Balancing Protein Stability and Activity in Cancer: A New Approach for Identifying Driver Mutations Affecting CBL Ubiquitin Ligase Activation

Oncogenic mutations in the monomeric Casitas B-lineage lymphoma (Cbl) gene have been found in many tumors, but their significance remains largely unknown. Several human c-Cbl (CBL) structures have recently been solved, depicting the protein at different stages of its activation cycle and thus providing mechanistic insight underlying how stability-activity tradeoffs in cancer-related proteins-may influence disease onset and progression. In this study, we computationally modeled the effects of missense cancer mutations on structures representing four stages of the CBL activation cycle to identify driver mutations that affect CBL stability, binding, and activity. We found that recurrent, homozygous, and leukemia-specific mutations had greater destabilizing effects on CBL states than random noncancer mutations. We further tested the ability of these computational models, assessing the changes in CBL stability and its binding to ubiquitin-conjugating enzyme E2, by performing blind CBL-mediated EGFR ubiquitination assays in cells. Experimental CBL ubiquitin ligase activity was in agreement with the predicted changes in CBL stability and, to a lesser extent, with CBL-E2 binding affinity. Two thirds of all experimentally tested mutations affected the ubiquitin ligase activity by either destabilizing CBL or disrupting CBL-E2 binding, whereas about one-third of tested mutations were found to be neutral. Collectively, our findings demonstrate that computational methods incorporating multiple protein conformations and stability and binding affinity evaluations can successfully predict the functional consequences of cancer mutations on protein activity, and provide a proof of concept for mutations in CBL.

Abstract 4965: Multiple ubiquitin-conjugating enzymes modulate the ubiquitination and downregulation of the EGFR by the Cbl RING finger ubiquitin ligase

Receptor tyrosine kinases (RTKs) are known drivers of malignant transformation. Many RTKs (e.g., EGFR, MET) are negatively regulated by ubiquitination and degradation mediated by Cbl proteins, a family of RING finger (RF) ubiquitin ligases (E3s). Loss of Cbl protein function is associated with malignant transformation driven by increased RTK activity. E3s such as the Cbl proteins confer specificity to the ubiquitination process and direct the conjugation of ubiquitin to one or more lysines on the target proteins in collaboration with ubiquitin-conjugating enzymes (E2s). We used enzymatic and yeast two-hybrid assays to characterize the E2s that can interact with Cbl proteins. Using an in vitro E3 assay, we found that only the Ube2d family of E2s mediates autoubiquitination of the Cbl proteins. Subsequently, using the yeast two-hybrid system, we found that Ube2e1, Ube2e2, Ube2e3, Ube2l3, Ube2u, Ube2w and Ube2z can interact with Cbl even though they do not support autoubiquitination of Cbl in the in vitro E3 assay. Among these E2s, three Ube2e family members and Ube2w bind to the RF domain of Cbl as demonstrated by the loss of interaction when the RF domain is disrupted. This suggests that Ube2e and Ube2w are relevant to the ubiquitination and degradation of substrates by Cbl. Knockdown of Ube2w decreases downregulation of EGFR in Hela cells. In the in vitro E3 assay we found that Ube2w can increase autoubiquitination of Cbl mediated by ube2d2. Surprisingly, we found that knockdown of Ube2e increases downregulation and ubiquitination of EGFR in HeLa cells. Mechanistically we found that three Ube2e members inhibit autoubiquitination of Cbl mediated by Ube2d2 in vitro. Further, we showed that Ube2e does not affect ubiquitin charging of Ube2d2 by the ubiquitin-activating enzyme (E1) in vitro. This suggests that Ube2e does not compete with Ube2d2 for the E1 under these conditions. Thus, our data suggest that Ube2e acts as a positive modulator of EGFR signaling by competing for Cbl with Ube2d2 and thus prevents ubiquitination and downregulation of the EGFR by Cbl in combination with Ube2d2. Together these data demonstrate that there is an E2 network which modulates the ubiquitination and downregulation of the EGFR by Cbl.

Citation Format: Ke Ma, Philip Ryan, Rachel Klevit, Stanley Lipkowitz. Multiple ubiquitin-conjugating enzymes modulate the ubiquitination and downregulation of the EGFR by the Cbl RING finger ubiquitin ligase. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4965. doi:10.1158/1538-7445.AM2015-4965

Abstract CT326: Pharmacokinetic/pharmacodynamic study of sequence specificity of the PARP inhibitor, olaparib and carboplatin in recurrent women's cancers

Background: Olaparib/carboplatin are active in gBRCA1/2m+ or BRCA-like breast and ovarian cancer (Br/OvCa). Our in vitro data suggest that pretreatment with olaparib before carboplatin attenuates C-induced DNA double stranded breaks (DSBs) and cytotoxicity. We hypothesize olaparib/carboplatin sequence may affect DNA DSBs and toxicity in pts.

Methods: Eligible pts had recurrent women's cancers, normal end-organ function, and evaluable disease. Pts were randomized to arm A or B for intra-pt and inter-cohort analysis of PK/PD endpoints. 21 pts were required per arm for 80% power to determine one SD difference between arms. PBMCs were collected prior to and 24hrs after olaparib or carboplatin on cyc 1&2 for comet DNA damage assay and PAR incorporation ELISA. Toxicity was evaluated q3 wks, and response q2 cyc by RECISTv1.1.

