Abstract P5-16-18: Developing IpY: A novel inhibitor for the treatment of ER+ CDK4i-resistant breast cancer

Almost 270,000 US women will be diagnosed with breast cancer (BC) this year, anddespite advances in treatment, ~40,000 women will die. ER/PR+ (endocrineresponsive), Her2- tumors occur in approximately 40% of breast cancer patients andare candidates for drugs targeting estrogen responsiveness, such as letrozole orfulvestrant. CDK4 targeting drugs (CDK4i) like palbociclib, abemaciclib, or ribociclib arenow approved in combination with letrozole or fulvestrant as a front- and second-linetherapy for metastatic ER/PR+, Her2- patients. However, while combined ER andCDK4i treatment significantly extends Progression Free Survival (PFS), those treatedinvariably develop resistance. Thus, drug resistance remains an urgent unmet need, as current treatments only marginally improve Overall Survival (OS) for these patients.Resistance to palbociclib develops because of compensation by another kinase, CDK2, suggesting that to be effective, therapies must be developed to inhibit both CDK4 andCDK2. Concarlo has taken a different approach to inhibit CDK4 and CDK2 by targetingp27Kip1 (p27). p27 interacts specifically with CDK4/6 and CDK2, and is responsible forturning these kinases ON and OFF. This transition from ON to OFF is mediated by aspecific modification to p27 itself, by the tyrosine kinase BRK (breast tumor relatedkinase). Published work has shown that a naturally occurring ALTernatively splicedform of BRK, ALT, can bind to p27, blocking BRK's association, and preventing BRK'sphosphorylation of p27. This locks CDK4 and CDK2 into the OFF conformation andsimultaneously inhibits activities of both kinases. As the naked 144 aa ALT peptidedoes not enter cells, it was formulated within a lipid nano-particle (NP), and called IpY.1.IpY.1 inhibits proliferation of HR+ and triple negative (TN) BC cells, but not non-cancerous breast cells MCF10A. IpY.1 arrests CDK4i-resistant and endocrine-resistantBC cells and it is both cytostatic and cytotoxic, demonstrating that p27 is a viabletherapeutic target to combat drug resistance. In vivo, IpY reduces tumor volumes and increase OS in cell line-derived xenografts (CDX). In order to convert manufacturing of the therapeutic peptide portion of IpY from recombinant to synthetic production, Concarlo truncated the large ALT peptide and bioengineered it to a more stable form. IpY.20 has a comparable IC50 as IpY.1 in HR+and TNBC cells and does not cause growth arrest in non-cancerous MCF10A cells. Using the fluorescent-labeled variant of IpY.20 (fluo-IpY.20) injected into tumor-bearingsyngeneic CDX model, followed by IVIS imaging, we could detect fluo-IpY.20 in tumorsas early as 15 min and up to 24h post injection. 6-10% of the total fluorescent signal isallocated to tumor at all timepoints. In addition, fluo-IpY.20 inhibits the activation of itstarget in tumors within 24h, suggesting fluo-IpY.20 not only reaches tumors but alsoengages with its target. IpY.20 induces tumor regression in CDX models and animmunocompetent genetically engineered model that overexpresses the potent Erbb2oncogene. Overall, repeated dosing of IpY.20 does not exhibit significant adverseeffects and is well tolerated in immunocompetent mice. However, in these treated mice, there was an increase in platelets and production of some cytokines compared to vehicle-treated mice, suggesting that an immune response may have been initiated. By targeting p27 instead of the conserved CDK4 or CDK2 active sites, IpY.20 will bemore selective and have fewer off-target effects than the ATP-competitive smallmolecule CDK4is currently in use. As the majority of the drug resistance seen withCDK4 inhibitory drugs is a result of compensatory CDK2 activity, IpY.20 preventsacquired drug resistance by hitting both CDK4 and CDK2 simultaneously, resulting in amore durable response to the drug. Concarlo is currently in manufacturing with IpY.20.

Citation Format: Grace Chen, Stacy W Blain, Irina Jilishitz, Allison Vanlnwegen, Lingyue Yan, Yun Wu. Developing IpY: A novel inhibitor for the treatment of ER+ CDK4i-resistant breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P5-16-18.

NP-ALT, a Liposomal:Peptide Drug, Blocks p27Kip1 Phosphorylation to Induce Oxidative Stress, Necroptosis, and Regression in Therapy-Resistant Breast Cancer Cells

Resistance to cyclin D-CDK4/6 inhibitors (CDK4/6i) represents an unmet clinical need and is frequently caused by compensatory CDK2 activity. Here we describe a novel strategy to prevent CDK4i resistance by using a therapeutic liposomal:peptide formulation, NP-ALT, to inhibit the tyrosine phosphorylation of p27Kip1(CDKN1B), which in turn inhibits both CDK4/6 and CDK2. We find that NP-ALT blocks proliferation in HR+ breast cancer cells, as well as CDK4i-resistant cell types, including triple negative breast cancer (TNBC). The peptide ALT is not as stable in primary mammary epithelium, suggesting that NP-ALT has little effect in nontumor tissues. In HR+ breast cancer cells specifically, NP-ALT treatment induces ROS and RIPK1-dependent necroptosis. Estrogen signaling and ERα appear required. Significantly, NP-ALT induces necroptosis in MCF7 ESR^Y537S cells, which contain an ER gain of function mutation frequently detected in metastatic patients, which renders them resistant to endocrine therapy. Here we show that NP-ALT causes necroptosis and tumor regression in treatment naïve, palbociclib-resistant, and endocrine-resistant BC cells and xenograft models, demonstrating that p27 is a viable therapeutic target to combat drug resistance. IMPLICATIONS: This study reveals that blocking p27 tyrosine phosphorylation inhibits CDK4 and CDK2 activity and induces ROS-dependent necroptosis, suggesting a novel therapeutic option for endocrine and CDK4 inhibitor-resistant HR+ tumors.

