GEO series

Single-Cell Profiling of HDAC Inhibitor-Induced EBV Lytic Heterogeneity Defines Abortive and Refractory States in B Lymphoblasts

GSE319577 Homo sapiens (human) Single-cell RNA-seq 2 samples Submitted 2026/02/18 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 2 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Homo sapiens (human)
Topic: Nasopharyngeal carcinomaThis series is part of our curated briefing on it.
Samples: 2 samples
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: Single-cell profiling of HDAC inhibitor-induced EBV lytic heterogeneity defines abortive and refractory states in B lymphoblastsPLoS pathogens · 2026

Summary (written by the submitters)

Epstein-Barr virus (EBV) is associated with multiple malignancies including Burkitt lymphoma (BL), Hodgkin’s lymphomas, nasopharyngeal carcinomas (NPC), and gastric cancers. Canonically, EBV positive tumors display latent gene expression programs that are difficult to target pharmacologically. To overcome this hurdle, lytic reactivation therapies have been developed based on HDAC inhibition with limited mechanistic studies.

Read the full summary ↓

We therefore characterized the impact of pan-HDAC inhibitor, panobinostat, and class I HDAC inhibitor, nanatinostat, on the growth, survival, and lytic reactivation of four EBV-positive cell lines: P3HR1-ZHT BL, Jijoye BL, IBL-1 immunoblastic lymphoma, and de novo infection derived lymphoblastoid cell lines (LCL). All lines were sensitive, enabling us to define ranges of sensitivity within which to use single cell approaches to assess early EBV lytic gene expression, cell cycle state, and apoptosis. We observed that each EBV-positive model of malignancy responded uniquely to the same HDAC inhibitors and that lytic reactivation was successful in only a small percentage of the cell population. To elucidate the potential role of host factors in preventing successful lytic reactivation, we performed single-cell RNA sequencing on the P3HR1-ZHT BL line treated with the HDAC inhibitor panobinostat. We observed that abortive lytic cells, or cells that do not successfully progress through the lytic cycle, upregulated genes downstream of NF-kB activity. Additionally, genes involved in immune signaling including the CD137/CD137L signaling axis, were upregulated in abortive lytic cells. These data have important implications for how we approach oncolytic therapies for EBV-associated malignancies.

Published in

Single-cell profiling of HDAC inhibitor-induced EBV lytic heterogeneity defines abortive and refractory states in B lymphoblasts

Haynes LE, Barry AP, Luftig MA · PLoS pathogens 2026 · PMID 41871169 · doi:10.1371/journal.ppat.1013610

This dataset

Open GSE319577 in finder → Find more human RNA-seq datasets → Nasopharyngeal carcinoma 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 GSE319577_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1423778 and SRA study SRP677166. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41871169) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 2 more — browse all 2 samples with per-sample file links →

More Nasopharyngeal carcinoma datasets

GSE231689 Bulk-RNA and single-cell RNA sequencing of Nasopharyngeal Carcinoma Cell lines infected with Epstein-Barr virus (EBV) subjected to air-liquid interface (ALI)-induced reactivation 10 samples same disease briefing · shares ebv, single-cell
GSE309453 EBV infection in epithelial malignancies induces resistance to the anti-tumor function of natural killer cells via CD73-mediated metabolism of AMP [NK cells] 18 samples same disease briefing · shares ebv
GSE309452 EBV infection in epithelial malignancies induces resistance to the anti-tumor function of natural killer cells via CD73-mediated metabolism of AMP [cell line] 12 samples same disease briefing · shares ebv
GSE266679 Characterizing resistant cellular states in nasopharyngeal carcinoma during EBV lytic induction 10 samples same disease briefing · shares ebv
GSE231687 Bulk-RNA Sequencing of Nasopharyngeal Carcinoma Cell Lines infected with Epstein-Barr virus (EBV) subjected to air-liquid interface (ALI)-induced reactivation 6 samples same disease briefing · shares ebv
GSE271486 Construction of a Transferable NGS Algorithmic Model for Predicting EBV-Associated Nasopharyngeal Cancer and High-risk Mutation 6 samples same disease briefing · shares ebv
GSE185644 Upregulation of SNAP25 by HDAC inhibition ameliorates NPC disease phenotypes via autophagy induction 4 samples same disease briefing · shares hdac
GSE231688 Single cell RNA sequencing of Nasopharyngeal Carcinoma Cell lines infected with Epstein-Barr virus (EBV) subjected to air-liquid interface (ALI)-induced reactivation 4 samples same disease briefing · shares ebv

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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.