1
|
Feng C, Song C, Ning Z, Ai B, Wang Q, Xu Y, Li M, Bai X, Zhao J, Liu Y, Li X, Zhang J, Li C. ce-Subpathway: Identification of ceRNA-mediated subpathways via joint power of ceRNAs and pathway topologies. J Cell Mol Med 2018; 23:967-984. [PMID: 30421585 PMCID: PMC6349186 DOI: 10.1111/jcmm.13997] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/28/2018] [Accepted: 10/17/2018] [Indexed: 12/19/2022] Open
Abstract
Competing endogenous RNAs (ceRNAs) represent a novel mechanism of gene regulation that may mediate key subpathway regions and contribute to the altered activities of pathways. However, the classical methods used to identify pathways fail to specifically consider ceRNAs within the pathways and key regions impacted by them. We proposed a powerful strategy named ce-Subpathway for the identification of ceRNA-mediated functional subpathways. It provided an effective level of pathway analysis via integrating ceRNAs, differentially expressed (DE) genes and their key regions within the given pathways. We respectively analysed one pulmonary arterial hypertension (PAH) and one myocardial infarction (MI) data sets and demonstrated that ce-Subpathway could identify many subpathways whose corresponding entire pathways were ignored by those non-ceRNA-mediated pathway identification methods. And these pathways have been well reported to be associated with PAH/MI-related cardiovascular diseases. Further evidence showed reliability of ceRNA interactions and robustness/reproducibility of the ce-Subpathway strategy by several data sets of different cancers, including breast cancer, oesophageal cancer and colon cancer. Survival analysis was finally applied to illustrate the clinical application value of the ceRNA-mediated functional subpathways using another data sets of pancreatic cancer. Comprehensive analyses have shown the power of a joint ceRNAs/DE genes and subpathway strategy based on their topologies.
Collapse
Affiliation(s)
- Chenchen Feng
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China
| | - Chao Song
- Department of Pharmacology, Daqing Campus, Harbin Medical University, Daqing, China
| | - Ziyu Ning
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China
| | - Bo Ai
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China
| | - Qiuyu Wang
- School of Nursing, Daqing Campus, Harbin Medical University, Daqing, China
| | - Yong Xu
- The fifth Affiliated Hospital of Harbin Medical University, Daqing, China
| | - Meng Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China
| | - Xuefeng Bai
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China
| | - Jianmei Zhao
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China
| | - Yuejuan Liu
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China
| | - Xuecang Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China
| | - Jian Zhang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China
| | - Chunquan Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China
| |
Collapse
|
2
|
Fusion of CT coronary angiography and whole-heart dynamic 3D cardiac MR perfusion: building a framework for comprehensive cardiac imaging. Int J Cardiovasc Imaging 2017; 34:649-660. [DOI: 10.1007/s10554-017-1260-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 10/19/2017] [Indexed: 10/18/2022]
|
3
|
Taylor R, Dobson A, Mirzaei M. Contribution of changes in risk factors to the decline of coronary heart disease mortality in Australia over three decades. ACTA ACUST UNITED AC 2016; 13:760-8. [PMID: 17001216 DOI: 10.1097/01.hjr.0000220581.42387.d4] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Coronary heart disease has been a major cause of mortality in Australian adults, but the rate has declined by 83% from the 1968 peak by the year 2000. The study objective is to determine the contribution of changes in population risk factors - mean serum cholesterol and diastolic blood pressure and tobacco smoking prevalence - to the decline in coronary heart disease mortality in Australia over three decades. METHODS Coronary heart disease deaths (International Classification of Disease-9, 410-414) and population by year, age group and sex were obtained from the Australian Bureau of Statistics. Risk factor levels were obtained from population surveys and estimated average annual changes by period were used to calculate average annual 'attributable' proportional declines in CHD mortality by period (age 35-64 years). RESULTS Over the period 1968-2000, 74% of male decline and 81% of the female decline in coronary heart disease mortality rate was accounted for by the combined effect of reductions in the three risk factors. In males 36% of the decline was contributed by reductions in diastolic blood pressure, 22% by cholesterol and 16% by smoking. For females 56% was from diastolic blood pressure reduction, 20% from cholesterol and 5% from smoking. Effects of reductions in serum cholesterol on coronary heart disease mortality occurred mainly in the 1970s. Declines in diastolic blood pressure had effects on coronary heart disease mortality over the three decades, and declines in tobacco smoking had a significant effect in males in the 1980s. CONCLUSION Most of the spectacular decline in coronary heart disease mortality over the last three decades in Australia can be ascribed to reductions in population risk factors from primary and secondary prevention.
