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Qi L, Tang Z. Prognostic model revealing pyroptosis-related signatures in oral squamous cell carcinoma based on bioinformatics analysis. Sci Rep 2024; 14:6149. [PMID: 38480853 PMCID: PMC10937718 DOI: 10.1038/s41598-024-56694-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 03/09/2024] [Indexed: 03/17/2024] Open
Abstract
One of the most common oral carcinomas is oral squamous cell carcinoma (OSCC), bringing a heavy burden to global health. Although progresses have been made in the intervention of OSCC, 5 years survival of patients suffering from OSCC is poor like before regarding to the high invasiveness of OSCC, which causes metastasis and recurrence of the tumor. The relationship between pyroptosis and OSCC remains to be further investigated as pyroptosis in carcinomas has gained much attention. Herein, the key pyroptosis-related genes were identified according to The Cancer Genome Atlas (TCGA) dataset. Additionally, a prognostic model was constructed based upon three key genes (CTLA4, CD5, and IL12RB2) through least absolute shrinkage and selection operator (LASSO) analyses, as well as univariate and multivariate COX regression in OSCC. It was discovered that the high expression of these three genes was associated with the low-risk group. We also identified LAIR2 as a hub gene, whose expression negatively correlated with the risk score and the different immune cell infiltration. Finally, we proved that these three genes were independent prognostic factors linked to overall survival (OS), and reliable consequences could be predicted by this model. Our study revealed the relationship between pyroptosis and OSCC, providing insights into new treatment targets for preventing and treating OSCC.
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Affiliation(s)
- Lu Qi
- Hunan Key Laboratory of Oral Health Research, Hunan Clinical Research Center of Oral Major Diseases and Oral Health, Xiangya Stomatological Hospital, Xiangya School of Stomatology, Central South University, Changsha, 410000, China
| | - Zhangui Tang
- Hunan Key Laboratory of Oral Health Research, Hunan Clinical Research Center of Oral Major Diseases and Oral Health, Xiangya Stomatological Hospital, Xiangya School of Stomatology, Central South University, Changsha, 410000, China.
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Wang Z, Mu L, Feng H, Yao J, Wang Q, Yang W, Zhou H, Li Q, Xu L. Expression patterns of platinum resistance-related genes in lung adenocarcinoma and related clinical value models. Front Genet 2022; 13:993322. [PMID: 36506331 PMCID: PMC9730711 DOI: 10.3389/fgene.2022.993322] [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: 07/13/2022] [Accepted: 10/21/2022] [Indexed: 11/25/2022] Open
Abstract
The purpose of this study was to explore platinum resistance-related biomarkers and mechanisms in lung adenocarcinoma. Through the analysis of gene expression data of lung adenocarcinoma patients and normal patients from The Cancer Genome Atlas, Gene Expression Omnibus database, and A database of genes related to platinum resistance, platinum resistance genes in lung adenocarcinoma and platinum resistance-related differentially expressed genes were obtained. After screening by a statistical significance threshold, a total of 252 genes were defined as platinum resistance genes with significant differential expression, of which 161 were up-regulated and 91 were down-regulated. The enrichment results of up-regulated gene Gene Ontology (GO) showed that TOP3 entries related to biological processes (BP) were double-strand break repair, DNA recombination, DNA replication, the down-regulated gene GO enriches the TOP3 items about biological processes (BP) as a response to lipopolysaccharide, muscle cell proliferation, response to molecule of bacterial origin. Gene Set Enrichment Analysis showed that the top three were e2f targets, g2m checkpoint, and rgf beta signaling. A prognostic model based on non-negative matrix factorization classification showed the characteristics of high- and low-risk groups. The prognostic model established by least absolute shrinkage and selection operator regression and risk factor analysis showed that genes such as HOXB7, NT5E, and KRT18 were positively correlated with risk score. By analyzing the differences in m6A regulatory factors between high- and low-risk groups, it was found that FTO, GPM6A, METTL3, and YTHDC2 were higher in the low-risk group, while HNRNPA2B1, HNRNPC, TGF2BP1, IGF2BP2, IGF2BP3, and RBM15B were higher in the high-risk group. Immune infiltration and drug sensitivity analysis also showed the gene characteristics of the platinum-resistant population in lung adenocarcinoma. ceRNA analysis showed that has-miR-374a-5p and RP6-24A23.7 were lower in the tumor expression group, and that the survival of the low expression group was worse than that of the high expression group. In conclusion, the results of this study show that platinum resistance-related differentially expressed genes in lung adenocarcinoma are mainly concentrated in biological processes such as DNA recombination and response to lipopolysaccharide. The validation set proved that the high-risk group of our prognostic model had poor survival. M6A regulatory factor analysis, immune infiltration, and drug sensitivity analysis all showed differences between high and low-risk groups. ceRNA analysis showed that has-miR-374a-5p and RP6-24A23.7 could be protective factors. Further exploration of the potential impact of these genes on the risk and prognosis of drug-resistant patients with lung adenocarcinoma would provide theoretical support for future research.
