1.Construction and validation of circadian rhythm genes-related prognostic risk model for lung adenocarcinoma
Yanqi CUI ; Hu ZHAO ; Yawei ZHANG ; Lin NI ; Duohuang LIAN ; Jingrong YANG ; Shixin YE ; Fengfeng XU ; Jincan ZHANG ; Zhiyong ZENG
Chinese Journal of Clinical Thoracic and Cardiovascular Surgery 2026;33(04):550-558
Objective To explore the relationship between circadian rhythm genes and the occurrence, development, prognosis, and tumor microenvironment (TME) of lung adenocarcinoma (LUAD). Methods The Cancer Genome Atlas data were used to evaluate the expression, copy number variation, and somatic mutation frequency of circadian gene sets in LUAD. Gene ontology, Kyoto encyclopedia of genes and genomes, and gene set enrichment analysis were used to explore the potential mechanisms by which circadian rhythm genes affected LUAD progression. Cox regression, least absolute shrinkage and selection operator regression, support vector machine recursive feature elimination, and random forest screened circadian genes and established prognostic models, and on this basis constructed nomogram to predict patients’ 1-, 3-, and 5-year survival rates. Kaplan-Meier survival curves, receiver operating characteristic (ROC) curves, and time-dependent ROC curves were drawn to evaluate the predictive ability of the model, and the external dataset of GEO further verified the prognostic value of the prediction model. In addition, we evaluated the association of the prognostic model with immune cells and immune checkpoint genes. Single cell RNA sequencing (scRNA-seq) analysis was used to explore the molecular characteristics between prognostically relevant circadian genes and different immune cell populations in TME. Results Differentially expressed circadian rhythm genes were mainly enriched in biological processes related to cGMP-PKG signaling pathway, lipid and atherosclerosis, and JAK-STAT signaling pathway. Seven circadian rhythm genes: LGR4, CDK1, KLF10, ARNTL2, RORA, NPAS2, PTGDS were screened out, and a RiskScore model was established. According to the median RiskScore, samples were divided into a high-risk group and a low-risk group. Compared with patients in the low-risk group, patients in the high-risk group showed a poorer prognosis (P<0.001). Immunological characterization analysis showed that there were differences in the infiltration of multiple immune cells between the low-risk group and high-risk group. Most immune checkpoint genes had higher expression levels in the high-risk group than those in the low-risk group, and RiskScore was positively correlated with the expression of CD276, TNFSF4, PDCD1LG2, CD274, and TNFRSF9, and negatively correlated with the expression of CD40LG and TNFSF15. The scRNA-seq analysis showed that RORA and KLF10 were mainly expressed in natural killer cells. Conclusion The prognostic model based on seven feature circadian rhythm genes has certain predictive value for predicting survival of LUAD patients. Dysregulated expression of circadian genes may regulate the occurrence, progression as well as prognosis of LUAD through affecting TME, which provides a possible direction for finding potential strategies for treating LUAD from the perspective of mechanism by which circadian disorder affects immune cells.
2.Construction of a prognostic prediction model for invasive lung adenocarcinoma based on machine learning
Yanqi CUI ; Jingrong YANG ; Lin NI ; Duohuang LIAN ; Shixin YE ; Yi LIAO ; Jincan ZHANG ; Zhiyong ZENG
Chinese Journal of Clinical Thoracic and Cardiovascular Surgery 2025;32(01):80-86
Objective To determine the prognostic biomarkers and new therapeutic targets of the lung adenocarcinoma (LUAD), based on which to establish a prediction model for the survival of LUAD patients. Methods An integrative analysis was conducted on gene expression and clinicopathologic data of LUAD, which were obtained from the UCSC database. Subsequently, various methods, including screening of differentially expressed genes (DEGs), Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and Gene Set Enrichment Analysis (GSEA), were employed to analyze the data. Cox regression and least absolute shrinkage and selection operator (LASSO) regression were used to establish an assessment model. Based on this model, we constructed a nomogram to predict the probable survival of LUAD patients at different time points (1-year, 2-year, 3-year, 5-year, and 10-year). Finally, we evaluated the predictive ability of our model using Kaplan-Meier survival curves, receiver operating characteristic (ROC) curves, and time-dependent ROC curves. The validation group further verified the prognostic value of the model. Results The different-grade pathological subtypes' DEGs were mainly enriched in biological processes such as metabolism of xenobiotics by cytochrome P450, natural killer cell-mediated cytotoxicity, antigen processing and presentation, and regulation of enzyme activity, which were closely related to tumor development. Through Cox regression and LASSO regression, we constructed a reliable prediction model consisting of a five-gene panel (MELTF, MAGEA1, FGF19, DKK4, C14ORF105). The model demonstrated excellent specificity and sensitivity in ROC curves, with an area under the curve (AUC) of 0.675. The time-dependent ROC analysis revealed AUC values of 0.893, 0.713, and 0.632 for 1-year, 3-year, and 5-year survival, respectively. The advantage of the model was also verified in the validation group. Additionally, we developed a nomogram that accurately predicted survival, as demonstrated by calibration curves and C-index. Conclusion We have developed a prognostic prediction model for LUAD consisting of five genes. This novel approach offers clinical practitioners a personalized tool for making informed decisions regarding the prognosis of their patients.
