Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Single-cell RNAseq of hiPSC derived alveolar-like lung organoids upon H3N2 infection

ABSTRACT: hiPSC from 2 different donors were differentiated into alveolar-like organoids (iPSC-aLOs) as previously described (DOI: 10.1038/s41596-019-0220-0). iPSC-aLOs were either kept in \"dome\" culture embedded in extracellular matrix or inverted in apical-out conformation to allow influenza H3N2 infection. Apical-out iPSC-aLOs were exposed or not to H3N2. At 24hs post-infection iPSC-aLOs were collected and dissociated into single cells. Samples were multiplexed using membrane lipid barcoding and we followed 10X Genomics instructions from single cell encapsulation to NGS. This data set is useful to compare iPSC-aLOs cell composition both in dome and apical-out culture conditions and iPSC-aLOs response to influenza virus H3N2 infection at a single timepoint of 24hs post-infection at MOI =1. Each sample (HUB 07-09) contains multiplexed conditions: control in dome culture, control in apical out (both non infected), infected 24 hpi. Due to human data sensitivity concerns, this experiment was submitted with processed data only.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: Valeria Fernandez Vallone

PROVIDER: E-MTAB-15980 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Extracellular vesicles derived from induced pluripotent stem cells (iPSC EVs) have immunoregulatory potential with the ability to alter monocyte-derived macrophages. Macrophages function in the propagation and resolution of inflammation which is mediated by their phenotype. Macrophages are an ideal therapeutic target as modulating their phenotype towards an anti-inflammatory pro-resolving state may be beneficial in chronic inflammatory diseases such as atherosclerosis. Macrophages are naturally phagocytotic cells and readily take up iPSC EVs however the contents of iPSC EVs and their effects on macrophages are poorly understood. Here iPSC EVs were characterized and analysed by mass-spectrometry based proteomics and a targeted microRNA (miR) panel. Their immunomodulatory effects on macrophages were assessed and a monocyte transmigration assay was used to assess the chemotactic potency of the secretome from iPSC EV treated macrophages. Proteomic analysis on iPSC EVs identified Podocalyxin-like protein 1 (PODXL1), Insulin (INS) and Solute Carrier Family 2 (Facilitated Glucose Transporter), Member 3 (SLC2A3) as the most abundant proteins unique to the iPSC EVs when compared to control NT-2 EVs. Notably, thioredoxin and peroxiredoxin related proteins were detected. miR-302d-3p was the most abundant miR in these iPSC EVs. miR-25-3p, previously reported to alter the macrophage phenotype, was significantly increased in comparison to the control NT-2 EVs. iPSC EVs increased expression of the anti-inflammatory associated MRC1 and miR-21 in human primary macrophages and decreased monocyte chemoattractant protein1 (MCP-1). Mass spectrometry based proteomics revealed that treated macrophages had decreased levels of secretory proteins, some of which have chemotactic properties, these included Azurocidin 1 (AZU1), Growth Differentiation Factor 15 (GDF15), and Ribosomal Protein S19 (RPS19). There was a decrease in monocyte transmigration towards conditioned media from macrophages treated with iPSC EVs. Collectively this study provides insights into the protein content and miR cargo of iPSC EVs and highlights their capacity to inhibit chemotactic proteins in macrophages and upregulate MRC1.

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Single-cell RNAseq of hiPSC derived alveolar-like lung organoids upon H3N2 infection

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