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Table 1 DEPs common to Jurkat and SUDHL5 after SAHA treatment, and their potential relevance to lymphomagenesis and/or response to HDACi treatment (fold changes are given in Fig. 1c)

From: HDACi mediate UNG2 depletion, dysregulated genomic uracil and altered expression of oncoproteins and tumor suppressors in B- and T-cell lines

Gene symbolProtein namePotential relevance to lymphomagenesis and/or HDACi treatment
Common upregulated
MGST3Microsomal glutathione S-transferase 3Oxidant detoxification. Potentially upregulated as a response to HDAC-induced activation of Nrf2
H1FXHistone 1 FXElusive
HLA-AHLA class I histocompatibility antigen, A-69 alpha chainSeveral HLA class I alleles and variants have been associated with lymphoma development (reviewed in [86])
EXOSC6Exosome complex component MTR3The RNA exosome has been implicated in both Ig CSR and SHM by targeting AID to transcribed dsDNA substrates and thus regulating its mutator activity [87]
NAXENAD(P)H-hydrate epimeraseNAXE (AI-BP) binds APOA1 and inhibits VEGFR2 signaling by promoting cholesterol efflux from caveolae/lipid rafts [88]
ANKRD13AAnkyrin repeat domain-containing protein 13APart of the BCR signalosome. Promotes endocytosis of EGFR [89]
ANXA2Annexin A2ANXA2 promotes binding of lymphoma cells to epithelial cells [90]
TMEM205Transmembrane protein 205Increases resistance to cisplatin, potentially by exocytosis of platinum-containing vesicles [91]
Common downregulated
UNG*Uracil-DNA glycosylaseMajor DNA glycosylase for excision of genomic uracil. Deficiency associated with increased lymphoma risk in mice [92]
TYMSThymidylate synthaseEssential in de novo dTTP synthesis. Target of cancer antimetabolites. Decreased levels improves response to 5-fluorouracil [93]
UBE2CUbiquitin-conjugating enzyme E2 CCorrelated to tumor aggressiveness in a variety of lymphomas and its downregulation may contribute to the clinical efficacy of HDAC inhibitors in such malignancies [94]
LARP4La-related protein 4Tumor suppressor that may reduce metastatic potential [95]
UHRF1E3 ubiquitin-protein ligase UHRF1Reader of DNA and histone methylation that is essential to proliferation and is overexpressed in many cancers [96]
UBTFNucleolar transcription factor 1Transcription factor for ribosomal RNA. Depletion induces DNA damage and genomic instability [97]
CCDC86Coiled-coil domain-containing protein 86Cooperates with Myc to drive aggressive lymphoma growth. Knockdown sensitizes lymphoma B cells to Rituximab [98]
USP22Ubiquitin carboxyl-terminal hydrolase 22Histone deubiquitinase and component of the SAGA HAT complex [99]. Putative stem-cell marker in ALL [100]
RWDD4RWD domain-containing protein 4Downregulation suppresses proliferation and invasion in bladder cancer cells [101]
DDX56Probable ATP-dependent RNA helicase DDX56Oncogene in colorectal cancer and associated with lymphatic invasion and metastasis [102]
CDO1Cysteine dioxygenase type 1In CD4 + CTCL, CDO1 overexpression contributed to apoptosis-inhibition and chemoprotection [103]
RPL7L160S ribosomal protein L7-like 1Elusive
  1. * UNG was quantified by SILAC in Jurkat only, but nuclear isoform UNG2 found to be robustly downregulated in SUDHL5 by western analysis, targeted MS and IHC