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APE1 INTERACTOME - Architecture of The Human Ape1 Interactome Defines Novel Cancers Signatures

ABSTRACT: The present work aimed at defining the association of the APE1-protein-protein interactions network in modulating its role in tumor progression and chemoresistance through proteomic and bionformatic analyses

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: CHIARA D'AMBROSIO

LAB HEAD: Andrea Scaloni

PROVIDER: PXD013368 | Pride | 2020-01-16

REPOSITORIES: Pride

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			Action	DRS
	CCE_APE_.msf	Msf
	CCE_APE_1.raw	Raw
	CCE_APE_10.raw	Raw
	CCE_APE_10BIS.raw	Raw
	CCE_APE_11.raw	Raw

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Publications

Architecture of The Human Ape1 Interactome Defines Novel Cancers Signatures.

Ayyildiz Dilara D Antoniali Giulia G D'Ambrosio Chiara C Mangiapane Giovanna G Dalla Emiliano E Scaloni Andrea A Tell Gianluca G Piazza Silvano S

Scientific reports 20200108 1

APE1 is essential in cancer cells due to its central role in the Base Excision Repair pathway of DNA lesions and in the transcriptional regulation of genes involved in tumor progression/chemoresistance. Indeed, APE1 overexpression correlates with chemoresistance in more aggressive cancers, and APE1 protein-protein interactions (PPIs) specifically modulate different protein functions in cancer cells. Although important, a detailed investigation on the nature and function of protein interactors re ...[more]

PMID: 31913336

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APE1 knock-in

Project description:APE1/Ref-1 protects cells from oxidative stress by acting as a central enzyme in base excision repair pathways of DNA lesions and through its independent activity as a redox transcriptional co-activator. To dissect between redox- and DNA-repair-mediated effects, here we performed transcription profiling of knock-in experiments using wild type and mutations C65S and 31-34A.

2011-10-01 | E-MEXP-2941 | biostudies-arrayexpress

AUF1 recognizes 8-oxo-guanosine embedded in DNA and stimulates APE1 endoribonuclease activity

Project description:The presence of rNMPs embedded in DNA represents a frequent genomic event able to destabilize the DNA backbone and to alter DNA replication and transcription. Usually, rNMPs are excised by RNase H2 and fully repaired by other enzymes belonging to the ribonucleotide excision repair pathway. The existence of modified rNMPs embedded in DNA, including 8-oxo-guanosine (8-oxo-G) and ribose monophosphate abasic site (rAP), have been recently highlighted by several works including ours. While eukaryotic RNase H2 is unable to process rAP and 8-oxo-G embedded in DNA, we demonstrated a role of APE1, a key enzyme of the base excision repair pathway, on these lesions. Notably, though APE1 activity on the repair of rAP sites results as efficient as the canonical dAP site, its incision repair activity on 8-oxo-G is very weak. Therefore, in order to guarantee an efficient repair activity of 8-oxo-G, additional processing mechanisms should be active in cells. In this work, by using an unbiased proteomic approach to isolate proteins able to recognize 8-oxo-G embedded in DNA, we discovered that AUF1 actively and specifically recognize 8-oxo-G and, interestingly, stimulates the APE1 enzymatic activity on this substrate. Although further structural analysis should be performed, it is reasonable that AUF1 facilitates the endoribonuclease activity of APE1 on 8-oxo-G by stabilizing the lesion substrate. Furthermore, by two orthogonal approaches including GST-pulldown and proximity ligation assay, we uncovered a novel protein-protein interaction between AUF1 and APE1. Remarkable, this interaction is modulated by H2O2-treatment, playing a putative biological role during cell response to oxidative stress.

2024-10-17 | PXD027252 | Pride

Gene expression influenced by human APE1 and mouse Ape1 in a mouse embryonic fibroblast line.

Project description:APE1 (AP-endonuclease 1) is an essential DNA repair protein but also it functions as a gene regulatory protein. A unique mouse embyonic fibroblast with almost undetectable levels of APE1 was isolated. Three isogenic derivatives of this cell line that contain either of the control vector, the human APE1 cDNA, and mouse Ape1 cDNA were analyzed for their global gene expression using Affymetrix mouse ST 2.0 chip set.