Results: 59 women (age 59 [25-74]; 47 OvCa (26 gBRCAm+)/10 triple negative BrCa [TNBC; 4 gBRCAm+]/1 uterine carcinosarcoma/1 endometrial Ca) were treated. All had prior therapy (median 5[2-14]). Intra-pt comparisons of PD endpoints indicated olaparib/carboplatin yields greater DNA DSBs than olaparib or carboplatin alone (median fold change compared to baseline; 1.21+/- 0.30 SD v. 1.13 or 0.97 [arm A], 1.33 +/- 0.67 SD v. 1.02 or 1.04 [arm B], both p<0.05). Intra-pt and inter-cohort comparisons show no significant differences in DNA DSBs, PAR incorporation and frequencies of Gr3/4 AEs as a function of the order of the schedule. Gr3/4 AEs included neutropenia (22%), anemia (12%), thrombocytopenia (10%), and carboplatin hypersensitivity (3%). Responses (54pts) included 1 CR (2%, 23mo; TNBC) and 23 PR (43%, 9[5-15]mo; 20 OvCa/3 TNBC). gBRCAm+ pts had a higher response rate (RR; 1CR/19 PR) compared to BRCAwt/unknown (4 PR; 65% v. 17%, p<0.001).

Conclusions: Combination O/C induced greater DNA damage than single agents, consistent with the higher than expected RR. However, the O/C sequence did not impact DNA damage, PAR incorporation or toxicity. Olaparib tablets 200mg bid x 7d with carboplatin AUC 4 q 21d is active and tolerable in recurrent women's cancers, especially for gBRCAm+ pts. (NCT01237067)

Treatment schedule armsCycle (cyc) 1Cyc 2Cyc 3-8Cyc 9+Arm AO tablet 200mg bid d1-7⇒C AUC4 d8C AUC4 d1⇒O tablet 200mg bid d2-8O tablet 200mg bid d1-7, C AUC4 d1or2maintenance O tablet 300mg bid

Citation Format: Victoria L. Chiou, Christina Annunziata, Stanley Lipkowitz, Lori Minasian, Nicolas Gordon, Minshu Yu, Seth Steinberg, Nicole Houston, Elise Kohn, Jung-min Lee. Pharmacokinetic/pharmacodynamic study of sequence specificity of the PARP inhibitor, olaparib and carboplatin in recurrent women's cancers. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr CT326. doi:10.1158/1538-7445.AM2015-CT326

Abstract 15: gp78 is a negative regulator of TRAIL-induced apoptosis in breast cancer cells

TNF-related apoptosis inducing ligand (TRAIL) selectively induces apoptosis in transformed cells by activating the extrinsic apoptotic pathway via its cognate receptors on the cell surface, TRAIL receptor 1 and TRAIL receptor 2. Triple negative breast cancer (TNBC) cells (so-called because TNBC lacks estrogen and progesterone receptor expression and Her-2 amplification) have been found to be sensitive to TRAIL while breast cancer cells of other subtypes of disease remain relatively resistant. Unfortunately, the mechanisms that govern sensitivity to TRAIL are not yet understood. The identification and characterization of novel regulators of the TRAIL pathway would provide new insights into the mechanisms that regulate TRAIL and potentially provide therapeutically exploitable molecular targets for the enhancement of TRAIL-based cancer treatments.

In order to identify candidate regulators of the TRAIL pathway, our lab carried out a high-throughput RNAi-mediated screen of ∼1300 genes using the TNBC cell line MB231. One hundred fifty candidate regulators were identified. The RING finger ubiquitin ligase gp78 (also known as AMFR) was identified as a candidate negative regulator of TRAIL sensitivity. gp78 is an endoplasmic reticulum (ER)-residing protein that helps facilitate the retrotranslocation of substrates across the ER membrane into the cytosol during ER-associated protein degradation. This process is critical to maintaining cellular homeostasis by promoting the proteasomal elimination of misfolded proteins and is integral to cell survival. Interestingly, gp78 has previously been found to promote metastasis in a mouse sarcoma model, and in this study, we have further characterized gp78 as an inhibitor of apoptosis.

The initial findings from the RNAi screen were confirmed by carrying out siRNA-mediated knockdown of gp78 in MB231 cells. The cells with inhibited gp78 expression were found to be significantly sensitive to TRAIL-induced caspase-3/7 activity and loss in viability. Knockdown of gp78 using in total 11 independent siRNAs demonstrated a reduction in gp78 expression is associated with TRAIL sensitization. Furthermore, pan-caspase inhibition with the pharmacologic inhibitor ZVAD-FMK completely abrogated sensitization to TRAIL with gp78 knockdown, demonstrating that loss in viability is caspase dependent. These results were further characterized by knocking down gp78 alone or along with one of the initiator caspases, 2, 8, 9, or 10. Loss of the initiator caspases 2 and 8 reduced sensitivity to TRAIL with gp78 knockdown, suggesting that pathways involved in the activation of these caspases in particular may be conferring sensitivity to TRAIL.

In summary, our lab has identified and characterized gp78 as a regulator of TRAIL sensitivity through a caspase-mediated mechanism in breast cancer cells. Continued study is warranted to fully elucidate the molecular mechanisms by which gp78 inhibits TRAIL-induced apoptosis.

