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Combination of a CCL21-gene modified dendritic cell vaccine and pembrolizumab induces immune responses in non-small cell lung cancer

GSE317309 Homo sapiens (human) RNA-seq (gene expression) 64 samples Submitted 2026/05/01 Platform GPL34284Platform GPL35012
At a glance

RNA-seq (gene expression) · human · 64 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)
Topic
Lung cancerThis series is part of our curated briefing on it.
Samples
64 samples: 19 conditions, mostly in duplicateGroups 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)
Immune checkpoint inhibitors (ICIs) have transformed treatment for non-small cell lung cancer (NSCLC), but resistance to these therapies is common. We report results from a phase I trial combining intratumoral administration of a CCL21-gene modified dendritic cell (CCL21-DC) vaccine with pembrolizumab in patients with advanced NSCLC. Among 23 patients that received trial therapy, there were no dose-limiting toxicities and a low incidence of treatment-related adverse events.
Read the full summary ↓
Although no objective responses were observed, 36.8% of patients had a best response of stable disease (SD). Correlative analyses of longitudinal tumor biopsies revealed that disease stability was associated with reduced tumor mutational heterogeneity and increased intratumoral T cell receptor diversity following therapy. Post-treatment tumor biopsies exhibited increased CD4+ T cell infiltration and the presence of novel T cell clones that predominantly possessed CD4+ memory T cell phenotypes. These novel clones experienced greater clonal expansion and a transition towards exhausted phenotypes in SD samples. However, many novel clones failed to persist over time, and immunosuppressive myeloid signaling signatures were identified especially in progressive disease samples. Our findings demonstrated that CCL21-DC vaccination combined with pembrolizumab is safe and can promote antitumor immune responses in a subset of patients. However, efficacy may have been constrained due to limited tumor specificity of the T cell response and an inability to fully reprogram the immunosuppressive tumor microenvironment.
This dataset
Open GSE317309 in finder → Find more RNA-seq datasets → Lung cancer 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 GSE317309_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 PRJNA1348488 and SRA study SRP663891. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
19 conditions, mostly in duplicate
Patient DCP09, 10x Genomics 5' V(D)J sequenci… ×3 Patient DCP10, 10x Genomics 5' V(D)J sequenci… ×3 Patient DCP14, 10x Genomics 5' V(D)J sequenci… ×3 Patient DCP22, 10x Genomics 5' V(D)J sequenci… ×3 Patient DCP25, 10x Genomics 5' V(D)J sequenci… ×3 Patient DCP30, 10x Genomics 5' V(D)J sequenci… ×3 Patient DCP31, 10x Genomics 5' V(D)J sequenci… ×3 Patient DCP12, 10x Genomics 5' V(D)J sequenci… ×2 +30 more

Supports a between-group comparison across 45 samples.

How we read this: 19 replicated groups read from 64 sample titles; they account for 45 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

+ 24 more — browse all 64 samples with per-sample file links →

More Lung cancer datasets

Search all RNA-seq datasets in GEO →

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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.