GEO series

Interaction between HIV-1 Tat and EBV Zta favours immune escape of B cells by downregulating HLA-ABC expression

GSE255092 Homo sapiens (human) RNA-seq (gene expression) 56 samples Submitted 2024/04/01 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 56 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: 56 samples: 16 conditions, mostly with about 4 replicates eachGroups 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: Interaction between HIV-1 Tat and EBV Zta favours immune escape of B cells by downregulating HLA-ABC expressionCellular and molecular life sciences : CMLS · 2026

Summary (written by the submitters)

Both Human immunodeficiency virus (HIV) and Epstein-Barr virus (EBV) are associated with an increased risk of malignancies. People living with HIV frequently have EBV reactivation and develop EBV-associated B-cell malignancies. In this study, we aimed to uncover the involvement of HIV-1 and EBV co-existence in the development of B-cell malignancies.

Read the full summary ↓

We studied two viral transcriptional activators (HIV-1 Tat and EBV Zta) and their possible interaction since they both have cell-penetration domains and can be found simultaneously in the blood or cells of people with HIV. We found that Tat and Zta directly bound each other in human B cells, T cells, and blood serum. Using RNA-sequencing, we found that combined Tat and Zta action in B cells differed from a simple combination of two proteins. A subset of genes, activated by Tat or Zta alone, that trigger an immune response and antigen presentation in B cells, remained unchanged when two proteins were combined. B cells, treated or transfected with Tat and Zta, exhibited a substantial decrease in HLA-ABC (MHC class I) expression, a critical component of the antigen processing and presentation pathway. HLA-ABC downregulation induced by Tat and Zta interaction conferred protection against cytotoxic T cell recognition of EBV-infected B cells. Tat and Zta interaction was also observed in serum from an HIV-positive individual. To conclude, we demonstrated for the first time the direct interaction between HIV-1 Tat and EBV Zta; this interaction can bring about immune evasion of EBV-infected or transformed B cells.

Published in

Interaction between HIV-1 Tat and EBV Zta favours immune escape of B cells by downregulating HLA-ABC expression

Shmakova A, Schwager A, Tsimailo I et al. · Cellular and molecular life sciences : CMLS 2026 · PMID 41627500 · doi:10.1007/s00018-025-06029-5

This dataset

Open GSE255092 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 GSE255092_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 PRJNA1073507 and SRA study SRP488269. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41627500) ↗

Study design

16 conditions, mostly with about 4 replicates each

B primary c 6h ×4 B primary c 48h ×4 B primary Tat 6h ×4 B primary Tat 48h ×4 B primary Zta 6h ×4 B primary Zta 48h ×4 B primaryTat-Zta 6h ×4 B primary Tat-Zta 48h ×4 +8 more

Supports a between-group comparison across 56 samples.

How we read this: 16 replicated groups read from 56 sample titles; they account for 56 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

GSM8063895 BLAS c 6h 1 BLAS c 6h
GSM8063896 BLAS c 6h 2 BLAS c 6h
GSM8063897 BLAS c 6h 3 BLAS c 6h
GSM8063898 BLAS c 48h 1 BLAS c 48h
GSM8063899 BLAS c 48h 2 BLAS c 48h
GSM8063900 BLAS c 48h 3 BLAS c 48h
GSM8063901 BLAS Tat 6h 1 BLAS Tat 6h
GSM8063902 BLAS Tat 6h 2 BLAS Tat 6h
GSM8063903 BLAS Tat 6h 3 BLAS Tat 6h
GSM8063904 BLAS Tat 48h 1 BLAS Tat 48h
GSM8063905 BLAS Tat 48h 2 BLAS Tat 48h
GSM8063906 BLAS Tat 48h 3 BLAS Tat 48h
GSM8063907 BLAS Zta 6h 1 BLAS Zta 6h
GSM8063908 BLAS Zta 6h 2 BLAS Zta 6h
GSM8063909 BLAS Zta 6h 3 BLAS Zta 6h
GSM8063910 BLAS Zta 48h 1 BLAS Zta 48h
GSM8063911 BLAS Zta 48h 2 BLAS Zta 48h
GSM8063912 BLAS Zta 48h 3 BLAS Zta 48h
GSM8063913 BLAS Tat-Zta 6h 1 BLAS Tat-Zta 6h
GSM8063914 BLAS Tat-Zta 6h 2 BLAS Tat-Zta 6h
GSM8063915 BLAS Tat-Zta 6h 3 BLAS Tat-Zta 6h
GSM8063916 BLAS Tat-Zta 48h 1 BLAS Tat-Zta 48h
GSM8063917 BLAS Tat-Zta 48h 2 BLAS Tat-Zta 48h
GSM8063918 BLAS Tat-Zta 48h 3 BLAS Tat-Zta 48h
GSM8063919 B primary c 6h 1 B primary c 6h
GSM8063920 B primary c 6h 2 B primary c 6h
GSM8063921 B primary c 6h 3 B primary c 6h
GSM8063922 B primary c 6h 4 B primary c 6h
GSM8063923 B primary c 48h 1 B primary c 48h
GSM8063924 B primary c 48h 2 B primary c 48h
GSM8063925 B primary c 48h 3 B primary c 48h
GSM8063926 B primary c 48h 4 B primary c 48h
GSM8063927 B primary Tat 6h 1 B primary Tat 6h
GSM8063928 B primary Tat 6h 2 B primary Tat 6h
GSM8063929 B primary Tat 6h 3 B primary Tat 6h
GSM8063930 B primary Tat 6h 4 B primary Tat 6h
GSM8063931 B primary Tat 48h 1 B primary Tat 48h
GSM8063932 B primary Tat 48h 2 B primary Tat 48h
GSM8063933 B primary Tat 48h 3 B primary Tat 48h
GSM8063934 B primary Tat 48h 4 B primary Tat 48h

+ 16 more — browse all 56 samples with per-sample file links →

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