Collapse
Affiliation(s)
- Richard Taylor
- School of Population Health, Faculty of Health Sciences, University of Queensland, Brisbane, Queensland, Australia.
| | | | | |
Collapse
|
4
|
The culprit lesion and its consequences: combined visualization of the coronary arteries and delayed myocardial enhancement in dual-source CT: a pilot study. Eur Radiol 2010; 20:2834-43. [DOI: 10.1007/s00330-010-1864-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2010] [Accepted: 05/04/2010] [Indexed: 01/10/2023]
|
5
|
Galassi AR, Tomasello SD, Costanzo L, Tamburino C. Retrograde approach for chronic total occlusion percutaneous revascularization. Interv Cardiol 2010. [DOI: 10.2217/ica.10.31] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
6
|
Shiau YC, Fan ST, Kuo TS, Chu SH. Backpropagation Neural Network for Motion Analysis on Blood-pool Gated Single Photon Emission Computed Tomography. CONFERENCE PROCEEDINGS : ... ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL CONFERENCE 2007; 2005:3157-60. [PMID: 17282914 DOI: 10.1109/iembs.2005.1617145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We used backpropagation neural network for left ventricular motion analysis on Tc-99m labeled RBC blood-pool gated single photon emission computed tomography (GSPECT). Phantom images by the model of solid spheres were generated to simulate the left ventricle. Training data sets were selected from the phantom images. After training, the neural network can perform motion analysis on the phantom images and all series of patients' GSPECT images. The results of motion analysis were displayed in the formats of vector fields superimposed on the original GSPECT images. The GSPECT of one patient with normal left ventricle and two patients with abnormal left ventricular motion were acquired and analyzed. The study showed that back propagation neural network was useful in the evaluation of left ventricular motion in GSPECT images.
Collapse
Affiliation(s)
- Yu-Chien Shiau
- Member, IEEE, Department of Nuclear Medicine, Far Eastern Memorial Hospital, No.21, Nan-Ya South Road, Section 2, Panchiao 22050 Taiwan (phone: +886-955-323-463; fax: +886-2-8966-8378; e-mail: )
| | | | | | | |
Collapse
|
7
|
Schoenhagen P, Stillman AE, Halliburton SS, Kuzmiak SA, Painter T, White RD. Non-invasive coronary angiography with multi-detector computed tomography: comparison to conventional X-ray angiography. Int J Cardiovasc Imaging 2005; 21:63-72. [PMID: 15915941 DOI: 10.1007/s10554-004-1887-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Selective coronary angiography introduced clinical coronary imaging in the late 1950s. The angiographic identification of high-grade coronary lesions in patients with acute and chronic symptomatic coronary artery disease (CAD) led to the development of surgical and percutaneous coronary revascularization. However, the fact that CAD remains the major cause of death in North America and Europe demonstrates the need for novel, complementary diagnostic strategies. These are driven by the need to characterize both increasingly advanced disease stages but also early, asymptomatic disease development. Complex revascularization techniques for patients with advanced disease stages will initiate a growing demand for 3-dimensional coronary imaging and integration of imaging modalities with new mechanical therapeutic devices. An emerging focus is atherosclerosis imaging with the goal to identify subclinical disease stages as the basis for pharmacological intervention aimed at disease stabilization or reversal. Non-invasive coronary imaging with coronary multidetector computed tomographic angiography (MDCTA) allows both assessment of luminal stenosis and subclinical disease of the arterial wall. Its complementary role in the assessment of early and advanced stages of CAD is increasingly recognized.
