scholarly journals Gene Expression in the Human Brain: The Current State of the Study of Specificity and Spatiotemporal Dynamics

2012 ◽  
Vol 84 (1) ◽  
pp. 76-88 ◽  
Author(s):  
Oksana Yu. Naumova ◽  
Maria Lee ◽  
Sergei Yu. Rychkov ◽  
Natalia V. Vlasova ◽  
Elena L. Grigorenko
Keyword(s):  
Gene Expression ◽  
Human Brain ◽  
Spatiotemporal Dynamics ◽  
Current State

scholarly journals Long non-coding RNAs in brain tumors

NAR Cancer ◽  
2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Keisuke Katsushima ◽  
George Jallo ◽  
Charles G Eberhart ◽  
Ranjan J Perera
Keyword(s):  
Gene Expression ◽  
Brain Tumors ◽  
Brain Cancer ◽  
Regulation Of Gene Expression ◽  
Therapeutic Targets ◽  
Diagnostic Biomarkers ◽  
Cancer Pathogenesis ◽  
Current State ◽  
Non Coding Rnas ◽  
Post Transcriptional Regulation

Abstract Long non-coding RNAs (lncRNAs) have been found to be central players in the epigenetic, transcriptional and post-transcriptional regulation of gene expression. There is an accumulation of evidence on newly discovered lncRNAs, their molecular interactions and their roles in the development and progression of human brain tumors. LncRNAs can have either tumor suppressive or oncogenic functions in different brain cancers, making them attractive therapeutic targets and biomarkers for personalized therapy and precision diagnostics. Here, we summarize the current state of knowledge of the lncRNAs that have been implicated in brain cancer pathogenesis, particularly in gliomas and medulloblastomas. We discuss their epigenetic regulation as well as the prospects of using lncRNAs as diagnostic biomarkers and therapeutic targets in patients with brain tumors.

Future trends in diagnosis using laboratory-on-a-chip technologies

Parasitology ◽  
1999 ◽  
Vol 117 (7) ◽  
pp. 191-203 ◽  
Author(s):  
M. S. TALARY ◽  
J. P. H. BURT ◽  
R. PETHIG
Keyword(s):  
Gene Expression ◽  
Lower Cost ◽  
Building Blocks ◽  
Cancer Diagnostics ◽  
Future Trends ◽  
Biotechnological Applications ◽  
Environmental Testing ◽  
Current State ◽  
Microelectronic Fabrication ◽  
Wide Range

There has been an enormous growth in the development of biotechnological applications, where advances in the techniques of microelectronic fabrication and the technologies of miniaturization and integration in semiconductor industries are being applied to the production of Laboratory-on-a-Chip devices. The aim of this development is to create devices that will perform the same processes that are currently carried out in the laboratory in reduced timescales, at a lower cost, requiring less reagents, and with a greater resolution of detection and specificity. The expectations of this Laboratory-on-a-Chip revolution is that this technology will facilitate rapid advances in gene discovery, genetic mapping and gene expression with broader applications ranging from infectious diseases and cancer diagnostics to food quality and environmental testing. A review of the current state of development in this field reveals the scale of the ongoing revolution and serves to highlight the advances that can be perceived in the development of Laboratory-on-a-Chip technologies. Since miniaturization can be applied to such a wide range of laboratory processes, some of the sub-units that can be used as building blocks in these devices are described, with a brief description of some of the fabrication processes that can be used to create them.

NF-κB is activated and ICAM-1 gene expression is upregulated during reoxygenation of human brain endothelial cells

1998 ◽  
Vol 248 (3) ◽  
pp. 199-203 ◽  
Author(s):  
Eugene F Howard ◽  
Qiang Chen ◽  
Charles Cheng ◽  
James E Carroll ◽  
David Hess
Keyword(s):  
Gene Expression ◽  
Endothelial Cells ◽  
Human Brain ◽  
Brain Endothelial Cells

scholarly journals A pH-eQTL interaction at the RIT2-SYT4 Parkinson's disease risk locus in the substantia nigra

2020 ◽  
Author(s):  
Sejal Patel ◽  
Derek Howard ◽  
Leon French
Keyword(s):  
Gene Expression ◽  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Substantia Nigra ◽  
Human Brain ◽  
Disease Risk ◽  
Brain Regions ◽  
Dopamine Neurons ◽  
Postmortem Human Brain ◽  
Increased Risk

