When protein destruction runs amok, malignancy is on the loose

Transforming growth factor beta facilitates beta-TrCP-mediated degradation of Cdc25A in a Smad3-dependent manner

Ubiquitin-dependent degradation of Cdc25A is a major mechanism for damage-induced S-phase checkpoint. Two ubiquitin ligases, the Skp1-cullin-beta-TrCP (SCFbeta-TrCP) complex and the anaphase-promoting complex (APCCdh1), are involved in Cdc25A degradation. Here we demonstrate that the transforming growth factor beta (TGF-beta)-Smad3 pathway promotes SCF(beta-TrCP)-mediated Cdc25A ubiquitination. Cells treated with TGF-beta, as well as cells transfected with Smad3 or a constitutively active type I TGF-beta receptor, exhibit increased ubiquitination and markedly shortened half-lives of Cdc25A. Furthermore, Cdc25A is stabilized in cells transfected with Smad3 small interfering RNA (siRNA) and cells from Smad3-null mice. TGF-beta-induced ubiquitination is associated with Cdc25A phosphorylation at the beta-TrCP docking site (DS82G motif) and physical association of Cdc25A with Smad3 and beta-TrCP. Cdc25A mutant proteins deficient in DS82G phosphorylation are resistant to TGF-beta-Smad3-induced degradation, whereas a Cdc25A mutant protein defective in APCCdh1 recognition undergoes efficient degradation. Smad3 siRNA inhibits beta-TrCP-Cdc25A interaction and Cdc25A degradation in response to TGF-beta. beta-TrCP2 siRNA also inhibits Smad3-induced Cdc25A degradation. In contrast, Cdh1 siRNA had no effect on Cdc25A down-regulation by Smad3. These data suggest that Smad3 plays a key role in the regulation of Cdc25A ubiquitination by SCFbeta-TrCP and that Cdc25A stabilization observed in various cancers could be associated with defects in the TGF-beta-Smad3 pathway.

Targeting beta-transducin repeat-containing protein E3 ubiquitin ligase augments the effects of antitumor drugs on breast cancer cells

beta-Transducin repeat-containing proteins (beta-TrCP) serve as substrate recognition component of E3 ubiquitin ligases that control stability of important regulators of cell cycle and signal transduction. beta-TrCP function is essential for the induction of nuclear factor kappaB transcriptional activities, which play a key role in proliferation and survival of cancer cells and are often constitutively up-regulated in human breast cancers. Here we show that inhibition of beta-TrCP either by RNAi approach or by forced expression of a dominant-negative beta-TrCP mutant suppresses growth and survival of human breast cancer cells. In addition, inhibition of beta-TrCP augments the antiproliferative effects of anticancer drugs such as doxorubicin, tamoxifen, and paclitaxel on human mammary tumor cells. These data provide the proof of principle that targeting beta-TrCP might be beneficial for anticancer therapies.

Cell cycle, proteolysis and cancer

Research in the past 15 years has shown that the mammalian cell cycle is controlled by the action of cyclin-dependent kinases (CDKs). A crucial substrate of the CDKs in G1-phase is the retinoblastoma tumor suppressor (pRB), which restrains proliferation largely by repressing the activity of the E2F transcription factors. More recent work has shown that the cell cycle is also a tale of two classes of ubiquitin ligases, referred to as SCF and APC/C ligases. CDKs, E2F and ubiquitin ligases reciprocally regulate each other, resulting in complex feedback loops. Perturbation of this network of molecular machines is associated with proliferative diseases, including cancer.

Mechanisms of delivery of ubiquitylated proteins to the proteasome: new target for anti-cancer therapy?

