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Viral triggers of Type 1 diabetes: Effects of Coxsackie B virus infection on transcriptome of trophoblast and pancreatic beta cell lines.

GSE278756 Homo sapiens (human) Non-coding RNA profiling 15 samples Submitted 2024/10/06 Platform GPL24676
At a glance

Non-coding RNA profiling · human · 15 samples

What it is
Non-coding RNA profilingLevels of RNAs that do not code for proteins, such as miRNA or lncRNA.
Organism
Homo sapiens (human)
Samples
15 samples: 3 × EndoC-βH1, CVB4-E2 infected, biol vs 3 × EndoC-βH1, CVB4-JVB infected, biol vs 3 × Sw.71, CVB4-JVB infected, biolGroups 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.
Paper
A novel microRNA promotes coxsackievirus B4 infection of pancreatic β cellsFrontiers in immunology · 2024
Summary (written by the submitters)
The epidemiological association of coxsackievirus B infection with type 1 diabetes suggests that therapeutic strategies that reduce viral load could delay or prevent disease onset. Moreover, recent studies suggest that treatment with antiviral agents against coxsackievirus B may help preserve insulin levels in type 1 diabetic patients.
Read the full summary ↓
In the current study, we performed small RNA-sequencing to show that infection of immortalized trophoblast cells with coxsackievirus caused differential regulation of several miRNAs. One of these, hsa-miR-AMC1, was similarly upregulated in human pancreatic β cells infected with coxsackievirus B4. Moreover, treatment of β cells with non-cytotoxic concentrations of an antagomir that targets hsa-miR-AMC1 led to decreased CVB4 infection, suggesting a positive feedback loop wherein this microRNA further promotes viral infection. Interestingly, some predicted target genes of hsa-miR-AMC1 are shared with hsa-miR-184, a microRNA that is known to suppress genes that regulate insulin production in pancreatic β cells. Consistently, treatment of coxsackievirus B4-infected β cells with the hsa-miR-AMC1 antagomir was associated with a trend toward increased insulin production. Taken together, our findings implicate novel hsa-miR-AMC1 as a potential early biomarker of coxsackievirus B4-induced type 1 diabetes and suggest that inhibiting hsa-miR-AMC1 may provide therapeutic benefit to type 1 diabetes patients. Our findings also support the use of trophoblast cells as a model for identifying microRNAs that might be useful diagnostic markers or therapeutic targets for coxsackievirus B-induced type 1 diabetes.
Published in
A novel microRNA promotes coxsackievirus B4 infection of pancreatic β cells
Lalani S, Knudsen J, Kenney J et al. · Frontiers in immunology 2024 · PMID 39697323 · doi:10.3389/fimmu.2024.1414894
This dataset
Open GSE278756 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 GSE278756_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 ↗

Also filed as BioProject PRJNA1168578 and SRA study SRP536517. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39697323) ↗
Study design
3 × EndoC-βH1, CVB4-E2 infected, biol vs 3 × EndoC-βH1, CVB4-JVB infected, biol vs 3 × Sw.71, CVB4-JVB infected, biol

Supports a case/control comparison: 9 samples read as cases, 6 as controls.

How we read this: 3 replicated groups read from 15 sample titles; they account for 9 of them. 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
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