Cellular Environment Remodels the Genomic Fabrics of Functional Pathways in Astrocytes

Abstract

We profiled the transcriptomes of primary mouse cortical astrocytes cultured alone or co-cultured with immortalized precursor oligodendrocytes (Oli-neu cells). Filters between the cell types prevented formation of hetero-cellular gap junction channels but allowed for free exchange of the two culture media. We previously reported that major functional pathways in the Oli-neu cells are remodeled by the proximity of non-touching astrocytes and that astrocytes and oligodendrocytes form a panglial transcriptomic syncytium in the brain. Here, we present evidence that the astrocyte transcriptome likewise changes significantly in the proximity of non-touching Oli-neu cells. Our results indicate that the cellular environment strongly modulates the transcriptome of each cell type and that integration in a heterocellular tissue changes not only the expression profile but also the expression control and networking of the genes in each cell phenotype. The significant decrease of the overall transcription control suggests that in the co-culture astrocytes are closer to their normal conditions from the brain. The Oli-neu secretome regulates astrocyte genes known to modulate neuronal synaptic transmission and remodels calcium, chemokine, NOD-like receptor, PI3K-Akt, and thyroid hormone signaling, as well as actin-cytoskeleton, autophagy, cell cycle, and circadian rhythm pathways. Moreover, the co-culture significantly changes the gene hierarchy in the astrocytes.

Genomic Fabric Remodeling in Metastatic Clear Cell Renal Cell Carcinoma (ccRCC): A New Paradigm and Proposal for a Personalized Gene Therapy Approach

“…Thus, when the analysis is applied to all 13,314 unredundantly quantified unigenes, the median REVs were: 41.51 (NOR), 31.45% (PTA), 37.21% (PTB) and 30.46% (MET). These results confirmed our previous findings in numerous human and animal samples (cited in [56]), that a diseased tissue has a stricter control of the expression level (hence less variability). The robust result of increased expression control is presumably an evolutionary adaptation to limit the disease (here cancer)-related damages.…”

“…In this report, we applied the Genomic Fabric Paradigm [35,53,56] to the transcriptomic profiles of three cancer nodules and the surrounding healthy tissue surgically removed from a patient with metastatic kidney cancer. GFP relies on the three independent expression characteristics (average level, variability and correlation with expression of each other genes) that can be assigned to every quantified gene in each region.…”

“…Also, ALG13, an important modifier of renal filtration defects [73], was oppositely coordinated with GADD45B, HDAC1 and MCM3 in the cancer nodules with respect to NOR. These opposite coordinations indicate the strong dependence of the gene interactions on the cellular phenotype [56] and genetic background [21] that are disregarded by the functional pathways built by popular software (KEGG, Ingenuity, DAVID, GennMapp etc. ).…”

“…However, profiling separately each cell phenotype is not the solution. We proved by comparing the gene expression profiles of astrocytes and oligodendrocytes cultured alone and co-cultured in insert systems that the cell transcriptome is very sensitive to the cellular environment [56,85]. Thus, the transcriptome of the heterogeneous tissue is not the sum of the transcriptomes of the separately profiled individual cell types.…”

“…We ranked the genes in each profiled region with respect to their Gene Commanding Height (GCH) scores [56]. As illustrated in Figure 8, the gene hierarchy is strongly perturbed by the cancer.…”