GEO series

Lithium partially rescues gene expression and enhancer activity from heterozygous knockout of AKAP11 while inducing novel differential changes [ChIP-Seq]

GSE290454 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 20 samples Submitted 2025/09/29 Platform GPL24676

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 20 samples

What it is: ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism: Homo sapiens (human)
Samples: 20 samples: 20 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.
Paper: Lithium partially rescues gene expression and enhancer activity from heterozygous knockout of AKAP11 while inducing novel differential changesScientific reports · 2025

Summary (written by the submitters)

Bipolar disorder (BD) is a complex psychiatric condition usually requiring long-term treatment. Lithium (Li) remains the most effective mood stabilizer for BD, yet it benefits only a subset of patients, and its precise mechanism of action remains elusive. Exome sequencing has identified AKAP11 (A-kinase anchoring protein 11) as a shared risk gene for BD and schizophrenia (SCZ).

Read the full summary ↓

Given that both the AKAP11-Protein Kinase A (PKA) complex and Li target and inhibit Glycogen Synthase Kinase-3 beta (GSK3β), we hypothesize that Li may partially normalize the transcriptomic and/or epigenomic alterations observed in heterozygous AKAP11-knockout (Het-AKAP11-KO) iPSC-derived neurons. In this study, we employed genome-wide approaches to assess the effects of Li on the transcriptome and epigenome of human iPSC-derived Het-AKAP11-KO neuronal culture. We show that chronic Li treatment in this cellular model upregulates key pathways that were initially downregulated by Het-AKAP11-KO, several of which have also been reported as downregulated in synapses of BD and SCZ post-mortem brain tissues. Moreover, we demonstrated that Li treatment partially rescues certain transcriptomic alterations resulting from Het-AKAP11-KO, bringing them closer to the WT state. We suggest two possible mechanisms underlying these transcriptomic effects: (1) Li modulates histone H3K27ac levels at intergenic and intronic enhancers, influencing enhancer activity and transcription factor binding, and (2) Li enhances GSK3β serine 9 phosphorylation, impacting WNT/β-catenin signaling and downstream transcription. These findings underscore Li's potential as a therapeutic agent for BD and SCZ patients carrying AKAP11 loss-of-function variants or exhibiting similar pathway alterations to those observed in Het-AKAP11-KO models.

Published in

Lithium partially rescues gene expression and enhancer activity from heterozygous knockout of AKAP11 while inducing novel differential changes

Farhangdoost N, Pietrantonio A, Liu Y et al. · Scientific reports 2025 · PMID 41162554 · doi:10.1038/s41598-025-21716-w

This dataset

Open GSE290454 in finder → Find more human ChIP / ATAC / CUT&Tag 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 GSE290454_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1228066 and SRA study SRP566236. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41162554) ↗

Study design

20 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 20 sample titles: 20 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

GSM8814782 ChIP-Seq, Het_AKAP11-KO-Clone 16_ChIP
GSM8814783 ChIP-Seq, Het_AKAP11-KO-Clone 20_ChIP
GSM8814784 ChIP-Seq, Het_AKAP11-KO-Clone 21_ChIP
GSM8814785 ChIP-Seq, WT_SBP009_Rep1_ChIP
GSM8814786 ChIP-Seq, WT_SBP009_Rep2_ChIP
GSM8814787 ChIP-Seq, WT_SBP009_Rep3_ChIP
GSM8814788 ChIP-Seq, Het_AKAP11-KO-Clone 16_Input
GSM8814789 ChIP-Seq, Het_AKAP11-KO-Clone 20_Input
GSM8814790 ChIP-Seq, Het_AKAP11-KO-Clone 21_Input
GSM8814791 ChIP-Seq, WT_SBP009_Input
GSM8814792 ChIP-Seq, Het_AKAP11-KO-Clone 16_Li_ChIP
GSM8814793 ChIP-Seq, Het_AKAP11-KO-Clone 20_Li_ChIP
GSM8814794 ChIP-Seq, Het_AKAP11-KO-Clone 21_Li_ChIP
GSM8814795 ChIP-Seq, WT_SBP009_Rep1_Li_ChIP
GSM8814796 ChIP-Seq, WT_SBP009_Rep2_Li_ChIP
GSM8814797 ChIP-Seq, WT_SBP009_Rep3_Li_ChIP
GSM8814798 ChIP-Seq, Het_AKAP11-KO-Clone 16_Li_Input
GSM8814799 ChIP-Seq, Het_AKAP11-KO-Clone 20_Li_Input
GSM8814800 ChIP-Seq, Het_AKAP11-KO-Clone 21_Li_Input
GSM8814801 ChIP-Seq, WT_SBP009_Li_Input

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