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Methamphetamine Induces Metallothionein 1 Expression and an Inflammatory Phenotype in Primary Human HIV-infected Macrophages [JW98_JW100]

GSE307858 Homo sapiens (human) RNA-seq (gene expression) 15 samples Submitted 2025/09/29 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 15 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
15 samples: 3 × Methampehtamine treated uninfected macrophages from donor coded JW100 vs 3 × HIV-infected untreated macrophages from donor coded JW100 vs 3 × HIV-infected methamphetamine treated macrophages from donor coded JW100 vs 2 × Uninfected untreated macrophages from donor coded JW100Groups 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
Methamphetamine Induces Metallothionein 1 Expression and an Inflammatory Phenotype in Primary Human HIV-Infected MacrophagesInternational journal of molecular sciences · 2025
Summary (written by the submitters)
HIV associated neurocognitive impairment (HIV-NCI), a comorbidity of HIV infection, affects up to 50% of people with HIV (PWH). HIV-infected monocytes that transmigrate across the blood brain barrier and differentiate into macrophages establish a CNS viral reservoir that activates and infects parenchymal cells, contributing to neuronal damage that characterizes HIV-NCI.
Read the full summary ↓
Methamphetamine (meth) use is prevalent in PWH and further impairs cognitive functioning. To examine whether meth-mediated dysregulation of macrophage functions may contribute to increased HIV-NCI, we characterized differential gene expression in primary human HIV-infected macrophages treated daily with meth for five days by RNA-sequencing. We identified increases in multiple gene isoforms of metallothionein 1 (MT1), a heavy metal binding protein involved in protective mechanisms against metal toxicity and oxidative stress. Nuclear localization of MT1 protein was previously shown to either positively or negatively affect NF-κB activity in a cell type specific manner, with nuclear MT1 contributing to LPS-induced TNF-α and IL-6 in macrophages. We found that daily meth treatment for one to five days increased nuclear localization of MT1 in macrophages acutely infected with HIV which was associated with increased LPS-induced CXCL8 and CCL8, and a trend towards increased basal and/or LPS-induced expression of other cytokines/chemokines, including TNF-α and IL-6, that was donor specific. ROS levels were not changed with meth treatment although there was a donor specific trend towards increased ROS with multiple days of meth treatment. These data indicate that repeated exposure of macrophages to meth in the context of HIV increases nuclear MT1 localization, which is associated with increased inflammatory mediator production, and therefore may be a mechanism that contributes to meth-mediated exacerbation of HIV-NCI.
Published in
Methamphetamine Induces Metallothionein 1 Expression and an Inflammatory Phenotype in Primary Human HIV-Infected Macrophages
Weiselberg J, Niu M, Hernandez CA et al. · International journal of molecular sciences 2025 · PMID 41009444 · doi:10.3390/ijms26188875
This dataset
Open GSE307858 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 GSE307858_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 PRJNA1327425. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41009444) ↗
Study design
3 × Methampehtamine treated uninfected macrophages from donor coded JW100 vs 3 × HIV-infected untreated macrophages from donor coded JW100 vs 3 × HIV-infected methamphetamine treated macrophages from donor coded JW100 vs 2 × Uninfected untreated macrophages from donor coded JW100

Supports a between-group comparison across 11 samples.

How we read this: 4 replicated groups read from 15 sample titles; they account for 11 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
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