Introduction
The SKP1, CUL1, F-box protein (SCF) complex is an E3 ubiquitin ligase that orchestrates the attachment of ubiquitin chains to protein targets, thereby regulating diverse biological processes such as protein localization, activity modulation, and proteolytic degradation through the ubiquitin-proteasome system (UPS). Among its functions, the poly-ubiquitination of proteins by the SCF complex leading to their degradation via the 26S proteasome is particularly well-studied and crucial for maintaining genome stability. This is achieved through the temporal regulation of various cellular processes, including signaling cascades, cell cycle progression, DNA repair, and apoptosis. Hence, genetic alterations in the SCF complex components can disrupt these processes and promote cancer development and progression.
Fig. 1 The SCF complex orchestrates proteolytic degradation by the 26S proteasome. (Thompson L. L., et al. 2021)
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Ubiquitin-Dependent Proteasomal Degradation
The UPS is a major intracellular protein degradation mechanism, essential for the temporal and spatial regulation of protein abundance. The UPS comprises proteins and enzymes that collectively regulate protein targets' abundance through two successive steps. First, a ubiquitin moiety covalently attaches to a lysine residue within a protein target and is modified by additional ubiquitin moieties, forming a poly-ubiquitin chain. The poly-ubiquitinated protein is then transported to the 26S proteasome for proteolytic degradation.
The 26S proteasome, a 2.5 megadalton macromolecular structure, contains a cylindrical 20S catalytic subunit with peptidase activity and a ring-shaped 19S regulatory subunit with structural components, ubiquitin receptors, and ATPases that bind, denature, and translocate protein targets into the 20S proteolytic core. Substrate poly-ubiquitination gives the UPS high specificity, facilitated by three successive enzymes: an E1 ubiquitin-activating enzyme, an E2 ubiquitin-conjugating enzyme, and an E3 ubiquitin ligase. These enzymes are responsible for ATP-dependent ubiquitin activation by E1, conjugation of ubiquitin to E2, and transfer of ubiquitin to the protein target by E3, forming a poly-ubiquitin chain linked by a series of lysine 48 (K48) to glycine 76 (G76) isopeptide bonds.
The E3 enzyme dictates the UPS substrate specificity, with approximately 650 E3 ubiquitin ligases existing within the human genome. These enzymes are categorized into four main groups based on their E2-binding structural motifs, including the HECT, U-box, PHD-finger, and RING-finger types. The largest subfamily is the Cullin-based, RING-finger type E3 enzyme, of which the SCF complex is considered the prototypical example.
The SCF Complex
The SCF complex consists of three invariable core components: RBX1, a RING-finger protein that recruits the E2 ubiquitin-conjugating enzyme; CUL1, the scaffolding protein; and SKP1, the invariable adaptor component bridging the core SCF complex with a variable F-box protein and its corresponding protein target. The F-box proteins impart target specificity to the SCF complex, recognizing and binding distinct sets of substrates. In humans, there are 69 F-box proteins, organized into three families based on their substrate recognition domains: FBXW, FBXL, and FBXO.
To control the abundance of specific protein targets, each F-box protein recruits one of its substrates (often phospho-activated) to the core SCF complex, facilitating polyubiquitination and subsequent degradation by the 26S proteasome. The presence of 69 different F-box genes implies up to 69 unique SCF complexes, each regulating myriad protein targets. Additionally, SCF complex members like SKP1 and RBX1 interact with non-prototypical binding partners to form additional E3 ubiquitin ligase complexes regulating other protein targets.
Unfortunately, the protein targets and functions for many F-box proteins and corresponding SCF complexes remain largely unknown in humans. However, a few well-characterized F-box proteins, like SKP2 and βTrCP, regulate essential genome stability processes like cell cycle progression and DNA repair. Thus, in-depth genetic and biochemical studies are crucial to advance our understanding of each SCF complex's specific protein targets and the biological processes they regulate. Understanding the roles of SCF complex components (e.g., SKP1, CUL1, RBX1, and the F-box proteins) is essential, as genetic alterations involving these E3 subunits significantly impact the cell and are often implicated in diseases like cancer.
The SCF Complex Regulates Transcription and Cancer-Associated Signaling Pathways
The SCF complex plays a crucial role in gene transcription regulation and numerous cancer-related cell signaling pathways. Specific SCF complexes, such as SCFβTrCP and SCFFBXO28, regulate the levels and activities of proto-oncogenic transcription factors such as Snail, β-catenin, and MYC. These transcription factors promote cancer-associated phenotypes like increased cellular proliferation and migration.
