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Cytoadhesion of Plasmodium falciparum-infected red blood cells changes the expression of cytokine-, histone- and antiviral protein-encoding genes in brain endothelial cells

GSE266399 Homo sapiens (human) RNA-seq (gene expression) 15 samples Submitted 2024/05/03 Platform GPL20301
At a glance

RNA-seq (gene expression) · human · 15 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Homo sapiens (human)
Samples
15 samples: 15 samples, each with a distinct title — no replicated groupsGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Summary (written by the submitters)
Introduction Malaria remains a significant global health problem, particularly due to the human malaria parasite Plasmodium falciparum, which is responsible for most fatal infections. Infected red blood cells (iRBCs) evade spleen clearance by adhering to endothelial cells (ECs), triggering capillary blockage, inflammatory cytokine release, endothelial dysfunction, and altered vascular permeability, prompting an endothelial transcriptional response.
Read the full summary ↓
Methods The iRBCIT4var04/HBEC-5i model, where iRBCs present IT4var04 (VAR2CSA) on their surface was employed to analyse the effects of iRBC binding on ECs. We used this model to investigate how cytoadhesion of iRBCs to ECs influences their expression profile depending on the temperature (37°C vs 40°C). Results Binding of non-infected RBCs (niRBCs) and fever alone significantly changes expression of hundreds of genes in ECs. Comparing the expression profile of HBEC-5i cultured either in the presence of iRBCs or in the presence of niRBCs, genes encoding proteins assigned to the GO terms immune response, nucleosome assembly, NF-kappa B signaling, angiogenesis, and antiviral immune response/interferon-alpha/beta signaling pathway were significantly up-regulated. If the cultivation temperature is increased from 37°C to 40°C, which simulates fever, a further significant increase in expression can be observed for most regulated genes, especially for genes coding for cytokines and proteins involved in angiogenesis. Conclusion The presence of iRBCs leads to the stimulation of ECs, activating several immunological signaling pathways and affecting antiviral (-parasitic) mechanisms and angiogenesis. Furthermore, to our knowledge, the induction of the interferon-alpha/beta signaling pathway in ECs in response to iRBCs has been described for the first time.
This dataset
Open GSE266399 in finder → Find more human RNA-seq datasets →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE266399_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1106906 and SRA study SRP505245. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
15 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 15 sample titles: 15 distinct titles with little repetition. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study
Datasets on a similar topic

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.