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Microenvironment-driven resistance to B-Raf inhibition in a melanoma patient is accompanied by broad changes of gene methylation and expression in distal fibroblasts. Transcriptomic study.

ABSTRACT: In this study, we compared gene expression and genome methylation of diverse fibroblast populations from a patient suffering from acrolentiginous melanoma (Breslow 4.0 mm, Clark IV, B-Raf V600E mutated). Stromal cells from the metastasis, i.e., melanoma associated fibroblasts (MAF), were positive for smooth muscle actin (SMA). Autologous control fibroblasts (ACF) isolated from distant uninvolved skin of the same patient during B-Raf inhibitor therapy and before clinical progression of the disease exhibited also strong SMA expression. Similar phenotype was observed in control dermal fibroblasts (CDF) from different donors yet exclusively after stimulation by TGF-Î²1. The identified differences in gene transcription as well as in DNA methylation indicate systemic activation of dermal fibroblasts in a patient with malignant melanoma. This dataset contains transcription profiling data, complementary methylation profiling data are available under accession E-MTAB-4965.

ORGANISM(S): Homo sapiens

SUBMITTER: Michal Kolar

PROVIDER: E-MTAB-4964 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Microenvironment-driven resistance to B-Raf inhibition in a melanoma patient is accompanied by broad changes of gene methylation and expression in distal fibroblasts. Genome methylation study.

Project description:In this study, we compared gene expression and genome methylation of diverse fibroblast populations from a patient suffering from acrolentiginous melanoma (Breslow 4.0 mm, Clark IV, B-Raf V600E mutated). Stromal cells from the metastasis, i.e., melanoma associated fibroblasts (MAF), were positive for smooth muscle actin (SMA). Autologous control fibroblasts (ACF) isolated from distant uninvolved skin of the same patient during B-Raf inhibitor therapy and before clinical progression of the disease exhibited also strong SMA expression. Similar phenotype was observed in control dermal fibroblasts (CDF) from different donors yet exclusively after stimulation by TGF-Î²1. The identified differences in gene transcription as well as in DNA methylation indicate systemic activation of dermal fibroblasts in a patient with malignant melanoma. This dataset contains genome methylation profiling data, complementary transcriptome profiling data are available under accession E-MTAB-4964.

2018-12-30 | E-MTAB-4965 | biostudies-arrayexpress

Targeting DDR1 and DDR2 overcomes matrix-mediated melanoma cell adaptation to BRAF-targeted therapy

Project description:To investigate the contribution of fibroblast-derived extracellular matrices (ECMs) to the resistance to targeted therapies in BRAF-mutated melanoma cells, we generated native-like 3D ECMs from human primary fibroblasts obtained from healthy individuals or melanoma patients. Cell-derived matrices from human dermal fibroblasts (HDF), skin melanoma associated fibroblasts (MAF) and two different lymph node fibroblast reticular cells (FRC) were denuded of cells and their composition was analyzed by mass spectrometry.

2021-11-12 | PXD026645 | Pride

Fibroblasts potentiate melanoma cells in vitro invasivity induced by UV-irradiated keratinocytes - transcription profiling

Project description:Melanoma represents a malignant disease with steadily increasing incidence. Despite a remarkable enrichment of therapeutic repertoire achieved in the last decade, primarily limited sensitivity to therapy or acquired resistance are common. These phenomena limit survival of patients in advanced stages of the disease. UV-irradiation is a very important factor in melanoma initiation. In this study, we tested the influence of normal dermal fibroblasts as well as cancer-associated fibroblasts isolated from melanoma on UV-irradiated keratinocytes as an inductor of melanoma cell migration in 3-D collagen gels. The introduction of normal dermal fibroblasts and mainly cancer-associated fibroblasts to such system further significantly stimulated melanoma cells invasivity. A panel of candidate gene products responsible for facilitation of melanoma cells invasion was defined with emphasis on IL6, IL8 and CXCL1.