The proteasome is the main proteolytic machinery of the cell. It is responsible for the basal turnover of many intracellular polypeptides, the elimination of abnormal proteins and the generation of the vast majority of peptides presented by class I major histocompatibility complex molecules. Proteasomal proteolysis is also involved in the control of virtually all cellular functions and major decisions through the spatially and timely regulated destruction of essential cell regulators. Therefore, the elucidation of its molecular mechanisms is crucial for the full understanding of the physiology of cells and whole organisms. Conversely, it is increasingly clear that proteasomal degradation is either altered in numerous pathological situations, including many cancers and diseases resulting from aberrant cell differentiation, or instrumental for the development of these pathologies. This, consequently, makes it an attractive target for therapeutical intervention. There is ample evidence that most cell proteins must be polyubiquitylated prior to proteasomal degradation. If the structure and the mode of functioning of the proteasome, as well as the enzymology of ubiquitylation, are relatively well understood, how substrates are delivered to and recognized by the proteolytic machine has remained mysterious till recently. The recent literature indicates that the mechanisms involved are multiple, complex and exquisitely regulated and provides new potential targets for anti-cancer pharmacological intervention.

Function and regulation of cullin-RING ubiquitin ligases

Cullin-RING complexes comprise the largest known class of ubiquitin ligases. Owing to the great diversity of their substrate-receptor subunits, it is possible that there are hundreds of distinct cullin-RING ubiquitin ligases in eukaryotic cells, which establishes these enzymes as key mediators of post-translational protein regulation. In this review, we focus on the composition, regulation and function of cullin-RING ligases, and describe how these enzymes can be characterized by a set of general principles.

La dégradation protéasomique : De l’adressage des protéins aux nouvelles perspectives thérapeutiques

The proteasome is the main intracellular proteolytic machinery. It is involved in all major cellular functions and decisions. It has long been thought that prior ubiquitinylation of almost all of its substrates was necessary for degradation. It has also long been considered that ubiquitinylation and degradation were two uncoupled mechanisms and that the recruitment of ubiquitinylated species was only performed by specialized subunits of the proteasome. The recent literature questions this simplified view. It also suggests that, on the one hand, the fraction of proteins hydrolyzed by the proteasome independently of their ubiquitinylation has largely been underestimated and, on the other hand, that the recognition of ubiquitinylated proteins involves complex addressing systems. Furthermore, it indicates a higher order structuration of the ubiquitin/proteasome pathway, a fraction of the proteasome and of ubiquitinylation enzymes being engaged in supramolecular complexes. Finally, proteasomal degradation is altered in a number of pathological situations. It, thus, constitutes a therapeutic target and the first applications are emerging.

In Vitro Screening for Substrates of the N‐End Rule–Dependent Ubiquitylation

We describe a systematic, high-throughput approach to the discovery of protein substrates of ubiquitylation. This method uses a library of cDNAs in combination with a reticulocyte lysate-based, transcription-translation system that acts as both an excellent means for high-throughput protein expression and a source of ubiquitylation enzymes. Ubiquitylation of newly expressed proteins occurs in this milieu from the action of any one of a number of E3 ligases that are present in the lysate. Specific detection of ubiquitylated proteins is carried out using electrochemiluminescence-based assays in conjunction with a multiplexing scheme that provides replicate measurements of the ubiquitylated products and two controls in each well of a microtiter plate. We used this approach to identify putative substrates of the N-end rule-dependent ubiquitylation (mediated by the UBR family of ubiquitin ligases), a system already well known to have high endogenous activity in reticulocyte lysates. We screened a library of approximately 18,000 cDNA clones, one clone per well, by expressing them in reticulocyte lysate and measuring the extent of modification. We selected approximately 500 proteins that showed significant ubiquitylation. This set of modified proteins was redacted to approximately 60 potential substrates of the N-end rule pathway in a secondary screen that involved looking for inhibition of ubiquitylation in reticulocyte lysates supplemented with specific inhibitors of the N-end rule ubiquitylation. We think our system provides a general approach that can be extended to the identification of substrates of other E3 ligases.