3.A case of mitochondrial and peroxisome fission deficiency-related encephalopathy caused by DNM1L gene mutation
Yuhui DU ; Xinlei JIA ; Daoqi MEI ; Qunqun ZHANG ; Jun SU ; Lidan CUI ; Yanqi LYU
Chinese Journal of Neurology 2024;57(1):74-79
Mitochondrial and peroxisome fission deficiency-related encephalopathy caused by DNM1L gene mutation is a rare and fatal epileptic encephalopathy, with clinical phenotype and genetic heterogeneity. The acute stage is drug-resistant epilepsy with poor prognosis and serious neurological sequelae. A case of genetically confirmed encephalopathy related to mitochondrial and peroxisome fission defects is reported, the clinical data, treatment process are summarized, and the previous literature is reviewed to improve the understanding of the rare disease.
4.Discussion on mechanism of Danggui Buxue Decoction for anti-myocardial ischemia- reperfusion injury and "treating different diseases with the same method" in ischemic stroke based on network pharmacology
Jiankun CUI ; Xichun HUANG ; Zeji NIU ; Yanqi SHAO ; Yuanting MEI ; Yiyan YANG ; Yan WANG
International Journal of Traditional Chinese Medicine 2023;45(5):612-619
Objective:To predict the mechanism of Danggui Buxue Decoction for anti-myocardial ischemia-reperfusion injury and "treating different diseases with the same method" in ischemic stroke based on network pharmacology and molecular docking.Methods:The active components and targets of Danggui Buxue Decoction were screened by retrieving the database of TCMSP and literature; the corresponding targets of myocardial ischemia-reperfusion injury and ischemic stroke were found by OMIM and GeneCards database; the intersection targets of Danggui Buxue Decoction and disease were obtained by using Venny diagram, and the common target network and protein-protein interaction network were constructed by Cytoscape 3.7.1 software and STRING database. The GO and KEGG pathways were enriched by David Database, and the Bio GPS database was used to obtain the tissue distribution information of the key targets. The molecular docking technology was used to verify the results.Results:There were 21 active components in Danggui Buxue Decoction, 181 effective targets and 93 cross targets with diseases. The key components were quercetin, Kaempferol, β-sitosterol, formononetin and isorhamnetin. The key targets were AKT1, TNF, IL6, IL-1β and VEGFA. The enrichment results showed that the main action pathways were fluid shear force and arteriosclerosis, lipid and arteriosclerosis, AGE-RAGE signal pathway in diabetic complications, and the core targets were mainly located in the medullary cells, dendritic cell, smooth muscle, prostate, thyroid and other tissues. The results of molecular docking showed that quercetin had the best binding effect to IL-1β, while isorhamnetin had the best binding effect to IL-1β.Conclusion:Danggui Buxue Decoction is against myocardial ischemia-reperfusion injury and ischemic stroke through hemodynamics, lipid metabolism, inflammatory reaction, oxidative stress, immune reaction and cell apoptosis, plays the role of "treating different diseases with the same method".
5.Clinical Observation on Treatment of 460 Community-acquired Pneumonia Cases in Children with Qing-Fei Tong-Luo Ointment
Xiuying ZHANG ; Xuefeng WANG ; Yunxiao SHANG ; Zhenze CUI ; Yan HUANG ; Yongsheng WANG ; Yingchun LI ; Tong FENG ; Yanqi SU ; Fengli YU ; Ling ZHANG ; Xueying JIN ; Aimin SUN ; Yixiang LIU ; Danhua SHI ; Han ZHANG ; Zhenqi WU ; Yue ZHAO
World Science and Technology-Modernization of Traditional Chinese Medicine 2017;19(12):2054-2057
This study was aimed to evaluate the clinical effect and safety of Qing-Fei Tong-Luo (QFTL) ointment for treating children with pneumonia.Randomized controlled trial (RCT) was conducted among 460 cases of children with pneumonia.The observation group was given QFTL ointment combined with basic treatment.And the control group was only treated by basic treatment.Evaluation was given on the total clinical efficacy,disappeared time of fever,cough,expectoration,shortness of breath,and medication safety.The incidence of respiratory diseases was followed up on the 30th days after drug withdrawal.The results showed that in the aspect of clinical efficacy between two groups,the cure rate of the observation group was 98.26%,and that of the control group was 93.89%,with statistic significance (P < 0.05).The cure rate of the observation group was better than that of the control group.There was statistical difference on expectoration disappeared time (P < 0.05).There was no statistical difference on disappeared time of fever,cough and shortness of breath (P > 0.05).There was statistical difference on the incidence of respiratory diseases on the 30th days followed-up after drug withdrawal (P < 0.05).There was no statistical difference on the incidence of upper respiratory tract infection,pneumonia and asthma (P > 0.05).No adverse reactions occurred in the observation group.It was concluded that QFTL ointment combined with basic therapy on the treatment of pneumonia in children was significantly better than the control group in the aspect of clinical efficacy,expectoration disappeared time and the incidence of bronchitis.It is safe and effective.The prognosis is good and worthy of promotion in the clinical practice.

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