2018-01-10 | E-MTAB-5973 | biostudies-arrayexpress

Global gene expression profiles of iPSC from SMA patient, unaffected father and iPS 19.9 compared to transcriptomic data obtained by corresponding fibroblasts

Project description:Spinal Muscular Atrophy (SMA) is an autosomal recessive motor neuron disease and is the second most common genetic disorder leading to death in childhood. Motoneurons derived from induced pluripotent stem cells (iPS cells) obtained by reprogramming SMA patient and his healthy father fibroblasts, and genetically corrected SMA-iPSC obtained converting SMN2 into SMN1 with target gene correction (TGC), were used to study gene expression and splicing events linked to pathogenetic mechanisms. Microarray technology was used to assess global gene expression profiles of iPSC from SMA patient, unaffected father and iPS 19.9 (Prof. J. Thomson's lab) compared to transcriptomic data obtained by corresponding fibroblasts. The microarray data derived from three different individuals: SMA patient, healthy father and control iPS cells (19.9). We analyzed iPSC from SMA patient (n=2), iPS- from healthy father (n=1) and iPS-19.9 from Prof. Thomson's lab (n=3). The expression profile was compared to SMA patient's fibroblasts (n=2) and healthy father's fibroblasts (n=1)

2013-01-04 | E-GEOD-27206 | biostudies-arrayexpress

Gene expression profiles from cultured skin fibroblasts of two MAF mutation-positive subjects

Project description:Total RNA was obtained from cultured skin fibroblasts of two MAF mutation-positive subjects and control (dermal adult skin fibroblasts, ATCC PCS-201-012) (each in duplicates), and was subjected for gene expression profiling to identify differentially expressed genes (DEG).

2015-07-31 | E-MTAB-3250 | biostudies-arrayexpress

Human Subperitoneal Fibroblasts and Cancer Cell Interaction Creates Microenvironment Enhancing Tumor Progression and Metastasis

Project description:Fibroblasts isolated from human colon submucosal and subperitoneal layer were stimulated by colon cancer cell line (DLD-1) cultured medium. Peritoneal invasion in colon cancer is an important prognostic factor, and the fibrosis with α-SMA was a significant pathological feature of the cancer microenvironment formed by peritoneal invasion (CMPI). The result indicated that the gene expression of subperitoneal fibroblasts showed more various gene modification than submucosal fibroblasts. And ACTA2 expression was higher in fibroblasts from subperitoneal layer than that from submucosal layer. Together with this concordant stromal protein expression in CMPI, this in vitro model is able to reflect the special microenvironment in CMPI. 3 cases of human colon submucosal and subperitoneal fibroblasts were isolated, and these fibroblasts were stimulated with DLD-1 cultured medium. Total RNA were extracted from these samples and hybridized in Affymetrix microarray to compare their gene expression changes through the DLD-1 stimulation

2014-02-20 | E-GEOD-53059 | biostudies-arrayexpress

Expression profiling of fibroblasts treated with melanosomes

Project description:mRNA profiling was performed on primary fibroblasts treated with melanosomes and untreated fibroblasts as control. The aim of this study was to explore whether melanoma-derived mature melanosomes functionally affect primary fibroblasts. A functional gene set enrichment analysis based on the resulting mRNA profiles predicted that an uptake of mature melanosomes by fibroblasts causes increased cell proliferation and cell motility. Expression profiling was performed for 3 replicates of primary human fibroblasts that were treated with mature melanosomes, 1 replicate of fibroblasts treated with early melanosomes and 3 replicates of untreated fibroblasts as controls. Melanosomes were extracted from the human melanoma cell line MNT-1. Fibroblasts were treated with melanosomes for 24h. Fold changes were calculed for fibroblasts treated with mature melanosomes vs. controls. The sample of fibroblasts treated with early melanosomes was considered for the normalization, but not for further analyses. Microarray Unit of the Core Facility Genomics and Proteomics DKFZ

