scholarly journals Multilayer Flows in Molecular Networks Identify Biological Modules in the Human Proteome

2020 ◽  
Vol 7 (1) ◽  
pp. 411-420 ◽  
Author(s):  
Giuseppe Mangioni ◽  
Giuseppe Jurman ◽  
Manlio De Domenico
2005 ◽  
Vol 27 (5-6) ◽  
pp. 281-292
Author(s):  
Remond J. A. Fijneman

Predisposition to non-familial, sporadic cancer is strongly influenced by multiple tumor susceptibility genes (TSGs), each with apparently minor effects on the cancer phenotype. Sequence analysis of the human genome has yielded numerous single nucleotide polymorphisms (SNPs), raising the expectation that new low-penetrance TSGs will be identified that can be used to estimate an individuals cancer risk. However, mouse models for human cancer showed that the effects of many low-penetrance TSGs are highly variable due to their involvement in epistatic interactions. Together, these interacting TSGs form large molecular networks, which represent cancer-associated biological modules that influence the tumorigenic process. As a consequence, although allelic variation in one TSG on a permissive genetic Background can have major effects on tumor development, the net effect of allelic variation in multiple interacting TSGs remains hard to predict. Therefore, the predictive value of SNP-analysis to estimate an individuals cancer risk will be restricted to those TSGs that exhibit single-gene effects. New strategies need to be developed to evaluate cancer risk associated with biological modules that are influenced by TSG-networks.


2016 ◽  
Vol 17 (10) ◽  
pp. 1198-1205 ◽  
Author(s):  
Gang Hu ◽  
Zhonghua Wu ◽  
Kui Wang ◽  
Vladimir N. Uversky ◽  
Lukasz Kurgan

2020 ◽  
Vol 17 ◽  
Author(s):  
Asma Babar ◽  
Kifayatullah Mengal ◽  
Abdul Hanan Babar ◽  
Shixin Wu ◽  
Mujahid Ali Shah ◽  
...  

: The world highest and largest altitude area is called the Qinghai-Tibetan plateau (QTB), which harbors unique animal and plant species. Mammals that inhabit the higher altitude regions have adapted well to the hypoxic conditions. One of the main stressors at high altitude is hypoxia. Metabolic responses to hypoxia play important roles in cell survival strategies and some diseases. However, the homeostatic alterations that equilibrate variations in the demand and supply of energy to maintain organismal function in a prolonged low O2 environment persist partly understood, making it problematic to differentiate adaptive from maladaptive responses in hypoxia. Tibetans and yaks are two perfect examples innate to the plateau for high altitude adaptation. By the scan of the whole-genome, EPAS1 and EGLN1 were identified as key genes associated with sustained haemoglobin concentration in high altitude mammals for adaptation. The yak is a much more ancient mammal which has existed on QTB longer than humans, it is, therefore, possible that natural selection represented a diverse group of genes/pathways in yaks. Physiological characteristics are extremely informative in revealing molecular networks associated with inherited adaptation, in addition to the whole-genome adaptive changes at the DNA sequence level. Gene-expression can be changed by a variety of signals originating from the environment, and hypoxia is the main factor amongst them. The hypoxia-inducible factors (HIF-1α and EPAS1/HIF-2α) are the main regulators of oxygen in homeostasis which play a role as maestro regulators of adaptation in hypoxic reaction of molecular mechanisms. (Vague) The basis of this review is to present recent information regarding the molecular mechanism involved in hypoxia that regulates candidate genes and proteins. Many transcriptional responses toward hypoxia are facilitated by HIFs that change the number of gene expressions and help in angiogenesis, erythropoiesis, metabolic reprogramming and metastasis. HIFs also activate several signals highlighting a strong association between hypoxia, the misfolded proteins’ accumulation in the endoplasmic reticulum in stress and activation of unfolded protein response (UPR). It was observed that at high-altitude, pregnancies yield a low birth weight ∼100 g per1000 m of the climb. (Vague) It may involve variation in the events of energy-demanding, like protein synthesis. Prolonged hypobaric hypoxia causes placental ER stress, which in turn, moderates protein synthesis and reduces proliferation. Further, Cardiac hypertrophy by cytosolic Ca2+ raises and Ca2+/calmodulin, calcineurin stimulation, NF-AT3 pathway might be caused by an imbalance in Sarcoplasmic reticulum ER Ca2, might be adaptive in beginning but severe later.


Author(s):  
Thaís Rodrigues Nogueira ◽  
Victor Alves de Oliveira ◽  
Irislene Costa Pereira ◽  
Cecília Maria Resende Gonçalves de Carvalho ◽  
Gilmara Péres-Rodrigues ◽  
...  

