Transcriptome profiling of Cryptosporidium parvum infected lung and intestinal organoids
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ABSTRACT:
PROVIDER: PRJNA449692 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6984250_1.fastq.gz | Fastqsanger.gz | |||
| SRR6984250_2.fastq.gz | Fastqsanger.gz | |||
| SRR6984260_1.fastq.gz | Fastqsanger.gz | |||
| SRR6984260_2.fastq.gz | Fastqsanger.gz | |||
| SRR6984270_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: Transcriptome profiling of Crytosporidium parvum infected lung and small intestinal organoids was performed to access the response of epithelial cells upon parasitic infection and to do a temporal analysis of the transcriptome of the parasite inside the organoid lumen. We isolated RNA from infected human lung and small intestinal organoids at 24 and 72 hour post infection. Methods: Organoids were grown in expansion or differentiation media and microinjected with equal amounts of Cryptosporidium oocysts. Media-injected organoids were used as a control .Expanding SI organoids were microinjected at 5-6 days after seeding, differentiated SI organoids were injected at 5 days after inducing differentiation. Lung organoids were incubated for 2 weeks after seeding for microinjection. RNA was extracted from 1-2 matrigel drops containing organoids. RNA was converted to cDNA and libraries were prepared using the CelSeq2 method and sequenced. Samples were sequenced on Illumina NextSeq500 by using 75-bp paired-end sequencing. Methods: Paired-end reads from Illumina sequencing were aligned to the human transcriptome genome and C. parvum transcriptome genome (Iowa strain) by BWA. DeSeq (v1.18.0) was used for read normalization and differential expression analysis (p-value adjustment 0.05 by method Benjamini-Hochberg). Gene set enrichment analysis (GSEA) was performed using gene lists for type I interferon response and regulation against normalized RNA-seq reads of injected SI and lung organoids using GSEA software v3.0 beta2. Results: At 24 hr post-infection,GO (gene ontology)-term analysis revealed that a substantial number of genes related to ‘cytoskeleton’ and ‘cell mobility’ were up-regulated in lung organoids. This suggests that infection by the parasites and subsequent formation of the intracellular stages within 24 hrs might affects cytoskeleton structures of host cells. After 72 hrs, many genes associated with the type I interferon pathway increased dramatically in lung and intestinal organoids. Results: After 72 hrs, many genes associated with the type I interferon pathway increased dramatically in lung and intestinal organoids. Multiple C. parvum genes were differentially expressed with a large fold change between 24 and 72 hr post-injection.At 24 hr post-infection, most of the enriched genes represented ribosomal proteins and ribosomal RNA subunits in both intestinal organoids and lung organoids. By contrast, at 72 hr post-infection, multiple oocyst-wall protein genes were up-regulated, confirming that the parasites formed new oocysts within the organoids. Conclusions: RNA sequencing of injected organoids revealed host epithelial responses upon parasite infection in differentiated SI organoids as well as in lung organoids.Upregulation of genes associated with type I interferon immunity in both SI and lung organoids.
2018-04-12 | GSE112991 | GEO
Project description:Purpose: The goal of this study was to identify transcriptional changes in HCT-8 cells treated with indole for 4 or 12 hours. Methods: Confluent HCT-8 monolayers were infected with excysted Cryptosporidium parvum sporozoites for 4 h, after which cells were washed to remove extracellular parasites. Cells were then treated with 1% DMSO in cell culture medium with or without 880 uM indole. RNA was collected in triplicate for each treatment type after 4 h and 12 h of treatment (8 and 16 hours post infection, respectively). Results: When the two time points were combined, indole significantly upregulated 57 genes and downregulated 11 genes. Of the upregulated genes,16 genes were primarily upregulated in cells exposed to indole for 4 h and then went back down by 12 h of exposure. These genes were primarily involved in pathways related to ER stress and the unfolded protein response (UPR). Conversely, 41 genes had higher gene expression after 12 h of indole exposure and were predominantly involved in membrane transport of carboxylic acids and amino acids. Conclusions: Indole treatment causes ER stress and upregulation of membrane transporters in a human adenocarcinoma cell line infected with Cryptosporidium parvum.
