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  • Frontiers Media SA  (6)
  • Xie, Xixi  (6)
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  • Frontiers Media SA  (6)
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  • 1
    Online Resource
    Online Resource
    Identification and validation of neurotrophic factor-related genes signature in HNSCC to predict survival and immune landscapes
    Frontiers Media SA ; 2022
    In:  Frontiers in Genetics Vol. 13 ( 2022-11-4)
    Details
    In: Frontiers in Genetics, Frontiers Media SA, Vol. 13 ( 2022-11-4)
    Abstract: Background: Head and neck squamous cell carcinoma (HNSCC) is the seventh most common type of cancer worldwide. Its highly aggressive and heterogeneous nature and complex tumor microenvironment result in variable prognosis and immunotherapeutic outcomes for patients with HNSCC. Neurotrophic factor-related genes (NFRGs) play an essential role in the development of malignancies but have rarely been studied in HNSCC. The aim of this study was to develop a reliable prognostic model based on NFRGs for assessing the prognosis and immunotherapy of HNSCC patients and to provide guidance for clinical diagnosis and treatment. Methods: Based on the TCGA-HNSC cohort in the Cancer Genome Atlas (TCGA) database, expression profiles of NFRGs were obtained from 502 HNSCC samples and 44 normal samples, and the expression and prognosis of 2601 NFRGs were analyzed. TGCA-HNSC samples were randomly divided into training and test sets (7:3). GEO database of 97 tumor samples was used as the external validation set. One-way Cox regression analysis and Lasso Cox regression analysis were used to screen for differentially expressed genes significantly associated with prognosis. Based on 18 NFRGs, lasso and multivariate Cox proportional risk regression were used to construct a prognostic risk scoring system. ssGSEA was applied to analyze the immune status of patients in high- and low-risk groups. Results: The 18 NFRGs were considered to be closely associated with HNSCC prognosis and were good predictors of HNSCC. The multifactorial analysis found that the NFRGs signature was an independent prognostic factor for HNSCC, and patients in the low-risk group had higher overall survival (OS) than those in the high-risk group. The nomogram prediction map constructed from clinical characteristics and risk scores had good prognostic power. Patients in the low-risk group had higher levels of immune infiltration and expression of immune checkpoints and were more likely to benefit from immunotherapy. Conclusion: The NFRGs risk score model can well predict the prognosis of HNSCC patients. A nomogram based on this model can help clinicians classify HNSCC patients prognostically and identify specific subgroups of patients who may have better outcomes with immunotherapy and chemotherapy, and carry out personalized treatment for HNSCC patients.
    Type of Medium: Online Resource
    ISSN: 1664-8021
    URL: Article
    DOI: 10.3389/fgene.2022.1010044
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2022
    detail.hit.zdb_id: 2606823-0
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  • 2
    Online Resource
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    Table_2.xls
    Frontiers Media SA ; 2023
    In:  Frontiers in Immunology Vol. 14 ( 2023-7-5)
    Details
    In: Frontiers in Immunology, Frontiers Media SA, Vol. 14 ( 2023-7-5)
    Abstract: The primary pathogenic cause of tooth loss in adults is periodontitis, although few reliable diagnostic methods are available in the early stages. One pathological factor that defines periodontitis pathology has previously been believed to be the equilibrium between inflammatory defense mechanisms and oxidative stress. Therefore, it is necessary to construct a model of oxidative stress-related periodontitis diagnostic markers through machine learning and bioinformatic analysis. Methods We used LASSO, SVM-RFE, and Random Forest techniques to screen for periodontitis-related oxidative stress variables and construct a diagnostic model by logistic regression, followed by a biological approach to build a Protein-Protein interaction network (PPI) based on modelled genes while using modelled genes. Unsupervised clustering analysis was performed to screen for oxidative stress subtypes of periodontitis. we used WGCNA to explore the pathways correlated with oxidative stress in periodontitis patients. Networks. Finally, we used single-cell data to screen the cellular subpopulations with the highest correlation by scoring oxidative stress genes and performed a proposed temporal analysis of the subpopulations. Results We discovered 3 periodontitis-associated genes ( CASP3, IL-1β , and TXN ). A characteristic line graph based on these genes can be helpful for patients. The primary hub gene screened by the PPI was constructed, where immune-related and cellular metabolism-related pathways were significantly enriched. Consistent clustering analysis found two oxidative stress categories, with the C2 subtype showing higher immune cell infiltration and immune function ratings. Therefore, we hypothesized that the high expression of oxidative stress genes was correlated with the formation of the immune environment in patients with periodontitis. Using the WGCNA approach, we examined the co-expressed gene modules related to the various subtypes of oxidative stress. Finally, we selected monocytes for mimetic time series analysis and analyzed the expression changes of oxidative stress genes with the mimetic time series axis, in which the expression of JUN, TXN, and IL-1β differed with the change of cell status. Conclusion This study identifies a diagnostic model of 3-OSRGs from which patients can benefit and explores the importance of oxidative stress genes in building an immune environment in patients with periodontitis.