Citation Format: Jennifer L. Dine, Sireesha V. Garimella, Kristie Gehlhaus, Magda Grandin, Daniel Letwin, Natasha Caplen, Stanley Lipkowitz. gp78 is a negative regulator of TRAIL-induced apoptosis in breast cancer cells. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 15. doi:10.1158/1538-7445.AM2015-15

Abstract P5-10-05: TRAIL receptor agonists target basal B triple negative breast Cancer (TNBC) that expresses vimentin and axl

Background:

Tumor Necrosis Factor Related Ligand (TRAIL) triggers apoptosis by binding to cell surface receptors. We previously showed that TRAIL receptor agonists preferentially kill TNBC cells with mesenchymal features (Basal B cell lines) through activation of TRAIL Receptor 2 (TRAIL-R2). We used preclinical models to identify predictive biomarkers of TRAIL sensitivity and tested expression of these markers in TNBC patient (pt) samples.

Methods:

We tested sensitivity to the TRAIL-R2 specific agonist drozitumab in vitro using cell viability and caspase assays. We examined expression of the mesenchymal proteins Axl and vimentin(vim) in breast cancer cell lines including TNBC by immunoblotting and using commercially available cDNA microarray data sets. Next, we performed an exploratory analysis on IHC tumor expression of vim and Axl in 53 African American pts with TNBC diagnosed between February 2003 and February 2009. In a retrospective cohort study, overall survival (OS) was calculated from date of surgery until date of death or last follow up. Disease-free survival (DFS) was calculated from the date that the pt was identified as being disease free until date of recurrence or date of last followed without recurrence. The significance of the difference among Kaplan-Meier curves was determined by a log-rank test. Axl, vim, and age at diagnosis values were divided approximately into quartiles based on data from all available pts before being used in actuarial analyses. A Cox proportional hazards analysis was also performed to determine if Axl or vim retained prognostic value after adjusting for other factors jointly associated with outcome. All p-values were two-tailed.

Results:

As previously demonstrated with TRAIL, drozitumab selectively killed Basal B TNBC cell lines. Gene analysis and protein expression demonstrated that vim and Axl were selectively expressed in drozitumab sensitive Basal B cells. Analysis of cDNA microarray data sets showed that approximately 40% of TNBC express high levels of both Axl and vim. IHC confirmed that expression of Axl and vim seen on cDNA microarray was in TNBC tumor cells. In an exploratory analysis of the relationship of vim and Axl expression to OS and DFS, Axl, vim, stage, and response to neoadjuvant chemotherapy were factors found to be potentially associated with OS in univariate analyses while Axl, vim, age and stage were associated with at least trends towards significance with respect to DFS in univariate analyses. Cox models showed that higher vim levels (p=0.08) and stage I and II disease (p=0.024) were potentially associated jointly with OS, while higher Axl levels (p=0.05), age (p=0.016) and stage I and II disease (p=0.0007) were jointly associated with DFS.

Conclusions:

Preclinical data suggest that expression of vim and Axl can identify TRAIL Receptor agonist sensitive TNBC cells. Based on microarray and IHC, a subset of TNBC tumors express these markers in tumor cells. In our exploratory analysis with limited pts, greater vim and Axl expression were associated with a trend towards better DFS and OS. Vim and Axl may be useful predictive biomarkers for identifying TNBC pts in whom to test TRAIL receptor agonists.

Research funding: Safeway Foundation and National Cancer Institute.

Citation Format: Ciara C O'Sullivan, Laleh Amiri-Kordestani, Sara Sinclair, Kathryn J Chavez, Jennifer L Dine, Brandon Stone, Stephen M Hewitt, Seth M Steinberg, Sandra M Swain, Stanley Lipkowitz. TRAIL receptor agonists target basal B triple negative breast Cancer (TNBC) that expresses vimentin and axl [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P5-10-05.

Molecular pathways: cbl proteins in tumorigenesis and antitumor immunity-opportunities for cancer treatment

The Cbl proteins are a family of ubiquitin ligases (E3s) that regulate signaling through many tyrosine kinase-dependent pathways. A predominant function is to negatively regulate receptor tyrosine kinase (RTK) signaling by ubiquitination of active RTKs, targeting them for trafficking to the lysosome for degradation. Also, Cbl-mediated ubiquitination can regulate signaling protein function by altered cellular localization of proteins without degradation. In addition to their role as E3s, Cbl proteins play a positive role in signaling by acting as adaptor proteins that can recruit signaling molecules to the active RTKs. Cbl-b, a second family member, negatively regulates the costimulatory pathway of CD8 T cells and also negatively regulates natural killer cell function. The different functions of Cbl proteins and their roles both in the development of cancer and the regulation of immune responses provide multiple therapeutic opportunities. Mutations in Cbl that inactivate the negative E3 function while maintaining the positive adaptor function have been described in approximately 5% of myeloid neoplasms. An improved understanding of how the signaling pathways [e.g., Fms-like tyrosine kinase 3 (Flt3), PI3K, and signal transducer and activator of transcription (Stat)] are dysregulated by these mutations in Cbl has helped to identify potential targets for therapy of myeloid neoplasms. Conversely, the loss of Cbl-b leads to increased adaptive and innate antitumor immunity, suggesting that inhibiting Cbl-b may be a means to increase antitumor immunity across a wide variety of tumors. Thus, targeting the pathways regulated by Cbl proteins may provide attractive opportunities for treating cancer.

