Ubiquitination and deubiquitination in cancer: from mechanisms to novel therapeutic approaches

Abstract

Ubiquitination, a pivotal posttranslational modification of proteins, plays a fundamental role in regulating protein stability. The dysregulation of ubiquitinating and deubiquitinating enzymes is a common feature in various cancers, underscoring the imperative to investigate ubiquitin ligases and deubiquitinases (DUBs) for insights into oncogenic processes and the development of therapeutic interventions. In this review, we discuss the contributions of the ubiquitin-proteasome system (UPS) in all hallmarks of cancer and progress in drug discovery. We delve into the multiple functions of the UPS in oncology, including its regulation of multiple cancer-associated pathways, its role in metabolic reprogramming, its engagement with tumor immune responses, its function in phenotypic plasticity and polymorphic microbiomes, and other essential cellular functions. Furthermore, we provide a comprehensive overview of novel anticancer strategies that leverage the UPS, including the development and application of proteolysis targeting chimeras (PROTACs) and molecular glues.

Keywords: Cancer hallmarks; Immunotherapies; Molecular mechanisms; Targeted therapies; Ubiquitination.

Fig. 1

The processes of ubiquitination and deubiquitination occur within the ubiquitin–proteasome system (UPS). Ubiquitination involves the sequential action of three enzyme classes: ubiquitin-activating enzymes (E1), ubiquitin-conjugating enzymes (E2), and ubiquitin-protein ligases (E3). Initially, E1 enzymes activate ubiquitin (Ub) in an ATP-dependent process. Subsequently, the activated Ub is transferred to E2 enzymes via a thioester bond. The final step is catalyzed by E3 ligases, which facilitate the transfer of Ub from E2 to the target substrate protein, marking it for degradation

Fig. 2

The various types of ubiquitin (Ub) linkages are as follows. a Mono-ubiquitination: A single ubiquitin protein is attached to a substrate protein. b Multi-monoubiquitination: Multiple ubiquitin proteins are each linked to different sites on the same substrate protein. c Homotypic polyubiquitination: Ubiquitin can bind to another ubiquitin through one of its seven lysine residues (K6, K11, K27, K29, K33, K48, and K63) or the N-terminal methionine residue (M1). Multiple identical ubiquitin proteins form a chain, which is then attached to a substrate protein. d Linear ubiquitination: A specific form of homotypic polyubiquitination where ubiquitin molecules are connected via Met1 linkages. e Mixed ubiquitin chain: A ubiquitin can be linked by two or more different connection methods within the same polymerization reaction, resulting in mixed ubiquitin chains. f Branched ubiquitin chain: Ubiquitin proteins in a chain are modified by adding more ubiquitin proteins at different binding sites. g Ubiquitin-like modified chain: A ubiquitin protein in the chain is linked to a ubiquitin-like protein. h Chemically modified chain: Ubiquitin proteins in the chain are modified by other protein modifications, such as phosphorylation or acetylation. The formation of mixed ubiquitin chains, branched ubiquitin chains, ubiquitin-like modified chains, and chemically modified ubiquitin chains are collectively referred to as heterotypic polyubiquitination

Fig. 3

Ubiquitination and deubiquitination regulation of the hallmarks of cancer. E3 ubiquitin ligases and deubiquitinating enzymes, by regulating the degradation and stability of proteins, significantly influence the hallmarks of malignant tumors, which include sustained proliferative signaling, evading growth suppressors, resisting cell death, enabling replicative immortality, inducing angiogenesis, activating invasion and metastasis, genome instability and mutation, tumor-promoting inflammation, reprogramming energy metabolism, evading immune destruction, unlocking phenotypic plasticity, nonmutational epigenetic reprogramming, polymorphic microbiomes, and senescent cells. Each cancer hallmark-associated E3 ligase and deubiquitinating enzyme (DUB) is listed in the corresponding box

Fig. 4

The ubiquitin–proteasome system (UPS) plays a vital role in resisting cell death through various mechanisms. a IBR domain containing 2 (IBRDC2) can target Bcl-2-associated X protein (BAX) for ubiquitination and degradation, which can prevent mitochondrial outer membrane permeabilization (MOMP) induced by active BAX and reduce cell apoptosis. Additionally, Cbl can target BimEL for ubiquitination and degradation, thereby inhibiting apoptosis. b A20 and USP22 can deubiquitinate receptor-interacting protein kinase 3 (RIPK3) to stabilize it, thus suppressing TNF-α-induced necroptosis. Pellino1 (Peli1) can mediate K63 ubiquitination on K115 of RIPK1 in a kinase-dependent manner, promoting the formation of necrosomes and facilitating necroptosis. c Tripartite motif 31 (TRIM31), F-box and leucine-rich repeat protein 2 (FBXL2), and casitas b-lineage lymphoma-b (Cbl-b) promote NLRP3 inflammasome protein 3 (NLRP3) polyubiquitination at different sites, thereby inhibiting the process of pyroptosis. USP18 inhibits pyroptosis in cancer cells via enhancing interferon-stimulated genes (ISGs), while USP48 promotes pyroptosis by stabilizing gasdermin E (GSDEM), and USP24 promotes pyroptosis by stabilizing gasdermin B (GSDEB). (d) Cullin3 (CUL3) and Parkin are responsible for ubiquitinating beclin 1 (BECN1) and voltage-dependent anion channel 1 (VDAC1), respectively, whereas USP19 and USP44 can deubiquitinate NLRP3 and H2B, respectively. e TRIM26 targets solute carrier family 7 member 11 (SLC7A11) for ubiquitination and degradation, promoting cellular ferroptosis. BRCA1-associated protein 1 (BAP1) removes H2A ubiquitination from the SLC7A11 promoter, resulting in decreased cystine uptake and increased ferroptosis. OTU deubiquitinase ubiquitin aldehyde-binding 1 (OTUB1) promotes glutathione peroxidase 4 (GPX4) deubiquitination, inhibiting ferroptosis in gastric cancer cells

