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Decoding breast cancer tissue-stroma interactions using species-specific sequencing

ABSTRACT: Decoding genome-wide effects of experimental tissue-tissue or cell-cell interactions is important, for example, to better understand tumor-stroma interactions after transplantation (xenografting). Transcriptome analysis of intermixed human and mouse cells has frequently relied on the need to separate the two cell populations prior to transcriptome analysis, which introduces confounding effects on gene expression. To circumvent this problem, we perform a bioinformatics-based genome-wide transcriptome analysis technique separating the mouse and human transcriptome part of a dataset, which allows a mixed mouse and human cell population to be sequenced without prior cell sorting. We use the new technology – which we call S3 (“S-cube” for Species-specific sequencing) technology – to provide new insights into the Notch downstream response following Notch ligand-stimulation and to explore transcriptional changes following transplantation of luminal (MCF7) and basal-type (MDA-MB-231) human breast cancer cells into mammary fat pad tissue in mice.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE66744 | GEO | 2015/08/12

SECONDARY ACCESSION(S): PRJNA277852

REPOSITORIES: GEO

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Decoding breast cancer tissue-stroma interactions using species-specific sequencing

Project description:Decoding genome-wide effects of experimental tissue-tissue or cell-cell interactions is important, for example, to better understand tumor-stroma interactions after transplantation (xenografting). Transcriptome analysis of intermixed human and mouse cells has frequently relied on the need to separate the two cell populations prior to transcriptome analysis, which introduces confounding effects on gene expression. To circumvent this problem, we perform a bioinformatics-based genome-wide transcriptome analysis technique separating the mouse and human transcriptome part of a dataset, which allows a mixed mouse and human cell population to be sequenced without prior cell sorting. We use the new technology – which we call S3 (“S-cube” for Species-specific sequencing) technology – to provide new insights into the Notch downstream response following Notch ligand-stimulation and to explore transcriptional changes following transplantation of luminal (MCF7) and basal-type (MDA-MB-231) human breast cancer cells into mammary fat pad tissue in mice. Analysis of Notch response to ligand in three settings: co-culture, immobilized ligand and xenografted tumors

2015-08-12 | E-GEOD-66744 | biostudies-arrayexpress

Transplanting FVIII/ET3-Secreting Cells in Fetal Sheep Increases FVIII Levels Long-Term Without Inducing Immunity or Toxicity

Project description:To investigate the differentiative fate of human PLCs following transplantation into fetal sheep and engraftment in various tissues/organs, we performed gene expression profiling analysis using data obtained from RNA-seq of human PLCs prior to in utero transplantation and of each engrafted fetal sheep tissue after filtering to remove any cross-reactivity with orthologous sheep transcripts

2023-06-01 | GSE230081 | GEO

Evolutionarily conserved effects of Notch signaling drive intestinal graft-versus-host disease in mice and non-human primates

Project description:Notch signaling promotes T-cell pathogenicity and graft-versus-host disease (GVHD) after allogeneic hematopoietic cell transplantation (allo-HCT) in mice, with a dominant role for the Delta-like ligand DLL4. To assess if Notch’s effects are evolutionarily conserved and identify key mechanisms, we studied antibody-mediated DLL4 blockade in a non-human primate (NHP) model similar to human allo-HCT. Short-term DLL4 blockade improved post-transplant survival with striking, durable protection from gastrointestinal GVHD, out of proportion to other disease sites. Unlike prior immunosuppressive strategies tested in the NHP GVHD model, anti-DLL4 interfered with a T-cell transcriptional program associated with intestinal infiltration. In cross-species investigations, Notch inhibition decreased surface abundance of the gut-homing integrin α4β7 in conventional T-cells while preserving α4β7 in regulatory T-cells, with findings suggesting increased 1 competition for 4 binding in conventional T-cells. Secondary lymphoid organ fibroblastic reticular cells emerged as the critical cellular source of Delta-like Notch ligands for Notch-mediated up-regulation of α4β7 integrin in T-cells after allo-HCT. Altogether, DLL4/Notch blockade decreased effector T-cell infiltration into the gut, with increased regulatory to conventional T-cell ratios early after allo-HCT. Our results identify a conserved, biologically unique and targetable role of DLL4/Notch signaling in GVHD.

