{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD055832/experimentaldesigntemplate.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD055832/checksum.txt"],"Xml":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD055832/mqpar.xml"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD055832/062_SS12.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD055832/055_SS05.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD055832/061_SS11.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD055832/054_SS04.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD055832/056_SS06.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD055832/060_SS10.raw"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD055832/txt.zip"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["carolyn.cummins@utoronto.ca"],"submitter":["Michael Saikali"],"technology_type":["Data-dependent acquisition","Mass Spectrometry"],"software":[""],"submitter_keywords":["Bioprinting","Immune response","Tissue engineering","Myocardium","Organ-on-a-chip","Cardiomyocytes","Vascularization"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD055832"],"sample_protocol":["Phenol red-free conditioned media was collected from three pooled fibrin-based tissues of two groups (CM/EC/DPSC and μtissue/EC/DPSC) on day 10 of culture. The media was centrifuged at 2500 x g for 20 minutes at 4°C to remove cell debris. The supernatant was concentrated 10-fold using a 3 kDa MWCO Amicon centrifuge filtration column (Millipore) at 4000 x g for 1 hour at 4°C, and then dried using a SpeedVac (Thermo Fisher Scientific) for 2 hours at medium heat. Twenty µg of conditioned media-derived proteins from each sample were denatured and reduced with 8 M urea, 10 mM DTT, and 100 mM Tris-HCl (pH 8.5) at 60°C for 30 minutes, followed by alkylation with 100 mM iodoacetamide for 15 minutes. Alkylation was quenched with DTT to a final concentration of 40 mM, and urea was diluted to less than 1 M with 50 mM ammonium bicarbonate. Proteins were digested with 0.2 μg of trypsin (Sigma-Aldrich) overnight at 37°C. The resulting peptides were acidified and desalted using in-house C18 pipette tips. Analysis was performed on an Easy nLC-1200 coupled to a Thermo Q Exactive HF mass spectrometer in Top 20 data-dependent acquisition mode. Peptides were separated on a PepMap RSLC C18 (2 μm, 75 μm x 50 cm) column and a PepMap 100 C18 (3 μm, 75 μm x 2 cm) precolumn with a 120-minute gradient from 5% to 40% Buffer B (0.1% formic acid in 80% acetonitrile)."],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["The raw MS data were analyzed using MaxQuant software. Proteins were identified by searching the human (UP000005640) proteomes from UniProtKB. Peptide spectral matches, and protein FDRs were set to 1%, and requiring a minimum of 1 unique peptide for identification. To increase the number of identified matches, “match between runs” was enabled with a match time window of 0.7 minutes. Protein abundancies were calculated using the label-free quantification (LFQ) algorithm in MaxQuant."],"omics_type":["Proteomics"],"labhead":["Carolyn L. Cummins"],"instrument_platform":[""],"labhead_affiliation":["Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Canada"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"submitter_mail":["michael.saikali@mail.utoronto.ca"],"publication":["40771434 Zhao Y, Khosravi R, Cheung K, Shen K, Wang Y, Landau S, Okhovatian S, Wu Q, Lu RXZ, Wagner KT, Bodenstein DF, Shawky SA, Vosoughi D, Beroncal EL, Yeager K, Cummins CL, Andreazza AC, Vunjak-Novakovic G, Radisic M. Geometrically controlled cardiac microtissues promote vascularization and reduce inflammation <i>in vitro</i> and <i>in vivo</i>. Cell Biomater. 2025 1(4):100075 10.1016/j.celbio.2025.100075"],"submitter_affiliation":["University of Toronto"],"submitter_country":["Canada"],"pubmed_abstract":["Cardiac tissue engineering faces challenges due to inadequate vascularization, poor engraftment, and ineffective strategies to control inflammation. This study explores the benefits of geometrically controlled cardiac microtissues over-dispersed cells. Microtissues derived from human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) and affixed between two polydimethylsiloxane (PDMS) pillars exhibited cellular alignment and contractile function and were necessary to serve as suitable building blocks for assembling larger tissues. Following implantation into the omentum in nude rats, these tissues exhibited robust engraftment, contractility, and vascularization, with significantly reduced inflammation. Compared to dispersed cells, microtissues demonstrated enhanced vessel network formation, reduced cell death (lower lactate dehydrogenase [LDH]), decreased cytotoxicity (lower cell-free mitochondrial DNA [mtDNA]), and decreased Yes-associated protein (YAP) activation in cardiomyocytes and associated non-cardiomyocyte populations. Cytokine analysis revealed elevated pro-angiogenic factors (placenta growth factor [PIGF], endocan, and angiopoietin-2) and reduced inflammatory markers (interleukin-31 receptor A [IL-31 RA], interleukin [IL]-2 R beta, and OX40 ligand) in microtissues compared with dispersed cells, offering a promising approach for cardiac repair and regeneration."],"pubmed_title":["Geometrically controlled cardiac microtissues promote vascularization and reduce inflammation <i>in vitro</i> and <i>in vivo</i>."],"pubmed_authors":["Zhao Yimu Y, Khosravi Ramak R, Cheung Krisco K, Shen Karen K, Wang Ying Y, Landau Shira S, Okhovatian Sargol S, Wu Qinghua Q, Lu Rick Xing Ze RXZ, Wagner Karl T KT, Bodenstein David F DF, Shawky Sarah A SA, Vosoughi Daniel D, Beroncal Erika Leigh EL, Yeager Keith K, Cummins Carolyn L CL, Andreazza Ana C AC, Vunjak-Novakovic Gordana G, Radisic Milica M"],"additional_accession":[]},"is_claimable":false,"name":"LC-MS/MS of conditioned media from vascularized tissue with and without cardiac microtissues.","description":"Geometrically controlled cardiac microtissues promote vascularization and reduce inflammation in vitro and in vivo   Cardiac tissue engineering faces challenges due to inadequate vascularization and lack of effective strategies to control inflammation post transplantation. . This study explores the benefits of geometrically optimized cardiac microtissues (μtissues) over dispersed cardiomyocytes (CMs) for in vitro and in vivo applications. Microtissues derived from human induced pluripotent stem cell-derived CMs (hiPSC-CMs) and compacted in between two PDMS pillars exhibit cellular alignment, contractile function and serve as suitable tissue building blocks. Constraining μtissue size to 300 µm ensures adequate oxygen diffusion, preventing necrotic core formation. In vivo, μtissues demonstrated improved engraftment, contractility, and vascularization in athymic nude rats, with significantly reduced inflammation and enhanced vessel ingrowth from the omental vasculature. This study highlights the potential of μtissues to advance cardiac tissue viability and function by creating contractile grafts with host endothelial ingrowth, offering a promising approach for cardiac repair and regeneration. When compared to dispersed CMs, μtissues show enhanced vessel network formation, reduced cell death (lower LDH), and decreased cytotoxicity (lower cell-free mtDNA). Cytokine analysis revealed elevated pro-angiogenic factors (PIGF, Endocan, Angiopoietin-2) and reduced inflammatory markers (IL-31 RA, IL-2 R beta, OX40 Ligand) in μtissues compared to dispersed 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