Breast cancer risk associated with genotypic polymorphism of the mitosis-regulating geneAurora-A/STK15/BTAK

Aneuploidy, an abnormal number of chromosomes, is relatively common and occurs early in breast cancer development. This observation supports a breast tumorigenic contribution of mechanisms responsible for maintaining chromosome number stability in which centrosomes play an essential role. We therefore speculated that the Aurora-A/STK15/BTAK gene, implicated in the regulation of centrosome duplication, may be associated with breast tumorigenesis. To test this hypothesis, we conducted a case-control study of 709 primary breast cancer patients and 1,972 healthy controls, examining single-nucleotide polymorphisms (SNPs), including a suggested functional Phe31Ile SNP, in Aurora-A. We were also interested in knowing whether any association between Aurora-A and breast cancer was modified by reproductive risk factors reflecting susceptibility to estrogen exposure. Our hypothesis is that, since estrogen is known to promote breast cancer development via its mitogenic effect leading to malignant proliferation on breast epithelium and since Aurora-A is involved in regulating mitosis, the discovery of a joint effect between the Aurora-A genotype and reproductive risk factors on cancer risk might yield valuable clues to the association of breast tumorigenesis with estrogen. Support for this hypothesis came from the following observations. (i) Two SNPs in Aurora-A were significantly associated with breast cancer risk (p < 0.05). (ii) Haplotype analyses, based on different combinations of multiple SNPs in Aurora-A, revealed a strong association with breast cancer risk; interestingly, the genotypic distribution of the suggested functional Phe31Ile SNP was not significantly different between breast cancer patients and controls, but the specific haplotype containing the putative at-risk Ile allele was more common in patients. (iii) This association between risk and putative high-risk genotypes was stronger and more significant in women thought to be more susceptible to estrogen, i.e., those with a longer interval between menarche and first full-term pregnancy. (iv) The protective effect conferred by a history of full-term pregnancy was significant only in women with a putative low-risk genotype of Aurora-A. Our study provides new findings supporting the mutator role of Aurora-A in breast cancer development, suggesting that breast cancer could be driven by genomic instability associated with variant Aurora-A, the tumorigenic contribution of which could be enhanced as a result of increased mitosis due to estrogen exposure.

Role of Cks1 overexpression in oral squamous cell carcinomas: cooperation with Skp2 in promoting p27 degradation

Down-regulation of p27 is frequently observed in various cancers due to an enhancement of its degradation. Skp2 is required for the ubiquitination and consequent degradation of p27 protein. Another protein called Cks1 is also required for p27 ubiquitination in the SCF(Skp2) ubiquitinating machinery. In the present study, we examined Cks1 expression and its correlation with p27 in oral squamous cell carcinoma (OSCC) derived from tongue and gingiva. By immunohistochemical analysis, high expression of Cks1 was present in 62% of OSCCs in comparison with 0% of normal mucosae. In addition, 65% of samples with low p27 expression displayed high Cks1 levels. Finally, Cks1 expression was well correlated with Skp2 expression and poor prognosis. To study the role of Cks1 overexpression in p27 down-regulation, we transfected Cks1 with or without Skp2 into OSCC cells. Cks1 transfection could not induce a p27 down-regulation by itself, but both Cks1 and Skp2 transfection strongly induced. Moreover, we inhibited Cks1 expression by small interference RNA (siRNA) in OSCC. Cks1 siRNA transfection induced p27 accumulation and inhibited the growth of OSCC cells. These findings suggest that Cks1 overexpression may play an important role for OSCC development through Skp2-mediated p27 degradation, and that Cks1 siRNA can be a novel modality of gene therapy.

