Protein degradation: expanding the toolbox to restrain cancer drug resistance

Abstract

Despite significant progress in clinical management, drug resistance remains a major obstacle. Recent research based on protein degradation to restrain drug resistance has attracted wide attention, and several therapeutic strategies such as inhibition of proteasome with bortezomib and proteolysis-targeting chimeric have been developed. Compared with intervention at the transcriptional level, targeting the degradation process seems to be a more rapid and direct strategy. Proteasomal proteolysis and lysosomal proteolysis are the most critical quality control systems responsible for the degradation of proteins or organelles. Although proteasomal and lysosomal inhibitors (e.g., bortezomib and chloroquine) have achieved certain improvements in some clinical application scenarios, their routine application in practice is still a long way off, which is due to the lack of precise targeting capabilities and inevitable side effects. In-depth studies on the regulatory mechanism of critical protein degradation regulators, including E3 ubiquitin ligases, deubiquitylating enzymes (DUBs), and chaperones, are expected to provide precise clues for developing targeting strategies and reducing side effects. Here, we discuss the underlying mechanisms of protein degradation in regulating drug efflux, drug metabolism, DNA repair, drug target alteration, downstream bypass signaling, sustaining of stemness, and tumor microenvironment remodeling to delineate the functional roles of protein degradation in drug resistance. We also highlight specific E3 ligases, DUBs, and chaperones, discussing possible strategies modulating protein degradation to target cancer drug resistance. A systematic summary of the molecular basis by which protein degradation regulates tumor drug resistance will help facilitate the development of appropriate clinical strategies.

Keywords: Chaperone-mediated autophagy; DUBs; Drug resistance; E3 ligase; Protein degradation.

Fig. 1

Ubiquitin-dependent and independent molecular mechanisms of protein degradation. a Ubiquitin conjugation system consists of ubiquitin-activating enzyme (E1), ubiquitin-conjugating enzyme (E2), and ubiquitin ligase (E3). Deubiquitylating enzymes (DUB) can remove ubiquitin chains from substrates. b Ubiquitin modification can be categorized as monoubiquitination, polyubiquitination, and branched ubiquitination, where Lys48 and Lys63 polyubiquitination chains are closely related to protein degradation. c The biological functions of substrates, including signaling transduction, protein conformation change, chromatin remodeling, proteasomal degradation, and lysosomal degradation, are further determined by the ubiquitin receptors. d Ubiquitin-independent targeted protein degradation includes 20S proteasome-mediated protein degradation and chaperone-mediated autophagy

Fig. 2

Protein degradation regulates drug efflux. ABCC1, ABCB1, and ABCG2 are the three main drug transporters. NEDDL ligases the ubiquitin chain to ABCC1, while USP22 and USP24 eliminate the ubiquitin chain. CUL3 regulates ABCC1 expression by modulating the degradation of NRF2. MARCH8, FBXO15, and FBXO21 ligase the ubiquitin chain on ABCB1, and USP24 acts as the DUB. USP24 is the DUB of ABCG2. RNF180 and UCHL3 indirectly regulate the expression of ABCG2

Fig. 3

Protein degradation modulates drug metabolism. Drug metabolism can be categorized into Phase I (oxidation, reduction, and hydrolysis) and Phase II (posttranslational modification), requiring different classes of drug metabolic enzymes. In Phase I drug metabolism, CHIP and AMFR can ubiquitinate the CYP3A family for degradation. In Phase II, SULT1A3 is regulated by ubiquitin-dependent protein degradation

