GEO series

Clonal replacement and differentiation of HIV-specific T-cells in people with HIV following anti-PD-1 in vivo

GSE278091 Homo sapiens (human) Single-cell RNA-seq 18 samples Submitted 2026/06/04 Platform GPL30209

At a glance

Single-cell RNA-seq · human · 18 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Homo sapiens (human)
Samples: 18 samples: 18 samples, each with a distinct title — no replicated groupsGroups 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.

Summary (written by the submitters)

Antiretroviral therapy (ART) in people with HIV (PWH) is highly effective but treatment is required lifelong given the persistence of virus in a latent form as well as ongoing immune dysfunction characterized by elevated expression of the exhaustion marker Programmed cell Death protein- 1 (PD-1) on HIV-specific T cells. We isolated tetramer+ HIV-specific CD8+ T-cells from PWH on ART with cancer who received anti-PD-1 (nivolumab) every 2 weeks.

Read the full summary ↓

and observed rapid changes following the first dose of anti-PD1, including a marked increase in the frequency of HIV-tetramer+ TEX cells in a subset of participants. Using single cell RNAseq on tetramer+ cells, we observed a distinct transcriptomic signature in tetramer+ central memory T (TCM) cells and the recruitment of multiple unique TCR clones. These findings are consistent with reinvigoration and rejuvenation of HIV-specific T-cells and evidence of clonal replacement of HIV-specific cells by anti-PD-1.

This dataset

Open GSE278091 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 GSE278091_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 PRJNA1165688. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

18 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 18 sample titles: 18 distinct titles with little repetition. 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

GSM8539501 Sample1B GEX
GSM8539502 Sample2A GEX
GSM8539503 Sample2B GEX
GSM8539504 Sample3A GEX
GSM8539505 Sample3B GEX
GSM8539506 Sample4A GEX
GSM8539507 Sample1B VDJ
GSM8539508 Sample2A VDJ
GSM8539509 Sample2B VDJ
GSM8539510 Sample3A VDJ
GSM8539511 Sample3B VDJ
GSM8539512 Sample4A VDJ
GSM8539513 Sample1B HTO
GSM8539514 Sample2A HTO
GSM8539515 Sample2B HTO
GSM8539516 Sample3A HTO
GSM8539517 Sample3B HTO
GSM8539518 Sample4A HTO

Datasets on a similar topic

GSE274848 Association of smoking with neurocognition, inflammatory and myeloid cell activation profiles in people with HIV on ART 165 samples shares hiv, people
GSE290636 RNAseq analysis of blood specimens from ART-suppressed people with HIV prior to analytical treatment interruption 74 samples shares hiv, people
GSE230738 Dysfunctional effector memory CD8 T cells in the bronchoalveolar compartment of people living with HIV 71 samples shares hiv, people
GSE332711 CD4/CD8 ratio is associated with structural reorganization of vaccine-induced immune responses in people living with HIV 60 samples shares hiv, people
GSE272734 Combination anti-PD-1 and anti-CTLA-4 therapy generates waves of clonal responses that include progenitor-exhausted CD8 T cells [dataset 2] 40 samples shares anti-pd-1, clonal
GSE231628 Dysfunctional effector memory CD8 T cells in the bronchoalveolar compartment of people living with HIV 33 samples shares hiv, people
GSE284755 Compromised Intestinal Barrier Resilience to Disruption in People with HIV [colon] 30 samples shares hiv, people
GSE284162 Efficacy of Neoadjuvant Chemotherapy Combined with Anti-PD-1 Monoclonal Antibody in Locally Advanced Resectable Oral Squamous Cell Carcinoma: A Single-Arm Phase II Clinical Trial 12 samples shares anti-pd-1, clonal

Search all human RNA-seq datasets in GEO →

Share this dataset

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.