Genome-scale profiling of gene expression in hepatocellular carcinoma: classification, survival prediction, and identification of therapeutic targets

The heterogeneous nature of human hepatocellular carcinoma (HCC) has hampered both treatment and prognostic predictions. Gene expression profiles of human HCC were analyzed to define the molecular characteristics of the tumors and to test the prognostic value of the expression profiles. By applying global gene expression analyses, including unsupervised and supervised methods, 2 distinctive subclasses of HCC that were highly homogeneous for both the underlying biology and the clinical outcome were discovered. Tumors from the low survival subclass had strong cell proliferation and antiapoptosis gene expression signatures. In addition, the low survival subclass displayed higher expression of genes involved in ubiquitination and sumoylation, suggesting an etiologic involvement of these processes in accelerating the progression of HCC. Genes most strongly associated with survival were identified by using the Cox proportional hazards survival analysis. This approach identified a limited number of genes that accurately predicted the length of survival and provided new molecular insights into the pathogenesis of HCC. Future studies will evaluate potential diagnostic markers and therapeutic targets identified during the global gene expression studies. Furthermore, cross-species similarity of gene expression patterns will also allow prioritization of a long list of genes obtained from human gene expression profiling studies and focus on genes whose expression is altered during tumorigenesis in both species.

The SCF ubiquitin ligase: insights into a molecular machine

Ubiquitin ligases are well suited to regulate molecular networks that operate on a post-translational timescale. The F-box family of proteins - which are the substrate-recognition components of the Skp1-Cul1-F-box-protein (SCF) ubiquitin ligase - are important players in many mammalian functions. Here we explore a unifying and structurally detailed view of SCF-mediated proteolytic control of cellular processes that has been revealed by recent studies.

N-Terminal ubiquitination of extracellular signal-regulated kinase 3 and p21 directs their degradation by the proteasome

Extracellular signal-regulated kinase 3 (ERK3) is an unstable mitogen-activated protein kinase homologue that is constitutively degraded by the ubiquitin-proteasome pathway in proliferating cells. Here we show that a lysineless mutant of ERK3 is still ubiquitinated in vivo and requires a functional ubiquitin conjugation pathway for its degradation. Addition of N-terminal sequence tags of increasing size stabilizes ERK3 by preventing its ubiquitination. Importantly, we identified a fusion peptide between the N-terminal methionine of ERK3 and the C-terminal glycine of ubiquitin in vivo by tandem mass spectrometry analysis. These findings demonstrate that ERK3 is conjugated to ubiquitin via its free NH(2) terminus. We found that large N-terminal tags also stabilize the expression of the cell cycle inhibitor p21 but not that of substrates ubiquitinated on internal lysine residues. Consistent with this observation, lysineless p21 is ubiquitinated and degraded in a ubiquitin-dependent manner in intact cells. Our results suggests that N-terminal ubiquitination is a more prevalent modification than originally recognized.

Classification and prediction of survival in hepatocellular carcinoma by gene expression profiling

We analyzed global gene expression patterns of 91 human hepatocellular carcinomas (HCCs) to define the molecular characteristics of the tumors and to test the prognostic value of the expression profiles. Unsupervised classification methods revealed two distinctive subclasses of HCC that are highly associated with patient survival. This association was validated via 5 independent supervised learning methods. We also identified the genes most strongly associated with survival by using the Cox proportional hazards survival analysis. This approach identified a limited number of genes that accurately predicted the length of survival and provides new molecular insight into the pathogenesis of HCC. Tumors from the low survival subclass have strong cell proliferation and antiapoptosis gene expression signatures. In addition, the low survival subclass displayed higher expression of genes involved in ubiquitination and histone modification, suggesting an etiological involvement of these processes in accelerating the progression of HCC. In conclusion, the biological differences identified in the HCC subclasses should provide an attractive source for the development of therapeutic targets (e.g., HIF1a) for selective treatment of HCC patients. Supplementary material for this article can be found on the HEPATOLOGY Web site (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html)

Control of DNA synthesis and mitosis by the Skp2-p27-Cdk1/2 axis

A new study reveals a novel role for p27 in inhibiting Cdk1 activity at G2/M and shows that p27 deficiency almost completely rescues the aberrations observed in Skp2(-/-) mice, demonstrating that p27 is the principal downstream effector of the SCF(Skp2) ubiquitin ligase.

