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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 symbol Protein name Potential relevance to lymphomagenesis and/or HDACi treatment
Common upregulated
MGST3 Microsomal glutathione S-transferase 3 Oxidant detoxification. Potentially upregulated as a response to HDAC-induced activation of Nrf2
H1FX Histone 1 FX Elusive
HLA-A HLA class I histocompatibility antigen, A-69 alpha chain Several HLA class I alleles and variants have been associated with lymphoma development (reviewed in [86])
EXOSC6 Exosome complex component MTR3 The 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]
NAXE NAD(P)H-hydrate epimerase NAXE (AI-BP) binds APOA1 and inhibits VEGFR2 signaling by promoting cholesterol efflux from caveolae/lipid rafts [88]
ANKRD13A Ankyrin repeat domain-containing protein 13A Part of the BCR signalosome. Promotes endocytosis of EGFR [89]
ANXA2 Annexin A2 ANXA2 promotes binding of lymphoma cells to epithelial cells [90]
TMEM205 Transmembrane protein 205 Increases resistance to cisplatin, potentially by exocytosis of platinum-containing vesicles [91]
Common downregulated
UNG* Uracil-DNA glycosylase Major DNA glycosylase for excision of genomic uracil. Deficiency associated with increased lymphoma risk in mice [92]
TYMS Thymidylate synthase Essential in de novo dTTP synthesis. Target of cancer antimetabolites. Decreased levels improves response to 5-fluorouracil [93]
UBE2C Ubiquitin-conjugating enzyme E2 C Correlated to tumor aggressiveness in a variety of lymphomas and its downregulation may contribute to the clinical efficacy of HDAC inhibitors in such malignancies [94]
LARP4 La-related protein 4 Tumor suppressor that may reduce metastatic potential [95]
UHRF1 E3 ubiquitin-protein ligase UHRF1 Reader of DNA and histone methylation that is essential to proliferation and is overexpressed in many cancers [96]
UBTF Nucleolar transcription factor 1 Transcription factor for ribosomal RNA. Depletion induces DNA damage and genomic instability [97]
CCDC86 Coiled-coil domain-containing protein 86 Cooperates with Myc to drive aggressive lymphoma growth. Knockdown sensitizes lymphoma B cells to Rituximab [98]
USP22 Ubiquitin carboxyl-terminal hydrolase 22 Histone deubiquitinase and component of the SAGA HAT complex [99]. Putative stem-cell marker in ALL [100]
RWDD4 RWD domain-containing protein 4 Downregulation suppresses proliferation and invasion in bladder cancer cells [101]
DDX56 Probable ATP-dependent RNA helicase DDX56 Oncogene in colorectal cancer and associated with lymphatic invasion and metastasis [102]
CDO1 Cysteine dioxygenase type 1 In CD4 + CTCL, CDO1 overexpression contributed to apoptosis-inhibition and chemoprotection [103]
RPL7L1 60S ribosomal protein L7-like 1 Elusive
  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