Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ECM of proliferative vs dormant HNSCC

ABSTRACT: The goal of this project is to characterize the ECM composition of actively proliferative and dormant head and neck squamous cell carcinoma xenografts and identify components of the ECM niche instructing tumor cell dormancy.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Homo Sapiens (human)

DISEASE(S): Neck Carcinoma

SUBMITTER: George Chlipala

LAB HEAD: Alexandra Naba

PROVIDER: PXD018883 | Pride | 2021-08-26

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

A tumor-derived type III collagen-rich ECM niche regulates tumor cell dormancy.

Di Martino Julie S JS Nobre Ana Rita AR Mondal Chandrani C Taha Isra I Farias Eduardo F EF Fertig Elana J EJ Naba Alexandra A Aguirre-Ghiso Julio A JA Bravo-Cordero Jose Javier JJ

Nature cancer 20211213 1

Cancer cells disseminate and seed in distant organs, where they can remain dormant for many years before forming clinically detectable metastases. Here we studied how disseminated tumor cells sense and remodel the extracellular matrix (ECM) to sustain dormancy. ECM proteomics revealed that dormant cancer cells assemble a type III collagen-enriched ECM niche. Tumor-derived type III collagen is required to sustain tumor dormancy, as its disruption restores tumor cell proliferation through DDR1-med ...[more]

PMID: 35121989

Similar Datasets

ECM of proliferative vs dormant HNSCC

Project description:The goal of this project is to characterize the ECM composition of actively proliferative and dormant head and neck squamous cell carcinoma xenografts and identify components of the ECM niche instructing tumor cell dormancy.

2021-08-26 | PXD019185 | Pride

ECM of proliferative vs dormant HNSCC

2022-09-06 | PXD036453 | Pride

FOXL1+ TELOCYTES IN MOUSE COLON ORCHESTRATE ECM BIODYNAMICS AND WOUND REPAIR RESOLUTION

Project description:Recent studies identified FoxL1+-Telocytes (TCFoxL1+) as key players in gut epithelial-mesenchymal interactions impacting the microenvironment. Disruption of BMP-signaling in TCFoxL1+ alters the physical and cellular microenvironment leading to gut pathophysiology, suggesting a role for TCFoxL1+ in stromagenesis. However, profiling studies from whole tissue can be misleading when analyzing the specific contribution of TCFoxL1+. We performed an ex vivo deconstruction of control and BmpR1a△FoxL1+ colons, isolated the mesenchyme-enriched fractions and determined the protein composition of in vivo ECM to compare the microenvironment. Matrisomic analysis of mesenchyme fractions revealed modulations in ECM proteins with functions associated to innate immunity, epithelial wound healing and collagen network. These results show that TCFoxL1+ have a critical role in orchestrating the colon ECM biodynamics. Dysfunctional TCFoxL1+ reprogram the microenvironment driving the epithelium toward pathologies. This method allows to truthfully investigate how TCFoxL1+ impacts matrix dynamics leading to a comprehensive ECM profiling in diseases.

2023-10-11 | PXD036294 | Pride

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

Matrisome of neonatal mouse dermal fibroblasts

Project description:The goal of this project is to compare the protein composition of the extracellular matrices (ECMs) deposited in vitro by wild type, heterozygous, or SPAG17 KO neonatal mouse dermal fibroblasts.

2022-09-22 | PXD019869 | Pride

Matrisome proteins of human and porcine cornea and amnion

Project description:In this project, for the first time, the Extracellular Matrix protein compositions of porcine cornea and human amnion (amniotic membrane) were characterized using LC/MS-MS based on an already developed protocol, "Matrisome Project".

2021-05-21 | PXD020606 | Pride

Global proteomic analysis of extracellular matrix in mouse and human brain highlights association with cerebrovascular disease

Project description:The extracellular matrix (ECM), a key interface between the cerebrovasculature and other cells within the neuro-glial-vascular unit , provides structural stability and modulates cell behaviour and signalling. These functions are dependent on ECM protein composition. Since ECM defects may contribute to a broad range of disorders including cerebrovascular disease, it is crucially important to characterize ECM composition to better understand the mechanisms by which the ECM modulates brain health and disease. To date, molecular studies of the cerebrovascular ECM have been limited. We therefore generated ECM extracts from vascular enriched tissues of both mouse and human post-mortem brain. We used mass spectrometry with off-line high-pH reversed-phase fractionation to increase proteome depth and characterized the identified proteins. This identified a large number of proteins (>1000 mouse, >2000 human) in the ECM-enriched fractions, with > 66% of the identified proteins covered in both human and mouse samples. We now report 147 ECM proteins, including collagens (as major ECM components), laminins, fibronectin and nidogens, that can be considered as the core constituents of the human brain vascular matrisome. We also identified 12 novel proteins in the ECM-enriched fraction, that may have regulate or interact with the matrisome, including several key regulators of neurovascular interactions, such as BCAM, CDH5 and PARVB. Many of the identified brain vascular matrisome proteins are encoded by genes identified in stroke and cerebral small vessel disease genome-wide association studies, underscoring the importance of the vascular ECM in health and disease. This brain vascular matrisome represents a powerful resource for investigating the impact of aging and disease on the cerebrovasculature.

2021-03-11 | PXD020436 | Pride

Comparative Wnt dependent Hydra ECM proteome

Project description:Comparative proteome of extracted Hydra vulgaris AEP extracellular matrix form Wnt9/10 knock out and Azakenpaullone treated animals. Used to analyse the changes in molecular composition of the mesoglea (ECM) of normal and Wnt depleted animals

2023-05-10 | PXD039846 | Pride

Profiling of the human Fallopian tube matrisome

Project description:Characterization of the protein composition of the extracellular matrix (ECM) of normal human Fallopian tube samples.

2021-11-02 | PXD023707 | Pride

Tumor decellularization reveals proteomic and mechanical characteristics of the extracellular matrix of primary liver cancer

Project description:Tumor initiation and progression are critically dependent on interaction of cancer cells with their cellular and extracellular microenvironment. Alterations in the composition, integrity, and mechanical properties of the extracellular matrix (ECM) dictate tumor processes including proliferation, migration, and invasion. Also in primary liver cancers, consisting of hepatocellular carcinoma (HCC) and cholangiocarcinoma (CCA), the dysregulation of the extracellular environment by liver fibrosis and tumor desmoplasia is pertinent. Yet, in-depth characterization of liver cancer ECM and underlying tumor-promoting mechanisms remain largely unknown. Herein, we used an integrative molecular and mechanical approach to extensively characterize the ECM of HCC and CCA tumors by utilizing decellularization techniques. We identified a myriad of ECM-related proteins in both tumor and adjacent liver tissue, highlighting the complexity of the primary liver cancer matrisome. The differences in ECM protein abundance result in divergent mechanical properties on a macro- and micro-scale that is tumor-type specific. Furthermore, we employed the decellularized tumor ECM to create a tumor-specific hydrogel that support patient-derived tumor organoids. This provides a new avenue for personalized medicine by combining patient-derived tumor ECM and cancer cells. Taken together, this study provides better understanding of alterations to key aspects of the ECM that occur during primary liver cancer development.

2023-03-28 | PXD035261 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data