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| Status |
Public on Apr 24, 2023 |
| Title |
Pro-inflammatory polarization and colorectal cancer modulate alternative and intronic polyadenylation in primary human macrophages |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Macrophages are essential cells of the immune system that alter their inflammatory profile depending on their microenvironment. Alternative polyadenylation in the 3'UTR (3'UTR-APA) and intronic polyadenylation (IPA) are mechanisms that modulate gene expression, in particular in cancer and activated immune cells. Yet, how polarization and colorectal cancer (CRC) cells microenvironment affect 3'UTR-APA and IPA in primary human macrophages remains unknown. Here, primary human monocytes were isolated from healthy donors, differentiated and polarized into a pro-inflammatory state and ChrRNA-Seq and 3'RNA-Seq were performed to quantify gene expression and characterize new 3’UTR-APA and IPA mRNA isoforms. Our results show that polarization of human macrophages from naïve to a pro-inflammatory state causes a marked increase both in proximal polyA site selection in the 3'UTR and in IPA events, in genes relevant for macrophage functions. Additionally, we found a negative correlation between differential gene expression and IPA during pro-inflammatory polarization of primary human macrophages. As macrophages are abundant immune cells in the CRC microenvironment that either promote or abrogate cancer progression, we investigated how indirect exposure to CRC cells affects macrophage gene expression and 3'UTR-APA and IPA mRNA events. Co-culture with CRC cells alters the inflammatory phenotype of macrophages, increases the expression of pro-tumoral genes and induce 3’UTR-APA alterations. Notably, some of these gene expression differences were also found in tumour-associated macrophages of CRC patients, indicating that they are physiological relevant. Upon macrophage pro-inflammatory polarization SRSF12 is the pre-mRNA processing gene that is most upregulated. After SRSF12 knockdown in M1 macrophages there is a global downregulation of gene expression, in particular in genes involved in gene expression regulation and in immune responses. Our results reveal new 3’UTR-APA and IPA mRNA isoforms produced during pro-inflammatory polarization of primary human macrophages and CRC co-culture that may be used in the future as diagnostic or therapeutic tools.
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| Overall design |
After treating primary human macrophages for 24 hours with pro-inflammatory stimuli - LPS + IFN-gamma - and 24 hours of exposure to CRC cells, we performed chromatin-bound RNA-Seq and 3'RNA-Seq. In unpolarised macrophages (M0), we performed 3'RNA-Seq
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| Web link |
https://pubmed.ncbi.nlm.nih.gov/37359548/
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| Contributor(s) |
Wilton J, Tellier M, Nojima T, Pereira-Castro I, Freitas J, Costa AM, Murpy S, Oliveira MJ, Proudfoot NJ, Moreira A, Lopes de Mendonça F |
| Citation(s) |
37359548 |
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| Submission date |
Dec 22, 2020 |
| Last update date |
Jul 24, 2023 |
| Contact name |
Joana Wilton |
| E-mail(s) |
[email protected]
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| Organization name |
i3S
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| Department |
IBMC
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| Lab |
Gene Regulation
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| Street address |
Rua Alfredo Allen, 208
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| City |
Porto |
| ZIP/Postal code |
4200-135 |
| Country |
Portugal |
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| Platforms (2) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (22)
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| Relations |
| BioProject |
PRJNA687266 |
| SRA |
SRP298980 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE163726_RAW.tar |
2.4 Gb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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