GEO series

Pomalidomide as an immune-enhancing agent in samples from people living with HIV

GSE244148 Homo sapiens (human) RNA-seq (gene expression) 14 samples Submitted 2025/12/09 Platform GPL18573

At a glance

RNA-seq (gene expression) · human · 14 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: 14 samples: 5 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: Pomalidomide enhances CD8(+) T and NK cell mediated killing of HIV-infected cellsEBioMedicine · 2025

Summary (written by the submitters)

Persisting immune dysfunction in people living with HIV (PLHIV) on suppressive antiretroviral therapy (ART) is a key challenge to finding a cure for HIV. We investigated pomalidomide, a well-tolerated immunomodulatory drug, as an agent to enhance HIV-directed immune responses. We collected peripheral blood mononuclear cells (PBMC) from PLHIV on ART, cultured these in the presence of HIV peptides and found that pomalidomide significantly expanded tetramer-positive HIV-specific CD8+ T-cells with reduced markers of exhaustion and enhanced CD8+ T-cell-mediated killing of HIV-target cells.

Read the full summary ↓

This was associated with an upregulation of carbon metabolism and cell cycle pathways, with MYB and BATF3 implicated as key regulators of the pomalidomide-mediated response. Pomalidomide also enhanced NK cell cytotoxicity against K562 as well as HIV-infected target cells by expanding polyfunctional cytotoxic NK cells. Given its immune-enhancing potential and good safety profile, pomalidomide should be further investigated as a therapeutic strategy for HIV control and cure.

Published in

Pomalidomide enhances CD8(+) T and NK cell mediated killing of HIV-infected cells

Pascoe RD, Gubser C, Chang JJ et al. · EBioMedicine 2025 · PMID 41232235 · doi:10.1016/j.ebiom.2025.106004

This dataset

Open GSE244148 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 GSE244148_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 PRJNA1021527 and SRA study SRP463390. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41232235) ↗

Study design

5 conditions, mostly in duplicate

HIV-specific CD8 T cell, DMSO, PRA ×3 HIV-specific CD8 T cell, Pom, PRA ×3 HIV-specific CD8 T cell, DMSO, UCSF ×2 HIV-specific CD8 T cell, Pom, UCSF ×2 CD8 T cell, DMSO, ×2 HIV-specific CD8 T cell, DMSO, LKA ×1 HIV-specific CD8 T cell, Pom, LKA ×1

Supports a between-group comparison across 12 samples.

How we read this: 5 replicated groups read from 14 sample titles; they account for 12 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

GSM7807841 HIV-specific CD8 T cell, DMSO, UCSF-2651 HIV-specific CD8 T cell…
GSM7807842 HIV-specific CD8 T cell, Pom, UCSF-2651 HIV-specific CD8 T cell…
GSM7807843 HIV-specific CD8 T cell, DMSO, UCSF-3162 HIV-specific CD8 T cell…
GSM7807844 HIV-specific CD8 T cell, Pom, UCSF-3162 HIV-specific CD8 T cell…
GSM7807845 HIV-specific CD8 T cell, DMSO, LKA12
GSM7807846 HIV-specific CD8 T cell, Pom, LKA12
GSM7807847 HIV-specific CD8 T cell, DMSO, PRA004 HIV-specific CD8 T cell…
GSM7807848 HIV-specific CD8 T cell, Pom, PRA004 HIV-specific CD8 T cell…
GSM7807849 HIV-specific CD8 T cell, DMSO, PRA007 HIV-specific CD8 T cell…
GSM7807850 HIV-specific CD8 T cell, Pom, PRA007 HIV-specific CD8 T cell…
GSM7807851 HIV-specific CD8 T cell, DMSO, PRA009 HIV-specific CD8 T cell…
GSM7807852 HIV-specific CD8 T cell, Pom, PRA009 HIV-specific CD8 T cell…
GSM7807853 CD8 T cell, DMSO, 01 CD8 T cell, DMSO,
GSM7807854 CD8 T cell, DMSO, 02 CD8 T cell, DMSO,

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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.