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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 22, 2023 |
| Title |
A549 NRF NT, mock and knockout RNAseq |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The NRF2 pathway is frequently activated in various cancer types, yet a comprehensive analysis of its effects across different malignancies is currently lacking. We developed a robust NRF2 activity metric and utilized it to conduct a pan-cancer wide analysis of oncogenic NRF2 signaling. We identified a distinct immunoevasive phenotype where high NRF2 activity is associated with low interferon-gamma (IFNγ), HLA-I expression and T-cell infiltration spanning non-small cell lung cancer (NSCLC) and squamous malignancies of head and neck area, cervix and esophagus. In squamous cell cancers, NRF2 overactive tumors comprise a molecular phenotype with SOX2/TP63 amplification, TP53 mutation and CDKN2A loss. These immune-cold NRF2 hyperactive diseases are associated with upregulation of immunomodulatory NAMPT, WNT5A, SPP1, SLC7A11 and SLC2A1 that represent candidate NRF2 target genes, suggesting direct modulation of the tumor immune milieu. Based on single-cell mRNA data, coupled with a priori information on intercellular ligand-receptor interactions, cancer cells of this subtype exhibit decreased expression of IFNγ responsive ligands, and increased expression of immunosuppressive ligands NAMPT, SPP1 and WNT5A that mediate signaling in intercellular crosstalk. As we observed differential cytokine mRNA expression with IFNγ treatment in NSCLC adenocarcinoma subtype, we explored the cytokine secretome in vitro. We found that secreted neutrophil chemoattractants interleukin-8 (CXCL8) and ENA-78 (CXCL5) are elevated in NRF2 overactive cells, suggesting contribution of immunosuppressive neutrophils in NRF2 driven immune escape. Importantly, as overactive NRF2 is associated with immune-cold characteristics, our results highlight the utility of NRF2 pathway activation as a putative biomarker for stratifying immune-checkpoint blockade responders and non-responders across NSCLC and squamous cancers.
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| Overall design |
RNAseq for A549 parental (NT), mock and NRF2 knockout by CRISPR/Cas9.
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| Contributor(s) |
Härkönen J |
| Citation(s) |
36867945 |
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| Submission date |
Nov 29, 2021 |
| Last update date |
Mar 23, 2023 |
| Contact name |
Anna-Liisa Levonen |
| Organization name |
University of Eastern Finland
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| Department |
A.I. Virtanen Institute
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| Lab |
ALL
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| Street address |
Neulaniementie 2
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| City |
Kuopio |
| State/province |
Savonia region |
| ZIP/Postal code |
70211 |
| Country |
Finland |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (9)
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| Relations |
| BioProject |
PRJNA784564 |
| SRA |
SRP348444 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE189804_A549_counts.txt.gz |
342.1 Kb |
(ftp)(http) |
TXT |
| GSE189804_IFNy_A549_counts.txt.gz |
821.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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