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| Status |
Public on Feb 04, 2024 |
| Title |
Identification of TREM1+CD163+ myeloid cells as a deleterious immune subset in HCC [bulk_RNA-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Hepatocellular carcinoma (HCC) is an inflammation-associated cancer arising from viral and non-viral etiologies. Expansion of suppressive myeloid cells is a hallmark of chronic inflammation and cancer, but their heterogeneity in HCC is not fully resolved and might underlie immunotherapy resistance in the steatohepatitis setting. Here, we present a high resolution atlas of hepatic innate immune cells from patients with HCC that unravels a steatohepatitis contexture characterized by influx of inflammatory and immunosuppressive myeloid cells. A discrete myeloid cell population identified by selective expression of TREM1 and CD163 expands in steatohepatitis-HCC. We refer to this population as TREM1+ regulatory myeloid cells (Mreg), as it potently suppresses T cell effector functions, highly expresses TGFB1 and IL13RA1 and localizes to HCC fibrotic lesions.
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| Overall design |
Single-cell RNA-seq (10x Genomics) on FACS-sorted CD45 + panTCRαβ - CD19 - innate immune cells freshly isolated from tumors (HCC) and adjacent non-tumoral (NT) liver sections were realized for 10 patients (10 HCC/CHC samples and 10 NT/TS samples). In parallel, we applied spatial transcriptomics (ST; Visium ® , 10x Genomics) on frozen tissue sections from the two of the previous patients (2 CHC visium samples). Furthermore, bulk RNA-seq sequencing were performed on innate immunity cells that were isolated using the same sorting strategy designed for scRNAseq experiments, for six of the previous patients. Bulk RNA-seq sequencing were also realized on FACS-sorted cell population, namely THBS1_M (c0, c3 and c4) populations that were isolated according to specific sorting strategy. In summary, available data concerns 20 scRNA-seq samples, 2 visium spatial transcriptomics and 9 bulk RNA-seq.
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| Contributor(s) |
Giraud J, Chalopin D, Ramel E, Boyer T, Zouine A, Derieppe M, Larmonier N, Adotevi O, Le Bail B, Blanc J, Laurent C, Chiche L, Derive M, Nikolski M, Saleh M |
| Citation(s) |
38350444 |
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| Submission date |
Oct 20, 2023 |
| Last update date |
May 12, 2024 |
| Contact name |
Maya Saleh |
| E-mail(s) |
maya.saleh@inrs.ca
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| Organization name |
INRS
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| Department |
Armand Frappier Santé Biotechnologie
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| Street address |
531 Boulevard des Prairies
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| City |
Laval |
| State/province |
Qc |
| ZIP/Postal code |
H7V 1B7 |
| Country |
Canada |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (9)
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| GSM7850787 |
innateCHC20, innate from patient 20 |
| GSM7850788 |
innateCHC23, innate from patient 23 |
| GSM7850789 |
innateCHC24, innate from patient 24 |
| GSM7850790 |
MDSC-c0, CD36high CD163- LOX1+, pool of 5 patients |
| GSM7850791 |
MDSC-c3, CD36high CD163- LOX1-, pool of 5 patients |
| GSM7850792 |
MDSC-c4, CD36high CD163+ LOX1med, pool of 5 patients |
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| This SubSeries is part of SuperSeries: |
| GSE245909 |
Identification of TREM1+CD163+ myeloid cells as a deleterious immune subset in HCC |
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| Relations |
| BioProject |
PRJNA1030367 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE245905_cpm_counts_RNAseq_matrix.tsv.gz |
1.1 Mb |
(ftp)(http) |
TSV |
| GSE245905_raw_counts_RNASeq_matrix.txt.gz |
672.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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