Differential gene expression in peritumoral brain zone of glioblastoma: role of SERPINA3 in promoting invasion, stemness and radioresistance of glioma cells and association with poor patient prognosis and recurrence

ABSTRACTIn contrast to the plethora of studies focusing on the genomic basis of adaptive phenotypic divergence, the role of gene expression during speciation has been much less investigated and consequently, less understood. Yet, the convergence of differential gene expression patterns between closely related species-pairs might reflect the role of natural selection during the process of ecological speciation. Here, we test for intercontinental convergence in differential transcriptional signatures between limnetic and benthic sympatric species-pairs of Lake Whitefish (Coregonus clupeaformis) and its sister-lineage, the European Whitefish (C. lavaretus), using six replicated sympatric species-pairs (two in North America, two in Norway and two in Switzerland). We characterized both sequence variation in transcribed regions and differential gene expression between sympatric limnetic and benthic species across regions and continents. Our first finding was that differentially expressed genes (DEG) between limnetic and benthic whitefish tend to be enriched in shared polymorphism among sister-lineages. We then used both genotypes and co-variation in expression in order to infer polygenic selection at the gene level. We identified parallel outliers and DEG involving genes primarily over-expressed in limnetic species relative to the benthic species. Our analysis finally revealed the existence of shared genomic bases underlying parallel differential expression across replicated species pairs from both continents, such as a cis-eQTL affecting the pyruvate kinase expression level involved in glycolysis. Our results are consistent with a longstanding role of natural selection in maintaining transcontinental diversity at phenotypic traits involved in ecological speciation between limnetic and benthic whitefishes.

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Activation of the nuclear transcription factor κB (NFκB) and differential gene expression in U87 glioma cells after exposure to the cytoprotector amifostine

International Journal of Radiation Oncology*Biology*Physics ◽

10.1016/s0360-3016(01)02820-6 ◽

2002 ◽

Vol 53 (1) ◽

pp. 180-189 ◽

Cited By ~ 22

Author(s):

Yasushi Kataoka ◽

Jeffrey S Murley ◽

Nikolai N Khodarev ◽

Ralph R Weichselbaum ◽

David J Grdina

Keyword(s):

Gene Expression ◽

Transcription Factor ◽

Differential Gene Expression ◽

Glioma Cells ◽

Nuclear Transcription Factor ◽

Differential Gene

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Alterations in gene expression in the spinal cord of mice lacking Nfix

BMC Research Notes ◽

10.1186/s13104-020-05278-w ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Elise Matuzelski ◽

Alexandra Essebier ◽

Lachlan Harris ◽

Richard M. Gronostajski ◽

Tracey J. Harvey ◽

...

Keyword(s):

Gene Expression ◽

Spinal Cord ◽

Transcription Factor ◽

Differential Gene Expression ◽

Cell Biology ◽

Wild Type ◽

Spinal Cord Development ◽

Differential Gene ◽

Developing Mouse Brain

Abstract Objective Nuclear Factor One X (NFIX) is a transcription factor expressed by neural stem cells within the developing mouse brain and spinal cord. In order to characterise the pathways by which NFIX may regulate neural stem cell biology within the developing mouse spinal cord, we performed an microarray-based transcriptomic analysis of the spinal cord of embryonic day (E)14.5 Nfix−/− mice in comparison to wild-type controls. Data description Using microarray and differential gene expression analyses, we were able to identify differentially expressed genes in the spinal cords of E14.5 Nfix−/− mice compared to wild-type controls. We performed microarray-based sequencing on spinal cords from n = 3 E14.5 Nfix−/− mice and n = 3 E14.5 Nfix+/+ mice. Differential gene expression analysis, using a false discovery rate (FDR) p-value of p < 0.05, and a fold change cut-off for differential expression of > ± 1.5, revealed 1351 differentially regulated genes in the spinal cord of Nfix−/− mice. Of these, 828 were upregulated, and 523 were downregulated. This resource provides a tool to interrogate the role of this transcription factor in spinal cord development.

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Genomic meta-analysis of the interplay between 3D chromatin organization and gene expression programs under basal and stress conditions

10.1101/337766 ◽

2018 ◽

Author(s):

Idan Nurick ◽

Ron Shamir ◽

Ran Elkon

Keyword(s):

Gene Expression ◽

Differential Gene Expression ◽

Cell Lines ◽

Meta Analysis ◽

Cell Types ◽

Chromatin Organization ◽

Cell Type ◽

Differential Gene ◽

Different Cell Types

AbstractBackgroundOur appreciation of the critical role of the 3D organization of the genome in gene regulation is steadily increasing. Recent 3C-based deep sequencing techniques elucidated a hierarchy of structures that underlie the spatial organization of the genome in the nucleus. At the top of this hierarchical organization are chromosomal territories and the megabase-scale A/B compartments that correlate with transcriptional activity within cells. Below them are the relatively cell-type invariant topologically associated domains (TADs), characterized by high frequency of physical contacts between loci within the same TAD and are assumed to function as regulatory units. Within TADs, chromatin loops bring enhancers and target promoters to close spatial proximity. Yet, we still have only rudimentary understanding how differences in chromatin organization between different cell types affect cell-type specific gene expression programs that are executed under basal and challenged conditions.ResultsHere, we carried out a large-scale meta-analysis that integrated Hi-C data from thirteen different cell lines and dozens of ChIP-seq and RNA-seq datasets measured on these cells, either under basal conditions or after treatment. Pairwise comparisons between cell lines demonstrated the strong association between modulation of A/B compartmentalization, differential gene expression and transcription factor (TF) binding events. Furthermore, integrating the analysis of transcriptomes of different cell lines in response to various challenges, we show that 3D organization of cells under basal conditions constrains not only gene expression programs and TF binding profiles that are active under the basal condition but also those induced in response to treatment.ConclusionsOur results further elucidate the role of dynamic genome organization in regulation of differential gene expression between different cell types, and indicate the impact of intra-TAD enhancer-promoter interactions that are established under basal conditions on both the basal and treatment-induced gene expression programs.

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