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Global DNA methylation analysis of cancer-associated fibroblasts reveals extensive epigenetic rewiring linked with RUNX1 upregulation in breast cancer stroma [co-culture]

ABSTRACT: We performed RNA seq to characterize the transcriptome of normal mammary fibroblasts (NMFs) co-cultured with 4T1 cancer cells for 3 and 5 days as well as mono-cultured NMFs.

ORGANISM(S): Mus musculus

PROVIDER: GSE213071 | GEO | 2022/11/08

REPOSITORIES: GEO

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Global DNA methylation analysis of cancer-associated fibroblasts reveals extensive epigenetic rewiring linked with RUNX1 upregulation in breast cancer stroma

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-11-08 | GSE195865 | GEO

Global DNA methylation analysis of cancer-associated fibroblasts reveals extensive epigenetic rewiring linked with RUNX1 upregulation in breast cancer stroma [ly6c]

Project description:We performed RNA seq to charachterize the transcriptome of specific cancer associates fibroblasts (pCAFs) sub-populations (Ly6c+ vs Ly6c- pCAFs)

2022-11-08 | GSE213074 | GEO

Global DNA methylation analysis of cancer-associated fibroblasts reveals extensive epigenetic rewiring linked with RUNX1 upregulation in breast cancer stroma [WGBS]

Project description:We preformed whole-genome bisulfite sequencing to charachterize the DNA methylation landscape of cancer associates fibroblasts (pCAF) compared to normal mammary fat pad fibroblasts (NMF)

2022-11-08 | GSE193518 | GEO

Global DNA methylation analysis of cancer-associated fibroblasts reveals extensive epigenetic rewiring linked with RUNX1 upregulation in breast cancer stroma [RNA-Seq]

Project description:We preformed RNA seq to charachterize the transcriptome of cancer associates fibroblasts (pCAF) compared to normal mammary fat pad fibroblasts (NMF)

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The tumor microenvironment shows a hierarchy of cell-cell interactions dominated by fibroblasts [cancer CM]

Project description:We preformed RNA seq on invitro fibroblasts after mono-cultured or co-cultured with macrophages in DMEM or with 4T1-conditioned medium , In order to understand the affect of cancer on macrophages-fibroblasts interactions

2023-08-27 | GSE218196 | GEO

Extensive rewiring of epithelial-stromal co-expression networks in breast cancer.

Project description:Epithelial-stromal crosstalk plays a critical role in invasive breast cancer pathogenesis; however, little is known on a systems level about how epithelial-stromal interactions evolve during carcinogenesis.We develop a framework for building genome-wide epithelial-stromal co-expression networks composed of pairwise co-expression relationships between mRNA levels of genes expressed in the epithelium and stroma across a population of patients. We apply this method to laser capture micro-dissection expression profiling datasets in the setting of breast carcinogenesis. Our analysis shows that epithelial-stromal co-expression networks undergo extensive rewiring during carcinogenesis, with the emergence of distinct network hubs in normal breast, and estrogen receptor-positive and estrogen receptor-negative invasive breast cancer, and the emergence of distinct patterns of functional network enrichment. In contrast to normal breast, the strongest epithelial-stromal co-expression relationships in invasive breast cancer mostly represent self-loops, in which the same gene is co-expressed in epithelial and stromal regions. We validate this observation using an independent laser capture micro-dissection dataset and confirm that self-loop interactions are significantly increased in cancer by performing computational image analysis of epithelial and stromal protein expression using images from the Human Protein Atlas.Epithelial-stromal co-expression network analysis represents a new approach for systems-level analyses of spatially localized transcriptomic data. The analysis provides new biological insights into the rewiring of epithelial-stromal co-expression networks and the emergence of epithelial-stromal co-expression self-loops in breast cancer. The approach may facilitate the development of new diagnostics and therapeutics targeting epithelial-stromal interactions in cancer.

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Expression data of 4T1 mammary cancer cells cultured in MSC-conditioned medium or co-cultured with MSCs

Project description:4T1 mammary cancer cells exihibit higher proliferation and metastatic ability when cultured in conditioned medium from mesenchymal stem cells . Also, co-implantation with MSCs, 4T1 tumors show higher tumor growth and metastasis. We used microarrays to detail the global programme of gene expression underlying the alteration of cell behaviour RNA was extrated from 4T1 cells cultured in MSC-CM or regular medium as well as 4T1 cells isolated from co-cultured with MSCs. Gene expression of these cell groups was acquired from Affymetrix microarray analysis using mouse 430 2.0 array chip.