: Breast cancer has a multifactorial etiology and, among the main causal factors, the dietary profile stands out, mainly the components of the pro-inflammatory diet and the interaction with genetic characteristics. In this sense, deciphering the molecular networks involved in the proliferation of cancer cells in breast tissue can determine ways of action of organic compounds that contain the pathogenesis of cancer, such as vitamin A and analogues, as well as their possible mechanisms of modulation of breast tumorigenesis. This is a review study conducted according to the guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-Analyzes (PRISMA) and by consulting the PubMed and Web of Science databases and including articles from the last five years, published in Portuguese, English and Spanish. 126 articles were obtained, of which 13 were selected for full reading and 6 were included in the study for meeting the eligibility criteria. The results of the compiled studies demonstrate the role that some retinol-binding proteins play in their metabolism, as well as in differentiation, cell proliferation and inflammation. Although controversial, the results point to the use of these structures as possible prognostic markers. The need for further studies in humans is also emphasized in order to assess the main effects of vitamin isoforms on tumor activity.


BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yang Xi ◽  
Zhuang Jing ◽  
Wu Wei ◽  
Zhang Chun ◽  
Qi Quan ◽  
...  

Abstract Background Sodium butyrate (NaB) is produced through the fermentation of dietary fiber that is not absorbed and digested by the small intestine. Purpose Here, we aimed to investigate the effects of NaB on the proliferation, invasion, and metastasis of CRC cells and their potential underlying molecular mechanism(s). Methods The cell counting kit-8 (CCK-8) assay and EdU assay were used to detect cell proliferation ability, flow cytometry was used to investigate the induction of apoptosis and cell cycle progression, and the scratch-wound healing and transwell assays were used to evaluate cell migration and invasion, respectively. The human CRC genome information for tissues and CRC cells treated with NaB obtained from the NCBI GEO database was reannotated and used for differential RNA analysis. Functional and pathway enrichment analyses were performed for differentially expressed lncRNAs and mRNAs. A protein-protein interaction (PPI) network for the hub genes was constructed using the Cytoscape software. Targeted miRNAs were predicted based on the lnCeDB database, and a ceRNA network was constructed using the Cytoscape software. The Kaplan-Meier method was used to analyze patient prognosis using the clinical information and exon-seq data for CRC obtained from the Broad Institute’s GDAC Firehose platform. Results NaB decreased the proliferation ability of CRC cells in a dose- and time-dependent manner. The number of apoptotic CRC cells increased with the increase in NaB concentrations, and NaB induced a G1 phase block in CRC cells. Moreover, NaB suppressed the migratory and invasive capabilities of CRC cells. There were 666 differentially expressed mRNAs and 30 differentially expressed lncRNAs involved in the CRC inhibition by NaB. The PPI network and ceRNA network were constructed based on the differentially expressed mRNAs and lncRNAs. Three differentially expressed mRNAs, including HMGA2, LOXL2, and ST7, were significantly correlated with the prognosis of CRC. Conclusion NaB induces the apoptosis and inhibition of CRC cell proliferation, invasion, and metastasis by modulating complex molecular networks. RNA prediction and molecular network construction need to be the focus of further research in this direction.


2007 ◽  
Vol 6 (9) ◽  
pp. 1666-1667
Author(s):  
Lennart Martens ◽  
Sandra Orchard ◽  
Rolf Apweiler ◽  
Henning Hermjakob
Keyword(s):  

Biology ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 417
Author(s):  
Ha Thi Nguyen ◽  
Salah Eddine Oussama Kacimi ◽  
Truc Ly Nguyen ◽  
Kamrul Hassan Suman ◽  
Roselyn Lemus-Martin ◽  
...  

MicroRNAs (miRNAs) are small non-coding RNAs. They can regulate the expression of their target genes, and thus, their dysregulation significantly contributes to the development of cancer. Growing evidence suggests that miRNAs could be used as cancer biomarkers. As an oncogenic miRNA, the roles of miR-21 as a diagnostic and prognostic biomarker, and its therapeutic applications have been extensively studied. In this review, the roles of miR-21 are first demonstrated via its different molecular networks. Then, a comprehensive review on the potential targets and the current applications as a diagnostic and prognostic cancer biomarker and the therapeutic roles of miR-21 in six different cancers in the digestive system is provided. Lastly, a brief discussion on the challenges for the use of miR-21 as a therapeutic tool for these cancers is added.


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