Abstract 5124: Identification and characterization of novel regulators of TRAIL-induced apoptosis in breast cancer cells

TNF-related apoptosis inducing ligand (TRAIL) is a member of the tumor necrosis factor super family and can induce apoptotic cell death upon binding to its cognate receptors, TRAIL Receptor 1 (TRAIL-R1) and TRAIL Receptor 2 (TRAIL-R2). TRAIL has been found to induce selectively cell death in triple negative breast cancer (TNBC) cell lines (so called because the breast cancer cells lack estrogen and progesterone receptor expression and Her-2 amplification). Other subtypes of breast cancer are relatively resistant to TRAIL-induced apoptosis. However, the mechanisms that underlie the sensitivity of TNBCs to TRAIL-induced apoptosis are not yet understood.

To identify regulators of TRAIL-induced apoptosis in the TNBC/mesenchymal cell line MB231, an siRNA screen of the kinome, phosphatome, and other potential regulators (∼1,300 genes) of the TRAIL pathway was carried out to measure the effects of loss of function of these genes on TRAIL-induced caspase-3/7 activation, capase-8 activation, and cell death. One hundred fifty negative regulators of the TRAIL pathway were identified, including 83 kinases, 4 phosphatases, and 63 non-kinases. The identified regulators were involved in diverse cell processes, including apoptosis, transcriptional regulation, growth factor receptor signaling, DNA repair, cell metabolism, and cell cycle regulation. Interestingly, no positive regulators were identified. A subset of the 150 candidates were rescreened in MB231 and three additional cell lines representative of other subytpes of breast cancer, including MB468 (TNBC/basal), SKBR3 (Her-2 amplified), and T47D (estrogen receptor positive). Interestingly, the TNBC/basal cell line MB468 was sensitized to TRAIL-induced caspase-3/7 activation by all of the candidates, whereas T47D and SKBR3 were sensitized to TRAIL by only two and three of the candidates, respectively. These findings demonstrate that breast cancer cell lines are varyingly sensitized to the effects of TRAIL. The anti-apoptotic protein Bcl-xL and the tyrosine kinase Src were also identified as negative regulators of TRAIL-induced apoptosis. We have further shown that pharmacologic inhibition of Bcl-xL or Src sensitize a wide range of breast cancer cell lines to TRAIL-induced apoptosis. These findings lend further support to the screen.

Overall, the siRNA screen has identified many regulators of TRAIL-induced apoptosis in the TNBC cell line MB231 and a smaller subset of regulators in breast cancer cell lines representative of other subtypes. These findings suggest targets for the rational development of combination therapy in breast cancer treatment.

Citation Format: Jennifer Dine, Sireesha Garimella, Kristie Gehlhaus, Magda Grandin, Natasha Caplen, Stanley Lipkowitz. Identification and characterization of novel regulators of TRAIL-induced apoptosis in breast cancer cells. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5124. doi:10.1158/1538-7445.AM2014-5124

Abstract 4441: Ube2e inhibits the ubiquitination and degradation of EGFR mediated by Cbl and Ube2d

Receptor tyrosine kinases (RTKs) have a demonstrated role as drivers of malignant transformation. Many RTKs (e.g., EGFR, MET, FLT3) are negatively regulated by ubiquitination and degradation mediated by Cbl proteins a family of RING finger (RF) ubiquitin ligases (E3s). There are three mammalian family members Cbl, Cbl-b and Cbl-c. All Cbl proteins have a highly conserved N-terminal tyrosine kinase binding domain and a C3HC4 (RF) domain. Loss of Cbl protein function has be associated with malignant transformation drive by increased RTK activity. E3s such as the Cbl proteins confer specificity to the ubiquitination process and direct the conjugation of ubiquitin to one or more lysines on the specific target proteins in collaboration with ubiquitin-conjugating enzymes (E2s). The E2s bind to the E3 and together they mediate ubiquitination of specific substrates. There are approximately 30 human E2s. All of the E2s have a highly conserved catalytic domain (UBC domain). In this study, we characterized the interaction of Cbl with E2s. Using an in vitro E3 assay, we found that only the Ube2d family (Ube2d1, Ube2d2, and Ube2d3) of E2s mediates autoubiquitination of the three Cbl proteins. Subsequently, using the yeast two-hybrid system, we found that Ube2e1, Ube2e2, Ube2e3, Ube2L3, Ube2u, Ube2w and Ube2z can interact with Cbl even though they do not support autoubiquitination of Cbl in vitro E3 assay. Among these E2s, three Ube2e family members and Ube2w bind to the RF domain of Cbl as demonstrated by the loss of interaction when the RF domain is disrupted. Further, we demonstrated that Ube2e family members are involved in regulation of EGFR activity mediated by Cbl in HeLa cells. Knockdown of Ube2e increases down-regulation and ubiquitination of EGFR in HeLa cells. We further showed that three Ube2e inhibit autoubiquitination of Cbl mediated by Ube2d2 in vitro. Together these data suggest that RTK degradation can be modulated by competition between E2s for the Cbl E3s.

