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Lentiviral-mediated phenotypic correction of type 1 and type 2 ABCA3 pathogenic variants

GSE302633 Homo sapiens (human) RNA-seq (gene expression) 10 samples Submitted 2025/08/30 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 10 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
10 samples: 5 × GFPGroups 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)
The ATP-binding cassette subfamily A member 3 (ABCA3) protein localizes to lamellar bodies in alveolar type 2 (AT2) cells and transports phospholipids required for pulmonary surfactant assembly. ABCA3 deficiency results from biallelic pathogenic variants in ABCA3 and causes progressive neonatal respiratory failure or childhood interstitial lung disease (chILD).
Read the full summary ↓
Supportive care or lung transplantation are the only current treatments for ABCA3 deficiency. Complementing defective ABCA3 production by gene addition has therapeutic potential. Previous studies show that repairing or complementing ABCA3 in induced pluripotent stem cell (iPSC) derived AT2 cells restores defining phenotypes (e.g., lamellar body morphology and surfactant phospholipid composition). ABCA3 pathogenic missense variants are rare or private and disrupt ABCA3 function through altered protein trafficking (type 1) or impairing phospholipid transport (type 2) into the lamellar bodies. Little is known about cellular responses to complementing mistrafficking or phospholipid transport variants. Here we used CRISPR/Cas9 to knockout ABCA3 from the A549 human pulmonary epithelial cell line to generate A549/ABCA3-/- cells stably expressing ABCA3 missense variant cDNAs from a single genomic locus: L101P (type 1), E292V (type 2), or E690K (type 2), or wild-type cDNA. Lentiviral-mediated ABCA3 delivery to each cell line phenotypically corrected the mutant cells. We observed restoration of lamellar body morphology and cell proliferation in ABCA3 complemented cells. Bulk RNA sequencing suggested that ABCA3 delivery ameliorated aberrant NF-kB signaling in p.E292V or p.E690K mutant cell lines, but not in p.L101P or knockout lines. These studies highlight important differences between ABCA3 pathogenic variant types that may influence genetic therapy outcomes.
This dataset
Open GSE302633 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 GSE302633_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 PRJNA1291622 and SRA study SRP600993. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
5 × GFP

Supports a between-group comparison across 5 samples.

How we read this: 1 replicated groups read from 10 sample titles; they account for 5 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
Datasets on a similar topic

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