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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