Mammalian APE1 controls miRNA processing and its interactome is linked to cancer RNA metabolism

Abstract

Mammalian apurinic/apyrimidinic endonuclease 1 is a DNA repair enzyme involved in genome stability and expression of genes involved in oxidative stress responses, tumor progression and chemoresistance. However, the molecular mechanisms underlying the role of apurinic/apyrimidinic endonuclease 1 in these processes are still unclear. Recent findings point to a novel role of apurinic/apyrimidinic endonuclease 1 in RNA metabolism. Through the characterization of the interactomes of apurinic/apyrimidinic endonuclease 1 with RNA and other proteins, we demonstrate here a role for apurinic/apyrimidinic endonuclease 1 in pri-miRNA processing and stability via association with the DROSHA-processing complex during genotoxic stress. We also show that endonuclease activity of apurinic/apyrimidinic endonuclease 1 is required for the processing of miR-221/222 in regulating expression of the tumor suppressor PTEN. Analysis of a cohort of different cancers supports the relevance of our findings for tumor biology. We also show that apurinic/apyrimidinic endonuclease 1 participates in RNA-interactomes and protein-interactomes involved in cancer development, thus indicating an unsuspected post-transcriptional effect on cancer genes.

Architecture of The Human Ape1 Interactome Defines Novel Cancers Signatures

“…Proteomic characterization of the APE1-PPI network. With this work, we wanted to study the relevance of APE1-PPIs in cancer using an unbiased functional proteomic approach in order to expand the number of known APE1 PPIs, as derived from studies from this and other groups 4,12 . To this purpose, we used HeLa cells stably expressing the APE1 FLAG-tagged protein 12 (WT), which were here managed to optimize the isolation of APE1-PPI complexes through co-immunoprecipitation experiments (Figs.…”

“…unbiased functional proteomic approach 4 . However, the reduced characterization of APE1 interaction with proteins involved in miRNA processing, e.g.…”

“…It is well known that the different functions of APE1 may depend on its interacting partners 13,14 ; for example, an alteration of its interaction networks has been reported to play a significant role in BER impairment. A recent hypothesis also suggests that APE1 functional dysregulation may impact on the RNome expression and, thus, on the expression of target genes playing a relevant role in the pathology onset 4 . Since several cancer-associated APE1 variants present mutations in the endonuclease domain, exhibiting only mild nuclease defects in vitro [15][16][17] , we hypothesize that APE1 non-canonical functions associated with its overexpression and/or an altered expression of its protein interacting partners should be related to cancer promotion.…”

“…Having a well-characterized cell model is essential when using unbiased strategies, such as genomics and proteomics, in order to easily interpret data and generate novel assumptions. In this context, few years ago, we developed a specific HeLa cell line stably expressing a flagged tagged APE1 form for selective and efficient protein complex immunocapture 4,17,26,27 . This cell line, and its corresponding products, were characterized in both cancer and genotoxic damage response contexts by means of different holistic approaches, including genomics, transcriptomics and proteomics 4,12 .…”

“…In this context, few years ago, we developed a specific HeLa cell line stably expressing a flagged tagged APE1 form for selective and efficient protein complex immunocapture 4,17,26,27 . This cell line, and its corresponding products, were characterized in both cancer and genotoxic damage response contexts by means of different holistic approaches, including genomics, transcriptomics and proteomics 4,12 . In this study, we wanted to improve our previous interactomic analyses by taking advantage of more sensitive mass spectrometry technologies, which were here applied to the analysis of extracts from different subcellular compartments.…”