A cyclin D-CDK6 dimer helps to reshuffle cyclin-dependent kinase inhibitors (CKI) to overcome TGF-beta-mediated arrest and maintain CDK2 activity

The cyclin D-CDK4/6 complex has two distinct functions. Its kinase-dependent role involves its ability to act as serine/threonine kinase, responsible for phosphorylation of substrates required for cell cycle transitions, while its kinase-independent function involves its ability to act as a reservoir for p27^Kip1. This association sequesters p27 from cyclin E-CDK2 complexes, allowing them to remain active. The aim of this current study is two-fold: to understand the contribution of the kinase-dependent and kinase-independent functions of CDK4 and CDK6 in epithelial cells and to directly compare CDK4 and CDK6 in a simple model system, TGF-β treatment, where arrest is initiated by the expression of p15^Ink4b. Cells that overexpressed a catalytically inactive, p15-insensitive CDK6 variant (p27 sequestration only mutant) were able to overcome TGF-β-mediated arrest by maintaining CDK2 activity, while cells expressing the identical mutations in CDK4 were not. This result can be partially explained by the presence of a previously unidentified cyclin D-CDK6 dimer, which serves as a sink for free p27 during TGF-β treatment, enabling CDK2 to remain inhibitor free. The use of the TGF-β model system and the characterization of CDK pool dynamics and p27 switching is relevant to the CDK4/6 specific inhibitors, such as palbociclib, whose mechanism of action may resemble that of p15.

The Ongoing Search for Biomarkers of CDK4/6 Inhibitor Responsiveness in Breast Cancer

CDK4 inhibitors (CDK4/6i), such as palbociclib, ribociclib, and abemaciclib, are approved in combination with hormonal therapy as a front-line treatment for metastatic HR+, HER2- breast cancer. Their targets, CDK4 and CDK6, are cell-cycle regulatory proteins governing the G1-S phase transition across many tissue types. A key challenge remains to uncover biomarkers to identify those patients that may benefit from this class of drugs. Although CDK4/6i addition to estrogen modulation therapy essentially doubles the median progression-free survival, overall survival is not significantly increased. However, in reality only a subset of treated patients respond. Many patients exhibit primary resistance to CDK4/6 inhibition and do not derive any benefit from these agents, often switching to chemotherapy within 6 months. Some patients initially benefit from treatment, but later develop secondary resistance. This highlights the need for complementary or companion diagnostics to pinpoint patients who would respond. In addition, because CDK4 is a bona fide target in other tumor types where CDK4/6i therapy is currently in clinical trials, the lack of target identification may obscure benefit to a subset of patients there as well. This review summarizes the current status of CDK4/6i biomarker test development, both in clinical trials and at the bench, with particular attention paid to those which have a strong biological basis as well as supportive clinical data.

Tyrosine Phosphorylation of p27Kip1 Correlates with Palbociclib Responsiveness in Breast Cancer Tumor Cells Grown in Explant Culture

Cdk4-targeting drugs, such as palbociclib, are approved for metastatic ER/PR⁺, Her2^- breast cancer. However, other than loss of retinoblastoma, which is very rare in this subset, there are no biomarkers to predict response. Cyclin D or cdk4 levels are not by themselves indicative, because p27Kip1 is required for cyclin D-cdk4 complex activation. Tyrosine phosphorylation of p27, including modification on residue Y88 (pY88), activates DK4-p27, and the pY88 level correlates with palbociclib responsiveness in cell lines. We developed dual IHC staining for p27 and pY88, and found that benign breast epithelium was negative, while breast cancer biopsies (of varied hormonal status) could be stratified for pY88 status. Lack of pY88 suggested that DK4 was inactive, and that these samples would not have the target required for palbociclib response. Tumor resection material was grown in explant culture, treated with palbociclib, and stained with Ki67 as a marker of response. Explants from the no pY88 group were nonresponsive, while explants from the low or high pY88 group responded to drug. IMPLICATIONS: Use of the pY88 biomarker, as a surrogate for cdk4 activity, may identify patients responsive to cdk4-targeting drugs and expand use of this therapy.Visual Overview: http://mcr.aacrjournals.org/content/molcanres/17/3/669/F1.large.jpg.

