Theory and Applications of the (Cardio) Genomic Fabric Approach to Post-Ischemic and Hypoxia-Induced Heart Failure

Iacobaş, Dumitru A.; Xi, Lei

doi:10.3390/jpm12081246

Cited by 9 publications

(12 citation statements)

References 73 publications

(120 reference statements)

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“…The results indicate that Cav1 is associated with Ngf. However, an inverse relationship between the protein levels of Cav1 and Ngf was found in the heart of a rat model of induced chronic ischemic heart failure compared to the corresponding control [44]. An increase of Ngf expression associated with Cav1 decrease was reported in the urinary bladder of rats following acute urinary retention after parturition [45].…”

Section: Discussionmentioning

confidence: 95%

“…Figure 8 presents the expression inter-coordination of 40 genes involved in 4 KEGGdetermined metabolic pathways: citrate cycle [42], fructose and mannose [43], glycolysis/gluconeogenesis [41], and pyruvate [44] pathways. (Aldehyde dehydrogenase 2 family), Aldh3/9a1 (Aldehyde dehydrogenase 3/9 family, member A1), Aldoa/c, Eno1/2/4 (Enolase 1/2/4), Fbp1, G6pc3 (Glucose 6 phosphatase, catalytic, 3), Gapdh (Glyceraldehyde-3-phosphate dehydrogenase), Gapdhs (Glyceraldehyde-3phosphate dehydrogenase, spermatogenic), Gck (glucokinase), Gpi (Glucose-6-phosphate isomerase), Hk1, Ldha/b (Lactate dehydrogenase A/B), Minpp1 (Multiple inositol-polyphosphate phosphatase 1), Pck2, Pdha1, Pfkl/m (Phosphofructokinase, liver/muscle), Pgam1 (Phosphoglycerate mutase 1), Pgk1 (Phosphoglycerate kinase 1), Tpi (Triosephosphate isomerase 1).…”

Section: Remodeling Of the Metabolic Genes Networkmentioning

confidence: 99%

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Metabolic Deregulation in Pulmonary Hypertension

Mathew¹,

Iacobaş²,

Huang³

et al. 2023

Preprint

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The high morbidity and mortality rate of the pulmonary arterial hypertension (PAH) is partially explained by the metabolic deregulation associated with the disease. The present study identified statistically significant increase of the glucose transporter solute carrier family 2 (Slc2a1), beta nerve growth factor (Ngf), and nuclear factor erythroid derived 2, like 2 (Nfe2l2) on three standard PAH rat models and their healthy counterpart. PAH was induced by subjecting the animals to hypoxia (HO group) or by injecting them with monocrotaline in either normal (CM) or hypoxic (HM) atmospheric conditions. The Western blot and double immunofluorescent experiments were complemented with the gene expression profiling of the animal lungs analyzed from the perspective of the Genomic Fabric Paradigm. We found substantial remodeling of the genomic fabrics of the citrate cycle, pyruvate metabolism, glycolysis/gluconeogenesis and fructose and manose pathways. According to the novel transcriptomic distance criterion, the most comprehensive measure of the transcriptomic alteration, glycolysis/gluconeogenesis was the most affected functional pathway in all three PAH models. PAH decoupled the coordinated expression of many metabolic genes and replaced Pmm2 with Pmm1 in the center of the fructose and mannose metabolism. Our data show that metabolic dysregulation is a major pathogenic factor of the PAH.

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Section: Discussionmentioning

confidence: 95%

Section: Remodeling Of the Metabolic Genes Networkmentioning

confidence: 99%

Metabolic Deregulation in Pulmonary Hypertension

Mathew¹,

Iacobaş²,

Huang³

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…In this report, we used the GFP algorithms [45] to reveal the novel characteristics of the transcriptome that are ignored by the traditional analysis limited to the genes' expression levels (e.g., [16,98]). Adding the independent REV and CORs characteristics to the AVE of each individual genes increased the information obtained from our gene expression experiments on thyroid cancer samples by almost 75 hundred times [49,52].…”