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Affiliation(s)
- Zhe Wang
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Lin Mu
- Department of Ophthalmology, Longhua Hospital Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - He Feng
- Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Zhejiang, China
| | - Jialin Yao
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Qin Wang
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Wenxiao Yang
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Huiling Zhou
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Qinglin Li
- Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Zhejiang, China,*Correspondence: Qinglin Li, ; Ling Xu,
| | - Ling Xu
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China,*Correspondence: Qinglin Li, ; Ling Xu,
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Zushi Y. Direct Prediction of Physicochemical Properties and Toxicities of Chemicals from Analytical Descriptors by GC-MS. Anal Chem 2022; 94:9149-9157. [PMID: 35700270 PMCID: PMC9246259 DOI: 10.1021/acs.analchem.2c01667] [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] [Indexed: 11/28/2022]
Abstract
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With advances in
machine learning (ML) techniques, the quantitative
structure–activity relationship (QSAR) approach is becoming
popular for evaluating chemicals. However, the QSAR approach requires
that the chemical structure of the target compound is known and that
it should be convertible to molecular descriptors. These requirements
lead to limitations in predicting the properties and toxicities of
chemicals distributed in the environment as in the PubChem database;
the structural information on only 14% of compounds is available.
This study proposes a new ML-based QSAR approach that can predict
the properties and toxicities of compounds using analytical descriptors
of mass spectrum and retention index obtained via gas chromatography–mass
spectrometry without requiring exact structural information. The model
was developed based on the XGBoost ML method. The root-mean-square
errors (RMSEs) for log Ko-w, log (molecular weight), melting point,
boiling point, log (vapor pressure), log (water solubility), log (LD50) (rat, oral), and log (LD50) (mouse, oral) are
0.97, 0.052, 51, 23, 0.74, 1.1, 0.74, and 0.6, respectively. The model
performed well on a chemical standard mixture measurement, with similar
results to those of model validation. It also performed well on a
measurement of contaminated oil with spectral deconvolution. These
results indicate that the model is suitable for investigating unknown-structured
chemicals detected in measurements. Any online user can execute the
model through a web application named Detective-QSAR (http://www.mixture-platform.net/Detective_QSAR_Med_Open/). The analytical descriptor-based approach is expected to create
new opportunities for the evaluation of unknown chemicals around us.
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Affiliation(s)
- Yasuyuki Zushi
- Research Institute of Science for Safety and Sustainability, National Institute of Advanced Industrial Science and Technology, 16-1 Onogawa, Tsukuba, Ibaraki 305-8506, Japan.,Graduate School of Science and Technology, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
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Immune Subtype Profiling and Establishment of Prognostic Immune-Related lncRNA Pairs in Human Ovarian Cancer. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:8338137. [PMID: 35578596 PMCID: PMC9107039 DOI: 10.1155/2022/8338137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/28/2022] [Indexed: 11/18/2022]
Abstract
This study collected immune-related genes (IRGs) and used gene expression data from TCGA database to construct a molecular subtype of ovarian cancer (OV) based on immune-related lncRNA gene pairs (IRLnc_GPs). The relationships between molecular subtypes and prognosis and clinical characteristics were further explored. IRGs were acquired from the ImmPort database, and round-robin pairing of immune-related lncRNAs was performed. The NMF algorithm was used to identify molecular subtypes, and the immune score of a single sample was calculated through ESTIMATE, TIMER, ssGSEA, MCPcounter, and CIBERSORT. The relationship between molecular subtypes and immune microenvironments was identified. A hypergeometric test was used to test the lncRNA pairs among the OV molecular subtypes (C1 and C2 subtypes). The BH method was used to screen the different lncRNA pairs, and a predictive risk model was constructed and verified. Finally, correlation analysis between the risk model, immune checkpoint genes, and chemotherapy drugs was carried out. Based on IRLnc_GP to classify 373 OV samples of TCGA, the samples were divided into two subtypes, and the prognosis between the subtypes showed significant differences. The C1 subtype with a poor prognosis was more related to the pathways of tumor occurrence and development. We identified 180 differential lncRNA pairs between subtypes and constructed a prognostic risk model based on 8 IRLnc_GPs. In the independent dataset, the distribution of subtypes in functional modules was different and highly repeatable. There were significant differences in the molecular and clinical characteristics of the subtypes and the drug sensitivity of immunotherapy/chemotherapy. In conclusion, the risk model established based on IRLnc_GP can better evaluate the prognosis of OV samples and can also assess the effects of different drug treatments in the high- and low-risk groups, providing new insights and ideas for the treatment of OV.