Abstract LB-214: pY88-p27Kip1 status acts as a biomarker to determine responsiveness to cdk4 inhibitor therapy

PURPOSE: Cdk4 targeting drugs (cdk4i), such as Palbociclib, are approved in combination with Estrogen modulation therapy for metastatic ER/PR+, Her2- breast cancer. However, there are no biomarkers to pinpoint patients who would respond to this type of therapy. 20-40% of metastatic ER/PR+, Her2- patients exhibit primary resistance to cdk4i therapy, highlighting the need for a companion diagnostic for cdk4i use. Rb- tumors appear resistant to cdk4i, but this is an infrequent event in HR+ breast cancer. In Rb+ tumors, Ki67, Cyclin D, cdk4, or p16 do not appear to stratify responsive and non-responsive subgroups. The levels of cyclin D or cdk4 themselves may not be reliable measures of responsiveness, due to the fact that a third protein, p27Kip1, is required for activation of the cyclin D-cdk4 (DK4) complex. Tyrosine (Y) phosphorylation of p27 on residue Y88 activates the DK4-p27 ternary complex, and the level of pY88-p27 correlates with cdk4 activity and Palbociclib responsiveness in tissue culture cells. We hypothesized the pY88-p27 status may serve as a biomarker for patients that are responsive to cdk4i therapy.

RESULTS: We developed a dual immunohistochemistry assay for p27 and pY88, which we used to analyze paraffin-embedded, archival breast cancer tumor samples. We used non-cancerous material obtained from core needle biopsies as non-neoplastic (control) and found that while strong p27 staining was detected (brown) in normal epithelial cells, all benign epithelium was negative for pY88 (pink staining). By examining a cohort of pathologically identical patients (ER/PR+, Her2- with similar Ki67 levels and grades), we were able to stratify them into three groups based on pY88 status: 21% had no pY88 staining (Group 0), 26% had a low percentage of pY88+ cells (Group 1), and 52% had very high pY88 staining (Group 2, >25% of cells pY88+). Similar groupings were detected in material analyzed from Her2+ or Triple Negative breast cancer patients. Lack of pY88 staining in Group 0 patients suggested that DK4 was not active, and these patients would not respond to Palbociclib, while those in Group 1 or 2, with some active DK4, would respond. To test this hypothesis, following informed consent, we stratified patients who were scheduled to undergo mastectomy or lumpectomy based on pY88 status. Post surgery fresh tumor material was grown in explant culture, followed by treatment with Palbociclib. 48 h. later samples were formalin-fixed, paraffin-embedded and stained with Ki67 as a marker of proliferation. We found that the explant material obtained from Group 0 patients was non-responsive to Palbociclib, while material obtained from Group 1 and 2 patients responded to Palbociclib-mediated inhibition in a statistically significant manner.

CONCLUSION: Our data suggest that pY88-p27 status, as a surrogate marker for cdk4 activity, determined responsiveness to Palbociclib treatment in explant culture. Use of the pY88 biomarker may aid in the expansion of cdk4i therapy into other breast cancer subgroups, where currently these therapies are not approved.

Citation Format: Stacy W. Blain, Susan R. Gottesman, Jonathan Somma, Lisa Dresner, Vladislav Tsiperson. pY88-p27Kip1 status acts as a biomarker to determine responsiveness to cdk4 inhibitor therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-214.

Dual Inhibition of CDK4 and CDK2 via Targeting p27 Tyrosine Phosphorylation Induces a Potent and Durable Response in Breast Cancer Cells

Cyclin-dependent kinase 4/6 (CDK4/6)-specific inhibitors, such as palbociclib, have shown clinical efficacy, but primary or secondary resistance has emerged as a problem. To develop more effective therapeutic approaches, investigation is needed into the mechanisms of resistance or adaption. Here, it is demonstrated that CDK2 compensates for loss of CDK4 activity to rescue palbociclib-arrested breast cancer cells, suggesting that inhibition of both kinases is required to achieve durable response. In addition, a novel strategy is described to inhibit tyrosine phosphorylation of p27Kip1 (CDKN1B) and simultaneously inhibit both CDK2 and CDK4. p27Kip1 is a required assembly factor for cyclin-CDK4 complexes, but it must be phosphorylated on residue Y88 to open or activate the complex. The Brk-SH3 peptide, ALT, blocks p27 Y88 phosphorylation, inhibiting CDK4. Nonphosphorylated p27 is no longer a target for ubiquitin-mediated degradation and this stabilized p27 now also inhibits CDK2 activity. Thus, ALT induction inhibits both the kinase that drives proliferation (CDK4) and the kinase that mediates resistance (CDK2), causing a potent and long-lasting cell-cycle arrest. ALT arrests growth of all breast cancer subgroups and synergizes with palbociclib to increase cellular senescence and to cause tumor regression in breast cancer xenograft models. The use of ALT demonstrates that both CDK4 and CDK2 need to be inhibited if long-term efficacy is to be achieved and represents a novel modality to inhibit breast cancer cells.Implications: Modulating tyrosine phosphorylation of p27 impacts both proliferative (CDK4) and resistance (CDK2) mechanisms in breast cancer and suggests that phospho-p27 status may serve as a biomarker for patients that are responsive to CDK4/6 inhibition. Mol Cancer Res; 16(3); 361-77. ©2018 AACR.