Citation Format: Ke Ma, Stanley Lipkowitz, Rachel Klevit, Mariya Sergeyevna Liyasova. Ube2e inhibits the ubiquitination and degradation of EGFR mediated by Cbl and Ube2d. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4441. doi:10.1158/1538-7445.AM2014-4441

Identification of novel molecular regulators of tumor necrosis factor-related apoptosis-inducing ligand (TRAIL)-induced apoptosis in breast cancer cells by RNAi screening

INTRODUCTION

Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) binds to its receptors, TRAIL-receptor 1 (TRAIL-R1) and TRAIL-receptor 2 (TRAIL-R2), leading to apoptosis by activation of caspase-8 and the downstream executioner caspases, caspase-3 and caspase-7 (caspase-3/7). Triple-negative breast cancer (TNBC) cell lines with a mesenchymal phenotype are sensitive to TRAIL, whereas other breast cancer cell lines are resistant. The underlying mechanisms that control TRAIL sensitivity in breast cancer cells are not well understood. Here, we performed small interfering RNA (siRNA) screens to identify molecular regulators of the TRAIL pathway in breast cancer cells.

METHODS

We conducted siRNA screens of the human kinome (691 genes), phosphatome (320 genes), and about 300 additional genes in the mesenchymal TNBC cell line MB231. Forty-eight hours after transfection of siRNA, parallel screens measuring caspase-8 activity, caspase-3/7 activity, or cell viability were conducted in the absence or presence of TRAIL for each siRNA, relative to a negative control siRNA (siNeg). A subset of genes was screened in cell lines representing epithelial TNBC (MB468), HER2-amplified breast cancer (SKBR3), and estrogen receptor-positive breast cancer (T47D). Selected putative negative regulators of the TRAIL pathway were studied by using small-molecule inhibitors.

RESULTS

The primary screens in MB231 identified 150 genes, including 83 kinases, 4 phosphatases, and 63 nonkinases, as potential negative regulators of TRAIL. The identified genes are involved in many critical cell processes, including apoptosis, growth factor-receptor signaling, cell-cycle regulation, transcriptional regulation, and DNA repair. Gene-network analysis identified four genes (PDPK1, IKBKB, SRC, and BCL2L1) that formed key nodes within the interaction network of negative regulators. A secondary screen of a subset of the genes identified in additional cell lines representing different breast cancer subtypes and sensitivities to TRAIL validated and extended these findings. Further, we confirmed that small-molecule inhibition of SRC or BCL2L1, in combination with TRAIL, sensitizes breast cancer cells to TRAIL-induced apoptosis, including cell lines resistant to TRAIL-induced cytotoxicity.

CONCLUSIONS

These data identify novel molecular regulators of TRAIL-induced apoptosis in breast cancer cells and suggest strategies for the enhanced application of TRAIL as a therapy for breast cancer.

Recruitment of Cbl-b to B cell antigen receptor couples antigen recognition to Toll-like receptor 9 activation in late endosomes

Casitas B-lineage lymphoma-b (Cbl-b) is a ubiquitin ligase (E3) that modulates signaling by tagging molecules for degradation. It is a complex protein with multiple domains and binding partners that are not involved in ubiquitinating substrates. Herein, we demonstrate that Cbl-b, but not c-Cbl, is recruited to the clustered B cell antigen receptor (BCR) and that Cbl-b is required for entry of endocytosed BCRs into late endosomes. The E3 activity of Cbl-b is not necessary for BCR endocytic trafficking. Rather, the ubiquitin associated (UBA) domain is required. Furthermore, the Cbl-b UBA domain is sufficient to confer the receptor trafficking functions of Cbl-b on c-Cbl. Cbl-b is also required for entry of the Toll-like receptor 9 (TLR9) into late endosomes and for the in vitro activation of TLR9 by BCR-captured ligands. These data indicate that Cbl-b acts as a scaffolding molecule to coordinate the delivery of the BCR and TLR9 into subcellular compartments required for productively delivering BCR-captured ligands to TLR9.

E3 ubiquitin ligase Cbl-b suppresses proallergic T cell development and allergic airway inflammation

E3 ubiquitin ligase Cbl-b has emerged as a gatekeeper that controls the activation threshold of the T cell antigen receptor and maintains the balance between tolerance and autoimmunity. Here, we report that the loss of Cbl-b facilitates T helper 2 (Th2) and Th9 cell differentiation in vitro. In a mouse model of asthma, the absence of Cbl-b results in severe airway inflammation and stronger Th2 and Th9 responses. Mechanistically, Cbl-b selectively associates with Stat6 upon IL-4 ligation and targets Stat6 for ubiquitination and degradation. These processes are heightened in the presence of T cell receptor (TCR)/ CD28 costimulation. Furthermore, we identify K108 and K398 as Stat6 ubiquitination sites. Intriguingly, introducing Stat6 deficiency into Cblb^−/− mice abrogates hyper-Th2 responses but only partially attenuates Th9 responses. Therefore, our data reveal a function for Cbl-b in the regulation of Th2 and Th9 cell differentiation.