2021-10-13 | GSE185652 | GEO
Project description:Cryptosporidium parvum is an important zoonotic parasitic disease worldwide, but the molecular mechanisms of the host–parasite interaction are not fully understood. Noncoding microRNAs (miRNAs) are considered key regulators of parasitic diseases. Therefore, we used microarray, qPCR, and bioinformatic analyses to investigate the intestinal epithelial miRNA expression profile after Cryptosporidium parvum infection.Twenty miRNAs were differentially expressed after infection (four upregulated and 16 downregulated). Further analysis of the differentially expressed miRNAs revealed that many important cellular responses were triggered by Cryptosporidium parvum infection, including cell apoptosis and the inflammatory and immune responses.This study demonstrates for the first time that the miRNA expression profile of human intestinal epithelium cells is altered by C. parvum infection. This dysregulation of miRNA expression may contribute to the regulation of host biological processes in response to C. parvum infection, including cell apoptosis and the immune responses. These results provide new insight into the regulatory mechanisms of host miRNAs during cryptosporidiosis, which may offer potential targets for future C. parvum control strategies.
2018-12-23 | GSE95365 | GEO
Project description:Cryptosporidium parvum is an important opportunistic parasite pathogen for immunocompromised individuals and a common cause of diarrhea in young children in developing countries. Infection by this parasite causes significant alterations in the gene expression profiles in infected host cells. This study aims to measure the genomic wide alterations in gene expression profiles in host intestinal epithelial cells following C. parvum infection. Mouse intestinal epithelial (IEC4.1) cells were grown to 80% confluence and exposed to C. parvum infection for 24h. Total RNA was collected for the genome-wide analysis. The Agilent SurePrint G3 mouse Gene Expression Microarray (G4852A) was used for the genome-wide analysis, which provides full coverage of genes and transcripts with the most up-to-date content, including mRNAs and lincRNAs (http://www.chem.agilent.com/store/en_US/Prod-G4852A/G4852A).
2018-12-19 | GSE112247 | GEO
Project description:Cryptosporidium parvum has been reported to induce digestive adenocarcinoma in a rodent model of chronic cryptosporidiosis. In the current study, the transcriptomes of C. parvum infected ileo-caecal regions of mice developing tumours were analysed to identifie potential genes involved in development of cancer
2021-12-29 | GSE188591 | GEO
Project description:Cryptosporidium parvum is one of the most important opportunistic enteric parasites, causing severe diarrhea in immunocomprised human and animals. However, few effective control agents were available for this parasite. circular RNA (circRNA) was discovered to play key roles in many diseases, and the well-known regulatory mechanism for circRNAs is that act as miRNA sponges competitively binding to miRNAs to block miRNA-mRNA interaction. Here, using microarray assay, we investigated the expression profiles of circRNAs in HCT-8 cells after the infection of C. parvum IId subtype, the prevalent subtype of China. A total of 178 circRNAs were dysregulated expressed in HCT-8 cells at 24 h post infection (pi) of C. parvum IId subtype.
2022-12-15 | GSE162990 | GEO
Project description:H69 cells were cultured in H69 medium with Cryptosporidium parvum oocysts(10 X 5 per well, for smaples 04, 05 and 06) or without oocysts(for samples 01, 02 and 03)for 8 hours and then collected for array analysis. Sample 07 was cells exposed to heated inactived oocysts. <br>
2010-02-11 | E-MEXP-2050 | biostudies-arrayexpress
Project description:To better understand the detailed interaction between the host and Cryptosporidium parvum, a large scale label-free proteomics study was conducted to characterize the changes to the proteome induced by C. parvum infection.
2021-07-29 | PXD027634 |