    Type of Medium: Online Resource
    ISSN: 1664-3224
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    DOI: 10.3389/fimmu.2023.1181467
    DOI: 10.3389/fimmu.2023.1181467.s001
    DOI: 10.3389/fimmu.2023.1181467.s002
    DOI: 10.3389/fimmu.2023.1181467.s003
    DOI: 10.3389/fimmu.2023.1181467.s004
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2023
    detail.hit.zdb_id: 2606827-8
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  • 3
    Online Resource
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    Table_4.xls
    Frontiers Media SA ; 2022
    In:  Frontiers in Endocrinology Vol. 13 ( 2022-12-8)
    Details
    In: Frontiers in Endocrinology, Frontiers Media SA, Vol. 13 ( 2022-12-8)
    Abstract: Uveal melanoma (UVM) is the most common primary intraocular malignancy in adults and is highly metastatic, resulting in a poor patient prognosis. Sphingolipid metabolism plays an important role in tumor development, diagnosis, and prognosis. This study aimed to establish a reliable signature based on sphingolipid metabolism genes (SMGs), thus providing a new perspective for assessing immunotherapy response and prognosis in patients with UVM. Methods In this study, SMGs were used to classify UVM from the TCGA-UVM and GEO cohorts. Genes significantly associated with prognosis in UVM patients were screened using univariate cox regression analysis. The most significantly characterized genes were obtained by machine learning, and 4-SMGs prognosis signature was constructed by stepwise multifactorial cox. External validation was performed in the GSE84976 cohort. The level of immune infiltration of 4-SMGs in high- and low-risk patients was analyzed by platforms such as CIBERSORT. The prediction of 4-SMGs on immunotherapy and immune checkpoint blockade (ICB) response in UVM patients was assessed by ImmuCellAI and TIP portals. Results 4-SMGs were considered to be strongly associated with the prognosis of UVM and were good predictors of UVM prognosis. Multivariate analysis found that the model was an independent predictor of UVM, with patients in the low-risk group having higher overall survival than those in the high-risk group. The nomogram constructed from clinical characteristics and risk scores had good prognostic power. The high-risk group showed better results when receiving immunotherapy. Conclusions 4-SMGs signature and nomogram showed excellent predictive performance and provided a new perspective for assessing pre-immune efficacy, which will facilitate future precision immuno-oncology studies.
    Type of Medium: Online Resource
    ISSN: 1664-2392
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    DOI: 10.3389/fendo.2022.1056310
    DOI: 10.3389/fendo.2022.1056310.s001
    DOI: 10.3389/fendo.2022.1056310.s002
    DOI: 10.3389/fendo.2022.1056310.s003
    DOI: 10.3389/fendo.2022.1056310.s004
    DOI: 10.3389/fendo.2022.1056310.s005
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2022
    detail.hit.zdb_id: 2592084-4
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  • 4
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    Table_2.xlsx
    Frontiers Media SA ; 2023
    In:  Frontiers in Immunology Vol. 14 ( 2023-3-10)
    Details
    In: Frontiers in Immunology, Frontiers Media SA, Vol. 14 ( 2023-3-10)
    Abstract: Head 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. Methods We 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. Results 6-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. Conclusion 6-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.