Enigma prevents Cbl-c-mediated ubiquitination and degradation of RETMEN2A

The Cbl proteins (Cbl, Cbl-b, and Cbl-c) are a highly conserved family of RING finger ubiquitin ligases (E3s) that function as negative regulators of tyrosine kinases in a wide variety of signal transduction pathways. In this study, we identify a new Cbl-c interacting protein, Enigma (PDLIM7). This interaction is specific to Cbl-c as Enigma fails to bind either of its closely related homologues, Cbl and Cbl-b. The binding between Enigma and Cbl-c is mediated through the LIM domains of Enigma as removal of all three LIM domains abrogates this interaction, while only LIM1 is sufficient for binding. Here we show that Cbl-c binds wild-type and MEN2A isoforms of the receptor tyrosine kinase, RET, and that Cbl-c enhances ubiquitination and degradation of activated RET. Enigma blocks Cbl-c-mediated RETMEN2A ubiquitination and degradation. Cbl-c decreased downstream ERK activation by RETMEN2A and co-expression of Enigma blocked the Cbl-c-mediated decrease in ERK activation. Enigma showed no detectable effect on Cbl-c-mediated ubiquitination of activated EGFR suggesting that this effect is specific to RET. Through mapping studies, we show that Cbl-c and Enigma bind RETMEN2A at different residues. However, binding of Enigma to RETMENA prevents Cbl-c recruitment to RETMEN2A. Consistent with these biochemical data, exploratory analyses of breast cancer patients with high expression of RET suggest that high expression of Cbl-c correlates with a good outcome, and high expression of Enigma correlates with a poor outcome. Together, these data demonstrate that Cbl-c can ubiquitinate and downregulate RETMEN2A and implicate Enigma as a positive regulator of RETMEN2A through blocking of Cbl-mediated ubiquitination and degradation.

E3 ubiquitin ligase Cbl-b regulates Pten via Nedd4 in T cells independently of its ubiquitin ligase activity

E3 ubiquitin ligase Cbl-b plays a crucial role in T cell activation and tolerance induction. However, the molecular mechanism by which Cbl-b inhibits T cell activation remains unclear. Here, we report that Cbl-b does not inhibit PI3K but rather suppresses TCR/CD28-induced inactivation of Pten. The elevated Akt activity in Cbl-b(-/-) T cells is therefore due to heightened Pten inactivation. Suppression of Pten inactivation in T cells by Cbl-b is achieved by impeding the association of Pten with Nedd4, which targets Pten K13 for K63-linked polyubiquitination. Consistent with this finding, introducing Nedd4 deficiency into Cbl-b(-/-) mice abrogates hyper-T cell responses caused by the loss of Cbl-b. Hence, our data demonstrate that Cbl-b inhibits T cell activation by suppressing Pten inactivation independently of its ubiquitin ligase activity.

WEE1 inhibition sensitizes basal breast cancer cells to TRAIL-induced apoptosis

TRAIL is a member of the TNF super family and has been shown to induce apoptosis in many cancer cell lines but not in normal cells. Breast cancers can be divided into different subgroups on the basis of the expression of estrogen and progesterone receptors, HER-2 amplification, or the lack of these three markers (known as triple-negative or basal-type breast cancer). Our group and others have shown previously that triple-negative breast cancer cell lines are sensitive to TRAIL whereas others are relatively resistant. In an earlier study, we reported that inhibition of WEE1, a cell-cycle checkpoint regulator, causes increased cell death in breast cancer cell lines. In this study, we tested the effects of WEE1 inhibition on TRAIL-mediated apoptosis in breast cancer cell lines. Pretreatment with WEE1 inhibitor or knockdown of WEE1 increased the toxicity of TRAIL in the basal/triple-negative breast cancer cell lines compared with WEE1 inhibitor or TRAIL treatment alone. The enhanced cell death is attributed to increased surface expression of death receptors, increased caspase activation which could be blocked by the pan-caspase inhibitor, Z-VAD-FMK, thereby rescuing cells from caspase-mediated apoptosis. The cell death was initiated primarily by caspase-8 because knockdown of caspase-8 and not of any other initiator caspases (i.e., caspase-2, -9, or -10) rescued cells from WEE1 inhibitor-sensitized TRAIL-induced cell death. Taken together, the data suggest that the combination of WEE1 inhibitor and TRAIL could provide a novel combination for the treatment of basal/triple-negative breast cancer.

RINGs of good and evil: RING finger ubiquitin ligases at the crossroads of tumour suppression and oncogenesis

The ubiquitin-proteasome system has numerous crucial roles in physiology and pathophysiology. Fundamental to the specificity of this system are ubiquitin-protein ligases (E3s). Of these, the majority are RING finger and RING finger-related E3s. Many RING finger E3s have roles in processes that are central to the maintenance of genomic integrity and cellular homeostasis, such as the anaphase promoting complex/cyclosome (APC/C), the SKP1-cullin 1-F-box protein (SCF) E3s, MDM2, BRCA1, Fanconi anaemia proteins, CBL proteins, von Hippel-Lindau tumour suppressor (VHL) and SIAH proteins. As a result, many RING finger E3s are implicated in either the suppression or the progression of cancer. This Review summarizes current knowledge in this area.

