PXD002571

PXD002571 is an original dataset announced via ProteomeXchange.

Title	Tissue and organ matrix arrays for high throughput screening and systems analysis of cell function
Description	Cell and protein arrays have demonstrated remarkable utility in the high-throughput evaluation of biological responses; however, they lack the complexity of native tissue and organs and cannot replicate the environment of mature normal or diseased tissues. Here, we describe the development of tissue and organ extracellular matrix (ECM) arrays for screening biological outputs and systems analysis. Tissues and organs were chemically and mechanically processed and then formulated as particles without any enzymatic breakdown. The tissue ECM particles were spotted as two-dimensional tissue ECM arrays or incorporated with cells to generate three-dimensional cell-ECM microtissue arrays, and these methods were compatible with tissues prepared with varied processing techniques. The physical and biochemical properties, including the proteomic composition, of the tissue ECM arrays were characterized and compared with native tissues. The 2D arrays were validated through quantitative analysis of tissue-specific biological outputs of cell matrix production, cell adhesion and proliferation, and cell shape following culture with stem cells, cancer cells, and macrophages. Tissue-specific stem cell osteogenic differentiation on the arrays was comparable between 2D and 3D ECM environments, and revealed lung as an unexpected promoter of osteogenesis. Further gene ontology analysis of lung tissue ECM proteomics showed enrichment for families of proteins associated with skeletal development and osteogenesis. Stem cell biological outputs, along with cancer line adhesion and macrophage shape, were correlated with tissue proteomics, and network analysis identified several protein determinants of cell function. Our methodology enables broad screening of tissue and organ ECMs to connect tissue-specific composition with biological responses via systems analysis, providing a new resource for research and translation.
HostingRepository	PRIDE
AnnounceDate	2015-09-28
AnnouncementXML	Submission_2015-10-26_04:59:02.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Akhilesh Pandey
SpeciesList	scientific name: Sus scrofa domesticus (domestic pig); NCBI TaxID: 9825;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive; LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2015-07-21 01:09:26	ID requested
1	2015-09-28 03:23:48	announced
⏵ 2	2015-10-26 04:59:03	announced	Updated publication reference for PubMed record(s): 26480475.

Beachley VZ, Wolf MT, Sadtler K, Manda SS, Jacobs H, Blatchley MR, Bader JS, Pandey A, Pardoll D, Elisseeff JH, Tissue matrix arrays for high-throughput screening and systems analysis of cell function. Nat Methods, 12(12):1197-204(2015) [pubmed]

curator keyword: Technical

submitter keyword: ECM, tissue array, organ array, matrix

Jennifer H. Elisseeff
contact affiliation	Translational Tissue Engineering Center, Wilmer Eye Institute and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21287, USA.
contact email	jhe@jhu.edu
lab head
Akhilesh Pandey
contact affiliation	Johns Hopkins University
contact email	pandey@jhmi.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/09/PXD002571

PRIDE project URI

• PRIDE
  1. PXD002571
     1. Label: PRIDE project
     2. Name: Tissue and organ matrix arrays for high throughput screening and systems analysis of cell function