2023-07-14 | GSE228838 | GEO

Homo sapiens

Project description:Microarray approach to investigate gene expression in human ovarian tissue after xenografting

| PRJNA206073 | ENA

Transplant Model Ischemic Conditioning Causes Tissue Leakage and Suppressed Inflammation in a Porcine Kidney

Project description:Background: Remote Ischemic Conditioning (RIC) has been proposed as a therapeutic intervention to circumvent the Ischemia/reperfusion injury (IRI) that is inherent to organ transplantation. Using a porcine kidney transplant model, we aimed to decipher the subclinical molecular effects of a RIC regime, compared to non-RIC controls. Methods: Kidney pairs (n = 8+8) were extracted from brain dead donor pigs and transplanted in juvenile recipient pigs following a period of cold ischemia. One kidney in each pair was subjected to RIC prior to reperfusion, while the other served as non-RIC control. We designed an advanced integrative -Omics strategy combining transcriptomics, proteomics, and phosphoproteomics to deduce molecular signatures in kidney tissue that could be attributed to RIC. Results: In kidney grafts taken out 10 h after transplantation we detected minimal molecular perturbations following RIC compared to non-RIC at the transcriptome level, but more pronounced effects at the proteome level. In particular, we noted that RIC resulted in response suppression of tissue inflammatory profiles. Furthermore, an accumulation of muscle extracellular matrix assembly proteins in RIC tissues was detected at the protein level, which may result in response to muscle tissue damage and/or fibrosis. Conclusions: Our data identifies subtle molecular phenotypes in porcine kidneys subjected to RIC which could aid further optimisation of remote ischaemia protocols in renal transplantation.

2022-04-04 | PXD025273 | Pride

Transcript Analysis of Human Mammary Cell Subsets using SAGE

2008-05-10 | GSE11387 | GEO

Transcriptional Profiling Provides New Insights into Organ Culture-Induced Changes in Human Donor Corneas

Project description:Corneal transplantation is one of the most common forms of tissue transplantation worldwide. Donor corneal tissue used in transplantation is provided by eye banks, which store the tissue in culture medium after procurement. To date, the effects of cell culture on human corneal tissue have not been fully elucidated. Using the 3’ RNA sequencing method for massive analysis of cDNA ends (MACE), we show that cultivation of corneal tissue leads to significant changes in a variety of molecular processes in human corneal tissue that go well beyond aspects of previously known culture effects. Functionally grouped network analysis revealed nine major groups of biological processes that were affected by corneal organ culture, among them keratinization, hypoxia, and angiogenesis, with genes from each group being affected by culture time. A cell type deconvolution analysis revealed significant modulations of the corneal immune cell profile in a time dependent manner. The results suggest that current culture conditions should be further refined and that prolonged cultivation may be detrimental. Recently, we showed that MACE enables transcrip-tional profiling of formalin-fixed and paraffin-embedded (FFPE) conjunctival tissue with high accuracy even after more than 10 years of storage. Here we demonstrate that MACE provides comparable results for native and FFPE corneal tissue, confirming that the technology is suitable for transcriptome analysis of a wide range of archived diseased corneal samples stored in histo-logical archives. Finally, our data underscore the feasibility of bioinformatics cell-type enrich-ment analysis in bulk RNA-seq data to profile immune cell composition in fixed and archived corneal tissue samples, for which RNA-seq analysis of individual cells is often not possible.

2022-11-22 | GSE214853 | GEO

Transcript Analysis of Human Mammary Cell Subsets using SAGE

Project description:Highly purified subpopulations of primitive bipotent and committed luminal progenitor cells as well as mature luminal and myoepithelial cells from normal human mammary tissue were isolated and compared their transcriptomes which were obtained using PCR-Long-SAGE technology. Keywords: mammary progenitors, stem cells, Notch signaling, gene expression Four SAGE libraries were constructed on RNA samples extracted from highly purified subpopulations of primitive bipotent and committed luminal progenitor cells as well as mature luminal and myoepithelial cells isolate from a normal human mammary tissue.

2008-05-09 | E-GEOD-11387 | biostudies-arrayexpress

Notch Pathway Activation Targets AML Cell Homeostasis and Differentiation: THP1 cell line

Project description:Expression data from untreated or Dll4-Fc treated THP1 cell line. We used Dll4-Fc stimulation of AML cells to study whether Notch activation has an impact on AML. We analyzed THP1 cell line in vitro treated with Dll4-Fc or vehicle control to determine genes affected by Notch activation. THP1 cell line was cultured on plate coated with 30 nM Dll4-Fc or vehicle for 48 hours prior to RNA extraction and hybridization to Human Genome U133 Plus 2.0 Affymetrix arrays.

2013-01-18 | E-GEOD-42259 | biostudies-arrayexpress

Donor lung tissues: Control vs. Primary graft dysfunction (PGD)

Project description:Primary graft dysfunction (PGD) continues to be a major cause of early death after lung transplantation. Moreover, there remains a lack of accurate pre-transplant molecular markers for predicting PGD. To identify distinctive gene expression signatures associated with PGD, we profiled human donor lungs using microarray technology prior to the graft implantation. The genomic profiles of 10 donor lung samples from patients who subsequently developed clinically defined severe PGD were compared with 16 case-matched donor lung samples from those who had a favorable outcome without PGD. Matched factors used were: recipient age (± 10 years), recipient gender, recipient lung disease, and type of transplantation (single or bilateral). Keywords: Observational case-control study

2008-09-15 | GSE9102 | GEO

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