Abstract 1220: Enigma blocks Cbl-c-mediated RET ubiquitination and degradation

RET (rearranged during transfection) is an RTK that is activated by glial cell-derived neurotrophic factors (GDNF) and is critical to neuronal and kidney development. RET mutations causing loss of function are associated with Hirschsprung's disease, while gain of function mutations are associated with thyroid carcinomas and mutiple endocrine neoplasias (MEN2A&B). Cbl proteins are a family of ubiquitin protein ligases that mediate RTK degradation and thereby serve as negative regulators of RTK signaling. Cbl-c (a.k.a. Cbl-3), the most recently identified of the human Cbl proteins, is restricted to epithelial cells and most resembles the Cbl proteins found in lower organisms. Cbl-c can ubiquitinate and downregulate RTKs including activated RET and EGFR. Through yeast two-hybrid screening, we identified the LIM protein Enigma (a.k.a. PDLIM7) as a Cbl-c interacting protein. Enigma is an adapter protein for kinase anchoring to the cytoskeleton and is required for the mitogenic signaling of the RET/PTC2 oncogene. The interaction was confirmed in mammalian cells through co-immunoprecipitation of transfected and endogenous Cbl-c and Enigma. Enigma did not co-immunoprecipitate with c-Cbl or Cbl-b indicating that this interaction is specific to Cbl-c. Cbl-c can ubiquitinate and downregulate an activated form of RET, RET-MEN2A and we show that Enigma prevents Cbl-c-mediated RET ubiquitination and downregulation. This effect is specific to RET as EGFR ubiquitination was unaffected by the presence of Enigma. An Enigma mutant, lacking the RET binding site, does not block Cbl-c recruitment and subsequent ubiquitination and downregulation of RET. Our data suggest that Enigma blocks Cbl-c binding to the RET receptor and prevents its ubiquitination. This is further supported by microscopy data which demonstrates maintained surface expression of RET in the presence of Enigma. Together these data demonstrate a novel interaction between a positive and negative regulator or RET signaling.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 1220. doi:10.1158/1538-7445.AM2011-1220

Abstract 4106: A functional genomic approach to identify novel molecular regulators of the TRAIL pathway in breast cancer

Tumor Necrosis Factor (TNF)-Related Apoptosis Inducing Ligand (TRAIL) is a member of the TNF family. The ligand binds to its receptors TRAIL-R1 or TRAIL-R2 leading to formation of the death-inducing signaling complex (DISC) which cleaves the initiator pro-caspase 8 to active caspase 8. This cleaved caspase 8 triggers the activation of the downstream executioner caspases (3/7) resulting in apoptosis. Earlier, we showed that triple-negative breast cancer cell lines with mesenchymal phenotype were sensitive to TRAIL while other breast cancer cell lines were resistant. To date the underlying mechanisms that control TRAIL sensitivity or resistance in breast cancer cells are not well understood. To identify potential molecular regulators of the TRAIL pathway, we carried out RNAi screens of the human kinome (691 genes), phosphatome (320 genes), and ≈300 additional genes in MB231, a triple-negative mesenchymal breast cancer cell line. Parallel RNAi screens targeting each gene with four different synthetic siRNAs in an arrayed 384 well plate format (one siRNA per well) were performed. Forty-eight hours post siRNA transfection, one screen received vehicle only, one a low concentration of TRAIL (62.5ng/ml), and one a high concentration of TRAIL (1000ng/ml). One hour after addition of TRAIL, caspase 3/7 activation was measured. The fold change in caspase activity was calculated relative to negative control-siRNA (siNeg) transfected cells. siRNAs corresponding to CASP8 and FLIP were used as assay specific controls. The silencing of CASP8 suppresses caspase 3/7 activation and FLIP enhances it. A gene was considered with high confidence as a potential regulator of TRAIL if three or more siRNAs induced a change in caspase 3/7 levels more than one standard deviation of the siNeg treated wells. These screens identified 45 genes, including 11 kinases and 34 non-kinases, where all four siRNAs induced a phenotype consistent with the targeted gene acting as a negative regulator of TRAIL. These effects were most evident at the high TRAIL dose. Of the 34 non-kinase genes, several known regulators of the TRAIL pathway including BCL2L1, BCL2L2, and BIRC2 were identified. Also, three of the four siRNAs corresponding to a further 126 genes were identified as potential negative regulators of TRAIL. These included 69 kinase genes, 33 phosphatase genes, and 24 genes encoding proteins with a variety of functions. High confidence hits (three or four siRNAs per gene) representing potential positive regulators of TRAIL were not identified, but two of four siRNAs corresponding to four kinases, eight phosphatases and one additional gene did suppress TRAIL activation more than one standard deviation. These screens suggest that a large number of genes act as negative regulators of TRAIL activity while there are fewer positive regulators. Validation of candidate regulators of the TRAIL pathway identified by these screens is in progress.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4106. doi:10.1158/1538-7445.AM2011-4106

The N terminus of Cbl-c regulates ubiquitin ligase activity by modulating affinity for the ubiquitin-conjugating enzyme