Fig. 4

Regulatory functions of ubiquitination in DNA repair. E3 ligases usually participate in DNA damage response and DNA double-strand repair through degradation-dependent function. Specifically, during DNA damage response, H2AX can be degraded through SMURF2 and HUWEI-mediated ubiquitination, and USP3, USP22, and USP17L2 can eliminate the ubiquitin chains. During homologous recombination, BRCA1 can be degraded by HERC2 and stabilized by USP9X. In the NHEJ process, XRCC4 is ubiquitinated by FBXW7 for degradation. DNA-PK is degraded through RNF144A-mediated ubiquitination. During mismatch repair, HDAC6 ubiquitinates MSH2 for further protein degradation, which can be reversed by USP10. In the regulation of cell cycle check points, RNF4 promotes ubiquitination of MDC1, and ataxin-3 and USP7 deubiquitinate MDC1, therefore controlling the stability of MDC1. MDM2 facilitates the ubiquitinoylation of p53 for degradation, while USP4, USP24, USP7, and USP28 remove the ubiquitin chain. USP7 stabilizes CDC25A. PIRH2 and SIAH2 promote ubiquitin-dependent degradation of CHK2, and USP39 eliminates the ubiquitin chains. HDAC6 and HUWEI induce CHK1 ubiquitination, while USP3 and USP7 deubiquitinate the CHK1

Fig. 5

Protein degradation regulates the efficacy of targeted therapy and chemotherapy. SOCS5, CGRRF1, and Cbl-b promote ubiquitination and subsequent endocytosis of the EGFR, while UPS22, STAMBP, UCHL1, and OTUD7B deubiquitinate EGFR. E3 ligases FBXW7 and RNF149 facilitate ubiquitination of BRAF. USP28 regulates the stability of BRAF by deubiquitinating FBXW7. ANAPC2, β-TrCP, and LZTR1/CUL3 complexes promote KRAS ubiquitination for degradation. E3 ligase TRIM15 and CYLD regulate the ubiquitination and deubiquitylation of ERK, respectively. E3 ligase MAGI3 and FBW7α facilitate the ubiquitination of c-Myc, and USP22, USP28, and OTUD6A stabilize c-Myc. Anti-apoptosis protein FLIP can be stabilized through USP2-mediated deubiquitylation. BCL-2 is ubiquitinated by AMFR and CHIP. MCL-1 can be ubiquitinated by HUWEI and deubiquitylated by USP9X, USP13, or USP17

Fig. 6

Protein degradation involved in EMT and cell stemness. Degradation of E-cadherin is regulated by E3 ligases RNF25, RNF43, and Hakai. Protein degradation of mesenchymal marker ZEB1 is mediated by E3 ligase SIAH1 and can be reversed by USP51. Snail is ubiquitinated by FBXO32 and deubiquitinated by USP1. For stemness sustaining pathways, β-TrCP participates in the ubiquitination of both YAP and β-catenin. In addition, STUB1 also facilitates the ubiquitination of YAP. USP10 facilitates deubiquitylation of YAP, and USP20, USP4, and USP22 deubiquitinate β-catenin

Fig. 7

Protein degradation modulates the tumor microenvironment. IKK can be stabilized by CYLD to facilitate the phosphorylation of IκB, which can be reversed by KEAP1-mediated ubiquitylation on IKK. β-TrCP induces activation of the NF-κB pathway by ubiquitinating IκB, resulting in nucleus translocation of the NF-κB complex. β-TrCP and KEAP1 facilitate NRF2 degradation, while USP17 can deubiquitinate NRF2. KEAP1 can also be regulated by DUB USP15. Under hypoxic conditions, HIF-1α can translocate into the nucleus and facilitate transcription of hypoxic genes. While under normoxia, HIF-1α can be oxidated and further ubiquitinated by VHL for degradation. USP22, USP29, and USP14 can deubiquitylate HIF-1α

Fig. 8

Current technologies targeting protein degradation. a PROTAC is designed to conjugate specific E3 ligases and proteins of interest for further degradation. b Based on the E3 ligase activity of IAPs, SNIPERs conjugate IAPs and proteins of interest for degradation. c TRIM21 has high affinity for antibodies. Therefore, using specific antibodies against the proteins of interest can lead to rapid degradation. d AUTAC is a heterobifunctional compound with a targeting warhead and a tag that recruits the autophagy system, which may lead to ubiquitin-dependent selective degradation through lysosomal degradation. e AUTOTAC connects the protein of interest and p62 for autophagy-induced protein degradation. f ATTEC conjugates the protein of interest and LC3 for degradation. g LYTAC interacts with membrane proteins or extracellular proteins and the CI-M6PR for endocytosis