Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomic characterization of stem cell-derived extracellular matrices

ABSTRACT: We characterized and compared the proteomic composition of ECM produced in vitro by bone marrow-derived MSC, adipose-derived MSC and neonatal fibroblasts isolated from different donors, employing a multidimensional proteomic approach coupled with label-based quantitative proteomics. Each cell-derived ECM displayed a specific and unique matrisome signature, yet they all shared a common set of proteins. We evaluated the biological response of cells cultured on the different matrices and compared them to cells on standard TCPS. The matrices lead to differential proliferation and gene expression profiles between the cell types and as compared to TCPS, indicating that the cell-derived ECM influence each cell type in a unique manner.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Embryonic Stem Cell

SUBMITTER: Amanda Del Rosario

LAB HEAD: Amanda Del Rosario

PROVIDER: PXD005521 | Pride | 2017-03-08

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	150219_122_HR_BM001.mgf	Mgf
	150219_122_HR_BM001.mzid.gz	Mzid
	150219_122_HR_BM001.pride.mgf.gz	Mgf
	150219_122_HR_BM001.pride.mztab.gz	Mztab
	150219_122_HR_BM001.raw	Raw

Items per page:

1 - 5 of 55

Similar Datasets

Analysis of ECM-enriched samples using different methods

Project description:Using LC-MS/MS, we analyzed ECM-enriched samples obtained from 1) human triple-negative breast cancer samples and matched adjacent normal mammary gland tissues, and 2) disease-free omentum from patient with non-metastatic ovarian cancer and high-grade- serous-ovarian- cancer-derived omental metastasis samples. We conducted the LC-MS/MS analysis on peptides obtained after solubilizing ECM-enriched samples using different methods (crude ECM extract, urea-soluble extract, urea-insoluble extract) and submitted to basic-reversed- phase separation or not.

2017-07-11 | PXD005554 | Pride

Long non-coding RNA H19 regulates matrisome signature and impacts cell behavior on MSC-engineered extracellular matrices

Project description:The vast and promising class of long non-coding RNAs (lncRNAs) has been under investigation for distinct therapeutic applications. Nevertheless, their role as molecular drivers of bone regeneration remains poorly studied. The lncRNA H19 mediates osteogenic differentiation of Mesenchymal Stem/Stromal Cells (MSCs) through the control of intracellular pathways. However, the effect of H19 on the extracellular matrix (ECM) components is still largely unknown. This research study was designed to decode the H19-mediated ECM regulatory network, and to reveal how the decellularized siH19-engineered matrices influence MSC proliferation and fate. This is particularly relevant for diseases in which the ECM regulation and remodelling processes are disrupted, such as osteoporosis.

2023-03-11 | PXD039001 | Pride

Proteomic characterization of stem cell-derived extracellular matrices

Project description:We characterized and compared the proteomic composition of ECM produced in vitro by bone marrow-derived MSC, adipose-derived MSC and neonatal fibroblasts isolated from different donors, employing a multidimensional proteomic approach coupled with label-based quantitative proteomics. Each cell-derived ECM displayed a specific and unique matrisome signature, yet they all shared a common set of proteins. We evaluated the biological response of cells cultured on the different matrices and compared them to cells on standard TCPS. The matrices lead to differential proliferation and gene expression profiles between the cell types and as compared to TCPS, indicating that the cell-derived ECM influence each cell type in a unique manner.

2017-03-29 | MSV000080731 | MassIVE

Transcriptional profiling by array of human adipose-derived stem cells to study the influence of cell-secreted ECM on the osteogenic differentiation process.

