GEO series

Loss of PTDSS1 in tumor cells improves immunogenicity and response to anti-PD-1 therapy [scRNAseq]

GSE292614 Mus musculus (mouse) Single-cell RNA-seq 24 samples Submitted 2025/09/10 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 24 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Mus musculus (mouse)
Samples: 24 samples: 8 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.

Summary (written by the submitters)

PTDSS1 (Phosphatidylserine synthase 1) encodes an enzyme that facilitates production of phosphatidylserine (PS), which mediates a global immunosuppressive signal. Here, based on in vivo CRISPR screen, we identified PTDSS1 as a target to improve anti-PD-1 therapy. Depletion of PTDSS1 in tumor cells increased expression of IFNγ-regulated genes, including B2m, Cxcl9, Cxcl10, and Stat1, even in the absence of IFNγ stimulation in vitro.

Read the full summary ↓

Loss of PTDSS1 in tumor cells also led to increased expression of MHC-I, which was associated with enhanced cytotoxicity of CD8+ T cells and increased frequency of an iNOS+ myeloid subset. A gene signature derived from the iNOS+ myeloid cell subset correlated with clinical benefit in patients treated with anti-PD-1 therapy. Moreover, genetic and pharmacological inhibition of PTDSS1 in different tumor models improved anti-PD-1 therapy. Together, our results provide insights on a new therapeutic strategy for overcoming immunosuppression by inhibiting PTDSS1 and provide rationale for development of a combination immunotherapy strategy comprised of PTDSS1 inhibition plus PD-1 blockade.

This dataset

Open GSE292614 in finder → Find more mouse 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 GSE292614_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 PRJNA1240302 and SRA study SRP572242. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

8 conditions, mostly with about 4 replicates each

Ptdss1 KD tumor, PBS treated, ×4 Ptdss1 KD tumor, anti-PD-1 treated, ×4 WT tumor, PBS treated, ×4 WT tumor, anti-PD-1 treated, ×4 batch1, Ptdss1 KD tumor, PBS treated, ×2 batch1, Ptdss1 KD tumor, anti-PD-1 treated, ×2 batch1, WT tumor, PBS treated, ×2 batch1, WT tumor, anti-PD-1 treated, ×2

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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

GSM8862421 Ptdss1 KD tumor, PBS treated, replicate 1 Ptdss1 KD tumor, PBS tr…
GSM8889453 Ptdss1 KD tumor, PBS treated, replicate 2 Ptdss1 KD tumor, PBS tr…
GSM8889454 Ptdss1 KD tumor, PBS treated, replicate 3 Ptdss1 KD tumor, PBS tr…
GSM8889455 Ptdss1 KD tumor, PBS treated, replicate 4 Ptdss1 KD tumor, PBS tr…
GSM8889456 Ptdss1 KD tumor, anti-PD-1 treated, replicate 1 Ptdss1 KD tumor, anti-P…
GSM8889457 Ptdss1 KD tumor, anti-PD-1 treated, replicate 2 Ptdss1 KD tumor, anti-P…
GSM8889458 Ptdss1 KD tumor, anti-PD-1 treated, replicate 3 Ptdss1 KD tumor, anti-P…
GSM8889459 Ptdss1 KD tumor, anti-PD-1 treated, replicate 4 Ptdss1 KD tumor, anti-P…
GSM8889460 WT tumor, PBS treated, replicate 1 WT tumor, PBS treated,
GSM8889461 WT tumor, PBS treated, replicate 2 WT tumor, PBS treated,
GSM8889462 WT tumor, PBS treated, replicate 3 WT tumor, PBS treated,
GSM8889463 WT tumor, PBS treated, replicate 4 WT tumor, PBS treated,
GSM8889464 WT tumor, anti-PD-1 treated, replicate 1 WT tumor, anti-PD-1 tre…
GSM8889465 WT tumor, anti-PD-1 treated, replicate 2 WT tumor, anti-PD-1 tre…
GSM8889466 WT tumor, anti-PD-1 treated, replicate 3 WT tumor, anti-PD-1 tre…
GSM8889467 WT tumor, anti-PD-1 treated, replicate 4 WT tumor, anti-PD-1 tre…
GSM8889468 batch1, Ptdss1 KD tumor, PBS treated, replicate 1 batch1, Ptdss1 KD tumor…
GSM8889469 batch1, Ptdss1 KD tumor, PBS treated, replicate 2 batch1, Ptdss1 KD tumor…
GSM8889470 batch1, Ptdss1 KD tumor, anti-PD-1 treated, replicate 1 batch1, Ptdss1 KD tumor…
GSM8889471 batch1, Ptdss1 KD tumor, anti-PD-1 treated, replicate 2 batch1, Ptdss1 KD tumor…
GSM8889472 batch1, WT tumor, PBS treated, replicate 1 batch1, WT tumor, PBS t…
GSM8889473 batch1, WT tumor, PBS treated, replicate 2 batch1, WT tumor, PBS t…
GSM8889474 batch1, WT tumor, anti-PD-1 treated, replicate 1 batch1, WT tumor, anti-…
GSM8889475 batch1, WT tumor, anti-PD-1 treated, replicate 2 batch1, WT tumor, anti-…

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GSE292462 Loss of PTDSS1 in tumor cells improves immunogenicity and response to anti-PD-1 therapy [RNA-seq] 12 samples shares anti-pd-1, ptdss1, immunogenicity, improves, therapy, loss
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GSE263240 Blocking CX3CR1+ Tumor-associated Macrophages Synergize with anti-PD-1 Therapy in Hepatocellular Carcinoma 16 samples shares anti-pd-1, therapy
GSE186854 The interactions among Tumor-infiltrating T lymphocytes (TILS) induced by Stellera chamaejasme and anti-PD-1 therapy with Sing-cell Expression Profiling 10 samples shares anti-pd-1, therapy
GSE334585 iNOS is a key mediator of anti-PD-1 melanoma therapy response 48 samples shares anti-pd-1, therapy
GSE282979 IL-2/IL-15 signaling induces NK cell production of FLT3LG which augments anti-PD-1 immunotherapy 24 samples shares anti-pd-1, therapy

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