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Comparison of transcriptomic profiles between dysplastic stem cell subpopulations

ABSTRACT: To investigate transcriptomic profiles of of two dysplastic stem cell (DSC) subpopulations, CD44v6neg/CD133+/CD166+ (DP-DSC) and CD44v6+/CD133+/CD166+ (TP-DSC), in dysplastic organoids (Meta4 organoids) established from active-Kras induced mouse stomachs

ORGANISM(S): Mus musculus

PROVIDER: GSE202191 | GEO | 2022/09/28

REPOSITORIES: GEO

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Single cell analysis of tumors developed from mouse dysplastic stem cells

Project description:To investigate whether the CD44v6neg/CD133+/CD166+ dysplastic stem cells are responsible for gastric adenocarcinoma development and cancer cell heterogeneity in the stomach, we used single cell RNA-seq (scRNA-seq) to examine gene expression profiles of heterogenous cancer cells in two types of gastric adenocarcinoma, cystic type and tubular type, developed from the dysplastic stem cell injection under the skin of immunodeficient nude mice.

2022-09-28 | GSE202192 | GEO

Targeting Stem Cells and Dysplastic Features with Dual MEK/ERK and STAT3 Suppression in Gastric Carcinogenesis

Project description:Pre-cancerous metaplasia progression to dysplasiasignificantlyincreases the risk of gastriccancer, and effective targeting strategies forpre-cancerouslesions are currently lacking.Weaimed to identify key signaling pathways critical for stem cell survival and function in dysplasia.Usingmouse and humanmetaplastic and dysplastic organoids, we evaluated responsestoPyrvinium, a putative anti-cancer drug.WhilePyrvinium induced growth arrest in metaplasticorganoids, itinducedcell death in dysplastic organoidsthrough a dual blockade of MEK/ERKand STAT3 signaling pathways. Pyrvinium specifically targeted stem cells andproliferating cellsin dysplastic organoids.Pyrviniumarrestedmetaplasia progression andpromoted repopulationof themousestomach mucosawith normal lineages.Furthermore, Pyrvinium exhibitedsuppressive effects on the growth and survival of human organoids with dysplastic features, through simultaneous blockingthe MEK/ERK and STAT3 signaling pathways.Therefore, ourfindings suggest that Pyrvinium is a promising therapeutic agent for reprogramming the pre-cancerous milieu to prevent of gastric cancer development.

2024-02-14 | GSE240890 | GEO

Human pluripotent stem cell-derived kidney organoids reveal tubular epithelial pathobiology of heterozygous HNF1B-associated dysplastic kidney malformations - cell line dataset

Project description:Hepatocyte nuclear factor 1B (HNF1B) encodes a transcription factor expressed in developing human kidney epithelia. Heterozygous HNF1B mutations are the commonest monogenic cause of dysplastic kidney malformations (DKMs). To understand their pathobiology, we generated heterozygous HNF1B mutant kidney organoids from CRISPR-Cas9 gene-edited human ESCs and iPSCs reprogrammed from a family with HNF1B-asscociated DKMs. Mutant organoids contained enlarged malformed tubules and displayed deregulated cell turnover. This submission is RNAseq of organoids from MAN13 embryonic stem cells.

2024-04-29 | E-MTAB-12824 | biostudies-arrayexpress

Human pluripotent stem cell-derived kidney organoids reveal tubular epithelial pathobiology of heterozygous HNF1B-associated dysplastic kidney malformations

2024-04-29 | E-MTAB-12822 | biostudies-arrayexpress

RNA-Seq of human fetal and adult scalp hair follicle dermal papilla (DP), dermal sheath cup (DSC), and interfollicular dermal (IFD) cells

