GEO series

X-Linked Cancer-Associated Polypeptide, Encoded by a Putative Noncoding RNA, Regulates Gene Expression and Cellular Pathways in Breast Cancer [RNA-seq]

GSE288868 Homo sapiens (human) RNA-seq (gene expression) 48 samples Submitted 2026/05/07 Platform GPL30173

At a glance

RNA-seq (gene expression) · human · 48 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: 48 samples: 14 conditions, mostly in duplicateGroups 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: X-linked cancer-associated polypeptide (XCP) from lncRNA1456 modulates PHF8 histone demethylase activity to regulate the epigenome, gene expression, and cellular pathways in breast cancerOncogene · 2026

Summary (written by the submitters)

Long noncoding RNAs (lncRNAs) have been found to play a critical role in cancer biology and other prevalent diseases. While most lncRNAs are poorly conserved and not evolutionarily neutral, they regulate biological processes at the RNA level. Recent studies have suggested that a subset of lncRNAs produce functional proteins, and in this study, we have discovered a protein named XCP ((X-linked Cancer-associated Polypeptide).

Read the full summary ↓

XCP is encoded by a pancreas- and testis-specific RNA annotated as a putative long noncoding RNA by Sun and Gadad et al. (lncRNA1456, aka RHOXF1P3), located on chromosome X. We found that lncRNA1456 and XCP are upregulated in luminal A, luminal B, and HER2 molecular subtypes of breast cancer, and XCP modulates estrogen-dependent as well as estrogen-independent growth of MCF-7 cells by regulating cancer pathways in xenograft models. We find that XCP shares homology with homeodomain-containing proteins and interacts with PHF8, which is also an X-linked gene, and demethylates H3K9me2 to activate transcription. Mechanistically, XCP positively regulates histone demethylase activity of PHF8 in vitro to regulate gene expression in breast cancer cells. These findings identify XCP as a coregulator of transcription and emphasize the need to interrogate the potential functional roles of open reading frames originating from noncoding RNAs.

Published in

X-linked cancer-associated polypeptide (XCP) from lncRNA1456 modulates PHF8 histone demethylase activity to regulate the epigenome, gene expression, and cellular pathways in breast cancer

Gadad SS, Camacho CV, Gong X et al. · Oncogene 2026 · PMID 41922576 · doi:10.1038/s41388-026-03740-w

This dataset

Open GSE288868 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 GSE288868_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 PRJNA1219653 and SRA study SRP561801. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41922576) ↗

Study design

14 conditions, mostly in duplicate

MCF-7 GFP ×8 MDA-MB-231 GFP ×8 MDA-MB-231 XCP ×8 MCF-7 XCP ×4 MCF-7, GFP, Control KD ×2 MCF-7, GFP, lncRNA1456 KD set1 ×2 MCF-7, GFP, lncRNA1456 KD set2 ×2 MCF-7, GFP, PHF8 KD set1 ×2 +6 more

Supports a between-group comparison across 48 samples.

How we read this: 14 replicated groups read from 48 sample titles; they account for 48 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