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Extensive and systematic rewiring of histone post-translational modifications in cancer model systems.

Project description:Histone post-translational modifications (PTMs) generate a complex combinatorial code that regulates gene expression and nuclear functions, and whose deregulation has been documented in different types of cancers. Therefore, the availability of relevant culture models that can be manipulated and that retain the epigenetic features of the tissue of origin is absolutely crucial for studying the epigenetic mechanisms underlying cancer and testing epigenetic drugs. In this study, we took advantage of quantitative mass spectrometry to comprehensively profile histone PTMs in patient tumor tissues, primary cultures and cell lines from three representative tumor models, breast cancer, glioblastoma and ovarian cancer, revealing an extensive and systematic rewiring of histone marks in cell culture conditions, which includes a decrease of H3K27me2/me3, H3K79me1/me2 and H3K9ac/K14ac, and an increase of H3K36me1/me2. While some changes occur in short-term primary cultures, most of them are instead time-dependent and appear only in long-term cultures. Remarkably, such changes mostly revert in cell line- and primary cell-derived in vivo xenograft models. Taken together, these results support the use of xenografts as the most representative models of in vivo epigenetic processes, suggesting caution when using cultured cells, in particular cell lines and long-term primary cultures, for epigenetic investigations.

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Regulatory Rewiring in a Cross Causes Extensive Genetic Heterogeneity.

Project description:Genetic heterogeneity occurs when individuals express similar phenotypes as a result of different underlying mechanisms. Although such heterogeneity is known to be a potential source of unexplained heritability in genetic mapping studies, its prevalence and molecular basis are not fully understood. Here we show that substantial genetic heterogeneity underlies a model phenotype--the ability to grow invasively--in a cross of two Saccharomyces cerevisiae strains. The heterogeneous basis of this trait across genotypes and environments makes it difficult to detect causal loci with standard genetic mapping techniques. However, using selective genotyping in the original cross, as well as in targeted backcrosses, we detected four loci that contribute to differences in the ability to grow invasively. Identification of causal genes at these loci suggests that they act by changing the underlying regulatory architecture of invasion. We verified this point by deleting many of the known transcriptional activators of invasion, as well as the gene encoding the cell surface protein Flo11 from five relevant segregants and showing that these individuals differ in the genes they require for invasion. Our work illustrates the extensive genetic heterogeneity that can underlie a trait and suggests that regulatory rewiring is a basic mechanism that gives rise to this heterogeneity.

| S-EPMC4596683 | biostudies-literature

Protein complex evolution does not involve extensive network rewiring.

Project description:The formation of proteins into stable protein complexes plays a fundamental role in the operation of the cell. The study of the degree of evolutionary conservation of protein complexes between species and the evolution of protein-protein interactions has been hampered by lack of comprehensive coverage of the high-throughput (HTP) technologies that measure the interactome. We show that new high-throughput datasets on protein co-purification in yeast have a substantially lower false negative rate than previous datasets when compared to known complexes. These datasets are therefore more suitable to estimate the conservation of protein complex membership than hitherto possible. We perform comparative genomics between curated protein complexes from human and the HTP data in Saccharomyces cerevisiae to study the evolution of co-complex memberships. This analysis revealed that out of the 5,960 protein pairs that are part of the same complex in human, 2,216 are absent because both proteins lack an ortholog in S. cerevisiae, while for 1,828 the co-complex membership is disrupted because one of the two proteins lacks an ortholog. For the remaining 1,916 protein pairs, only 10% were never co-purified in the large-scale experiments. This implies a conservation level of co-complex membership of 90% when the genes coding for the protein pairs that participate in the same protein complex are also conserved. We conclude that the evolutionary dynamics of protein complexes are, by and large, not the result of network rewiring (i.e. acquisition or loss of co-complex memberships), but mainly due to genomic acquisition or loss of genes coding for subunits. We thus reveal evidence for the tight interrelation of genomic and network evolution.

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