biostudies-arrayexpressSHOHEI WAKAOHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16736Stem cells undergo cytokine-driven differentiation, but this process often takes longer than several weeks to complete. A novel mechanism for somatic stem cell differentiation via phagocytosing 'model cells' (apoptotic differentiated cells) was found to require only a short time frame. Pluripotent-like Muse cells phagocytosed apoptotic differentiated cells via different phagocytic receptor subsets than macrophages. The phagocytosed-differentiated cell-derived contents (e.g., transcription factors) were quickly released into the cytoplasm, translocated into the nucleus, and bound to promoter regions of the stem cell genomes. Within 24 ~ 36 h, the cells expressed lineage-specific markers corresponding to the phagocytosed-differentiated cells, both in vitro and in vivo. This scRNA-seq experiment aimed to elucidate the transcriptional changes induced by the phagocytosis of dead cell fragments derived from differentiated cells, including cardiomyocytes, neural cells, and hepatocytes.biostudies-arrayexpressNucleic Acid Extraction - Cells for all samples were stained with barcode tag-conjugated β2-microglobulin antibody and CD298 antibody (BioLegend), counted and multiplexed, and prepared for single-cell capture.Sample Collection - Human bone marrow-mesenchymal stem cells (h-BM-MSCs) were purchased from Lonza (Basel, Switzerland, PT-2501). SSEA-3(+) Muse cells were collected by fluorescence-activated cell sorting (FACS; BD FACSAria™ II cell sorter, Becton Dickinson, San Jose, CA, USA). mCherry- or GFP-h-Muse cells (1 × 105) were incubated for 3 days with m-cardiomyocyte DDCs, r-neural cell DDCs, and r-hepatic cell DDCs derived from 2 × 105 cells to make Phago-cardio-, Phago-neuro-, and Phago-hepa-Muse cells, respectively, then washed out and cultured in medium (DMEM + 10% FBS) for 4 days.Library Construction - Single-cell capture and cDNA synthesis were performed by the BD Rhapsody Single-Cell Analysis System according to the manufacturer’s instructions.Sequencing - All libraries were sequenced using Novaseq 6000 to a read depth of at least 100,000 reads/cell.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Raw fastq files were mapped onto GRCh38 release-107 by STARsolo. The sequencing and initial analysis were performed using ImmunoGeneTeqs (Tokyo, Japan).UnknownTranscriptomicsGenomicsProteomicsBD RhapsodyIllumina NovaSeq 6000Stem cells undergo cytokine-driven differentiation, but this process often takes longer than several weeks to complete. A novel mechanism for somatic stem cell differentiation via phagocytosing 'model cells' (apoptotic differentiated cells) was found to require only a short time frame. Pluripotent-like Muse cells, multipotent mesenchymal stem cells (MSCs), and neural stem cells (NSCs) phagocytosed apoptotic differentiated cells via different phagocytic receptor subsets than macrophages. The phagocytosed-differentiated cell-derived contents (e.g., transcription factors) were quickly released into the cytoplasm, translocated into the nucleus, and bound to promoter regions of the stem cell genomes. Within 24 ~ 36 h, the cells expressed lineage-specific markers corresponding to the phagocytosed-differentiated cells, both in vitro and in vivo. At 1 week, the gene expression profiles were similar to those of the authentic differentiated cells and expressed functional markers. Differentiation was limited to the inherent potential of each cell line: triploblastic-, adipogenic-/chondrogenic-, and neural-lineages in Muse cells, MSCs, and NSCs, respectively. Disruption of phagocytosis, either by phagocytic receptor inhibition via small interfering RNA or annexin V treatment, impeded differentiation in vitro and in vivo. Together, our findings uncovered a simple mechanism by which differentiation-directing factors are directly transferred to somatic stem cells by phagocytosing apoptotic differentiated cells to trigger their rapid differentiation into the target cell lineage.RNA-seq of coding RNA from single cellsHomo sapiensPhagocytosing differentiated cell-fragments is a novel mechanism for controlling somatic stem cell differentiation within a short time frameWakao S, Oguma Y, Kushida Y, Kuroda Y, Tatsumi K, Dezawa MYO OGUMASHOHEI WAKAOMARI DEZAWAfalseSingle-cell RNA sequencing of multi-lineage differentiating stress-enduring (Muse) cells in the naïve state and after phagocytosis of cardiomyocyte-, neural cell-, or hepatic cell–derived fragmentsStem cells undergo cytokine-driven differentiation, but this process often takes longer than several weeks to complete. A novel mechanism for somatic stem cell differentiation via phagocytosing 'model cells' (apoptotic differentiated cells) was found to require only a short time frame. Pluripotent-like Muse cells phagocytosed apoptotic differentiated cells via different phagocytic receptor subsets than macrophages. The phagocytosed-differentiated cell-derived contents (e.g., transcription factors) were quickly released into the cytoplasm, translocated into the nucleus, and bound to promoter regions of the stem cell genomes. Within 24 ~ 36 h, the cells expressed lineage-specific markers corresponding to the phagocytosed-differentiated cells, both in vitro and in vivo. This scRNA-seq experiment aimed to elucidate the transcriptional changes induced by the phagocytosis of dead cell fragments derived from differentiated cells, including cardiomyocytes, neural cells, and hepatocytes.2026-04-21T00:00:00Z2026-04-21T01:03:28.413Z2026-03-30T21:38:16.41ZE-MTAB-1673636203068ERP191576EFO_0002944EFO_0004170EFO_0005684EFO_0005518EFO_0003816EFO_000418410.1007/s00018-022-04555-0