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The tumor associated antigen PRAME exhibits dualistic functions that are targetable in diffuse large B cell lymphoma

GSE190403 Homo sapiens (human) RNA-seq (gene expression) 30 samples Submitted 2024/12/04 Platform GPL16791
At a glance

RNA-seq (gene expression) · human · 30 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
Diffuse large B-cell lymphomaThis series is part of our curated briefing on it.
Samples
30 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.
Summary (written by the submitters)
PRAME is a prominent member of the cancer germline antigen family of proteins, which triggers autologous T-cell mediated immune responses. Integrative genomic analysis in diffuse large B-cell lymphoma (DLBCL) uncovered recurrent, and highly focal deletions of 22q11.22 including the PRAME gene, which were associated with poor outcome. PRAME-deleted tumors showed cytotoxic T-cell immune escape and were associated with cold tumor microenvironments.
Read the full summary ↓
In addition, PRAME down-modulation was strongly associated with somatic EZH2 Y641 mutations in DLBCL, and PRC2-regulated genes were repressed in isogenic PRAME KO vs. PRAME wt lymphoma cell lines, with PRAME directly interacting with EZH2 as a negative regulator. EZH2 inhibition with EPZ-6438 abrogated these extrinsic and intrinsic effects leading to PRAME and microenvironment restoration in vivo. Our data highlight multiple functions of PRAME during lymphomagenesis, and provide a preclinical rationale for synergistic therapies combining epigenetic re-programming with PRAME-targeted therapies.
This dataset
Open GSE190403 in finder → Find more human RNA-seq datasets → Diffuse large B-cell lymphoma 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 GSE190403_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 PRJNA786940 and SRA study SRP349682. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
14 conditions, mostly in duplicate
HBL1-MUT ×3 SUDHL-4_wt_bulk ×2 SUDHL-4_single_5 ×2 SUDHL-4_single_6 ×2 SUDHL-4_PRAME_A2-6 ×2 SUDHL-4_PRAME_A2-9 ×2 SUDHL-4_PRAME_A2-10 ×2 Karpas422_wt_bulk ×2 +7 more

Supports a between-group comparison across 29 samples.

How we read this: 14 replicated groups read from 30 sample titles; they account for 29 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
More Diffuse large B-cell lymphoma datasets

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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.