Project description:The aim of this study is to characterize how the extracellular matrix secreted by adipose-derived stem cells (ADSC) during osteogenesis affects the differentiation process. Specifically, ADSC undergo osteogenesis by following similar maturational phases as bone marrow-derived stem cells. However, it is unclear how the differentiation process is the same and how it differs. We first focused on ADSC behavior by analyzing whole transcriptome changes in response to osteogenic media supplements added into the tissue culture medium. We then developed osteogenic differentiation expression profiles for the ADSC and identify key genes and pathways that serve as an osteogenesis signature. This expression signature acted as a template for comparison of how extracellular matrix (ECM) affected ADSC differentiation. We studied ADSC induced to differentiate on ECM isolated from day 16 in the differentiation process (the midpoint in osteogenesis) as well as ECM from day 11 in the differentiation process. Ultimately, we aim to dissect the relationship between cells grown on ECM as an in vitro growth substrate and cells grown on tissue culture plastic; both in the presence of osteogenic supplements. This study, will allow us to determine the extent to which ECM affects the differentiation process.

2012-01-01 | E-MEXP-3340 | biostudies-arrayexpress

Comprehensive proteomic characterization of stem cell-derived extracellular matrices

Project description:In the stem-cell niche, the extracellular matrix (ECM) serves as a structural support that additionally provides stem cells with signals that contribute to the regulation of stem-cell function, via reciprocal interactions between cells and components of the ECM. Recently, cell-derived ECMs have emerged as in vitro cell culture substrates to better recapitulate the native stem-cell microenvironment outside the body. Significant changes in cell number, morphology and function have been observed when mesenchymal stem cells (MSC) were cultured on ECM substrates as compared to standard tissue-culture polystyrene (TCPS). As select ECM components are known to regulate specific stem-cell functions, a robust characterization of cell-derived ECM proteomic composition is critical to better comprehend the role of the ECM in directing cellular processes. Here, we characterized and compared the protein composition of ECM produced in vitro by bone marrow-derived MSC, adipose-derived MSC and neonatal fibroblasts isolated from different donors, employing quantitative proteomic methods. Each cell-derived ECM displayed a specific and unique matrisome signature, yet they all shared a common set of proteins. We evaluated the biological response of cells cultured on the different matrices and compared them to cells on standard TCPS. The matrices lead to differential survival and gene-expression profiles among the cell types and as compared to TCPS, indicating that the cell-derived ECMs influence each cell type in a different manner. This general approach to understanding the protein composition of different tissue-specific and cell-derived ECM will inform the rational design of defined systems and biomaterials that recapitulate critical ECM signals for stem-cell culture and tissue engineering.

2017-03-07 | GSE94667 | GEO

Dental Pulp Stem Cells LC-MS/MS analysis

Project description:This study focuses on the impact of ECM (extra-cellular matrix) over cell processes such as proliferation, differentiation or mineralization which is more specifically related to our dental pulp cells. We cultured these dental pulp stem cells (DPSC) in mineralization growth or normal growth conditions. After 21 days, cells were incubated in decellularized solution until no intact cells are seen. After ECM was washed, we studied the mineralization associated to these two different ECM. Matrisome proteins were identified through proteomics. DPSC matrisome is composed of 225 individual different proteins. We classified them according to different categories, the 3 core matrisome categories: glycoproteins, collagens, proteoglycans and the 3 matrisome associated proteins categories: the regulators, affiliated and secreted. When comparing the proteins in the N-ECM and OM-ECM, most of the core matrisome proteins are downregulated in OM conditions, except 3 glycoproteins, as well as regulators and secreted factors. However, annexins were found to be upregulated in OM condition. Cell adhesion, tensile strength and growth factor binding are over-represented in NM ECM. The collagen group and glycoproteins were higher in N-ECM than OM-ECM Thereafter, gingival stem cells (GSC), the less inherit osteogenic potency cells, were seeded on these N-ECM and OM-ECM. When GSCs were seeded on DPSC-derived ECM, the OM-ECM dramatically promoted mineral deposition compared with N-ECM. We hypothesize that annexins could participate in the osteogenic inductive properties. ECM plays a pivotal role in many physiological processes, it regulates cells behavior and can orient cell differentiation. Dental pulp and oral mucosa share embryological origins but differ in their reactions to insults. Dental pulp can mineralize while oral mucosa heals ad integrum. We hypothesize that ECM participate in these characteristics.

