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Conserved long noncoding RNA TILAM promotes liver fibrosis in humans and mice.

GSE238159 Homo sapiens (human) RNA-seq (gene expression) 18 samples Submitted 2024/07/22 Platform GPL20301Platform GPL17021
At a glance

RNA-seq (gene expression) · human · 18 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
18 samples: 6 conditions, mostly in triplicateGroups 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
Conserved long noncoding RNA TILAM promotes liver fibrosis through interaction with PML in HSCsHepatology (Baltimore, Md.) · 2025
Summary (written by the submitters)
Fibrosis is the common endpoint for all forms of chronic liver injury, and progression of fibrosis is responsible for the development of end stage liver disease and liver failure. The activation of hepatic stellate cells (HSCs) and their transition to HSC myofibroblasts is a key step in the disease process, as these cells are the primary source of the extracellular matrix (ECM) proteins, which form the fibrotic scar.
Read the full summary ↓
Long noncoding (lnc) RNAs can regulate the activity of HSCs, and lncRNAs that promote the fibrotic activity of HSCs may provide targets for antifibrotic therapies. Here, we identified and defined the functional mechanisms of a conserved lncRNA that plays a critical role in promoting liver fibrosis. We found that TILAM is conserved between human and mouse HSCs, and regulates expression of type 1 collagen, a major component of the ECM. To determine the role of TILAM in vivo, we annotated the mouse ortholog (Tilam), generated Tilam-deficient GFP-reporter mice, and challenged these mice in two different models of liver fibrosis. Analysis of GFP expression revealed that Tilam is induced in murine HSCs with the development of fibrosis in vivo. In both male and female mice, we also observed that loss of Tilam resulted in reduced fibrosis in the setting of injury induced by carbon tetrachloride (CCl4) and choline-deficient L-amino acid defined high fat diet (CDA-HFD). Finally, we found that TILAM interacts with PML to stabilize PML protein expression and promote the fibrotic activity of HSCs. Together, these results define an lncRNA conserved between humans and mice that is activated uniquely in HSCs to drive the development of fibrosis and could provide a therapeutic target to combat the development of end stage liver disease.
Published in
Conserved long noncoding RNA TILAM promotes liver fibrosis through interaction with PML in HSCs
Sun C, Zhou C, Daneshvar K et al. · Hepatology (Baltimore, Md.) 2025 · PMID 38563629 · doi:10.1097/HEP.0000000000000822
This dataset
Open GSE238159 in finder → Find more 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 GSE238159_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 PRJNA998066 and SRA study SRP451199. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38563629) ↗
Study design
6 conditions, mostly in triplicate
Hepatic stellate cells (Lrat-cre_zsgreen) con… ×3 Hepatic stellate cells (Lrat-cre_zsgreen) CCl4 ×3 Primary Hepatic stellate cells, LNA control A ×3 Primary Hepatic stellate cells, siPML 17# ×3 Primary Hepatic stellate cells, siRNA control… ×3 Primary Hepatic stellate cells, TILAM LNA ×3

Supports a between-group comparison across 18 samples.

How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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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