BACKGROUND: Parkinson's disease (PD) causes severe motor and cognitive disabilities that result from the progressive loss of dopamine neurons in the substantia nigra. The rs12456492 variant in the RIT2 gene has been repeatedly associated with increased risk for Parkinson's disease. From a transcriptomic perspective, a meta-analysis found that RIT2 gene expression is correlated with pH in the human brain. OBJECTIVE: To assess pH associations at the RIT2-SYT4 locus. METHODS: Linear models to examine two datasets that assayed rs12456492, gene expression, and pH in the postmortem human brain. RESULTS: Using the BrainEAC dataset, we replicate the positive correlation between RIT2 gene expression and pH in the human brain. Furthermore, we found that the relationship between expression and pH is influenced by rs12456492. When tested across ten brain regions, this interaction is specifically found in the substantia nigra. A similar association was found for the co-localized SYT4 gene. In addition, SYT4 associations are stronger in a combined model with both genes, and the SYT4 interaction appears to be specific to males. In the GTEx dataset, the pH associations involving rs12456492 and expression of either SYT4 and RIT2 was not seen. This null finding may be due to the short postmortem intervals (PMI) of the GTEx tissue samples. In the BrainEAC data, we tested the effect of PMI and only observed the interactions in the longer PMI samples. CONCLUSIONS: These previously unknown associations suggest novel mechanistic roles for rs12456492, RIT2, and SYT4 in the regulation of pH in the substantia nigra.

scholarly journals Brain organoids and insights on human evolution

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 760 ◽  
Author(s):  
Alysson R. Muotri
Keyword(s):  
Stem Cells ◽  
Human Brain ◽  
Human Health ◽  
Human Evolution ◽  
Pluripotent Stem Cells ◽  
Disease Modeling ◽  
State Of The Art ◽  
Future Perspectives ◽  
Promising Technique ◽  
Current State

Human brain organoids, generated from pluripotent stem cells, have emerged as a promising technique for modeling early stages of human neurodevelopment in controlled laboratory conditions. Although the applications for disease modeling in a dish have become routine, the use of these brain organoids as evolutionary tools is only now getting momentum. Here, we will review the current state of the art on the use of brain organoids from different species and the molecular and cellular insights generated from these studies. Besides, we will discuss how this model might be beneficial for human health and the limitations and future perspectives of this technology.

scholarly journals Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts

2020 ◽  
Author(s):  
Ammar Zaghlool ◽  
Adnan Niazi ◽  
Åsa K. Björklund ◽  
Jakub Orzechowski Westholm ◽  
Adam Ameur ◽  
...  
Keyword(s):  
Gene Expression ◽  
Subcellular Localization ◽  
Human Brain ◽  
Expression Analysis ◽  
Differential Expression Analysis ◽  
Adult Brain ◽  
Sequencing Data ◽  
Human Brain Tissue ◽  
Protein Coding ◽  
The Impact

AbstractTranscriptome analysis has mainly relied on analyzing RNA sequencing data from whole cells, overlooking the impact of subcellular RNA localization and its influence on our understanding of gene function, and interpretation of gene expression signatures in cells. Here, we performed a comprehensive analysis of cytosolic and nuclear transcriptomes in human fetal and adult brain samples. We show significant differences in RNA expression for protein-coding and lncRNA genes between cytosol and nucleus. Transcripts displaying differential subcellular localization belong to particular functional categories and display tissue-specific localization patterns. We also show that transcripts encoding the nuclear-encoded mitochondrial proteins are significantly enriched in the cytosol compared to the rest of protein-coding genes. Further investigation of the use of the cytosolic or the nuclear transcriptome for differential gene expression analysis indicates important differences in results depending on the cellular compartment. These differences were manifested at the level of transcript types and the number of differentially expressed genes. Our data provide a resource of RNA subcellular localization in the human brain and highlight differences in using the cytosolic or the nuclear transcriptomes for differential expression analysis.

scholarly journals Chromatin interaction aware gene regulatory modeling with graph attention networks

2021 ◽  
Author(s):  
Alireza Karbalayghareh ◽  
Merve Sahin ◽  
Christina S Leslie
Keyword(s):  
Gene Expression ◽  
Deep Learning ◽  
Chromatin Interaction ◽  
Learning Approach ◽  
Chromosome Conformation ◽  
Attention Networks ◽  
Current State ◽  
Regulatory Impact ◽  
Sequence Elements ◽  
Gene Expression Levels

Linking distal enhancers to genes and modeling their impact on target gene expression are longstanding unresolved problems in regulatory genomics and critical for interpreting non-coding genetic variation. Here we present a new deep learning approach called GraphReg that exploits 3D interactions from chromosome conformation capture assays in order to predict gene expression from 1D epigenomic data or genomic DNA sequence. By using graph attention networks to exploit the connectivity of distal elements and promoters, GraphReg more faithfully models gene regulation and more accurately predicts gene expression levels than dilated convolutional neural networks (CNNs), the current state-of-the-art deep learning approach for this task. Feature attribution used with GraphReg accurately identifies functional enhancers of genes, as validated by CRISPRi-FlowFISH and TAP-seq assays, outperforming both CNNs and the recently proposed Activity-by-Contact model. GraphReg therefore represents an important advance in modeling the regulatory impact of epigenomic and sequence elements.

Localization and gene expression of serotonin1A (5HT1A) receptors in human brain postmortem

1994 ◽  
Vol 658 (1-2) ◽  
pp. 55-59 ◽  
Author(s):  
D. Marazziti ◽  
S. Marracci ◽  
L. Palego ◽  
A. Rotondo ◽  
C. Mazzanti ◽  
...  
Keyword(s):  
Gene Expression ◽  
Human Brain ◽  
5Ht1a Receptors
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