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Shi Y, Wang Y, Yang R, Zhang W, Zhang Y, Feng K, Lv Q, Niu K, Chen J, Li L, Zhang Y. Glycosylation-related molecular subtypes and risk score of hepatocellular carcinoma: Novel insights to clinical decision-making. Front Endocrinol (Lausanne) 2022; 13:1090324. [PMID: 36605944 PMCID: PMC9807760 DOI: 10.3389/fendo.2022.1090324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is the fifth most common cancer and the third leading cause of cancer deaths worldwide, seriously affecting human community health and care. Emerging evidence has shown that aberrant glycosylation is associated with tumor progression and metastasis. However, the role of glycosylation-related genes in HCC has notbeen reported. METHODS Weighted gene coexpression network analysis and non-negative matrix factorization analysis were applied to identify functional modules and molecularm subtypes in HCC. The least absolute shrinkage and selection operator Cox regression was used to construct the glycosylation-related signature. The independent prognostic value of the risk model was confirmed and validated by systematic techniques, including principal component analysis, T-distributed random neighbor embedding analysis, Kaplan-Meier survival analysis, the ROC curve, multivariate Cox regression, the nomogram, and the calibration curve. The single-sample gene set enrichment analysis, gene set variation analysis, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes analyses were evaluated by the immune microenvironment and potential biological processes. The quantitative real-time polymerase chain reaction and immunohistochemistry analysis were used to verify the expression of five genes. RESULTS We identified the glycosylation-related genes with bioinformatics analysis to construct and validate a five-gene signature for the prognosis of HCC patients. Patients with HCC in the high-risk group had a worse prognosis. The risk score could be an independent factor and was associated with clinical features, such as the grade and stage. The nomogram exhibited an accurate score that included the risk score and clinical parameters. The infiltration levels of antitumor cells were upregulated in the low-risk group, including B_cells, Mast_cells, neutrophils, NK_cells, and T_helper_cells. Moreover, glycosylation was more sensitive to immunotherapy, and may play a critical role in the metabolic processes of HCC, such as bile acid metabolism and fatty acid metabolism. In addition, the five-gene messenger RNA (mRNA) and protein expression were overexpressed in HCC cells and tissues. CONCLUSIONS The glycosylation-related signature is effective for prognostic recognition, immune efficacy evaluation, and substance metabolism in HCC, providing a novel insight for therapeutic target prediction and clinical decision-making.
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Affiliation(s)
- Yanlong Shi
- Hepatopancreatobiliary Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yizhu Wang
- Hepatopancreatobiliary Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Rui Yang
- Hepatopancreatobiliary Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Wenning Zhang
- Hepatopancreatobiliary Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yu Zhang
- The Second Clinical Medical College, Lanzhou University, Lanzhou, Gansu, China
| | - Kun Feng
- Hepatopancreatobiliary Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Qingpeng Lv
- Hepatopancreatobiliary Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Kaiyi Niu
- Hepatopancreatobiliary Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jiping Chen
- Hepatopancreatobiliary Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Li Li
- Department of General Surgery, Fuyang Hospital of Anhui Medical University, Fuyang, Anhui, China
- *Correspondence: Li Li, ; Yewei Zhang,
| | - Yewei Zhang
- Hepatopancreatobiliary Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- *Correspondence: Li Li, ; Yewei Zhang,
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