Cbl proteins are ubiquitin ligases (E3s) that play a significant role in regulating tyrosine kinase signaling. There are three mammalian family members: Cbl, Cbl-b, and Cbl-c. All have a highly conserved N-terminal tyrosine kinase binding domain, a catalytic RING finger domain, and a C-terminal proline-rich domain that mediates interactions with Src homology 3 (SH3) containing proteins. Although both Cbl and Cbl-b have been studied widely, little is known about Cbl-c. Published reports have demonstrated that the N terminus of Cbl and Cbl-b have an inhibitory effect on their respective E3 activity. However, the mechanism for this inhibition is still unknown. In this study we demonstrate that the N terminus of Cbl-c, like that of Cbl and Cbl-b, inhibits the E3 activity of Cbl-c. Furthermore, we map the region responsible for the inhibition to the EF-hand and SH2 domains. Phosphorylation of a critical tyrosine (Tyr-341) in the linker region of Cbl-c by Src or a phosphomimetic mutation of this tyrosine (Y341E) is sufficient to increase the E3 activity of Cbl-c. We also demonstrate for the first time that phosphorylation of Tyr-341 or the Y341E mutation leads to a decrease in affinity for the ubiquitin-conjugating enzyme (E2), UbcH5b. The decreased affinity of the Y341E mutant Cbl-c for UbcH5b results in a more rapid turnover of bound UbcH5b coincident with the increased E3 activity. These data suggest that the N terminus of Cbl-c contributes to the binding to the E2 and that phosphorylation of Tyr-341 leads to a decrease in affinity and an increase in the E3 activity of Cbl-c.

Cbl and human myeloid neoplasms: the Cbl oncogene comes of age

Cbl was originally discovered in 1989 as the cellular homolog of the v-Cbl oncogene, the transforming gene of the Cas NS-1 murine retrovirus that causes myeloid leukemia and lymphomas in mice. Cbl is a member of a family of RING finger ubiquitin ligases that negatively regulate signaling by tyrosine kinases and that function as adaptor proteins to regulate signaling positively. Until the past 2 years, there was little evidence that Cbl proteins were involved in human malignancies. Recent publications have shown homozygous mutations in Cbl in human myeloid neoplasms. Although in vitro and animal transformation models suggested that mutant forms of Cbl acted as an oncogene, the cellular role suggested that the protein could serve as a tumor suppressor gene. The recent data begin to reconcile this paradox as the loss of ubiquitin ligase function (the tumor suppressor function) is coupled to the maintenance of the positive signaling function (the oncogene function). These data also provide insight into potential therapeutic approaches to myeloid disorders harboring Cbl mutations.

CBL is frequently altered in lung cancers: its relationship to mutations in MET and EGFR tyrosine kinases

Background

Non-small cell lung cancer (NSCLC) is a heterogeneous group of disorders with a number of genetic and proteomic alterations. c-CBL is an E3 ubiquitin ligase and adaptor molecule important in normal homeostasis and cancer. We determined the genetic variations of c-CBL, relationship to receptor tyrosine kinases (EGFR and MET), and functionality in NSCLC.

Methods and Findings

Using archival formalin-fixed paraffin embedded (FFPE) extracted genomic DNA, we show that c-CBL mutations occur in somatic fashion for lung cancers. c-CBL mutations were not mutually exclusive of MET or EGFR mutations; however they were independent of p53 and KRAS mutations. In normal/tumor pairwise analysis, there was significant loss of heterozygosity (LOH) for the c-CBL locus (22%, n = 8/37) and none of these samples revealed any mutation in the remaining copy of c-CBL. The c-CBL LOH also positively correlated with EGFR and MET mutations observed in the same samples. Using select c-CBL somatic mutations such as S80N/H94Y, Q249E and W802* (obtained from Caucasian, Taiwanese and African-American samples, respectively) transfected in NSCLC cell lines, there was increased cell viability and cell motility.

Conclusions

Taking the overall mutation rate of c-CBL to be a combination as somatic missense mutation and LOH, it is clear that c-CBL is highly mutated in lung cancers and may play an essential role in lung tumorigenesis and metastasis.

Identification of WEE1 as a potential molecular target in cancer cells by RNAi screening of the human tyrosine kinome

Breast cancers can be classified into those that express the estrogen (ER) and progesterone (PR) receptors, those with ERBB2 (HER-2/Neu) amplification, and those without expression of ER, PR, or amplification of ERBB2 (referred to as triple-negative or basal-like breast cancer). In order to identify potential molecular targets in breast cancer, we performed a synthetic siRNA-mediated RNAi screen of the human tyrosine kinome. A primary RNAi screen conducted in the triple-negative/basal-like breast cancer cell line MDA-MB231 followed by secondary RNAi screens and further studies in this cell line and two additional triple-negative/basal-like breast cancer cell lines, BT20 and HCC1937, identified the G2/M checkpoint protein, WEE1, as a potential therapeutic target. Similar sensitivity to WEE1 inhibition was observed in cell lines from all subtypes of breast cancer. RNAi-mediated silencing or small compound inhibition of WEE1 in breast cancer cell lines resulted in an increase in gammaH2AX levels, arrest in the S-phase of the cell cycle, and a significant decrease in cell proliferation. WEE1-inhibited cells underwent apoptosis as demonstrated by positive Annexin V staining, increased sub-G1 DNA content, apoptotic morphology, caspase activation, and rescue by the pan-caspase inhibitor, Z-VAD-FMK. In contrast, the non-transformed mammary epithelial cell line, MCF10A, did not exhibit any of these downstream effects following WEE1 silencing or inhibition. These results identify WEE1 as a potential molecular target in breast cancer.