GEO series
Immunosuppressive monocytes are enriched in hepatocellular carcinoma patients with liver dysfunction in a phase II trial of combination sorafenib and nivolumab [CITE-Seq]
GSE313642
Homo sapiens (human)
Single-cell RNA-seq
194 samples
Submitted 2025/12/12
Platform GPL24676
At a glance
Single-cell RNA-seq · human · 194 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)
- Samples
- 194 samples: 38 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.
- Paper
- Phase II trial with nivolumab and sorafenib in HCC identified enrichment of immunosuppressive monocytes in patients with Child-Pugh B liver dysfunctionJHEP reports : innovation in hepatology · 2026
Summary (written by the submitters)
Background and aims: Immune checkpoint inhibition (ICI) and anti-angiogenic therapies are active in hepatocellular carcinoma (HCC), although patients with impaired hepatic function have worse outcomes. Methods: We conducted a multi-center, open-label phase II clinical trial to assess the safety and efficacy of the multikinase inhibitor, sorafenib, combined with nivolumab, in patients with advanced or unresectable HCC and varying liver function.
Read the full summary ↓
In a Part 1 safety lead-in, we investigated the primary endpoint of the maximum-tolerated dose (MTD) of the combination in patients with Child-Pugh A or B7 HCC. In Part 2, we enrolled patients with Child-Pugh B HCC with the primary endpoint of grade >/=3 treatment-related adverse events (TRAE) incidence. Exploratory endpoints included immunologic biomarkers. Results: Overall, 25 patients were consented and 16 eligible patients enrolled. In Part 1, dose-limiting toxicity occurred in 1 of 6 patients in Dose Level -1, and 2 of 5 patients in Dose Level 1; Dose Level -1 was determined to be the MTD. In total, 69% of patients experienced a Grade >/=3 TRAE, with similar distribution for patients with Child-Pugh A and B liver function (70%, 95% CI: 0.35, 0.93 vs 66.7%, 95% CI: 0.22, 0.96). The objective response rate was 6%. We found that patients with Child-Pugh B liver disease harbored more circulating suppressive CD14+ monocytes at baseline. Conclusions: While the combination of sorafenib and nivolumab demonstrated acceptable safety at the MTD in both Child-Pugh subgroups, the objective response rate was below the pre-specified threshold to be declared worthy of further exploration. A distinct immune cell profile in Child-Pugh B patients may define mechanisms of resistance and potential therapeutic targets in this population with unmet clinical need
Published in
Keenan BP, Fan Z, Le BK et al.
· JHEP reports : innovation in hepatology 2026
· PMID 41831609
· doi:10.1016/j.jhepr.2026.101817
This dataset
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.
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 GSE313642_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1380453 and SRA study SRP654876. Searching any of these in the dataset finder brings you back here.
Study design
38 conditions, mostly in duplicate
PBMC healthy donor scRNA-seq replicate 3 ×10
PBMC healthy donor CITE-seq replicate 3 ×10
PBMC healthy donor scRNA-seq replicate 1 ×6
PBMC healthy donor CITE-seq replicate 1 ×6
PBMC healthy donor scRNA-seq replicate 2 ×5
PBMC healthy donor CITE-seq replicate 2 ×5
HCC PBMC patient A-33 timepoint C1D1 scRNA-seq ×3
HCC PBMC patient A-33 timepoint C1D1 CITE-seq ×3
+116 more
Supports a case/control comparison: 134 samples read as cases, 42 as controls.
