GEO series

AR coactivators, CBP/p300, are critical mediators of DNA repair in prostate cancer [RNA-seq: 22RV1]

GSE275778 Homo sapiens (human) RNA-seq (gene expression) 20 samples Submitted 2024/09/04 Platform GPL34281

At a glance

RNA-seq (gene expression) · human · 20 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)
Topic: Prostate cancerThis series is part of our curated briefing on it.
Samples: 20 samples: 5 conditions, mostly with about 4 replicates eachGroups 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: AR coactivators, CBP/p300, are critical mediators of DNA repair in prostate cancerOncogene · 2024

Summary (written by the submitters)

Castration resistant prostate cancer (CRPC) remains an incurable disease stage with ineffective treatments options. Here, the androgen receptor (AR) coactivators CBP/p300, which are histone acetyltransferases, were identified as critical mediators of DNA damage repair (DDR) to potentially enhance therapeutic targeting of CRPC. Key findings demonstrate that CBP/p300 expression increases with disease progression and selects for poor prognosis in metastatic disease.

Read the full summary ↓

CBP/p300 bromodomain inhibition enhances response to standard of care therapeutics. Functional studies, CBP/p300 cistrome mapping, and transcriptome in CRPC revealed that CBP/p300 regulates DDR. Further mechanistic investigation showed that CBP/p300 attenuation via therapeutic targeting and genomic knockdown decreases homologous recombination (HR) factors in vitro, in vivo, and in human prostate cancer (PCa) tumors ex vivo. Similarly, CBP/p300 expression in human prostate tissue correlates with HR factors. Lastly, targeting CBP/p300 impacts HR-mediate repair and patient outcome. Collectively, these studies identify CBP/p300 as drivers of PCa tumorigenesis and lay the groundwork to optimize therapeutic strategies for advanced PCa via CBP/p300 inhibition, potentially in combination with AR-directed and DDR therapies.

Published in

AR coactivators, CBP/p300, are critical mediators of DNA repair in prostate cancer

Sardar S, McNair CM, Ravindranath L et al. · Oncogene 2024 · PMID 39266679 · doi:10.1038/s41388-024-03148-4

This dataset

Open GSE275778 in finder → Find more human RNA-seq datasets → Prostate cancer landscape →

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 GSE275778_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 PRJNA1152964 and SRA study SRP528933. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39266679) ↗

Study design

5 conditions, mostly with about 4 replicates each

22RV1_CCS ×4 22RV1_shCBP ×4 22RV1_shCON ×4 22RV1_shP300 ×4 22RV1_Veh ×4

Supports a between-group comparison across 20 samples.

How we read this: 5 replicated groups read from 20 sample titles; they account for 20 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

GSM8484419 22RV1_CCS_1 22RV1_CCS
GSM8484420 22RV1_CCS_2 22RV1_CCS
GSM8484421 22RV1_CCS_3 22RV1_CCS
GSM8484422 22RV1_CCS_4 22RV1_CCS
GSM8484423 22RV1_shCBP_1 22RV1_shCBP
GSM8484424 22RV1_shCBP_2 22RV1_shCBP
GSM8484425 22RV1_shCBP_3 22RV1_shCBP
GSM8484426 22RV1_shCBP_4 22RV1_shCBP
GSM8484427 22RV1_shCON_1 22RV1_shCON
GSM8484428 22RV1_shCON_2 22RV1_shCON
GSM8484429 22RV1_shCON_3 22RV1_shCON
GSM8484430 22RV1_shCON_4 22RV1_shCON
GSM8484431 22RV1_shP300_1 22RV1_shP300
GSM8484432 22RV1_shP300_2 22RV1_shP300
GSM8484433 22RV1_shP300_3 22RV1_shP300
GSM8484434 22RV1_shP300_4 22RV1_shP300
GSM8484435 22RV1_Veh_1 22RV1_Veh
GSM8484436 22RV1_Veh_2 22RV1_Veh
GSM8484437 22RV1_Veh_3 22RV1_Veh
GSM8484438 22RV1_Veh_4 22RV1_Veh

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GSE300947 A novel six-biomarker panel identified from male breast cancer-associated fibroblasts demonstrates prognostic power for prostate tumors 6 samples same disease briefing · shares prostate
GSE242541 ONECUT2 is a druggable driver of luminal to basal breast cancer plasticity 12 samples same disease briefing
GSE71008 Plasma extracellular RNA profiles in healthy and cancer patients 192 samples same disease briefing
GSE275777 AR coactivators, CBP/p300, are critical mediators of DNA repair in prostate cancer [ChIP-seq] 13 samples shares p300, cbp, coactivators, mediators, critical, prostate
GSE255133 Targeting histone H2B acetylated enhanceosomes via p300/CBP degradation in prostate cancer (RNA-Seq) 32 samples shares p300, cbp, prostate, rna-seq

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