Abstract 2348: Targeting the p27kip1/cdk4/cdk2/Rb axis in breast cancer using a peptidomimetic of Brk’s SH3 domain

Purpose: Cyclin D-cdk4 (DK4) has been a highly sought after therapeutic target because it drives cancer proliferation in a majority of human tumors. We have explored the clinical utility of a recently discovered mechanism of cell cycle control exerted on DK4 by p27Kip1 and its activator, the Breast tumor Related Kinase (Brk), in predicting responsiveness to therapy and as a new target for treatment. Although known as a DK4 assembly factor and cdk2 inhibitor, p27 also acts as a DK4 ON/OFF “switch.” Tyrosine (Y) phosphorylation of p27 (pY) by Brk gatekeeps both ATP binding and CAK phosphorylation of cdk4’s T loop, essential for DK4 activation. This function is restricted to cdk4: p27’s association with cdk2, whether Y phosphorylated or not, appears to be inhibitory. However, in vivo Y phosphorylated p27 is a target for cdk2-dependent ubiquitin-mediated degradation, reducing p27’s association with cdk2, indirectly activating this complex. We showed that blocking p27 pY inactivates cdk4 directly AND cdk2 indirectly, and thus represents a novel way to block cancer cell proliferation. pY also serves as a predictive biomarker of cdk4 activity and tumor response.

Methods: We used a small peptide, ALT, which contains a portion of Brk’s SH3 domain. ALT binds to p27, blocks Brk’s association and ability to phosphorylate p27, inhibiting cdk4 and increasing p27’s ability to inhibit cdk2. We engineered a lipid-based nanoparticle delivery vehicle (NP-ALT), permitting us to test ALT as a first generation therapeutic in breast cancer cell lines that were both responsive and non-responsive to cdk4i therapy. ALT was also used with Palbociclib to determine if combination therapy reduced drug resistance. We developed a dual IHC assay for p27 and pY, which we used to analyze paraffin-embedded, archival human tumor samples, to determine whether we could pinpoint patients who would have responded to cdk4 inhibition therapy.

Results: NP-ALT blocks pY, cdk4 and cdk2 activity, and proliferation in both Palbociclib sensitive and resistant cell lines. As a dual therapy, ALT treatment synergized with Palbociclib to arrest cells for >30 days, increased senescence, and in animal models caused tumor regression instead of just slowing tumor growth as seen with Palbociclib alone. Analysis of human cancer, obtained from archival sources, demonstrated that pY is never detected in quiescent benign mammary tissue, but is detected in about half of the advanced ER/PR+/Her2- tumors analyzed, and using explant culture techniques, we were able to stratify pY with Palbociclib response.

Conclusion: Use of an Brk SH3 based peptide (NP-ALT) has proven effective in blocking p27 pY, inhibiting both cdk2 and cdk4, inducing senescence and increased durability. pY levels correlate with Palbociclib sensitivity in low, moderate and non-responders, suggesting that this may be a biomarker highlighting responsiveness to cdk4i therapy.

Citation Format: Stacy W. Blain, Jason Quinones, Priyank Patel, Vladislav Tsiperson, Susan Gottesman, Jonathan Somma, Yun Wu. Targeting the p27kip1/cdk4/cdk2/Rb axis in breast cancer using a peptidomimetic of Brk’s SH3 domain [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2348. doi:10.1158/1538-7445.AM2017-2348

Designing a broad-spectrum integrative approach for cancer prevention and treatment

Targeted therapies and the consequent adoption of "personalized" oncology have achieved notable successes in some cancers; however, significant problems remain with this approach. Many targeted therapies are highly toxic, costs are extremely high, and most patients experience relapse after a few disease-free months. Relapses arise from genetic heterogeneity in tumors, which harbor therapy-resistant immortalized cells that have adopted alternate and compensatory pathways (i.e., pathways that are not reliant upon the same mechanisms as those which have been targeted). To address these limitations, an international task force of 180 scientists was assembled to explore the concept of a low-toxicity "broad-spectrum" therapeutic approach that could simultaneously target many key pathways and mechanisms. Using cancer hallmark phenotypes and the tumor microenvironment to account for the various aspects of relevant cancer biology, interdisciplinary teams reviewed each hallmark area and nominated a wide range of high-priority targets (74 in total) that could be modified to improve patient outcomes. For these targets, corresponding low-toxicity therapeutic approaches were then suggested, many of which were phytochemicals. Proposed actions on each target and all of the approaches were further reviewed for known effects on other hallmark areas and the tumor microenvironment. Potential contrary or procarcinogenic effects were found for 3.9% of the relationships between targets and hallmarks, and mixed evidence of complementary and contrary relationships was found for 7.1%. Approximately 67% of the relationships revealed potentially complementary effects, and the remainder had no known relationship. Among the approaches, 1.1% had contrary, 2.8% had mixed and 62.1% had complementary relationships. These results suggest that a broad-spectrum approach should be feasible from a safety standpoint. This novel approach has potential to be relatively inexpensive, it should help us address stages and types of cancer that lack conventional treatment, and it may reduce relapse risks. A proposed agenda for future research is offered.