For example, Snail, a transcriptional repressor of E-cadherin, is poly-ubiquitinated and targeted for degradation by SCFβTrCP following phosphorylation by glycogen synthase kinase 3 (GSK3). Disruption of this process leads to increased Snail levels, driving epithelial to mesenchymal transition (EMT), cellular migration, and cancer metastasis. Similarly, β-catenin, a key component of the canonical WNT signaling pathway, is phospho-activated by GSK3, enabling SCFβTrCP-mediated poly-ubiquitination and degradation. Mutations interfering with β-catenin phosphorylation lead to β-catenin accumulation and constitutive WNT pathway activation, driving tumor development.
Interestingly, not all poly-ubiquitinated SCF substrates are targeted for proteasomal degradation. For instance, FBXO28 acts as a transcriptional co-factor to positively regulate MYC target gene expression. Rather than being targeted for degradation, poly-ubiquitinated MYC interacts with phosphorylated FBXO28 at MYC target gene promoters to recruit chromatin remodeling enzymes, increasing MYC-driven transcription and promoting tumorigenesis.
SCF Complex Activity in Cell Cycle Control and Tumorigenesis
The SCF complex is vital in controlling cell cycle progression, coordinating with the anaphase-promoting complex/cyclosome (APC/C) for regulated transitions through cell cycle phases. It facilitates G1 to S-phase transition by degrading inhibitors and promoting cyclin-CDK activities necessary for DNA synthesis. Similarly, SCF complexes regulate S-phase progression and mitotic entry by targeting and degrading specific cell cycle regulators.
Disruptions in SCF functions, such as mutations in βTrCP and SKP2, are linked to cancers, leading to unchecked proliferation and genome instability. βTrCP and SKP2 overexpression or loss in specific cancers (colorectal, pancreatic, gastric) correlates with tumor progression. Conversely, tumor suppressor F-box proteins like FBXO4 and FBXW7 often exhibit loss-of-function mutations in cancers, disrupting cell cycle control.
Core SCF Complex Members Alterations in Cancer
Genetic aberrations in the core SCF components (SKP1, CUL1, RBX1) can inflict broader disruptions than those in individual F-box proteins. Reduced expression of these core components induces chromosomal instability (CIN), driving cancer development and progression. The Cancer Genome Atlas (TCGA) data suggests that SKP1, CUL1, and RBX1 are altered in various cancers, with significant copy number variations contributing to dysregulation.
The distribution of mutations throughout SKP1, CUL1, and RBX1 genes indicates their potential tumor suppressor roles, necessitating further research to delineate their impacts on cell cycle and tumorigenesis. Gene expression analyses reveal positive correlations between copy number variations and altered gene expression in cancers, aligning with observed tumor suppressor- and oncogene-like activities.
Targeting the SCF Complex for Cancer Treatments
Exploiting SCF complex components for cancer treatment is complex due to their extensive role in regulating critical pathways. Broad-spectrum approaches like proteasome inhibitors (e.g., Bortezomib) or indirect SCF inhibitors (e.g., MLN4924) have shown some effectiveness in treating leukemia, lymphoma, and myeloma. Therapeutic strategies targeting aberrant SKP1, CUL1, or RBX1 expression and function represent promising avenues.
Synthetic genetic approaches, such as synthetic lethality or dosage lethality, could exploit genetic aberrations driving cancer development. Low-dose SCF inhibitors may benefit cancers with shallow deletions. Another emerging strategy is PROTACS, chimeric proteins that link a protein target to an F-box protein for SCF-mediated degradation, targeting overexpressed proteins in specific tissues.
Conclusion
The SCF complex's involvement in numerous biological pathways critical for cell cycle control, genome stability, and transcription regulation underlines its significance in cancer pathogenesis. Genetic and biochemical studies must advance our understanding of SCF components to translate these insights into clinical therapies effectively. Exploiting aberrations in SCF complex expression holds potential for novel precision medicine approaches, ultimately aiming to improve cancer patient outcomes. Understanding the intricate dynamics of SCF complexes will pave the way for innovative therapeutic strategies targeting the underlying genetic and molecular foundations of cancer.
References
- Thompson L. L., et al. The SCF complex is essential to maintain genome and chromosome stability. International Journal of Molecular Sciences. 2021, 22(16): 8544.
- Yumimoto K., et al. F-box proteins and cancer. Cancers. 2020, 12(5): 1249.
- Skaar J. R., et al. SCF ubiquitin ligase-targeted therapies. Nature reviews Drug discovery. 2014, 13(12): 889-903.
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