DGs are the most common primary malignant brain tumours in adults, with an age-adjusted mortality rate of 4.25/100,000 per year in the United States [1]. To understand gliomagenesis, molecular changes in large cohorts of DGs have been described previously [2,3]. These large-scale studies established the full spectrum of genomic alterations and revealed extensive molecular heterogeneity among individuals. Recent genomic studies have documented that individual cancer samples display genetic heterogeneity and contain subclonal populations [4]. The presence of multiple clones within a single tumour has been explained as a Darwinian evolutionary
Gliomas represent 80% of malignant brain tumors. Because of the high heterogeneity, the oncogenic mechanisms in gliomas are still unclear. In this study, we developed a new approach to identify dysregulated competitive endogenous RNA (ceRNA) interactions driven by copy number variation (CNV) in both lower-grade glioma (LGG) and glioblastoma multiforme (GBM). By analyzing genome and transcriptome data from The Cancer Genome Atlas (TCGA), we first found out the protein coding genes and long non-coding RNAs (lncRNAs) significantly affected by CNVs and further determined CNV-driven dysregulated ceRNA interactions by a customized pipeline. We obtained 13,776 CNV-driven dysregulated ceRNA pairs (including 3,954 mRNAs and 306 lncRNAs) in LGG and 262 pairs (including 221 mRNAs and 11 lncRNAs) in GBM, respectively. Our results showed that most of the ceRNA interactions were weakened by CNVs in both LGG and GBM, and many CNV-driven genes shared the same ceRNAs in the dysregulated ceRNA networks. Functional analysis indicated that the CNV-driven ceRNA network involved in some important mechanisms of tumorigenesis, such as cell cycle, p53 signaling pathway and TGF-beta signaling pathway. Further investigation of the ceRNA pairs in the communities from the dysregulated ceRNA network revealed more detailed biological functions related to the oncogenesis of malignant gliomas. Moreover, by exploring the association of CNV-driven ceRNAs with prognosis and histological subtype, we found that the copy number status of MTAP, KLHL9, and ELAVL2 related to the overall survival in LGG and showed high correlation with histological subtype. In conclusion, this study provided new insight into the molecular mechanisms and clinical biomarkers in gliomas.
Objective. Atherosclerotic is a chronic systemic disease that may occur in multiple vascular beds, including the carotid arteries, renal arteries, lower limb arteries, and cerebral vessels. Coronary atherosclerosis shares similar risk factors, pathogenesis, and pathophysiological basis with the atherosclerotic lesions of arteries at these sites. Arterial ultrasound assessment data were used to explore the correlation of atherosclerotic disease with CHD lesions and their severity and the number of lesion branches, as well as to evaluate its value in predicting CHD risk, in combination with traditional risk factors. Methods. A total of 363 inpatients with suspected CHD in the Department of Cardiology of the First Hospital of Harbin Medical University from November 2017 to June 2021 were selected. Patient clinical data, blood biochemical examination results, and ultrasound examination of neck vessels, abdominal arteries, and limb arteries were collected to obtain atherosclerosis assessment data. We then compared the differences between the CHD group and the control group, analyzed their correlation with CHD lesions and severity and the number of lesion branches, and evaluated the correlation with the coronary Gensini score. After adjustment for traditional risk factors, logistic regression was applied to analyze the relationship between arterial ultrasound assessment data and the risk of CHD. In addition, ROC plots were drawn to evaluate the risk of arterial ultrasound assessment data, combined with traditional risk factors, to predict CHD. Results. With regard to abnormal blood biochemical index values, differences in lipids, HDL-C, FIB, CK-MB, hs-cTnI, BNP, and GGT were found between the CHD group and the control group. Carotid plaque count, abdominal aortic flow velocity, inferior mesenteric artery flow velocity, classification of the number of stenotic branches of abdominal aortic branch arteries, lower-extremity-artery plaque count, degree of lower-extremity-artery stenosis, and lower-extremity-artery AS were risk factors for arterial ultrasound assessment data of CHD. Carotid plaque count, carotid artery AS, inferior mesenteric artery flow velocity, abdominal aortic flow velocity, abdominal aortic plaque count, abdominal aortic branch artery stenosis branch classification, lower-extremity-artery plaque count, lower-extremity-artery stenosis branch classification, degree of lower-extremity-artery stenosis, and lower-extremity-artery AS, combined with traditional risk factors, were mostly more effective than traditional risk factor models in predicting CHD, its severity, and the number of branch lesions; moreover, the predictive value was higher. Specifically, carotid plaque count, carotid AS, lower-extremity-artery AS, the degree of stenosis of lower-extremity arteries, and abdominal aortic branch artery stenosis branch classification can be used as predictor variables for CHD risk. Among these variables, the carotid plaque count can be used as an independent predictor of CHD. Conclusion. The incidence of arterial intima–media thickening (IMT), plaques, and stenosis can provide a reference for understanding the pattern of systemic atherogenesis and the distribution of atherosclerosis.
The clonal mutations in driver genes enable cells to gradually acquire growth advantage in tumor development. Therefore, revealing the functions of clonal driver gene mutations is important. Here, we proposed the method FCMP that considered evolutionary dependencies to analyze the functions of clonal driver gene mutations in a single patient. Applying our method to five cancer types from The Cancer Genome Atlas, we identified specific functions and common functions of clonal driver gene mutations. We found that the clonal driver gene mutations in the same patient played multiple functions. We also found that clonal mutations in the same driver gene performed different functions in different patients. These findings suggested that the clonal driver gene mutations showed strong tumor heterogeneity. In the pan-cancer analysis, the immune-related functions for clonal driver gene mutations were shared by multiple cancer types. In addition, clonal mutations in some driver genes predicted the survival of patients in cancers.
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