Nanoelectronic circuit elements based on nanoscale metal–molecular networks

: 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.

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Vitamin A: Modulating Effect on Breast Carcinogenesis

Current Nutrition & Food Science ◽

10.2174/1573401316999200706011813 ◽

2020 ◽

Vol 16 ◽

Author(s):

Thaís Rodrigues Nogueira ◽

Victor Alves de Oliveira ◽

Irislene Costa Pereira ◽

Cecília Maria Resende Gonçalves de Carvalho ◽

Gilmara Péres-Rodrigues ◽

...

Keyword(s):

Vitamin A ◽

Breast Tissue ◽

Web Of Science ◽

Prognostic Markers ◽

Molecular Networks ◽

Breast Tumorigenesis ◽

Eligibility Criteria ◽

Genetic Characteristics ◽

Review Study ◽

Main Effects

: 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.

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Inhibitory effect of sodium butyrate on colorectal cancer cells and construction of the related molecular network

BMC Cancer ◽

10.1186/s12885-021-07845-1 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Yang Xi ◽

Zhuang Jing ◽

Wu Wei ◽

Zhang Chun ◽

Qi Quan ◽

...

Keyword(s):

Cell Proliferation ◽

Sodium Butyrate ◽

Molecular Network ◽

Differentially Expressed ◽

Cell Counting ◽

Molecular Networks ◽

Ppi Network ◽

Invasion And Metastasis ◽

Cerna Network ◽

Proliferation Ability

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.

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MiR-21 in the Cancers of the Digestive System and Its Potential Role as a Diagnostic, Predictive, and Therapeutic Biomarker

Biology ◽

10.3390/biology10050417 ◽

2021 ◽

Vol 10 (5) ◽

pp. 417

Author(s):

Ha Thi Nguyen ◽

Salah Eddine Oussama Kacimi ◽

Truc Ly Nguyen ◽

Kamrul Hassan Suman ◽

Roselyn Lemus-Martin ◽

...

Keyword(s):

Digestive System ◽

Potential Role ◽

Target Genes ◽

Prognostic Biomarker ◽

Cancer Biomarkers ◽

Cancer Biomarker ◽

Molecular Networks ◽

Therapeutic Tool ◽

Comprehensive Review ◽

Non Coding Rnas

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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A Detailed Catalogue of Multi-Omics Methodologies for Identification of Putative Biomarkers and Causal Molecular Networks in Translational Cancer Research

International Journal of Molecular Sciences ◽

10.3390/ijms22062822 ◽

2021 ◽

Vol 22 (6) ◽

pp. 2822

Author(s):

Efstathios Iason Vlachavas ◽

Jonas Bohn ◽

Frank Ückert ◽

Sylvia Nürnberg

Keyword(s):

Cancer Research ◽

Clinical Information ◽

Disease Diagnosis ◽

Molecular Data ◽

Molecular Networks ◽

Biological Knowledge ◽

Omics Data ◽

Translational Cancer Research ◽

Using Data ◽

Biological Entities

Recent advances in sequencing and biotechnological methodologies have led to the generation of large volumes of molecular data of different omics layers, such as genomics, transcriptomics, proteomics and metabolomics. Integration of these data with clinical information provides new opportunities to discover how perturbations in biological processes lead to disease. Using data-driven approaches for the integration and interpretation of multi-omics data could stably identify links between structural and functional information and propose causal molecular networks with potential impact on cancer pathophysiology. This knowledge can then be used to improve disease diagnosis, prognosis, prevention, and therapy. This review will summarize and categorize the most current computational methodologies and tools for integration of distinct molecular layers in the context of translational cancer research and personalized therapy. Additionally, the bioinformatics tools Multi-Omics Factor Analysis (MOFA) and netDX will be tested using omics data from public cancer resources, to assess their overall robustness, provide reproducible workflows for gaining biological knowledge from multi-omics data, and to comprehensively understand the significantly perturbed biological entities in distinct cancer types. We show that the performed supervised and unsupervised analyses result in meaningful and novel findings.

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Competing Endogenous RNAs in Cervical Carcinogenesis: A New Layer of Complexity

Processes ◽

10.3390/pr9060991 ◽

2021 ◽

Vol 9 (6) ◽

pp. 991

Author(s):

Fernanda Costa Brandão Berti ◽

Sara Cristina Lobo-Alves ◽

Camila de Freitas Oliveira-Toré ◽

Amanda Salviano-Silva ◽

Karen Brajão de Oliveira ◽

...

Keyword(s):

Gene Expression ◽

Fine Tuning ◽

Molecular Networks ◽

Cervical Carcinogenesis ◽

Molecular Changes ◽

Cellular Processes ◽

Target Mrnas ◽

Competing Endogenous Rnas ◽

Cervical Cells ◽

Post Transcriptional Regulation

MicroRNAs (miRNAs) regulate gene expression by binding to complementary sequences within target mRNAs. Apart from working ‘solo’, miRNAs may interact in important molecular networks such as competing endogenous RNA (ceRNA) axes. By competing for a limited pool of miRNAs, transcripts such as long noncoding RNAs (lncRNAs) and mRNAs can regulate each other, fine-tuning gene expression. Several ceRNA networks led by different lncRNAs—described here as lncRNA-mediated ceRNAs—seem to play essential roles in cervical cancer (CC). By conducting an extensive search, we summarized networks involved in CC, highlighting the major impacts of such dynamic molecular changes over multiple cellular processes. Through the sponging of distinct miRNAs, some lncRNAs as HOTAIR, MALAT1, NEAT1, OIP5-AS1, and XIST trigger crucial molecular changes, ultimately increasing cell proliferation, migration, invasion, and inhibiting apoptosis. Likewise, several lncRNAs seem to be a sponge for important tumor-suppressive miRNAs (as miR-140-5p, miR-143-3p, miR-148a-3p, and miR-206), impairing such molecules from exerting a negative post-transcriptional regulation over target mRNAs. Curiously, some of the involved mRNAs code for important proteins such as PTEN, ROCK1, and MAPK1, known to modulate cell growth, proliferation, apoptosis, and adhesion in CC. Overall, we highlight important lncRNA-mediated functional interactions occurring in cervical cells and their closely related impact on cervical carcinogenesis.

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