Sustained proliferation in cancer: Mechanisms and novel therapeutic targets

Proliferation is an important part of cancer development and progression. This is manifest by altered expression and/or activity of cell cycle related proteins. Constitutive activation of many signal transduction pathways also stimulates cell growth. Early steps in tumor development are associated with a fibrogenic response and the development of a hypoxic environment which favors the survival and proliferation of cancer stem cells. Part of the survival strategy of cancer stem cells may manifested by alterations in cell metabolism. Once tumors appear, growth and metastasis may be supported by overproduction of appropriate hormones (in hormonally dependent cancers), by promoting angiogenesis, by undergoing epithelial to mesenchymal transition, by triggering autophagy, and by taking cues from surrounding stromal cells. A number of natural compounds (e.g., curcumin, resveratrol, indole-3-carbinol, brassinin, sulforaphane, epigallocatechin-3-gallate, genistein, ellagitannins, lycopene and quercetin) have been found to inhibit one or more pathways that contribute to proliferation (e.g., hypoxia inducible factor 1, nuclear factor kappa B, phosphoinositide 3 kinase/Akt, insulin-like growth factor receptor 1, Wnt, cell cycle associated proteins, as well as androgen and estrogen receptor signaling). These data, in combination with bioinformatics analyses, will be very important for identifying signaling pathways and molecular targets that may provide early diagnostic markers and/or critical targets for the development of new drugs or drug combinations that block tumor formation and progression.

Abstract P5-08-01: Tyrosine phosphorylation of p27kip1 regulates the activity of cyclin D-cdk4 complexes in breast cancer

The oncogenes Cyclin D and cdk4 are overexpressed in breast cancer, but the levels of these proteins are not always accurate indicators of oncogenic activity because p27Kip1 is required to assemble this otherwise unstable dimer. However, p27’s association activates or alternatively inhibits cyclin D-cdk4, serving as a bona fide ON/OFF "switch." Tyrosine (Y) phosphorylation of residues Y88/89 in p27 displaces its C-terminus from the cdk4 active site, permitting both ATP binding and CAK phosphorylation of cdk4’s T loop. This model leads to the following hypothesis: modulation of p27 pY controls cdk4 activity, which in turn regulates efficient cell cycle passsage, and in breast cancer where cdk4 activity is deregulated, p27 may be constitutively switched ON. Deregulated Src Family Kinase (SFK) signaling in cancer may increase p27 pY, constitutively activating oncogenic cdk4, causing continuous cell cycling. Using our p27 pY phosphospecific antibody, we have shown in primary tumors, that p27 pY is not detected in benign tissue regions, but is detected in grade 1 and progressively higher grade tumors, suggesting that p27 pY may be a marker for increased oncogenic cdk4 activity and cdk4 inhibitor sensitivity. We identified an SH3 recruitment domain within p27 that controls p27 pY, and in turn controls cdk4 activity. Blocking the SH3:p27 interaction with small peptides prevents p27 pY and cdk4 activity in vitro and in vivo. Using a phage-ELISA assay, we identified PTK6/Brk (Protein Tyrosine Kinase 6/Breast Tumor Kinase) that functions as a high-affinity kinase, able to phosphorylate p27 in vitro and associate with phosphorylated p27 in vivo. Overexpression of PTK6 in vivo increases p27 pY and increases resistance to specific cdk4 inhibition by the chemical inhibitor, PD0332991. An ALTernatively spliced form of PTK6 (ALT), which contains the SH3 domain, specifically associates with p27 in cells arrested by contact or serum-starvation, blocking pY and acting as an endogenous inhibitor of cdk4. As PTK6/Brk is overexpressed in more than 60% of human breast carcinomas, our data suggest that PTK6/Brk overexpression facilitates cell cycle progression by increasing cdk4 activity through direct p27 Y phosphorylation. As PD0332991 moves into the clinic, p27 pY could serve as a marker to identify tumors sensitive to cdk4 inhibition, while blocking the PTK6:p27 interaction with small molecules represents a novel therapeutic option to inhibit cdk4 activation.

Citation Format: Priyank Patel, Elina Shetyn, Cindy Gomez, Susan RS Gottesman, Angela Tyner, Benedikt Asbach, Ralf Wagner, Stacy W Blain. Tyrosine phosphorylation of p27kip1 regulates the activity of cyclin D-cdk4 complexes in breast cancer [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 P5-08-01.

Abstract LB-123: PTK6/BRK modulates tyrosine phosphorylation of p27Kip1 and the activity of the oncogene cyclin D-cdk4

