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

GSE292462 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2025/09/10 Platform GPL19057

At a glance

RNA-seq (gene expression) · mouse · 12 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: Mus musculus (mouse)
Samples: 12 samples: 3 × WT, vs 3 × Ptdss1 KD#1, vs 3 × Ptdss1 KD#2, vs 3 × Ptdss1 KD#3,Groups 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 GSE292462 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 GSE292462_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 PRJNA1238825 and SRA study SRP571893. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

3 × WT, vs 3 × Ptdss1 KD#1, vs 3 × Ptdss1 KD#2, vs 3 × Ptdss1 KD#3,

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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

GSM8859538 WT, replicate 1 WT,
GSM8859539 WT, replicate 2 WT,
GSM8859540 WT, replicate 3 WT,
GSM8859541 Ptdss1 KD#1, replicate 1 Ptdss1 KD#1,
GSM8859542 Ptdss1 KD#1, replicate 2 Ptdss1 KD#1,
GSM8859543 Ptdss1 KD#1, replicate 3 Ptdss1 KD#1,
GSM8859544 Ptdss1 KD#2, replicate 1 Ptdss1 KD#2,
GSM8859545 Ptdss1 KD#2, replicate 2 Ptdss1 KD#2,
GSM8859546 Ptdss1 KD#2, replicate 3 Ptdss1 KD#2,
GSM8859547 Ptdss1 KD#3, replicate 1 Ptdss1 KD#3,
GSM8859548 Ptdss1 KD#3, replicate 2 Ptdss1 KD#3,
GSM8859549 Ptdss1 KD#3, replicate 3 Ptdss1 KD#3,

Datasets on a similar topic

GSE292614 Loss of PTDSS1 in tumor cells improves immunogenicity and response to anti-PD-1 therapy [scRNAseq] 24 samples shares anti-pd-1, ptdss1, immunogenicity, improves, therapy, loss
GSE266110 7aaRGD - a novel SPP1/integrin signaling-blocking peptide reverses immunosuppression and improves anti-PD-1 immunotherapy outcomes in experimental gliomas 40 samples shares anti-pd-1, improves, therapy
GSE292089 Cancer-induced nerve injury promotes resistance to anti-PD-1 therapy [RNA-seq] 6 samples shares anti-pd-1, therapy, rna-seq
GSE263274 Insights into the mechanisms of serplulimab: a distinctive anti-PD-1 monoclonal antibody, in combination with a TIGIT or LAG3 inhibitor in preclinical tumor immunotherapy studies 45 samples shares anti-pd-1, therapy
GSE273488 Mapping the genetic landscape establishing a tumor immune microenvironment favorable for anti-PD-1 response in mice and humans (RNA-Seq II). 42 samples shares anti-pd-1, rna-seq
GSE262811 Lack of TREM2 during anti-PD-1 therapy reprograms intestinal macrophages and microbiota to enhance tumor rejection 32 samples shares anti-pd-1, therapy
GSE273487 Mapping the genetic landscape establishing a tumor immune microenvironment favorable for anti-PD-1 response in mice and humans (RNA-Seq I). 23 samples shares anti-pd-1, rna-seq
GSE263240 Blocking CX3CR1+ Tumor-associated Macrophages Synergize with anti-PD-1 Therapy in Hepatocellular Carcinoma 16 samples shares anti-pd-1, therapy

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