Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Correlation between immune lymphoid cells and plasmacytoid DCs in colon cancer

ABSTRACT: Correlation between immune lymphoid cells and plasmacytoid DCs in colon cancer

PROVIDER: PRJNA525832 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR8689900.fastq.gz	Fastqsanger.gz
	SRR8689910.fastq.gz	Fastqsanger.gz
	SRR8689920.fastq.gz	Fastqsanger.gz
	SRR8689901.fastq.gz	Fastqsanger.gz
	SRR8689911.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 28

Similar Datasets

Correlation between immune lymphoid cells and plasmacytoid DCs in colon cancer

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to use RNA-seq to compare ILC3s and pDCs gene expression in colon cancer. Results: Using an optimized data analysis workflow, More than >60 million clean reads were obtained from each sample group after elimination of low-quality reads. A total of 14,943 in ILC3s and 10,840 in pDCs DEGs were found up-regulated and 4,213 in ILC3s and 11,549 DEGs in pDC s down-regulated on comparison of ILC3s and pDCs from tumor samples and controls samples transcripts with TopHat workflow. RNA-seq data confirmed stable expression of 25 known housekeeping genes, and 12 of these were validated with qRT–PCR. RNA-seq data had a linear relationship with qRT–PCR for more than four orders of magnitude and a goodness of fit (R2) of 0.8798. Approximately 10% of the transcripts showed differential expression between the WT and Nrl−/− retina, with a fold change ≥1.5 and p value <0.05. Altered expression of 25 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to retinal function. Data analysis with BWA and TopHat workflows revealed a significant overlap yet provided complementary insights in transcriptome profiling. Conclusion: These findings highlighting the important roles of ILC3s and pDCs in the processes of tumor progression and inhibition in colon cancer promote the development of new strategies for inducing antitumor immune responses in metastatic and recurrent colon cancer.

2021-03-16 | GSE127934 | GEO

Correlation Between Immune Lymphoid Cells and Plasmacytoid Dendritic Cells in Human Colon Cancer.

Project description:BackgroundInnate lymphoid cells (ILCs), so far studied mostly in mouse models, are important tissue-resident innate immune cells that play important roles in the colorectal cancer microenvironment and maintain mucosal tissue homeostasis. Plasmacytoid dendritic cells (pDCs) present complexity in various tumor types and are correlated with poor prognosis. pDCs can promote HIV-1-induced group 3 ILC (ILC3) depletion through the CD95 pathway. However, the role of ILC3s in human colon cancer and their correlation with other immune cells, especially pDCs, remain unclear.MethodsWe characterized ILCs and pDCs in the tumor microenvironment of 58 colon cancer patients by flow cytometry and selected three patients for RNA sequencing.ResultsILC3s were negatively correlated, and pDCs were positively correlated, with cancer pathological stage. There was a negative correlation between the numbers of ILC3s and pDCs in tumor tissues. RNA sequencing confirmed the correlations between ILC3s and pDCs and highlighted the potential function of many ILC- and pDC-associated differentially expressed genes in the regulation of tumor immunity. pDCs can induce apoptosis of ILC3s through the CD95 pathway in the tumor-like microenvironment.ConclusionsOne of the interactions between ILC3s and pDCs is via the CD95 pathway, which may help explain the role of ILC3s in colon cancer.

| S-EPMC7940519 | biostudies-literature

Mechanosensing regulates plasmacytoid DCs activation in the skin through NRF2 activation

Project description:Mechanosensing regulates plasmacytoid DCs activation in the skin through NRF2 activation

| PRJNA1189818 | ENA

Mechanosensing regulates plasmacytoid DCs activation in the skin through NRF2 activation

Project description:Mechanosensing regulates plasmacytoid DCs activation in the skin through NRF2 activation

| PRJNA1189544 | ENA

Suppression of plasmacytoid dendritic cell migration by compounds derived from natural medicines

