Potential roles of UCH family deubiquitinases in tumorigenesis and chemical inhibitors developed against them

Abstract

Deubiquitinating enzymes (DUBs) are a large group of proteases that reverse ubiquitination process and maintain protein homeostasis. The DUBs have been classified into seven subfamilies according to their primary sequence and structural similarity. As a small subfamily of DUBs, the ubiquitin C-terminal hydrolases (UCHs) subfamily only contains four members including UCHL1, UCHL3, UCHL5, and BRCA1-associated protein-1 (BAP1). Despite sharing the deubiquitinase activity with a similar catalysis mechanism, the UCHs exhibit distinctive biological functions which are mainly determined by their specific subcellular localization and partner substrates. Besides, growing evidence indicates that the UCH enzymes are involved in human malignancies. In this review, the structural information and biological functions of the UCHs are briefly described. Meanwhile, the roles of these enzymes in tumorigenesis and the discovered inhibitors against them are also summarized to give an insight into the cancer therapy with the potential alternative strategy.

Keywords: Deubiquitinase; UCH family; cancer; inhibitors.

Figure 1

Schematic demonstration of the structural domains and ribbon representation of the solved crystal structures for the UCH family members. All UCH family members including UCHL1, UCHL3, UCHL5 and BAP1 share a conserved UCH catalytic domain featured with a canonical αβα fold. Besides the UCH domain, UCHL5 contains an additional C-terminal ULD structural domain composed of four α-helices in its structure. BAP1 is composed of three domains including the UCH catalytic domain, the C-terminal domain, and a long non-organized regions (NORS) inserted in the middle of the enzyme. The NORS insertion unique to vertebrates contains multiple binding motifs which are responsible for BAP1’s interacting with chromosome-associated proteins, and the C-terminal domain of BAP1 contains a nuclear localization signal (NLS) at its tail. ULD, UCHL5-like domain; NBD, nucleosome binding domain; NLS, nuclear localization signal.

Figure 2

Sequence alignment of UCH catalytic domain for UCH family members. The conserved residues through the UCH family are highlighted in red. The catalytic triad (C90, H161 & D176 for UCHL1) is marked with green star. The secondary structural elements observed in the crystal structure of UCHL1 are shown and labeled. The sequence alignment result was generated by using MEGA and ESPript 3.0.

Figure 3

Schematic illustration of the roles for UCHL1 in tumorigenesis. As an oncogene, UCHL1 stabilizes EGFR, TGFβR1, HIF-α, and β-catenin through its DUB activity. Meanwhile, it balances the mTOR complexes by disrupting mTORC1 and promoting mTORC2 assembly. UCHL1 could also act as a tumor suppressor by regulating the p14ARF-MDM2-p53 tumor suppression pathway and promoting cell apoptosis through the caspase-dependent pathway. TGFβR, transforming growth factor-β receptor; EGFR, epidermal growth factor receptor; Smad, drosophila mothers against decapentaplegic protein; mTORC1, mechanistic target of rapamycin complex 1; mTORC2, mechanistic target of rapamycin complex 2; 4EBP1, eukaryotic translation initiation factor 4E (eIF4E)-binding protein 1; eIF4F, eukaryotic translation initiation factor 4; HIF-α, hypoxia-inducible factor α; TCF/Lef, T-cell factor/lymphoid enhancer-binding factor.

Figure 4

Genetic alterations of UCHL1 in specific types of cancer. A. Data from Cancer Cell Line Encyclopedia (Broad, 2019), including mutations, structural variant, copy number alterations (CNA) and mRNA expression z-scores relative to diploid samples [RNA Seq RPKM; threshold 2.0], was analyzed using cBioportal software and visualized using the standard Oncoprint output. The Onco Query Language (OQL) used in the analysis was ‘UCHL1: MUT AMP GAIN EXP ≥ 2 HOMDEL HETLOSS EXP ≤ -2’. B. Lung cancer patients with high UCHL1 expression level suffered from shorter overall survival time as compared to those with low UCHL1 expression level.

Figure 5

Schematic illustration of the roles for UCHL3 in tumorigenesis. UCHL3 stabilizes TRAF2, RAD51, and AhR through its DUB activity. Also, it upregulates the phosphorylation levels of Akt and mTOR. mTOR, mammalian target of rapamycin; AhR, aryl hydrocarbon receptor; TRAF, tumor necrosis factor receptor-associated factors; RAD51, RADiation sensitive 51.

Figure 6

Schematic illustration of the roles for UCHL5 in tumorigenesis. UCHL5 modulates the pathogenesis process of cancer mainly through stabilizing the key players of tumorigenesis-associated signaling pathways. TGFβR, transforming growth factor-β receptor; Smad, drosophila mothers against decapentaplegic protein; Smurf1/2, Smad ubiquitination regulatory factor 1/2; Smo, Smoothened; ELK3, ETS Transcription Factor ELK3; Axin1, axis inhibition protein 1.

Figure 7

Genetic alterations in UCHL5 in specific types of cancer. A. Data from Cancer Cell Line Encyclopedia (Broad, 2019), including mutations, structural variant, copy number alterations (CNA) and mRNA expression z-scores relative to diploid samples [RNA Seq RPKM; threshold 2.0], was analyzed using cBioportal software and visualized using the standard Oncoprint output. The Onco Query Language (OQL) used in the analysis was ‘UCHL5: MUT AMP GAIN EXP ≥ 2 HOMDEL HETLOSS EXP ≤ -2’. B. Myeloma patients with high UCHL5 expression level suffered from shorter overall survival time as compared to those with low UCHL5 expression level.

Figure 8

Schematic illustration of the roles for BAP1 in tumorigenesis. BAP1 plays a key role in the chromatin’s epigenetic modulation by modifying the levels of H2AK119Ub and H3K27me3 through the formation of multi-protein complexes composed of ASXLs, BAP1, HCF-1, YY1, FOXK1/2, OGT, MBD5/6 without or with COMPASS. Moreover, BAP1-containing complexes play an important role in cell cycle regulation through removing ubiquitin from non-histone substrates including its core component of HCF-1 and facilitating the recruitment of transcription factors of KLF5, YY1 and FOXK2. Besides cell cycle regulation, BAP1 modulates DNA repair through its interactions with BRCA1/BARD1 and INO80. Finally, BAP1 BAP1 could induce cytochrome C-dependent apoptosis by deubiquitinating the inositol-1,4,5-triphosphate receptor (IP3R3) and promote ferroptosis by downregulating the expression of SLC7A11. Me, H3K27me3; ASXLs, additional sex comb-like proteins; YY1, Ying Yang 1; HCF-1, Host cell factor 1; OGT, O-linked- N-acetylglucosamine transferase; FOXK1/2, factor forkhead box proteins K1/2; COMPASS, complex of proteins associated with Set1; E2F1, E2F transcription factor 1; KLF5, Kruppel-like factor 5; BRAD1, BRCA1 breast cancer type 1 susceptibility protein; SLC7A11, Solute Carrier Family 7 Member 11; IP3R, Inositol 1,4,5-triphosphate receptor.

Figure 9

Chemical structures and determined potencies of small molecule inhibitors against the UCH family members.