Interwoven Ubiquitination Oscillators and Control of Cell Cycle Transitions

Ubiquitin-mediated proteolysis has emerged as a paramount mechanism for regulating the cell division cycle. Changes in the activities of certain E3 ligases can promote the interconversion of cell cycle states or transitions. Recent studies have revealed how distinct E3 ligases control the activity of other E3 ligases and how the interplay between these degradation machines sets up the timing of cell cycle transitions. For example, during G1, the anaphase-promoting complex in conjunction with Cdh1 (APC(Cdh1)) catalyzes destruction of the S-phase activator Skp2, helping to define the G1 state. In response to poorly defined signals, APC(Cdh1) activity is reduced, allowing accumulation of Skp2 and therefore entry into S phase. In many cases, E3 ligases also function to ubiquitinate proteins that negatively regulate cell cycle transitions. Recent work indicates that cyclin-dependent kinase 2 and Polo kinase collaborate to phosphorylate Wee1, thereby promoting its ubiquitination by SCF(beta-TRCP). Thus, activation of the mitotic transition produces feedback signals that help to turn off the negative upstream pathway to further reenforce the transition.

Oncogenic aberrations of cullin-dependent ubiquitin ligases

Accumulating evidence points to a key role of the ubiquitin-proteasome pathway in oncogenesis. Aberrant proteolysis of substrates involved in cellular processes such as the cell division cycle, gene transcription, the DNA damage response and apoptosis has been reported to contribute significantly to neoplastic transformation. Cullin-dependent ubiquitin ligases (CDLs) form a class of structurally related multisubunit enzymes central to the ubiquitin-mediated proteolysis of many important biological substrates. In this review, we describe the role of CDLs in the ubiquitinylation of cancer-related substrates and discuss how altered ubiquitinylation by CDLs may contribute to tumor development.

Control of the SCFSkp2–Cks1 ubiquitin ligase by the APC/CCdh1 ubiquitin ligase

Skp2 and its cofactor Cks1 are the substrate-targeting subunits of the SCF(Skp2-Cks1) (Skp1/Cul1/F-box protein) ubiquitin ligase complex that regulates entry into S phase by inducing the degradation of the cyclin-dependent kinase inhibitors p21 and p27 (ref. 1). Skp2 is an oncoprotein that often shows increased expression in human cancers; however, the mechanism that regulates its cellular abundance is not well understood. Here we show that both Skp2 and Cks1 proteins are unstable in G1 and that their degradation is mediated by the ubiquitin ligase APC/C(Cdh1) (anaphase-promoting complex/cyclosome and its activator Cdh1). Silencing of Cdh1 by RNA interference in G1 cells stabilizes Skp2 and Cks1, with a consequent increase in p21 and p27 proteolysis. Depletion of Cdh1 also increases the percentage of cells in S phase, whereas concomitant downregulation of Skp2 reverses this effect, showing that Skp2 is an essential target of APC/C(Cdh1). Expression of a stable Skp2 mutant that cannot bind APC/C(Cdh1) induces premature entry into S phase. Thus, the induction of Skp2 and Cks1 degradation in G1 represents a principal mechanism by which APC/C(Cdh1) prevents the unscheduled degradation of SCF(Skp2-Cks1) substrates and maintains the G1 state.

Fluorescent probes for proteolysis: tools for drug discovery

Our body contains many different protease and proteolytic systems that are involved in the recycling of proteins into amino acids, and also in a multitude of regulatory events inside and outside cells. Proteases are prominent drug targets because of their well-defined chemistry and their implication in a large number of diseases, such as cancer, neurodegeneration, arteriosclerosis, inflammation and infection.

Fluorescent reporter substrates can be used to directly probe the activities of proteases in their natural environment — that is, in cells and organisms. Conceptually different strategies have been used for this purpose depending on the location and the nature of the protease of interest.

Fluorescent reporters for the ubiquitin–proteasome system have been generated by linking constitutively active degradation signals to green fluorescent protein (GFP). These GFP-based substrates can be used for functional analysis of the ubiquitin–proteasome system in cells and transgenic animals.