Project description:Much is still unknown about the molecular regulatory networks which govern the dermal papilla’s (DP) ability to induce hair follicle regeneration, a capacity which gradually decreases with age. DP and dermal sheath cup (DSC) cells from mature, anagen phase, hair follicles were manually microdissected from fresh frozen sections of 16-18 week human fetal scalp and 30-60 year old adult male scalp. Interfollicular dermal (IFD) fibroblasts were harvested for comparison. RNA-seq libraries from each cell population were prepared with Nugen’s Ovation RNA-Seq and Ultralow Library systems, sequenced to approximately 100 million total reads. A set of 121 genes was identified as significantly upregulated in fetal DP cells, as compared to both fetal DSC and IFD populations. Wnt/β-catenin, Shh, FGF, BMP, and Notch signaling pathways were significantly enriched among those genes differentially expressed between fetal and adult DP cells. Among them, Spondin-1, a Wnt agonist, was chosen for verification and can rescue hair follicle regeneration in skin reconstitution assays using cells from adult mice. Additionally, twenty-nine transcription factors were significantly upregulated in fetal DP compared to adult DP cells. Of those, seven transcription factor binding motifs were significantly enriched in the candidate promoter regions of differentially expressed genes between fetal and adult DP cells, suggesting a combinatorial regulatory role in the fetal DP phenotype. Further investigation into these regulators is warranted to determine if these proteins and/or associated pathways plays a role in the maintenance or modulation of DP cells to induce hair regeneration.

2020-11-16 | GSE149189 | GEO

Epigenome analysis of cirrhosis and dysplastic liver samples

Project description:Epigenome analysis of cirrhosis and dysplastic liver samples

| PRJNA663577 | ENA

Epigenome analysis of cirrhosis and dysplastic liver samples

Project description:Genome-wide DNA methylation profiling of cirrhosis and dysplastic liver samples. The Illumina Infinium 450k Human DNA methylation BeadChip was used to obtain DNA methylation profiles across approximately 485,577 CpGs sites. Samples included 130 cirrhosis and 8 exhibiting dysplasia. The manuscript includes an integrative analysis of these samples along with samples from normal liver and HCC already deposited under GSE63898.

2021-06-02 | GSE157973 | GEO

Gene Expression Changes in Non-Dysplastic Mucosa from Patients with Ulcerative Colitis Harboring Remote Neoplastic Lesions

Project description:Background and Aims: Individuals with ulcerative colitis (UC) are at increased risk for colorectal cancer, although underlying mechanisms are incompletely understood. We sought to identify a potential gene expression signature in non-dysplastic distal mucosa that as a “genetic field effect” could be a marker for remote neoplastic lesions. Results: 468 genes were significantly up-regulated and 541 genes were significantly down-regulated >2-fold in UC patients with neoplasia compared to UC patients without neoplasia. Nine genes (ACSL1, BIRC3, CLC, CREM, ELTD1, FGG, S100A9, THBD, and TPD52L1) were progressively and significantly up-regulated from controls to quiescent non-dysplastic UC to UC with neoplasia. Immunostaining of proteins revealed increases in tissue expression of S100A9 and REG1 in UC-associated cancer and in non-dysplastic tissue from UC patients harboring remote neoplasia, compared to UC patients without dysplasia and normal controls. Conclusions: Gene expression changes occur as a field effect in UC patients without active inflammation who harbor a remote dysplastic lesion. Further characterization of these genes and proteins might elucidate pathways of carcinogenesis in IBD and lead to the development of more accurate, less invasive markers of dysplasia in those at increased risk.

2012-04-20 | GSE37283 | GEO

Progressive immune activation and negative immunoregulation from common melanocytic nevi to dysplastic nevi to melanoma

Project description:The purpose of this study was to comprehensively study and compare the molecular gene expression profiles of common melanocytic nevi (GSE53223), dysplastic nevi (GSE53223), and primary melanoma.

2018-10-25 | GSE114445 | GEO

Knockdown of PGC-1α suppresses dysplastic oral keratinocyte cells proliferation through reprogramming energy metabolism

Project description:To investigate the effects of knockdown PGC1α on human dysplastic oral keratinocyte (DOK) cell proliferation, cell cycle, apoptosis, xenograft tumor, mitochondrial DNA (mtDNA), mitochondrial electron transport chain complexes (ECT), ROS, oxygen consumption rate (OCR), extracellular acidification rate (ECAR), and glucose uptake

2023-09-13 | GSE224317 | GEO

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