GEO series

CMPK2 restricts Mycobacterium tuberculosis replication and regulates macrophage gene expression

GSE331078 Homo sapiens (human) RNA-seq (gene expression) 18 samples Submitted 2026/05/15 Platform GPL30173

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)
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: CMPK2 restricts Mycobacterium tuberculosis replication and regulates macrophage gene expressionbioRxiv : the preprint server for biology · 2026

Summary (written by the submitters)

Host cell metabolic pathways influence innate immune responses to intracellular pathogens, but the contribution of nucleotide metabolism to antimicrobial defense remains incompletely defined. Here, we identify the mitochondrial nucleoside monophosphate kinase CMPK2 as a regulator of macrophage responses to Mycobacterium tuberculosis (Mtb).

Read the full summary ↓

Using a targeted genetic screen of candidate host factors, we found that depletion of CMPK2 enhances intracellular Mtb replication in human macrophages. This phenotype was confirmed using both shRNA-mediated knockdown and CRISPR-Cas9-mediated knockout approaches. CMPK2 expression increased following macrophage activation and Mtb infection. Transcriptomic profiling revealed that loss of CMPK2 is associated with broad alterations in gene expression, including reduced expression of genes linked to innate immune and inflammatory responses early after infection. In contrast, myeloid-specific deletion of Cmpk2 in mice did not significantly alter bacterial burden or survival following aerosol Mtb infection, indicating that the contribution of CMPK2 to host defense is context dependent. Together, these findings identify CMPK2 as a host factor that limits Mtb replication in human macrophages and shapes innate immune gene expression programs.

Published in

CMPK2 restricts Mycobacterium tuberculosis replication and regulates macrophage gene expression

Neff J, Ektnitphong VA, Campos PC et al. · bioRxiv : the preprint server for biology 2026 · PMID 42239409 · doi:10.64898/2026.05.19.726211

This dataset

Open GSE331078 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 GSE331078_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 PRJNA1466864 and SRA study SRP700905. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42239409) ↗

Study design

6 conditions, mostly in triplicate

THP1 WT, uninfected, biol ×3 THP1 CMPK2 KO, uninfected, biol ×3 THP1 WT, infected with MTB Erdman, 4H, biol ×3 THP1 CMPK2 KO, infected with MTB Erdman, 4H,… ×3 THP1 WT, infected with MTB Erdman, 24H, biol ×3 THP1 CMPK2 KO, infected with MTB Erdman, 24H… ×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

GSM9738614 THP1 WT, uninfected, biol rep 1 THP1 WT, uninfected, bi…
GSM9738615 THP1 WT, uninfected, biol rep 2 THP1 WT, uninfected, bi…
GSM9738616 THP1 WT, uninfected, biol rep 3 THP1 WT, uninfected, bi…
GSM9738617 THP1 CMPK2 KO, uninfected, biol rep 1 THP1 CMPK2 KO, uninfect…
GSM9738618 THP1 CMPK2 KO, uninfected, biol rep 2 THP1 CMPK2 KO, uninfect…
GSM9738619 THP1 CMPK2 KO, uninfected, biol rep 3 THP1 CMPK2 KO, uninfect…
GSM9738620 THP1 WT, infected with MTB Erdman, 4H, biol rep 1 THP1 WT, infected with …
GSM9738621 THP1 WT, infected with MTB Erdman, 4H, biol rep 2 THP1 WT, infected with …
GSM9738622 THP1 WT, infected with MTB Erdman, 4H, biol rep 3 THP1 WT, infected with …
GSM9738623 THP1 CMPK2 KO, infected with MTB Erdman, 4H, biol rep 1 THP1 CMPK2 KO, infected…
GSM9738624 THP1 CMPK2 KO, infected with MTB Erdman, 4H, biol rep 2 THP1 CMPK2 KO, infected…
GSM9738625 THP1 CMPK2 KO, infected with MTB Erdman, 4H, biol rep 3 THP1 CMPK2 KO, infected…
GSM9738626 THP1 WT, infected with MTB Erdman, 24H, biol rep 1 THP1 WT, infected with …
GSM9738627 THP1 WT, infected with MTB Erdman, 24H, biol rep 2 THP1 WT, infected with …
GSM9738628 THP1 WT, infected with MTB Erdman, 24H, biol rep 3 THP1 WT, infected with …
GSM9738629 THP1 CMPK2 KO, infected with MTB Erdman, 24H, biol rep 1 THP1 CMPK2 KO, infected…
GSM9738630 THP1 CMPK2 KO, infected with MTB Erdman, 24H, biol rep 2 THP1 CMPK2 KO, infected…
GSM9738631 THP1 CMPK2 KO, infected with MTB Erdman, 24H, biol rep 3 THP1 CMPK2 KO, infected…

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