Project description:Background and Aims. Dendritic cells (DCs) play a pivotal role in maintaining immunological homeostasis by orchestrating innate and adaptive immune responses via migration to inflamed sites and the lymph nodes (LNs). Plasmacytoid DCs (pDCs) have been reported to accumulate in the colon of inflammatory bowel disease (IBD) patients and dextran sulfate sodium (DSS)-induced colitis mice. However, the role of pDCs in the progression of colonic inflammation remains unclear. Methods. 80 compounds in natural medicines were searched for inhibitors of pDC migration using bone marrow-derived pDCs (BMpDCs) and conventional DCs (BMcDCs). BALB/c mice were given 3% DSS in the drinking water for 7 days to induce acute colitis. Compounds, which specifically inhibited pDC migration, were administrated into DSS-induced colitis mice. Results. Astragaloside IV (As-IV) and oxymatrine (Oxy) suppressed BMpDC migration but not BMcDC migration. In DSS-induced colitis mice, the number of pDCs was markedly increased in the colonic lamina propria (LP), and the expression of CCL21 was obviously observed in colonic isolated lymphoid follicles (ILFs). As-IV and Oxy reduced symptoms of colitis and the accumulation of pDCs in colonic ILFs but not in the colonic LP. Moreover, in a BMpDC adoptive transfer model, BMpDC migration to colonic ILFs was significantly decreased by treatment with As-IV or Oxy. Conclusion. pDCs accumulated in the colon of DSS-induced colitis mice, and As-IV and Oxy ameliorated DSS-induced colitis by suppressing pDC migration to colonic ILFs. Accordingly, the selective inhibition of pDC migration may be a potential therapeutic approach for treating colonic inflammatory diseases.

2021-07-06 | GSE167388 | GEO

Clonal lineage tracing reveals shared origin of conventional and plasmacytoid dendritic cells

Project description:Developmental origins of dendritic cells (DCs) including conventional DCs (cDCs, comprising cDC1 and cDC2 subsets) and plasmacytoid DCs (pDCs) remain unclear. We studied DC development in unmanipulated adult mice using inducible lineage tracing combined with clonal DNA "barcoding" and single-cell transcriptome and phenotype analysis (CITE-Seq). Inducible tracing of Cx3cr1+ hematopoietic progenitors in the bone marrow showed that they simultaneously produce all DC subsets including pDCs, cDC1s and cDC2s. Clonal tracing of hematopoietic stem cells (HSCs) and of Cx3cr1+ progenitors revealed clone sharing between cDC1s and pDCs, but not between the two cDC subsets or between pDCs and B cells. Accordingly, CITE-Seq analyses of differentiating HSCs and Cx3cr1+ progenitors identified progressive stages of pDC development including Cx3cr1+ Ly-6D+ propDCs that were distinct from lymphoid progenitors. These results reveal the shared origin of pDCs and cDCs, and suggest a revised scheme of DC development whereby pDCs share clonal relationship with cDC1s

2022-02-16 | GSE193733 | GEO

Common lymphoid progenitor derivation of plasmacytoid dendritic cells is mediated by Bcl11a

Project description:Common lymphoid progenitor derivation of plasmacytoid dendritic cells is mediated by Bcl11a

| PRJNA415465 | ENA

Common lymphoid progenitor derivation of plasmacytoid dendritic cells is mediated by Bcl11a

Project description:Common lymphoid progenitor derivation of plasmacytoid dendritic cells is mediated by Bcl11a

| PRJNA937378 | ENA

Proteomics of human dendritic cell subsets

Project description:We exploited label-free quantitative mass spectrometry to compare primary human blood Dendritic cells (DCs) subsets protein expression to identify new markers. Subsets distinguished are: Plasmacytoid DCs (pDC) and BDCA3+ and CD1c+ myeloid DCs and CD16+ monocytes. The dendritic cells were analyzed by LC-MS/MS and processed by MaxQuant for identification and LFQ quantification.

2016-09-27 | PXD004678 | Pride

Plasmacytoid dendritic cells develop from Ly6D+ lymphoid progenitors distinct from the myeloid lineage

Project description:Plasmacytoid dendritic cells develop from Ly6D+ lymphoid progenitors distinct from the myeloid lineage

| PRJNA542142 | ENA