GEO series

Emerin Dysregulation Drives the Very-Small-Nuclear Phenotype and Lineage Plasticity that Associates with a Clinically Aggressive Subtype of Prostate Cancer

GSE288991 Homo sapiens (human) RNA-seq (gene expression) 18 samples Submitted 2025/02/11 Platform GPL24676

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)
Topic: Prostate cancerThis series is part of our curated briefing on it.
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: Emerin Dysregulation Drives the Very-Small-Nuclear Phenotype and Lineage Plasticity That Associate with a Clinically Aggressive Subtype of Prostate CancerClinical cancer research : an official journal of the American Association for Cancer Research · 2025

Summary (written by the submitters)

Background: Circulating tumor cells (CTCs) with a very-small-nuclear phenotype (vsnCTCs) in prostate cancer (PCa) are characterized by nuclei smaller than 8.5 μm. Our previous studies established an association between vsnCTCs and visceral metastasis. Reduction of emerin (EMD), a nuclear envelope protein, contributes to PCa metastasis and nuclear shape instability.

Read the full summary ↓

Here we investigated the correlation between EMD expression and the vsnCTC phenotype and its clinical impact. Methods: We analyzed CTCs from 93 mCRPC patients and categorized them as either vsnCTC+ or vsnCTC- and compared overall survival (OS) and progression-free survival (PFS). C4-2B, 22Rv1, and DU145 with EMD knockdown were developed and characterized by nuclear size and gene expression by GSEA analysis. Abiraterone- and enzalutamide-resistant (Abi-R/Enza-R) C4-2B cells were also characterized by nuclear size and EMD expression. Results: vsnCTC+ patients had significantly worse OS and PFS compared to vsnCTC- patients. EMD expression was markedly reduced in CTCs from vsnCTC+ patients compared to vsnCTC- patients, with a significant positive correlation between EMD expression and CTC nuclear size. EMD knockdown in PCa cells resulted in smaller nuclei, enhanced invasion, and the upregulation of genes associated with lineage plasticity. Additionally, C4-2B Abi-R/Enza-R cells had smaller nuclei and lower EMD expression. vsnCTC+ cells also showed enhanced platinum sensitivity. Conclusions: The presence of vsnCTCs represents a novel hallmark of an aggressive subtype of mCRPC, closely linked to EMD loss and lineage plasticity. These findings highlight the importance of EMD dysregulation in the vsn phenotype, disease progression, and therapeutic resistance in patients with PCa.

Published in

Emerin Dysregulation Drives the Very-Small-Nuclear Phenotype and Lineage Plasticity That Associate with a Clinically Aggressive Subtype of Prostate Cancer

Zhang L, Teng PC, Cavassani KA et al. · Clinical cancer research : an official journal of the American Association for Cancer Research 2025 · PMID 40063516 · doi:10.1158/1078-0432.CCR-24-3660

This dataset

Open GSE288991 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 GSE288991_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 PRJNA1220194 and SRA study SRP562088. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40063516) ↗

Study design

6 conditions, mostly in triplicate

C42B Control Sample ×3 C42B EMD KD Sample ×3 22RV1 Control Sample ×3 22RV1 EMD KD Sample ×3 DU145 Control Sample ×3 DU145 EMD KD Sample ×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

GSM8780515 C42B Control Sample 1 C42B Control Sample
GSM8780516 C42B Control Sample 2 C42B Control Sample
GSM8780517 C42B Control Sample 3 C42B Control Sample
GSM8780518 C42B EMD KD Sample 1 C42B EMD KD Sample
GSM8780519 C42B EMD KD Sample 2 C42B EMD KD Sample
GSM8780520 C42B EMD KD Sample 3 C42B EMD KD Sample
GSM8780521 22RV1 Control Sample 1 22RV1 Control Sample
GSM8780522 22RV1 Control Sample 2 22RV1 Control Sample
GSM8780523 22RV1 Control Sample 3 22RV1 Control Sample
GSM8780524 22RV1 EMD KD Sample 1 22RV1 EMD KD Sample
GSM8780525 22RV1 EMD KD Sample 2 22RV1 EMD KD Sample
GSM8780526 22RV1 EMD KD Sample 3 22RV1 EMD KD Sample
GSM8780527 DU145 Control Sample 1 DU145 Control Sample
GSM8780528 DU145 Control Sample 2 DU145 Control Sample
GSM8780529 DU145 Control Sample 3 DU145 Control Sample
GSM8780530 DU145 EMD KD Sample 1 DU145 EMD KD Sample
GSM8780531 DU145 EMD KD Sample 2 DU145 EMD KD Sample
GSM8780532 DU145 EMD KD Sample 3 DU145 EMD KD Sample

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GSE242541 ONECUT2 is a druggable driver of luminal to basal breast cancer plasticity 12 samples same disease briefing · shares plasticity
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
GSE120181 Human prostate cancer cell line, 22Rv1: Control vs. luteolin treatment 2 samples same disease briefing · shares prostate
GSE71008 Plasma extracellular RNA profiles in healthy and cancer patients 192 samples same disease briefing
GSE302864 DNMT3B drives neuroendocrine lineage plasticity and aggressive progression in prostate cancer 12 samples shares plasticity, aggressive, prostate
GSE309034 Combined BET Bromodomain and DNMT Inhibition Targets Lineage Plasticity in Prostate Cancer [BETi_DNMTi_human_RNAseq] 44 samples shares plasticity, prostate

Search all human RNA-seq datasets in GEO →

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.