The oncogenes Cyclin D and cdk4 are overexpressed in a variety of tumors, but the levels of these proteins are not always accurate indicators of oncogenic activity because p27Kip1 is required to assemble this otherwise unstable dimer. However, p27’s association activates or alternatively inhibits cyclin D-cdk4, serving as a bona fide ON/OFF “switch.” Tyrosine (Y) phosphorylation of residues Y88/89 in p27 displaces its C-terminus from the cdk4 active site, permitting both ATP binding and CAK phosphorylation of cdk4’s T loop. This model leads to the following hypothesis: modulation of p27 Y phosphorylation controls cdk4 activity, which in turn regulates efficient cell cycle passsage, and in cancers where cdk4 activity is deregulated, p27 may be constitutively switched ON. Deregulated Src Family Kinase (SFK) signaling in cancer may increase p27 Y phosphorylation, constitutively activating oncogenic cdk4, causing continuous cell cycling. Using our p27 Y88 phosphospecific antibody, we have shown in primary tumors, that p27 Y phosphorylation is not detected in benign tissue regions, but is detected in grade 1 and progressively higher grade tumors, suggesting that p27 Y phosphorylation may be a marker for increased oncogenic cdk4 activity and cdk4 inhibitor sensitivity. Although SFKs have been implicated in p27 Y phosphorylation, little is known about the domains involved on either the SFK or p27. We identified two SH3 recruitment domains within p27 that modulate Y88 phosphorylation, thereby modulating cdk4 activity. Mutation of these domains results in loss of Y88 phosphorylation, while the prior addition of an SH3 peptide is able to prevent Y88 phosphorylation. Using a phage-ELISA assay, we identified PTK6/Brk, (Protein Tyrosine Kinase 6/Breast Tumor Kinase), that functions as a high-affinity kinase, able to phosphorylate p27 in vitro and associate with phosphorylated p27 in vivo. Overexpression of PTK6 in vivo increases Y88 phosphorylation and increases resistance to specific cdk4 inhibition by the chemical inhibitor, PD0332991, in a kinase-dependent fashion. As PTK6/Brk is overexpressed in more than 60% of human breast carcinomas, our data suggest that PTK6/Brk overexpression facilitates cell cycle progression by increasing cdk4 activity through direct p27 Y phosphorylation. As PD0332991 moves into the clinic, p27 Y phosphorylation could serve as a marker to identify tumors sensitive to cdk4 inhibition, while blocking the PTK6:p27 interaction represents a novel therapeutic option to inhibit cdk4 activation.

Citation Format: Stacy W. Blain, Cindy Gomez, Elina Shteyn, Priyank Patel, Susan R.S. Gottesman, Benedikt Asbach, Ralf Wagner, Angela L. Tyner. PTK6/BRK modulates tyrosine phosphorylation of p27Kip1 and the activity of the oncogene cyclin D-cdk4. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-123. doi:10.1158/1538-7445.AM2013-LB-123

Tyrosine phosphorylation of the p21 cyclin-dependent kinase inhibitor facilitates the development of proneural glioma

Phosphorylation of Tyr-88/Tyr-89 in the 3(10) helix of p27 reduces its cyclin-dependent kinase (CDK) inhibitory activity. This modification does not affect the interaction of p27 with cyclin-CDK complexes but does interfere with van der Waals and hydrogen bond contacts between p27 and amino acids in the catalytic cleft of the CDK. Thus, it had been suggested that phosphorylation of this site could switch the tumor-suppressive CDK inhibitory activity to an oncogenic activity. Here, we examined this hypothesis in the RCAS-PDGF-HA/nestin-TvA proneural glioma mouse model, in which p21 facilitates accumulation of nuclear cyclin D1-CDK4 and promotes tumor development. In these tumor cells, approximately one-third of the p21 is phosphorylated at Tyr-76 in the 3(10) helix. Mutation of this residue to glutamate reduced inhibitory activity in vitro. Mutation of this residue to phenylalanine reduced the tumor-promoting activity of p21 in the animal model, whereas glutamate or alanine substitution allowed tumor formation. Consequently, we conclude that tyrosine phosphorylation contributes to the conversion of CDK inhibitors from tumor-suppressive roles to oncogenic roles.

Chk1 has an essential role in the survival of differentiated cortical neurons in the absence of DNA damage

Neuronal death in the central nervous system contributes to the development of age-related neurodegeneration. The ATR/Chk1 pathway appears to function neuroprotectively to prevent DNA damage induced by cytotoxic agents. Here, we examine the function of Chk1 on cell viability of cortical neurons in the absence of additional DNA damaging stimuli. The Chk1-specific inhibitor, UCN-01, and the ATR inhibitor, Caffeine, cause neuronal apoptosis in differentiated neurons in the absence of additional treatment, whereas inhibition of ATM or Chk2, does not. UCN-01 treatment increased the detection of γ-H2AX phosphorylation, DNA strand breaks, and an activated p53-dependent DNA damage response (DDR), suggesting that Chk1 normally helps to maintain genomic stability. UCN-01 treatment also enhanced the apoptosis seen in neurons treated with DNA damaging agents, such as camptothecin (CPT). Our results indicate that Chk1 is essential for neuronal survival, and perturbation of this pathway increases a cell's sensitivity to naturally accumulating DNA damage.

