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A radical switch in clonality reveals the formation of a stem cell niche in the epiphyseal growth plate

ABSTRACT: A radical switch in clonality reveals the formation of a stem cell niche in the epiphyseal growth plate

PROVIDER: PRJNA454724 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7095960.fastq.gz	Fastqsanger.gz
	SRR7095970.fastq.gz	Fastqsanger.gz
	SRR7095980.fastq.gz	Fastqsanger.gz
	SRR7095990.fastq.gz	Fastqsanger.gz
	SRR7096000.fastq.gz	Fastqsanger.gz

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A radical switch in clonality reveals the formation of a stem cell niche in the epiphyseal growth plate

Project description:A radical switch in clonality reveals the formation of a stem cell niche in the epiphyseal growth plate

2019-01-03 | GSE113982 | GEO

GNPS Phoenicin switch: Penicillium atrosanguineum on various growth media

Project description:Part of the publication: Phoenicin Switch: Discovering the trigger for radical phoenicin production in multiple wild type Penicillium species.

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Niche modulated versus niche modulating genes in multiple myeloma

Project description:Background. Multiple myeloma (MM) cells depend on the bone marrow (BM) niche for growth and survival. However, the tumor genes regulated by the niche are largely unknown. Design and Methods. BM aspiration samples were obtained from MM-patients with a high tumor load. Gene expression profile (GEP) was recorded immediately following aspiration and at subsequent time points. Identification of niche-regulated genes relied on spontaneous gene modulation following loss of niche regulation. Results. Compared to the reference samples fixed immediately following aspiration, the BM samples fixed after longer delay acquired numerous changes in GEP. The top modulated genes included a common subset of ~ 60 genes displaying prompt and sustained “switch” in expression consistently, among which were oncogenes (FOS, JUN) and genes regulating homing (CD69, RGS1), expansion and angiogenesis (AREG, PTGS2, RGS2, NR4A2). Interestingly, the “switch” in GEP was reversible and turned “off” and “on” in culture conditions resuming cell-cell-matrix contact versus re-spread into suspension, respectively. Moreover, the resuming of contact prolonged the survival of the tumor cells out-of-niche and the regression of the “contactless switch” was followed by induction of a new set of genes this time mostly encoding extracellular proteins, including angiogenic factors (IL8, CXCL5), extracellular-matrix proteins (SPP1, FN1), chemokines (CXCL5, CCL2, CCL20) and growth factors (CCL2, IL6). Conclusions. Our dataset, being unique in authentic expression design, uncovered contact-regulated genes capable of controlling homing, expansion and tumorigenesis. The adaptive response of the tumor cells to culture conditions deficient of integral niche components (e.g., vascular vessels) uncovered inducible niche-regulating tumor genes.

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A biphasic epigenetic switch controls immunoevasion, virulence and niche adapatation in non-typeable Haemophilus influenzae

Project description:Non-typeable Haemophilus influenzae (NTHi) contains an N6-adenine DNA-methyltransferase (ModA), that is subject to phase variable expression (random ON/OFF switching). Five modA alleles, modA2, 4, 5, 9 and 10, account for over two-thirds of clinical otitis media isolates surveyed. Single Molecule Real Time (SMRT) methylome analysis identified the DNA recognition motifs for all five of these modA alleles. Phase variation of these alleles regulated multiple proteins, including vaccine candidates. ON/OFF switching of modA alleles resulted in differential regulation of key virulence phenotypes, such as antibiotic resistance (modA2, 5, 10), biofilm formation (modA2) and immunoevasion (modA4). Analysis of the modA2 strain, 723, in the chinchilla model of otitis media showed a clear selection for switching from modA2OFF to ON in the middle ear. This is the first report of a biphasic epigenetic switch controlling bacterial virulence, immunoevasion and niche adaptation in an animal model system Direct comparison of biological triplicates of wild type and mutant strains

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Neuroinflammation creates an immune regulatory niche at the meningeal lymphatic vasculature near the cribriform plate

Project description:We report the use of single cell RNA sequencing of meningeal lymphatic endothelial cells near the cribriform plate in both naïve mice, and during experimental autoimmune encephalomyelitis (EAE), a mouse model of multiple sclerosis. By sorting for meningeal lymphatics near the cribriform plate, we identified that these lymphatic endothelial cells acquire an altered phenotype during neuroinflammation, where they become enriched in genes involved in leukocyte crosstalk including adhesion molecules, antigen processing and presentation, and tolerance, thus becoming a unique site of immune regulation.

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Neuroinflammation creates an immune regulatory niche at the meningeal lymphatic vasculature near the cribriform plate

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Epigenetic clonality confers por prognosis in colorrectal cancer patients (SNP)

Project description:In CRC, 1) to identify epigenetic changes at inter-tumor and intra-tumor level, and 2) to relate intra-tumor clonality to clinical, molecular and histopathologic parameters. From 79 FFPE tumors, 3 different regions were macrodissected: invasive front (IF), digestive tract surface (DTS) and central bulk (CB). Clinical, molecular, and histopathologic parameters were stablished. Epigenetic analysis was performed using Infinium 450K beadchip (Illumina) and R statistics. Intra-tumor regions clustered together by patient. The biggest epigenetic changes were in IF vs DTS/CB. By patient, the most often divergent region was IF (49.4%) comparing with DTS and CB (25.3% in both). It did not correlate with histopathologic, molecular and clinical parameters.Epigenetic clonality is higher at intra-tumor level. The highest changes are observed in IF vs DTS/CB. No association with histopathologic, molecular, and clinical characteristics was found. SNP characterization of 9 patients of teh discovery cohort were hibridized on Infinium HumanOncoArray-500 v1 beadchip, to asses the genetic clonality of the samples among the three intratumoral regions studied.

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Protein-coding and MicroRNA Biomarkers of Recurrence of Prostate Cancer Following Radical Prostatectomy

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