Fig. 5

The ubiquitin–proteasome system regulates tumor metabolism in several pathways. a Glycolysis: Hexokinase 2 (HK2) can be ubiquitinated by E3 ligases membrane-associated RING-CH protein 8 (MARCH8) and tripartite motif protein 36 (TRIM36), a process that can be reversed by the deubiquitinase ubiquitin-specific protease 7 (USP7). Pyruvate kinase M2 (PKM2) can be ubiquitinated by E3 ligases TRIM9, TRIM29, STIP1 homology and U-box-containing protein 1 (STUB1), and TRIM35. Conversely, PKM2 can be deubiquitinated by proteasome non-ATPase regulatory subunit 14 (PSMD14), OTU domain-containing ubiquitin aldehyde-binding protein 2 (OTUB2), and USP35. b Fatty acid (FA) metabolism: Acetyl-CoA carboxylase 1 (ACC1) and fatty acid synthase (FASN), both involved in fatty acid metabolism, can be ubiquitinated by E3 ligases tribbles pseudokinase 1 (Trib1)-constitutive photomorphogenic 1 (COP1), and F-box and WD repeat domain containing 7β (FBXW7β), respectively. In contrast, FASN can be deubiquitinated by USP38. c Glutaminolysis: Glutaminase C (GAC), which catalyzes the initial step of glutamine decomposition into glutamic acid and ammonia, can be ubiquitinated by the E3 ligase TRIM21. This leads to K63-linked ubiquitination that inhibits GAC activity. Glutamate dehydrogenase (GDH), another key enzyme in glutamine catabolism, can be ubiquitinated by E3 ligases ring finger protein 213 (RNF213) and STUB1

Fig. 6

The ubiquitin–proteasome system regulates tumor immunity. a Components of the tumor microenvironment include cancer-associated fibroblasts (CAFs), dendritic cells (DCs), natural killer (NK) cells, tumor-associated macrophages (TAMs), and T lymphocytes. b CAFs secrete a variety of chemokines, cytokines, and other effector molecules, such as transforming growth factor-β (TGF-β), interleukin-6 (IL-6), C-X-C chemokine ligand 12 (CXCL12), C–C chemokine ligand 2 (CCL2), stromal cell-derived factor 1 (SDF-1), vascular endothelial growth factor (VEGF), indoleamine 2,3-dioxygenase (IDO), and prostaglandin E2 (PGE2). These molecules regulate the function of immune cell populations in the TME, mediated by immune cells to inhibit immune responses. c E3 ligases and deubiquitinases that directly target PD-L1. E3 ligases USP7, USP22, CSN5, USP8, and USP9X stabilize PD-L1. Conversely, deubiquiting enzymes SPOP, FBXO38, FBXO22, and NEDD4 degrade PD-L1 through ubiquitination. The following list comprises the E3 ligases and deubiquitinating enzymes involved in processes that affect PD-L1 transcription. FBW7 and RNF31 inhibit PD-L1 transcription through the PI3K/AKT/GSK-3β signaling pathway and the Hippo/YAP/PD-L1 axis. USP22 and HERC2 promote PD-L1 transcription through the USP22-CSN5-PD-L1 axis and the JAK2/STAT3 signaling pathway, respectively. d The involvement of the ubiquitin–proteasome system in the TGF-β signaling pathway includes USP11 acting on the TGF-β type II receptor, USP15, and USP4 acting on the TGF-β type I receptor, and USP3, USP11, A20, and USP27X acting on EMT transcription factors

Fig. 7

Schematic diagram of ubiquitin–proteasome system regulating proteins and its corresponding treatment strategies. Drugs targeting proteasome: bortezomib, carfilzomib, oprozomib and ixazomib. Drugs targeting El enzyme: TAK-243, pevonedistat, TAK-981 andTAS4464. Drugs targeting E2 enzyme: Leucetta A, manado sterols A, manado sterols B andCC0651. Drugs targeting E3 ligase: S-phase kinase-associated protein 2 (SKP2) inhibitors and homologous to the E6AP C-terminus (HECT)-type E3 ligase inhibitors, HOlL-1 interacting protein (HOIP) inhibitors, mouse double minute 2 (MDM2) inhibitors and IAPs inhibitors. Drugs targeting deubiquitinase (DUB): Broad-range DUB inhibitors, inhibitors targeting USP7, inhibitors targeting USP14, and inhibitors targeting UCH-L1