2021-09-23 | PXD018951 | Pride

Graphene Oxide Substrate Promotes Neurotrophic Factor Secretion and Survival of Human Schwann-Like Adipose Mesenchymal Stromal Cells - RNAseq

Project description:Mesenchymal stromal cells from adipose tissue (AD-MSCs) exhibit favourable clinical traits for autologous transplantation and can develop a ‘Schwann-like’ phenotype (sAD-MSCs) to improve peripheral nerve regeneration, where severe injuries yield insufficient recovery. However, sAD-MSCs regress without biochemical stimulation and detach from conduits under unfavourable transplant conditions, negating their paracrine effects. Graphene-derived materials support AD-MSC attachment, regulating cell adhesion and function through physiochemistry and topography. We report graphene oxide (GO) as a suitable substrate for human sAD-MSCs incubation towards severe peripheral nerve injuries, through evaluating transcriptome changes, neurotrophic factor expression over a 7-day period, and cell viability in apoptotic conditions. Transcriptome changes from GO incubation across four patients were minor compared to biological variance.

2021-03-08 | E-MTAB-10078 | biostudies-arrayexpress

Secreted proteins extracted (3M NaCl) from EP/LP MSCs grown on soft/stiff substrates for 8 days

Project description:Tissues are maintained by homeostatic feedback mechanisms in which cells can respond to, but also modify, the chemical and mechanical properties of the surrounding extracellular matrix (ECM). Mechano-sensitive mesenchymal stem cells (MSCs) resident in the marrow niche experience a diverse mechanical environment, but ageing can affect the composition and quality of bone and marrow tissues. Here we quantified the compounded effects of substrate stiffness and replication-induced senescence on MSC morphology and their ability to modify their environments through secretion of ECM proteins. The ECM proteome was found to be sensitive to substrate stiffness, but pharmacological inhibition of cellular contractility perturbed this response, decreasing levels of tenascin-C, fibulins and fibronectin. A corresponding change in the ECM of senescent cells, concomitant with a loss of mechano-responsive morphological features, suggested a decoupling of mechanotransduction pathways. Intracellular proteomic and transcriptomic analyses confirmed a decrease in all components of the cytoskeletal protein homeostasis machinery in senescent MSCs. These results demonstrate a senescence-mediated perturbation to cytoskeletal homeostasis, pathways of mechanotransduction and the secretion of ECM proteins considered necessary for tissue maintenance.

2022-10-10 | PXD013241 | Pride

Proteomics analysis of the matrisome from MC38 experimental mouse liver metastases

Project description:Dissemination of primary tumors to distant anatomical sites has a substantial negative impact on patient prognosis. The liver is a common site for metastases from colorectal cancer, and patients with hepatic metastases have generally much shorter survival, raising a need to develop and implement novel strategies for targeting metastatic disease. The extracellular matrix (ECM) is a meshwork of highly crosslinked, insoluble, high molecular weight proteins maintaining tissue integrity and establishing cell-cell interactions. Emerging evidence identifies the importance of the ECM in cancer cell migration, invasion, intravasation, and metastasis. Here, we isolated the extracellular matrix from MC38 mouse liver metastases using our optimized method of mild detergent solubilization followed by biochemical enrichment. The matrices were subjected to label-free quantitative mass spectrometry analysis, revealing proteins highly abundant in the metastatic matrisome. The resulting list of differentially expressed proteins significantly predicted survival in patients with colorectal cancer but not other cancers with strong involvement of the extracellular matrix component. One of the proteins upregulated in liver metastatic ECM, Annexin A1, was not previously studied in the context of cancer-associated matrisome. Here we show that Annexin A1 was markedly upregulated in colon cancer cell lines compared to cancer cells of other origin, and also overrepresented in human primary colorectal lesions as well as hepatic metastases in comparison with their adjacent healthy tissue counterparts. In conclusion, our study provides a comprehensive ECM characterization of MC38 experimental liver metastases and proposes Annexin A1 as a putative target for this disease.

2020-05-26 | PXD013350 | Pride

MSCs on soft/stiff substrates treated with ROCK or myosin II inhibitors

2022-10-12 | PXD013239 | Pride