Section: Discussionmentioning

confidence: 99%

“…The analyses were carried out from the Genomic Fabric Paradigm (GFP) perspective which provides the most theoretically possible characterization of the transcriptome [45] and is able to identify the most legitimate targets for personalized anti-cancer gene therapy [46]. In addition to the traditional average expression level (AVE), GFP characterizes each gene with the Relative Expression Variation (REV) across biological replicas and Expression Coordination (COR), with each other gene in the same condition.…”

Section: Introductionmentioning

confidence: 99%

Papillary Thyroid Cancer Remodels the Genetic Information Processing Pathways

Iacobas,

Iacobas

2024

Genes

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The genetic causes of the differentiated, highly treatable, and mostly non-fatal papillary thyroid cancer (PTC) are not yet fully understood. The mostly accepted PTC etiology blames the altered sequence or/and expression level of certain biomarker genes. However, tumor heterogeneity and the patient’s unique set of favoring factors question the fit-for-all gene biomarkers. Publicly accessible gene expression profiles of the cancer nodule and the surrounding normal tissue from a surgically removed PTC tumor were re-analyzed to determine the cancer-induced alterations of the genomic fabrics responsible for major functional pathways. Tumor data were compared with those of standard papillary and anaplastic thyroid cancer cell lines. We found that PTC regulated numerous genes associated with DNA replication, repair, and transcription. Results further indicated that changes of the gene networking in functional pathways and the homeostatic control of transcript abundances also had major contributions to the PTC phenotype occurrence. The purpose to proliferate and invade the entire gland may explain the substantial transcriptomic differences we detected between the cells of the cancer nodule and those spread in homo-cellular cultures (where they need only to survive). In conclusion, the PTC etiology should include the complex molecular mechanisms involved in the remodeling of the genetic information processing pathways.

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“…Precision medicine is a medical model for prevention, diagnosis, and treatment that aims to achieve an optimal therapeutic regimen for an individual ( Yan et al, 2021 ). It has become a focal area of interest and development in medicine of the 21st century ( Iacobas and Xi, 2022 ). Previous researchers such as Zaki et al (2018) ; Zulkifley et al (2019) , and Zamani et al (2020) was based on the two-class detection of pterygium.…”

Section: Discussionmentioning

confidence: 99%

Application of artificial intelligence models for detecting the pterygium that requires surgical treatment based on anterior segment images

et al. 2022

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Background and aimA pterygium is a common ocular surface disease, which not only affects facial appearance but can also grow into the tissue layer, causing astigmatism and vision loss. In this study, an artificial intelligence model was developed for detecting the pterygium that requires surgical treatment. The model was designed using ensemble deep learning (DL).MethodsA total of 172 anterior segment images of pterygia were obtained from the Jiangxi Provincial People’s Hospital (China) between 2017 and 2022. They were divided by a senior ophthalmologist into the non-surgery group and the surgery group. An artificial intelligence model was then developed based on ensemble DL, which was integrated with four benchmark models: the Resnet18, Alexnet, Googlenet, and Vgg11 model, for detecting the pterygium that requires surgical treatment, and Grad-CAM was used to visualize the DL process. Finally, the performance of the ensemble DL model was compared with the classical Resnet18 model, Alexnet model, Googlenet model, and Vgg11 model.ResultsThe accuracy and area under the curve (AUC) of the ensemble DL model was higher than all of the other models. In the training set, the accuracy and AUC of the ensemble model was 94.20% and 0.978, respectively. In the testing set, the accuracy and AUC of the ensemble model was 94.12% and 0.980, respectively.ConclusionThis study indicates that this ensemble DL model, coupled with the anterior segment images in our study, might be an automated and cost-saving alternative for detection of the pterygia that require surgery.

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Theory and Applications of the (Cardio) Genomic Fabric Approach to Post-Ischemic and Hypoxia-Induced Heart Failure

Cited by 9 publications

References 73 publications

Metabolic Deregulation in Pulmonary Hypertension

Metabolic Deregulation in Pulmonary Hypertension

Papillary Thyroid Cancer Remodels the Genetic Information Processing Pathways

Application of artificial intelligence models for detecting the pterygium that requires surgical treatment based on anterior segment images

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