GSM8777111 MCF-7 GFP 1 MCF-7 GFP
GSM8777112 MCF-7 GFP 2 MCF-7 GFP
GSM8777113 MCF-7 GFP 3 MCF-7 GFP
GSM8777114 MCF-7 GFP 4 MCF-7 GFP
GSM8777115 MCF-7 GFP 5 MCF-7 GFP
GSM8777116 MCF-7 GFP 6 MCF-7 GFP
GSM8777117 MCF-7 GFP 7 MCF-7 GFP
GSM8777118 MCF-7 GFP 8 MCF-7 GFP
GSM8777119 MCF-7 XCP 1 MCF-7 XCP
GSM8777120 MCF-7 XCP 2 MCF-7 XCP
GSM8777121 MCF-7 XCP 3 MCF-7 XCP
GSM8777122 MCF-7 XCP 4 MCF-7 XCP
GSM8777123 MDA-MB-231 GFP 1 MDA-MB-231 GFP
GSM8777124 MDA-MB-231 GFP 2 MDA-MB-231 GFP
GSM8777125 MDA-MB-231 GFP 3 MDA-MB-231 GFP
GSM8777126 MDA-MB-231 GFP 4 MDA-MB-231 GFP
GSM8777127 MDA-MB-231 GFP 5 MDA-MB-231 GFP
GSM8777128 MDA-MB-231 GFP 6 MDA-MB-231 GFP
GSM8777129 MDA-MB-231 GFP 7 MDA-MB-231 GFP
GSM8777130 MDA-MB-231 GFP 8 MDA-MB-231 GFP
GSM8777131 MDA-MB-231 XCP 1 MDA-MB-231 XCP
GSM8777132 MDA-MB-231 XCP 2 MDA-MB-231 XCP
GSM8777133 MDA-MB-231 XCP 3 MDA-MB-231 XCP
GSM8777134 MDA-MB-231 XCP 4 MDA-MB-231 XCP
GSM8777135 MDA-MB-231 XCP 5 MDA-MB-231 XCP
GSM8777136 MDA-MB-231 XCP 6 MDA-MB-231 XCP
GSM8777137 MDA-MB-231 XCP 7 MDA-MB-231 XCP
GSM8777138 MDA-MB-231 XCP 8 MDA-MB-231 XCP
GSM8777139 MCF-7, GFP, Control KD Rep1 MCF-7, GFP, Control KD
GSM8777140 MCF-7, GFP, Control KD Rep2 MCF-7, GFP, Control KD
GSM8777141 MCF-7, GFP, lncRNA1456 KD set1 Rep1 MCF-7, GFP, lncRNA1456 …
GSM8777142 MCF-7, GFP, lncRNA1456 KD set1 Rep2 MCF-7, GFP, lncRNA1456 …
GSM8777143 MCF-7, GFP, lncRNA1456 KD set2 Rep1 MCF-7, GFP, lncRNA1456 …
GSM8777144 MCF-7, GFP, lncRNA1456 KD set2 Rep2 MCF-7, GFP, lncRNA1456 …
GSM8777145 MCF-7, GFP, PHF8 KD set1Rep1 MCF-7, GFP, PHF8 KD set1
GSM8777146 MCF-7, GFP, PHF8 KD set1 Rep2 MCF-7, GFP, PHF8 KD set1
GSM8777147 MCF-7, GFP, PHF8 KD set2 Rep1 MCF-7, GFP, PHF8 KD set2
GSM8777148 MCF-7, GFP, PHF8 KD set2 Rep2 MCF-7, GFP, PHF8 KD set2
GSM8777149 MCF-7, XCP, Control KD Rep1 MCF-7, XCP, Control KD
GSM8777150 MCF-7, XCP, Control KD Rep2 MCF-7, XCP, Control KD

+ 8 more — browse all 48 samples with per-sample file links →

Datasets on a similar topic

GSE288983 X-Linked Cancer-Associated Polypeptide, Encoded by a Putative Noncoding RNA, Regulates Gene Expression and Cellular Pathways in Breast Cancer 55 samples shares cancer-associated, polypeptide, noncoding, x-linked, putative, cellular, encoded
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GSE250293 G-quadruplexes within the SVA retrotransposon modulate TAF1 gene expression in X-linked Dystonia Parkinsonism [RNA-Seq] 63 samples shares x-linked, rna-seq
GSE279728 The X-linked chromatin modifier SMC1A is deregulated in lupus female monocytes and promotes autoimmunity [RNA-Seq] 61 samples shares x-linked, rna-seq
GSE286577 Cancer-associated snaR-A noncoding RNA interacts with core splicing machinery and disrupts processing of mRNA subpopulations II 24 samples shares cancer-associated, noncoding
GSE271350 Cancer-Associated Fibroblasts Promote Vasculogenic Mimicry of Colorectal Cancer by Epigenetic Silencing of Decorin [RNA-Seq] 24 samples shares cancer-associated, rna-seq
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