S phase entry causes homocysteine-induced death while ataxia telangiectasia and Rad3 related protein functions anti-apoptotically to protect neurons

A major phenotype seen in neurodegenerative disorders is the selective loss of neurons due to apoptotic death and evidence suggests that inappropriate re-activation of cell cycle proteins in post-mitotic neurons may be responsible. To investigate whether reactivation of the G1 cell cycle proteins and S phase entry was linked with apoptosis, we examined homocysteine-induced neuronal cell death in a rat cortical neuron tissue culture system. Hyperhomocysteinaemia is a physiological risk factor for a variety of neurodegenerative diseases, including Alzheimer's disease. We found that in response to homocysteine treatment, cyclin D1, and cyclin-dependent kinases 4 and 2 translocated to the nucleus, and p27 levels decreased. Both cyclin-dependent kinases 4 and 2 regained catalytic activity, the G1 gatekeeper retinoblastoma protein was phosphorylated and DNA synthesis was detected, suggesting transit into S phase. Double-labelling immunofluorescence showed a 95% co-localization of anti-bromodeoxyuridine labelling with apoptotic markers, demonstrating that those cells that entered S phase eventually died. Neurons could be protected from homocysteine-induced death by methods that inhibited G1 phase progression, including down-regulation of cyclin D1 expression, inhibition of cyclin-dependent kinases 4 or 2 activity by small molecule inhibitors, or use of the c-Abl kinase inhibitor, Gleevec, which blocked cyclin D and cyclin-dependent kinase 4 nuclear translocation. However, blocking cell cycle progression post G1, using DNA replication inhibitors, did not prevent apoptosis, suggesting that death was not preventable post the G1-S phase checkpoint. While homocysteine treatment caused DNA damage and activated the DNA damage response, its mechanism of action was distinct from that of more traditional DNA damaging agents, such as camptothecin, as it was p53-independent. Likewise, inhibition of the DNA damage sensors, ataxia-telangiectasia mutant and ataxia telangiectasia and Rad3 related proteins, did not rescue apoptosis and in fact exacerbated death, suggesting that the DNA damage response might normally function neuroprotectively to block S phase-dependent apoptosis induction. As cell cycle events appear to be maintained in vivo in affected neurons for weeks to years before apoptosis is observed, activation of the DNA damage response might be able to hold cell cycle-induced death in check.

Switching cyclin D-Cdk4 kinase activity on and off

The cyclin-cdks are master regulators of cell proliferation. These serine/threonine kinases are the motors that both start and stop the cell cycle in response to proliferative or antiproliferative signals. They phosphorylate substrates required to trigger orderly cell cycle progression, and thus their activity is tightly regulated in order to prevent inappropriate activation. One of the main interfaces between the extraceullar environment and the cell cycle machinery is the interaction of the cyclin-cdks with two families of stoichiometric cyclin kinase inhibitors (CKIs), the Ink4s and the Cip/Kips. As their name suggests, the CKIs have historically been considered negative regulators of the cyclin-cdks, responsible for rapidly and effectively turning off cyclin-cdk activity. However, the interaction of cyclin D-cdk4 with the Cip/Kip family, and with p27Kip1 in particular, appeared complex. In addition to its ability to inhibit cyclin D-cdk4, p27 appeared to be a required assembly factor for the complex, binding in a non-inhibitory mode at least some of the time. Whether p27 was a cyclin D-cdk4/6 inhibitor or not was controversial, and how it might switch between these two modes was unknown. Arguing for a two state mechanism, we have recently shown that p27 can be both a cdk4 bound-inhibitor and a bound-non-inhibitor, depending on the growth state of the cell. This perspective highlights the significance of this finding in terms of normal cell cycle progression and tumor development.

Differential modification of p27Kip1 controls its cyclin D-cdk4 inhibitory activity

Whether p27 is a cyclin D-cdk4/6 inhibitor or not is controversial, and how it might switch between these two modes is unknown. Arguing for a two-state mechanism, we show that p27 bound to cyclin D-cdk4 can be both inhibitory and noninhibitory, due to its differential-growth-state-dependent tyrosine phosphorylation. We found that p27 from proliferating cells was noninhibitory but that p27 from arrested cells was inhibitory, and the transition from a bound noninhibitor to a bound inhibitor was not due to an increase in p27 concentration. Rather, two tyrosine residues (Y88 and Y89) in p27's cdk interaction domain were phosphorylated preferentially in proliferating cells, which converted p27 to a noninhibitor. Concordantly, mutation of these sites rendered p27 resistant to phosphorylation and locked it into the bound-inhibitor mode in vivo and in vitro. Y88 was directly phosphorylated in vitro by the tyrosine kinase Abl, which converted p27 to a cdk4-bound noninhibitor. These data show that the growth-state-dependent tyrosine phosphorylation of p27 modulates its inhibitory activity in vivo.

Different sensitivity of the transforming growth factor-beta cell cycle arrest pathway to c-Myc and MDM-2

Recently, the oncoprotein MDM-2 was implicated in the transforming growth factor-beta (TGF-beta) growth inhibitory pathway by the finding that prolonged, constitutive expression of MDM-2 in mink lung epithelial cells could overcome the antiproliferative effect of TGF-beta (Sun, P., Dong, P., Dai, K., Hannon, G. J., and Beach, D. (1998) Science 282, 2270-2272). However, using Mv1Lu cells conditionally expressing MDM-2, we found that MDM-2 does not overcome TGF-beta-mediated growth arrest. No detectable changes were observed in various TGF-beta responses, including cell cycle arrest, activation of transcriptional reporters, and TGF-beta-dependent Smad2/3 nuclear accumulation. This finding was in direct contrast to the effect of forcing c-Myc expression, a bona fide member of the TGF-beta growth inhibitory pathway, which renders cells refractory to TGF-beta-induced cell cycle arrest. Our results suggest that an MDM-2-dependent increase in cell cycle progression may allow the acquisition of additional mutations over time and that these alterations then allow cells to evade a TGF-beta-mediated growth arrest. Our conclusion is that, whereas c-Myc down-regulation by TGF-beta is a required event in the cell cycle arrest response of epithelial cells, MDM-2 is not a direct participant in the normal TGF-beta antiproliferative response.