A collection of different proteases is involved in degradation of small peptide fragments. This process can be followed in real time in living cells by confocal laser scanning microscopy after microinjection of internally quenched peptide substrates.

Extracellular and lysosomal proteases have the advantage that they are accessible for membrane-impermeable reporter substrates. Near-infrared fluorescence (NIRF) substrates are quenched fluorescent peptides that, because of their near-infrared excitation, can be readily detected in living animals and used for in vivo monitoring of, for example, lysosomal cathepsins or surface matrix metalloproteinases.

By combining specific pairs of fluorescent proteins (GFP and its variants with shifted excitation and emission spectra) in fusion proteins, fluorescence energy transfer (FRET) reporter substrates have been generated for initiator and effector caspases.

A fluorescent intracellular reporter for human immunodeficiency virus (HIV-1) protease activity was constructed by fusing a protease precursor protein composed of HIV-1 protease and GFP. Cells will only survive and emit fluorescence when the toxic protease activity is sufficiently blocked by drugs.

The diffusion rate of the endoplasmic reticulum-resident peptide transporter complex TAP correlates with activity and thus cytosolic peptide levels. By measuring the diffusion of TAP–GFP fusions with fluorescence recovery after photobleaching (FRAP), the kinetics of peptide generation can be followed in living cells.

Cells contain numerous proteases, which are found at many different locations. These proteases recognize an even larger number of different substrates and are involved in almost every process in the cell. Aberrations in proteolysis are linked to a plethora of diseases, such as cancer, inflammation, arteriosclerosis, neurodegeneration and infection. Because of their well-defined chemistry and key role in pathologies, proteases have been important targets for drug development. Recent progress in the development of fluorescent probes has opened up the possibility of visualizing protease activities in the natural environment of the cell. We will describe various strategies to follow protease activities in cells and organisms.

Regulation of lung cancer cell growth and invasiveness by ?-TRCP

Beta-transducin-repeat-containing protein (beta-TRCP) serves as a substrate-recognition subunit of Skp1/Cullin/F-box (SCF)(beta-TRCP) E3 ligases, involved in regulation of several important signaling molecules. SCF(beta-TRCP) E3 ligases play a critical role in cell mitosis as well as in various signaling pathways. Here, we provide evidence to support that beta-TRCP negatively regulates cell growth and motility of lung cancer cells. With specific antibodies, we detect loss of beta-TRCP1 protein in several lung cancer cell lines. One cell line contains an inactivated mutation of the beta-TRCP1 gene. Loss of beta-TRCP1 protein is also found in subsets of lung cancer specimens. We observe that retrovirus-mediated stable expression of beta-TRCP1 in beta-TRCP1 negative cells inhibits cell growth in soft-agar and tumor formation in nude mice. Furthermore, expression of beta-TRCP1 alters cell motility, as indicated by morphological changes and a reduced level of active matrix metalloproteinase (MMP)11. Conversely, inactivation of beta-TRCP1 by specific siRNA accelerates cell invasion. Of the 10 known substrates of SCF(beta-TRCP) E3 ligases, the protein level of cell division cycle 25 (CDC25)A is clearly affected in these lung cancer cells. Cells treated with CDC25A inhibitors become less invasive. Thus, loss of beta-TRCP1 may promote both growth and cell motility of lung cancer cells, possibly through regulation of CDC25A and the MMP11 level.

Defective autophagy leads to cancer

Cellular proteins are degraded within two distinct compartments: the proteasome and the lysosome. Alterations in proteasomal degradation can contribute to carcinogenesis. In contrast, alterations in autophagic protein degradation through the lysosome have not been linked to cancer. Now two reports demonstrate that the autophagic gene, Beclin 1, is a haploinsufficient tumor suppressor gene. These new data suggest that autophagic degradation provides an important mechanism to prevent cellular transformation.