023; 26:107693. [PMID: 37680482 PMCID: PMC10480314 DOI: 10.1016/j.isci.2023.107693] [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: 03/31/2023] [Revised: 07/25/2023] [Accepted: 08/17/2023] [Indexed: 09/09/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are the largest family of membrane proteins and play a critical role as pharmacological targets. An improved understanding of GPCRs' involvement in tumor microenvironment may provide new perspectives for cancer therapy. This study used machine learning to classify head and neck squamous cell carcinoma (HNSCC) patients into two GPCR-based subtypes. Notably, these subtypes showed significant differences in prognosis, gene expression, and immune microenvironment, particularly CD8+ T cell infiltration. S1PR4 emerged as a key regulator distinguishing the subtypes, positively correlated with CD8+ T cell proportion and cytotoxicity in HNSCC. It was predominantly expressed in CX3CR1+CD8+ T cells among T cells. Upregulation of S1PR4 enhanced T cell function during CAR-T cell therapy, suggesting its potential in cancer immunotherapy. These findings highlight S1PR4 as an immune modulator for favorable prognosis in HNSCC, and offer a potential GPCR-targeted therapeutic option for HNSCC treatment.
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Affiliation(s)
- Chenshen Huang
- Department of Gastrointestinal Surgery, Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China
- Department of General Surgery, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Fengshuo Zhu
- Department of Oral Maxillofacial-Head and Neck Oncology, Shanghai Ninth People’s Hospital, College of Stomatology, Shanghai, China
- Jiao Tong University School of Medicine, National Clinical Research Center for Oral Disease, Shanghai Key Laboratory of Stomatology and Shanghai Research Institute of Stomatology, Shanghai, China
| | - Hao Zhang
- Department of Neurosurgery, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Ning Wang
- Department of Hepatobiliary and Pancreatic Surgery, Huzhou Central Hospital, Affiliated Hospital of Zhejiang University, Huzhou, China
| | - Qi Huang
- Department of General Surgery, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
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Sun Y, Li R, Chen Y, Yang B, Li X, Li Z, He J, Zhou Z, Li J, Guo X, Wang X, Wu Y, Zhang W, Guo G. The value of basement membrane-associated genes in the prognosis and immune regulation of glioma. Medicine (Baltimore) 2023; 102:e33935. [PMID: 37335645 DOI: 10.1097/md.0000000000033935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/21/2023] Open
Abstract
Gliomas have a high incidence rate in central nervous tumors. Although many breakthroughs have been made in the pathogenesis and treatment of glioma, the recurrence and metastasis rates of patients have not been improved based on the uniqueness of glioma. Glioma destroys the surrounding basement membrane (BM), leading to local infiltration, resulting in the corresponding clinical and neurological symptoms. Therefore, exploring the biological roles played by BM associated genes in glioma is particularly necessary for a comprehensive understanding of the biological processes of glioma and its treatment. Differential expression and univariate COX regression analyses were used to identify the basement membrane genes (BMGs) to be included in the model. LASSO regression was used to construct the BMG model. The Kaplan-Meier (KM) survival analysis model was used to assess the prognosis discrimination between training sets, validation sets, and clinical subgroups. Receiver-operating characteristic (ROC) analysis was used to test the prognostic efficacy of the model. Use calibration curves to verify the accuracy of nomograms. Gene ontology (GO), Kyoto encyclopedia of genes and genomes (KEGG), and gene set enrichment analysis (GSEA) were used to analyze the function and pathway enrichment among the model groups. ESTIMATE and other 7 algorithms including CIBERSORT were used to evaluate the immune microenvironment. "pRRophetic" was used to evaluate drug sensitivity. This study demonstrated that high-risk genes (LAMB4, MMP1, MMP7) promote glioma progression and negatively correlate with patient prognosis. In the tumor microenvironment (TME), high-risk genes have increased scores of macrophages, neutrophils, immune checkpoints, chemokines, and chemokine receptors. This study suggests that BMGs, especially high-risk-related genes, are potential sites for glioma therapy, a new prospect for comprehensively understanding the molecular mechanism of glioma.
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Affiliation(s)
- Yanqi Sun
- Department of Emergency, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Ren Li
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yang Chen
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Biao Yang
- Department of Emergency, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xuepeng Li
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Ziao Li
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Jianhang He
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Zihan Zhou
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Jiayu Li
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xiaolong Guo
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xiaogang Wang
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yongqiang Wu
- Department of Emergency, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Wenju Zhang
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Geng Guo
- Department of Emergency, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
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Chi H, Yang J, Peng G, Zhang J, Song G, Xie X, Xia Z, Liu J, Tian G. Circadian rhythm-related genes index: A predictor for HNSCC prognosis, immunotherapy efficacy, and chemosensitivity. Front Immunol 2023; 14:1091218. [PMID: 36969232 PMCID: PMC10036372 DOI: 10.3389/fimmu.2023.1091218] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 02/27/2023] [Indexed: 03/12/2023] Open
Abstract
BackgroundHead and neck squamous cell carcinoma (HNSCC) is the most common head and neck cancer and is highly aggressive and heterogeneous, leading to variable prognosis and immunotherapy outcomes. Circadian rhythm alterations in tumourigenesis are of equal importance to genetic factors and several biologic clock genes are considered to be prognostic biomarkers for various cancers. The aim of this study was to establish reliable markers based on biologic clock genes, thus providing a new perspective for assessing immunotherapy response and prognosis in patients with HNSCC.MethodsWe used 502 HNSCC samples and 44 normal samples from the TCGA-HNSCC dataset as the training set. 97 samples from GSE41613 were used as an external validation set. Prognostic characteristics of circadian rhythm-related genes (CRRGs) were established by Lasso, random forest and stepwise multifactorial Cox. Multivariate analysis revealed that CRRGs characteristics were independent predictors of HNSCC, with patients in the high-risk group having a worse prognosis than those in the low-risk group. The relevance of CRRGs to the immune microenvironment and immunotherapy was assessed by an integrated algorithm.Results6-CRRGs were considered to be strongly associated with HNSCC prognosis and a good predictor of HNSCC. The riskscore established by the 6-CRRG was found to be an independent prognostic factor for HNSCC in multifactorial analysis, with patients in the low-risk group having a higher overall survival (OS) than the high-risk group. Nomogram prediction maps constructed from clinical characteristics and riskscore had good prognostic power. Patients in the low-risk group had higher levels of immune infiltration and immune checkpoint expression and were more likely to benefit from immunotherapy.Conclusion6-CRRGs play a key predictive role for the prognosis of HNSCC patients and can guide physicians in selecting potential responders to prioritise immunotherapy, which could facilitate further research in precision immuno-oncology.
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Affiliation(s)
- Hao Chi
- Clinical Medical College, Southwest Medical University, Luzhou, China
| | - Jinyan Yang
- School of Stomatology, Southwest Medical University, Luzhou, China
| | - Gaoge Peng
- Clinical Medical College, Southwest Medical University, Luzhou, China
| | - Jinhao Zhang
- School of Stomatology, Southwest Medical University, Luzhou, China
| | - Guobin Song
- School of Stomatology, Southwest Medical University, Luzhou, China
| | - Xixi Xie
- School of Stomatology, Southwest Medical University, Luzhou, China
| | - Zhijia Xia
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, Germany
- *Correspondence: Zhijia Xia, ; Jinhui Liu, ; Gang Tian,
| | - Jinhui Liu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- *Correspondence: Zhijia Xia, ; Jinhui Liu, ; Gang Tian,
| | - Gang Tian
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- *Correspondence: Zhijia Xia, ; Jinhui Liu, ; Gang Tian,
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