Myc downregulation by transforming growth factor beta required for activation of the p15(Ink4b) G(1) arrest pathway

The antimitogenic action of transforming growth factor beta (TGF-beta) in epithelial cells involves cyclin-dependent kinase (cdk) inhibitory gene responses and downregulation of c-Myc expression. Although the cdk inhibitory responses are sufficient for G(1) arrest, enforced expression of c-Myc prevents G(1) arrest by TGF-beta. We investigated the basis of this antagonism by using Mv1Lu lung epithelial cell lines that conditionally express levels of human c-Myc. We show that c-Myc prevents induction of the cdk4 inhibitor p15(Ink4b) and the subsequent inhibition of G(1) cdks by TGF-beta. We assessed the significance of this effect by analyzing the oligomeric state of cdk4 in these cells. In proliferating cells, endogenous cdk4 is distributed among three populations: an abundant high-molecular-mass (>400-kDa) pool of latent cdk4 that serves as a source of cdk4 for cyclin D, a low-abundance pool containing active cyclin D-cdk4 complexes, and an inactive population of monomeric cdk4. Cell stimulation with TGF-beta converts the latent and active cdk4 pools into inactive cdk4, an effect that is specifically mimicked by overexpression of p15 but not by other forms of G(1) arrest. This process of TGF-beta-induced cdk4 inactivation is completely blocked by expression of c-Myc, even though the latent and active cdk4 complexes from c-Myc-expressing cells remain sensitive to dissociation by p15 in vitro. c-Myc causes a small increase in cyclin D levels, but this effect contributes little to the loss of TGF-beta responses in these cells. The evidence suggests that c-Myc interferes with TGF-beta activation of the p15 G(1) arrest pathway. TGF-beta must therefore downregulate c-Myc in order to activate this pathway.

Differential interaction of the cyclin-dependent kinase (Cdk) inhibitor p27Kip1 with cyclin A-Cdk2 and cyclin D2-Cdk4

Although p27(Kip1) has been considered a general inhibitor of G1 and S phase cyclin-dependent kinases, we report that the interaction of p27 with two such kinases, cyclin A-Cdk2 and cyclin D-Cdk4, is different. In Mv1Lu cells containing a p27 inducible system, a 6-fold increase over the basal p27 level completely inhibited Cdk2 and cell cycle progression. In contrast, the same or a larger increase in p27 levels did not inhibit Cdk4 or its homologue Cdk6, despite extensive binding to these kinases. A p27-cyclin A-Cdk2 complex formed in vitro was essentially inactive, whereas a p27-cyclin D2-Cdk4 complex was active as a retinoblastoma kinase and served as a substrate for the Cdk-activating kinase Cak. High concentrations of p27 inhibited cyclin D2-Cdk4, apparently by conversion of active complexes into inactive ones by the binding of additional p27 molecules. In contrast to their differential interaction, cyclin A-Cdk2 and cyclin D2-Cdk4 were similarly inhibited by bound p21(Cip1/Waf1). Roles of cyclin A-Cdk2 as a p27 target and cyclin D2-Cdk4 as a p27 reservoir may result from the differential ability of bound p27 to inhibit the kinase subunit in these complexes.

Differential effects of Moloney murine leukemia virus reverse transcriptase mutations on RNase H activity in Mg2+ and Mn2+

We have previously described the in vitro and in vivo characterization of a panel of mutations affecting the RNase H domain of Moloney murine leukemia virus reverse transcriptase (Blain, S. W., and Goff, S.P. (1993) J. Biol. Chem. 268, 23585-23592; Blain, S. W., and Goff, S. P. (1995) J. Virol. 69, 4440-4452). We were intrigued by a discrepancy between in vitro and in vivo RNase H results for two of the mutants. While delta C and delta 5E appeared to have nearly wild-type RNase H activity in vitro, they were unable to degrade their genomic RNA in vivo and thus were effectively RNase H null mutants in this context. In this present report, we describe the differential effects of these mutations on RNase H activity in vitro in the presence of Mg2+ versus Mn2+: mutants delta C and delta 5E were active in the presence of the less biologically relevant Mn2+ and not in the presence of Mg2+. We also describe three mutants with only partial activity in Mg2+. The presence of the different cations can also affect DNA polymerization and processivity of an RNase H-deficient mutant.

Reversion of a Moloney murine leukemia virus RNase H mutant at a second site restores enzyme function and infectivity

The reverse transcriptase of retroviruses contains an RNase H activity essential for the proper synthesis of the viral DNA copy of the RNA genome. We have previously characterized a number of point mutations altering the RNase domain of the Moloney murine leukemia virus reverse transcriptase (S. W. Blain and S. P. Goff, J. Biol. