PXD008293

PXD008293 is an original dataset announced via ProteomeXchange.

Title	Histone deacetylase inhibitors mediate selective degradation of nuclear uracil-DNA glycosylase 2 and increased genomic uracil
Description	HDAC inhibitors (HDACi) belong to a new group of chemotherapeutics that are increasingly used to treat B-cell-derived malignancies. Such malignancies regularly carry mutational signatures that conform to off-target induction of uracil by the AID/APOBEC family of cytidine deaminases, or downstream processing of uracil. . HDACi suppress thymidylate synthase increasing the cellular dUTP/dTTP ratio and leading to increased pressure on uracil repair machinery due to misincorporated uracil lesions. To investigate potential effect upon other enzymes involved in genomic uracil induction and processing, Jurkat (T-cell lymphoma) and SUDHL5 (B-cell lymphoma) cells were treated with pan-HDACi SAHA prior to SILAC based MS/MS investigation. HDACi treatment mediated significant differential expression of xx and xx proteins in Jurkat and SUDHL5, respectively, and had a substantial impact upon enzymes involved in in pyrimidine metabolism. Surprisingly, uracil N-glycosylase, UNG, was strongly downregulated by HDACi treatment. Further analysis in HEK and HeLa cells revealed that HDACis induce specific loss of the nuclear isoform UNG2 independent of transcription and cell-cycle alterations. More than 80% of UNG2 is degraded proteasomally after 24 hours treatment with SAHA, MS275, Valproate or Na-butyrate, indicating a universal ability of HDACis to mediate loss of UNG2. Targeted MS/MS analysis in HEK cells against a panel of proteins involved in DNA repair, translesion synthesis and nucleotide metabolism, revealed that UNG2 was the most pronounced differentially expressed among these after HDACi treatment. 48 hour treatment lead to a 30-40% increase in uracil lesions in the nuclear genome of HeLa and HEK cells and MS275 treatment in murine CH12F3 cell line mediated robust UNG2-loss accompanied by reduced class switch recombination. Furthermore, our analysis identified the PCNA-associated factor PAF15 among the downregulated proteins. PAF15 is overexpressed in many cancers and suppress TLS by inducing double monoubiquitinylation of PCNA and recruitment of the replicative polymerases. In summary, our findings demonstrate that HDAC inhibition affects the levels of proteins involved in DNA base excision repair, translesion synthesis and pyrimidine metabolism. These findings are important for a wide range of clinical applications of HDACi, such as in rheumatology, HIV-, and cancer treatment.
HostingRepository	PRIDE
AnnounceDate	2020-04-14
AnnouncementXML	Submission_2020-04-13_22:48:31.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Animesh Sharma
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-11-24 05:25:28	ID requested
⏵ 1	2020-04-13 22:48:32	announced

Iveland TS, Hagen L, Sharma A, Sousa MML, Sarno A, Wollen KL, Liabakk NB, Slupphaug G, HDACi mediate UNG2 depletion, dysregulated genomic uracil and altered expression of oncoproteins and tumor suppressors in B- and T-cell lines. J Transl Med, 18(1):159(2020) [pubmed]

curator keyword: Biological

submitter keyword: AA, amino acid

AID, activation induced deaminase;

Geir Slupphaug
contact affiliation	Professor i molekylærbiologi og faglig leder av PROMEC Institutt for klinisk og molekylær medisin Erling Skjalgssons g 1, aboratoriesenteret * * Laboratoriesenter Norwegian University of Science and Technology Trondheim 7030 Norway ( lab head )
contact email	geir.slupphaug@ntnu.no
lab head
Animesh Sharma
contact affiliation	Engineer at NTNU, Norway
contact email	sharma.animesh@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD008293
     1. Label: PRIDE project
     2. Name: Histone deacetylase inhibitors mediate selective degradation of nuclear uracil-DNA glycosylase 2 and increased genomic uracil