Collapse
Affiliation(s)
- Paul Schoenhagen
- Department of Radiology, Center for Integrated Non-Invasive Cardiovascular Imaging, The Cleveland Clinic Foundation, Cleveland, OH 44195, USA.
| | | | | | | | | | | |
Collapse
|
8
|
Wong CYO, Tatini VR, Bis K. Combined CT-PET criteria for myocardial viability and scar: a preliminary report. Int J Cardiovasc Imaging 2005; 20:487-91. [PMID: 15856631 DOI: 10.1007/s10554-004-2784-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Identification of hibernating myocardium and its differentiation from scar tissue is an important clinical task for implementing different treatment options. The recognition of combined criteria in spiral-CT and PET for hibernating myocardium and scar will be important as hybrid CT-PET moves into the main stream of routine oncologic and cardiovascular imaging. A review of three cases, initially referred for CT evaluation of cardiac or pulmonary conditions with subsequent F-18 FDG body PET imaging, was presented for illustration as a combined CT-PET cardiac evaluation. The real value of this combined anatomical and functional evaluation will be with the upcoming concurrent CT and PET imaging using dedicated multi-slice CT-PET scanners.
Collapse
Affiliation(s)
- Ching-yee Oliver Wong
- Positron Diagnostic Center and Cyclotron, Department of Nuclear Medicine, William Beaumont HOspital, Michigan 48073-6769, USA.
| | | | | |
Collapse
|
9
|
Abstract
Magnetic resonance imaging and/or contrast-enhanced multidetector computed tomography may be used separately or, often more effectively, in an integrated fashion, to address important issues in patients with coronary artery disease causing ischemic cardiac disease (ICD). These issues include complications of myocardial infarction, such as ventricular dysfunction, myocardial wall rupture, aneurysm formation, intracavitary thrombus, mitral insufficiency, and pericarditis, as well as aspects of planning and monitoring therapy for ICD, such as revascularization and ventricular aneurysm repair.
Collapse
Affiliation(s)
- Richard D White
- Center for Integrated Non-Invasive Cardiovascular Imaging, Department of Radiology, Cleveland Clinic Foundation, Cleveland, Ohio 44195, USA.
| |
Collapse
|
10
|
Abstract
The vascular endothelium is an active, dynamic tissue that controls many important functions, including regulation of vascular tone and maintenance of blood circulation, fluidity, coagulation, and inflammatory responses. Cardiovascular risk factors affect many of the normal functions of the endothelium. In particular, oxidized low-density lipoprotein cholesterol initiates a series of events that begin with cell activation, endothelial dysfunction, local inflammation, and a procoagulant vascular surface. These conspire to result in plaque formation and ultimately plaque rupture and cardiovascular events. Endothelial dysfunction may be evaluated by means of invasive techniques, such as coronary artery reactivity to acetylcholine, or noninvasive techniques, such as brachial artery ultrasonography. Loss of endothelium-dependent vasodilation is a characteristic feature throughout the development of atherosclerosis, and it is independently related to future adverse cardiovascular risk. Therefore, measurement of endothelial function can possibly be used to determine risk, to triage management, and to improve outcomes. At the same time, inflammation is a crucial factor in the atherosclerotic disease process. To identify and monitor the ongoing inflammatory process, markers of inflammation such as C-reactive protein (CRP) have been studied. Scientific evidence shows that elevated plasma CRP values add to the predictive ability of other established risk factors; moreover, elevated values appear to augment the Framingham Coronary Risk Score in identifying individuals who should be considered for cardioprotective treatment programs. Interestingly, thiazolidinediones (TZDs), peroxisome proliferator-activated receptor-gamma agonists that are effective in the treatment of type 2 diabetes mellitus, not only increase insulin sensitivity but can benefit endothelial function because they exhibit anti-inflammatory effects. For many individuals, including those with the metabolic syndrome and/or type 2 diabetes, endothelial dysfunction and elevated plasma CRP levels indicate increased risk of cardiovascular disease. Notably, the TZDs have been shown to reduce CRP levels and may improve endothelial function.
Collapse
Affiliation(s)
- Manuel A Gonzalez
- Cardiovascular Division, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | |
Collapse
|
11
|
Raggi P. Introduction. Am J Cardiol 2002. [DOI: 10.1016/s0002-9149(02)02952-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|