How we read this: 38 replicated groups read from 194 sample titles; they account for 108 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
- GSM9371441 HCC PBMC patient A-07 timepoint C2D1 scRNA-seq replicate 1 HCC PBMC patient A-07 t…
- GSM9371442 HCC PBMC patient B-23 timepoint C3D1 scRNA-seq
- GSM9371443 HCC PBMC patient B-21 timepoint C1D1 scRNA-seq
- GSM9371444 HCC PBMC patient B-10 timepoint C2D1 scRNA-seq
- GSM9371445 HCC PBMC patient B-03 timepoint C1D1 scRNA-seq
- GSM9371446 HCC PBMC patient B-22 timepoint C3D1 scRNA-seq
- GSM9371447 HCC PBMC patient A-04 timepoint C2D1 scRNA-seq replicate 1 HCC PBMC patient A-04 t…
- GSM9371448 PBMC healthy donor scRNA-seq replicate 1-1 PBMC healthy donor scRN…
- GSM9371449 HCC PBMC patient A-32 timepoint C1D1 scRNA-seq
- GSM9371450 HCC PBMC patient A-12 timepoint baseline scRNA-seq replicate 1 HCC PBMC patient A-12 t…
- GSM9371451 HCC PBMC patient A-04 timepoint C2D1 scRNA-seq replicate 2 HCC PBMC patient A-04 t…
- GSM9371452 HCC PBMC patient B-17 timepoint C1D1 scRNA-seq
- GSM9371453 HCC PBMC patient B-12 timepoint C2D1 scRNA-seq
- GSM9371454 HCC PBMC patient B-22 timepoint C2D15 scRNA-seq
- GSM9371455 HCC PBMC patient B-08 timepoint C1D1 scRNA-seq
- GSM9371456 PBMC healthy donor scRNA-seq replicate 1-3 PBMC healthy donor scRN…
- GSM9371457 HCC PBMC patient B-13 timepoint C2D1 scRNA-seq
- GSM9371458 HCC PBMC patient B-02 timepoint C1D1 scRNA-seq
- GSM9371459 HCC PBMC patient A-08 timepoint C1D1 scRNA-seq replicate 1 HCC PBMC patient A-08 t…
- GSM9371460 HCC PBMC patient A-12 timepoint baseline scRNA-seq replicate 2 HCC PBMC patient A-12 t…
- GSM9371461 HCC PBMC patient B-09 timepoint baseline scRNA-seq
- GSM9371462 HCC PBMC patient A-21 timepoint baseline scRNA-seq
- GSM9371463 HCC PBMC patient A-07 timepoint C2D1 scRNA-seq replicate 2 HCC PBMC patient A-07 t…
- GSM9371464 HCC PBMC patient B-03 timepoint C7D1 scRNA-seq
- GSM9371465 HCC PBMC patient B-23 timepoint C1D15 scRNA-seq
- GSM9371466 HCC PBMC patient B-05 timepoint C1D1 scRNA-seq
- GSM9371467 HCC PBMC patient B-14 timepoint C2D1 scRNA-seq replicate 1 HCC PBMC patient B-14 t…
- GSM9371468 HCC PBMC patient A-05 timepoint C4D1 scRNA-seq replicate 1 HCC PBMC patient A-05 t…
- GSM9371469 PBMC healthy donor scRNA-seq replicate 1-5 PBMC healthy donor scRN…
- GSM9371470 HCC PBMC patient A-30 timepoint C1D1 scRNA-seq replicate 1 HCC PBMC patient A-30 t…
- GSM9371471 HCC PBMC patient B-10 timepoint C1D1 scRNA-seq
- GSM9371472 HCC PBMC patient B-17 timepoint C2D1 scRNA-seq
- GSM9371473 HCC PBMC patient B-11 timepoint baseline scRNA-seq replicate 1 HCC PBMC patient B-11 t…
- GSM9371474 HCC PBMC patient B-17 timepoint Safety follow up scRNA-seq
- GSM9371475 HCC PBMC patient B-12 timepoint C1D1 scRNA-seq
- GSM9371476 HCC PBMC patient B-06 timepoint C1D1 scRNA-seq
- GSM9371477 HCC PBMC patient B-02 timepoint C2D1 scRNA-seq
- GSM9371478 HCC PBMC patient B-08 timepoint C7D1 scRNA-seq
- GSM9371479 PBMC healthy donor scRNA-seq replicate 1-6 PBMC healthy donor scRN…
- GSM9371480 HCC PBMC patient A-02 timepoint C1D1 scRNA-seq
+ 154 more — browse all 194 samples with per-sample file links →
Datasets on a similar topic
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- GSE299340 Single-cell RNA sequencing reveals B cell-related immunosuppressive landscape and a potential suppressor in hepatocellular carcinoma 10 samples shares immunosuppressive, hepatocellular
- GSE272993 Combination anti-PD-1 and anti-CTLA-4 therapy generates waves of clonal responses that include progenitor-exhausted CD8 T cells [dataset 1] 360 samples shares combination
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