2016-01-31 | GSE55765 | GEO

Apurinic/apyrimidinic endonuclease/redox factor-1 (Ape1/Ref-1) activates Notch signaling through Jagged1 expression and promotes colon cancer progression

Project description:To investigate the possible role of Ape1/Ref-1 in tumorigenicity of colon cancer and explored the oncogenic mechanism of Ape1/Ref-1 in colon cancer cells. Control and Ref-1 overexpressing SW480cells, control and Ref-1-deficient SW480 cells. Duplicate

2013-04-17 | E-GEOD-45912 | biostudies-arrayexpress

The role of FKBP51 in the activation of Akt oncogenic pathway

Project description:FKBP51 is an immunophilin with a relevant role in sustaining cancer cell growth and aggressiveness, particularly in melanoma. Thanks to its scaffold and isomerase activities, mediated by its TPR and FK1 domains, respectively, FKBP51 participates in several signaling pathways. Akt is a serine-threonine kinase that is constitutively active in many tumors with a role in cancer growth and resistance. FKBP51 forms a complex with Akt and PH-domain leucine-rich repeat protein phosphatase (PHLPP), which is reported to deactivate Akt. The effect of FKBP51 on Akt activation is far from being fully elucidated and opposite data emerge from literature. We recently identified a spliced FKBP51 isoform. In this paper, we interrogated the two FKBP51 isoforms in the regulation of Akt activation and the underlying mechanisms. Our finding shows that the pAkt levels were upregulated by the canonical but not the spliced FKBP51. We show that the TPR domain mediates Akt-K63-ubiquitination, an essential aspect of Akt activation. The spliced FKBP51s, lacking such domain, could not link K63-Ub residues to Akt. Unexpectedly, PHLPP silencing did not foster phosphorylation of Akt, and its overexpression even induced phosphorylation of Akt. Our finding shows that PHLPP stabilizes levels of the E3-ubiquitin ligase TRAF6, a known FKBP51 interactor. We observed an increased K63-ubiquitination of Akt upon PHLPP overexpression. A mass spectrometry-based proteome profile of melanoma cells highlighted a relevant role for such phosphatase in improving oncogenic hallmarks, first, cell proliferation. In conclusion, we show that canonical FKBP51 promotes Akt activation by serving as a scaffold to build the macro complex deputed to Akt ubiquitination and phosphorylation. The short FKBP51 isoform, even if it retains the ability to bind to Akt, cannot support Akt phosphorylation, being unable to engage K63-ubiquitin.

2023-03-11 | PXD033828 | Pride

Single-cell RNA-seq following APE1/Ref-1 knockdown in Pancreatic Ductal Adenocarcinoma

Project description:APE1 was knocked down using siRNA in low passage patient-derived PDAC cells and the resulting cells, along with control cells were analysed using scRNA-seq to identify differentially expressed genes and pathways as a result of APE1 knock-down.

2018-02-14 | GSE99305 | GEO

Single-cell RNA-seq following APE1/Ref-1 knockdown in Pancreatic Ductal Adenocarcinoma

2021-04-28 | GSE173433 | GEO

The DNA-repair protein APE1 contributes with hnRNPA2B1 to motif-enriched miRNA secretion

Project description:The base excision repair (BER) Apurinic/apyrimidinic endonuclease 1 (APE1) enzyme is endowed with several non-repair activities, such as the cell response to genotoxic stress, the regulation of gene expression and miRNAs processing. We recently demonstrated that APE1 can be actively secreted by mammalian cells through exosomes. The role of APE1 in exosomes is still unknown, especially regarding the molecular mechanism involving small non-coding RNAs vesicular secretion. miRNAs loading into exosomes is a regulated and selective process, since not all the expressed miRNAs are indistinctly conveyed into exosomes. Through a dedicated transcriptomic analysis on cellular and vesicular small RNAs, we identified secreted miRNAs characterized by enriched sequence motifs and possible binding sites for APE1. In 50 out of 53 DE-miRNA precursors, we surprisingly found EXO motifs and proved that APE1 cooperates with hnRNPA2B1 for the EV-sorting of a subsets of miRNAs, including miR-1246, through a direct binding to GGAG stretch. We provide evidence of a new post-transcriptional role for this ubiquitous DNA-repair enzyme towards miRNAs secretion mechanisms, that could be exploited to interfere with tumor microenvironment.

2024-07-24 | GSE230874 | GEO

RNAi knock down of the DNA-repair enzyme and transcriptional co-activator APE1 in human HeLa cells

Project description:Transcriptional profiling was done following APE1/Ref1 silencing using conditional gene expression knockdown by RNA interference (RNAi) technology in HeLa cell lines. APE1 is a DNA-repair enzyme and transcriptional co-activator. Knockdown leads to cell-growth arrest, apoptosis and impairment in the intracellular redox state and cytoskeletal perturbation.

2009-02-02 | E-MEXP-1315 | biostudies-arrayexpress

Apurinic/apyrimidinic endonuclease/redox factor-1 (Ape1/Ref-1) activates Notch signaling through Jagged1 expression and promotes colon cancer progression

Project description:To investigate the possible role of Ape1/Ref-1 in tumorigenicity of colon cancer and explored the oncogenic mechanism of Ape1/Ref-1 in colon cancer cells.

2013-04-17 | GSE45912 | GEO

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