2016-08-09 | E-GEOD-72229 | biostudies-arrayexpress

Global gene expression profile and splicing events of iPS-derived motorneurons from SMA patient, unaffected father and TGC-treated cells

Project description:Spinal Muscular Atrophy (SMA) is an autosomal recessive motor neuron disease and is the second most common genetic disorder leading to death in childhood. Motoneurons derived from induced pluripotent stem cells (iPSC) obtained by reprogramming SMA patient and his healthy father fibroblasts, and genetically corrected SMA-iPSC obtained converting SMN2 into SMN1 with target gene correction (TGC), were used to study gene expression and splicing events linked to pathogenetic mechanisms. Microarray technology was used to assess the global gene expression profile as well as splicing events of iPS-derived motorneurons from SMA patient, unaffected father and TGC-treated cells. The microarray data derived from three different groups: SMA patient, healty father and treated SMA patient's cells. Each population consists of three RNA profiling cell samples.

2013-01-04 | E-GEOD-27205 | biostudies-arrayexpress

Transcription profiling of human spinal muscular atrophy patient induced pluripotent stem cells

Project description:Spinal muscular atrophy (SMA) is one of the most common inherited forms of neurological disease leading to infant mortality. Patients exhibit selective loss of lower motor neurons resulting in muscle weakness, paralysis, and often death. Although patient fibroblasts have been used extensively to study SMA, motor neurons have a unique anatomy and physiology which may underlie their vulnerability to the disease process. Here we report the generation of induced pluripotent stem (iPS) cells from skin fibroblast samples taken from a child with SMA. These cells expanded robustly in culture, maintained the disease genotype, and generated motor neurons that showed selective deficits compared to those derived from the childâs unaffected mother. This is the first study to show human iPS cells can be used to model the specific pathology seen in a genetically inherited disease. As such, it represents a promising resource to study disease mechanisms, screen novel drug compounds, and develop new therapies. Experiment Overall Design: A total of 10 samples were hybridized to the human genome U133 Plus 2.0 GeneChip arrays carrying 54,675 probe sets (Affimetrix). Experiment Overall Design: H1L, H7, H9, H13B, and H14A embryonic stem cells are controls for the iPS cells Experiment Overall Design: iPS(SMA) 3.5 and iPS(SMA)3.6 are from the patient. The clone iPS(SMA) 4.2. is from the parent.

2009-01-13 | E-GEOD-13828 | biostudies-arrayexpress

Heterotypic signaling between dermal fibroblasts and melanoma cells induces phenotypic plasticity and proteome rearrangement in malignant cells

Project description:The signaling events triggered by soluble mediators released from both transformed and stromal cells shape the phenotype of tumoral cells and have significant implications in cancer development and progression. In this study we performed an in vitro heterotypic signaling assay by evaluating the proteome diversity of human dermal fibroblasts after stimulation with the conditioned media obtained from malignant melanoma cells. In addition, we also evaluated the changes in the proteome of melanoma cells after stimulation with their own conditioned media as well as with the conditioned medium from melanoma-stimulated fibroblasts. Our results pointed out to a significant rearrangement in the proteome of stromal and malignant cells upon crosstalk of soluble mediators. The main proteome signature of stimulated cells was related to protein synthesis, which may indicate that this process might be an early response of stimulated stromal cells. In addition, the conditioned medium derived from ‘primed’ stromal cells (melanoma-stimulated fibroblasts) was more effective in altering the functional phenotype (cell migration) of malignant cells than the fibroblast conditioned medium alone. Collectively, self- and cross-stimulation may play a key role in shaping the tumor microenvironment and, more importantly, enable tumoral cells to succeed in the process of melanoma progression and metastasis. Although the proteome landscape of cells participating in such a heterotypic signaling represents a snapshot of a highly dynamic state, understanding the diversity of proteins and enriched biological pathways resulting from stimulated cell states may allow for targeting specific cell regulatory motifs involved in melanoma progression and metastasis.

2020-08-31 | PXD020426 | Pride

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