    Type of Medium: Online Resource
    ISSN: 1664-3224
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    DOI: 10.3389/fimmu.2023.1091218
    DOI: 10.3389/fimmu.2023.1091218.s001
    DOI: 10.3389/fimmu.2023.1091218.s002
    DOI: 10.3389/fimmu.2023.1091218.s003
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2023
    detail.hit.zdb_id: 2606827-8
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  • 5
    Online Resource
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    Table1.xls
    Frontiers Media SA ; 2023
    In:  Frontiers in Pharmacology Vol. 14 ( 2023-9-26)
    Details
    In: Frontiers in Pharmacology, Frontiers Media SA, Vol. 14 ( 2023-9-26)
    Abstract: Background: Uveal melanoma (UVM) is a primary intraocular malignancy that poses a significant threat to patients’ visual function and life. The basement membrane (BM) is critical for establishing and maintaining cell polarity, adult function, embryonic and organ morphogenesis, and many other biological processes. Some basement membrane protein genes have been proven to be prognostic biomarkers for various cancers. This research aimed to develop a novel risk assessment system based on BMRGs that would serve as a theoretical foundation for tailored and accurate treatment. Methods: We used gene expression profiles and clinical data from the TCGA-UVM cohort of 80 UVM patients as a training set. 56 UVM patients from the combined cohort of GSE84976 and GSE22138 were employed as an external validation dataset. Prognostic characteristics of basement membrane protein-related genes (BMRGs) were characterized by Lasso, stepwise multifactorial Cox. Multivariate analysis revealed BMRGs to be independent predictors of UVM. The TISCH database probes the crosstalk of BMEGs in the tumor microenvironment at the single-cell level. Finally, we investigated the function of ITGA5 in UVM using multiple experimental techniques, including CCK8, transwell, wound healing assay, and colony formation assay. Results: There are three genes in the prognostic risk model (ADAMTS10, ADAMTS14, and ITGA5). After validation, we determined that the model is quite reliable and accurately forecasts the prognosis of UVM patients. Immunotherapy is more likely to be beneficial for UVM patients in the high-risk group, whereas the survival advantage may be greater for UVM patients in the low-risk group. Knockdown of ITGA5 expression was shown to inhibit the proliferation, migration, and invasive ability of UVM cells in vitro experiments. Conclusion: The 3-BMRGs feature model we constructed has excellent predictive performance which plays a key role in the prognosis, informing the individualized treatment of UVM patients. It also provides a new perspective for assessing pre-immune efficacy.
    Type of Medium: Online Resource
    ISSN: 1663-9812
    URL: Article
    URL: Article
    DOI: 10.3389/fphar.2023.1264345
    DOI: 10.3389/fphar.2023.1264345.s001
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2023
    detail.hit.zdb_id: 2587355-6
    SSG: 15,3
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  • 6
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    Table_2.xlsx
    Frontiers Media SA ; 2023
    In:  Frontiers in Immunology Vol. 14 ( 2023-3-15)
    Details
    In: Frontiers in Immunology, Frontiers Media SA, Vol. 14 ( 2023-3-15)
    Abstract: Hepatocellular carcinoma (HCC), the third most prevalent cause of cancer-related death, is a frequent primary liver cancer with a high rate of morbidity and mortality. T-cell depletion (TEX) is a progressive decline in T-cell function due to continuous stimulation of the TCR in the presence of sustained antigen exposure. Numerous studies have shown that TEX plays an essential role in the antitumor immune process and is significantly associated with patient prognosis. Hence, it is important to gain insight into the potential role of T cell depletion in the tumor microenvironment. The purpose of this study was to develop a trustworthy TEX-based signature using single-cell RNA-seq (scRNA-seq) and high-throughput RNA sequencing, opening up new avenues for evaluating the prognosis and immunotherapeutic response of HCC patients. Methods The International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA) databases were used to download RNA-seq information for HCC patients. The 10x scRNA-seq. data of HCC were downloaded from GSE166635, and UMAP was used for clustering descending, and subgroup identification. TEX-related genes were identified by gene set variance analysis (GSVA) and weighted gene correlation network analysis (WGCNA). Afterward, we established a prognostic TEX signature using LASSO-Cox analysis. External validation was performed in the ICGC cohort. Immunotherapy response was assessed by the IMvigor210, GSE78220, GSE79671, and GSE91061cohorts. In addition, differences in mutational landscape and chemotherapy sensitivity between different risk groups were investigated. Finally, the differential expression of TEX genes was verified by qRT-PCR. Result 11 TEX genes were thought to be highly predictive of the prognosis of HCC and substantially related to HCC prognosis. Patients in the low-risk group had a greater overall survival rate than those in the high-risk group, according to multivariate analysis, which also revealed that the model was an independent predictor of HCC. The predictive efficacy of columnar maps created from clinical features and risk scores was strong. Conclusion TEX signature and column line plots showed good predictive performance, providing a new perspective for assessing pre-immune efficacy, which will be useful for future precision immuno-oncology studies.
    Type of Medium: Online Resource
    ISSN: 1664-3224
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    DOI: 10.3389/fimmu.2023.1137025
    DOI: 10.3389/fimmu.2023.1137025.s001
    DOI: 10.3389/fimmu.2023.1137025.s002
    DOI: 10.3389/fimmu.2023.1137025.s003
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2023
    detail.hit.zdb_id: 2606827-8
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