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Reconstruction of intercellular communication and signaling impacting de novo HSC emergence using CellComm platform

ABSTRACT: Reconstruction of intercellular communication and signaling impacting de novo HSC emergence using CellComm platform

PROVIDER: PRJNA673448 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12955100_1.fastq.gz	Fastqsanger.gz
	SRR12955100_2.fastq.gz	Fastqsanger.gz
	SRR12955101_1.fastq.gz	Fastqsanger.gz
	SRR12955101_2.fastq.gz	Fastqsanger.gz
	SRR12955102_1.fastq.gz	Fastqsanger.gz

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Reconstruction of intercellular communication and signaling impacting de novo HSC emergence using CellComm platform

Project description:Cellular transitions are shaped by cross-talk between cell-intrinsic and extrinsic factors. Signals derived from the cell’s microenvironment are integrated and processed by the cell to modulate gene expression programs to instruct cell function and fate. Recent advances in single-cell technologies and analytics have provided an unprecedented resolution to study intercellular communication and differentiation trajectories. Here, we developed CellComm, a systems biology platform to infer intercellular communication networks and transcriptional regulators downstream of cell surface receptors predicted to mediate cellular interactions. We applied CellComm to investigate how the unique cellular niche of the aorta-gonad-mesonephros (AGM) region is involved in hematopoietic stem cell emergence and identified key cell types and microenvironmental signals implicated in hematopoietic development. We extensively validated CellComm’s predictions in three different species - zebrafish, mouse and human - and found both known and novel genes involved in developmental hematopoiesis, such as Stat3, Nr0b2, Ybx1 and, surprisingly, App, which is often reported in neurodegenerative disorders. Strikingly, CellComm revealed extensive cross-talk of signaling pathways feeding into the same transcriptional regulators, indicating a tightly regulated developmental program ensuring dynamic adaptation to changes in the embryonic environment. Taken together, our work contributes to a better understanding on how the embryonic niche is involved in developmental hematopoiesis as well as provides a new algorithm and data resource for the scientific community.

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Transient restriction of intercellular communication is required for root regeneration

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Developmental gene regulation by an ancient intercellular communication system in social amoebae

Project description:In the social amoebae (Dictyostelia) quorum sensing system mediates aggregation of single cells into multicellular aggregates by chemotactic movement towards gradients of diffusible molecules known as acrasins. The acrasin of P. violaceum is the unusual dipeptide N-propionyl-gamma-L-glutamyl-L-ornithine-delta-lactam-ethylester, known as glorin. Phylogenetic analysis has indicated that P. violaceum is more related to the most derived group 4 dictyostelids than to the ancient group 2 polysphondylids such as P. pallidum. Nevertheless it has been reported that P. pallidum cells respond to glorin in chemotaxis assays. This has led to the assumption that glorin-based communication may be the most ancient form of intercellular communication that Dictyostelia invented to organize early steps of multicellular development. In this study we show that glorin mediates rapid changes in gene expression at the transition from vegetative growth to aggregation, apparently without pronounced cross-talk with the cyclic AMP-based communication system that coordinates post-aggregation events in this species. We describe glorin-mediated changes in gene expression in the social amoeba Polysphondylium pallidum at the transition from unicellular growth to multicellular development. Comparison of gene expression in growing cells versus cells starving for 2 or 3 hours in the presence or absence of glorin.

2010-10-29 | E-GEOD-24911 | biostudies-arrayexpress

Transient restriction of intercellular communication is required for root regeneration

Project description:Transient restriction of intercellular communication is required for root regeneration

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Adolescent bone sarcomas have distinct immune signatures and intercellular communication networks

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Adolescent bone sarcomas have distinct immune signatures and intercellular communication networks

Project description:Ewing and osteosarcoma are bone sarcomas that occur predominantly in adolescents. In the setting of metastatic or recurrent disease, overall prognosis is poor. While immunotherapy is effective for some adult soft tissue sarcoma, limited success has been achieved with immunotherapy for pediatric bone sarcomas. To better understand antitumor immunity in Ewing and osteosarcoma patients, we performed single-cell RNAseq on peripheral blood and tumor infiltrating immune populations using 10X Genomics droplet-based approach. We also included peripheral blood from healthy adolescent blood donors as a comparator. Utilizing these transcriptional profiles, we characterized tumor infiltrating CD8+ T cells and myeloid cells and identified intercellular communication networks in both primary and recurrent disease.

2022-08-31 | GSE198896 | GEO

Developmental gene regulation by an ancient intercellular communication system in social amoebae

2010-10-29 | GSE24911 | GEO

Intercellular communication via miR-143-containing microvesicles controls osteoblastic bone formation in vivo

Project description:Intercellular communication via miR-143-containing microvesicles controls osteoblastic bone formation in vivo

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Intercellular communication via miR-143-containing microvesicles controls osteoblastic bone formation in vivo

Project description:Osteoblasts are the only somatic cell type with bone-forming ability. While the cellular and molecular mechanisms underlying their differentiation and function have been identified, their dynamic control in vivo is unclear. By intravital multiphoton microscopy of live bone tissues of osteoblast fluorescent reporter mice, we visualized intact mature osteoblasts in vivo and found that they actively secrete and capture extracellular microvesicles. Microvesicles from mature osteoblasts contain the microRNA miR-143-3p, which inhibits osteoblast differentiation. Osteoblast-specific deletion of miR-143 increased bone formation and miR-143-deficient microvesicles induced recovery from bone defect. In sum, we report a novel mode of intercellular communication in vivo via microRNA-containing extracellular vesicles, which controls bone homeostasis.

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