Pro-inflammatory polarization and colorectal cancer modulate alternative and intronic polyadenylation in primary human macrophages

Abstract

Macrophages are essential cells of the immune system that alter their inflammatory profile depending on their microenvironment. Alternative polyadenylation in the 3prime UTR (3prime 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 3prime 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 3prime RNA-Seq were performed to quantify gene expression and characterize new 3prime UTR-APA and iPA mRNA isoforms. Our results show that polarization of human macrophages from naive to a pro-inflammatory state causes a marked increase both in proximal polyA site selection in the 3prime 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 3prime 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 3prime UTR-APA alterations. Notably, some of these gene expression differences were also found in tumor-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 3prime 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.

Non-canonical isoforms of the mRNA polyadenylation factor WDR33 regulate STING-mediated immune responses

“… 36 Recently, Wilton et al reported an increase in V2, but not V1 or V3, in primary human macrophages as they were polarized into a pro-inflammatory state or were co-cultured with cancer cells. 63 This finding also suggests that V2 might contribute to macrophage anti-tumor activity. This is not surprising, given that V2 can increase autophagic activity and that autophagy regulates many macrophage functions, such as antigen presentation 64 and several other functions.…”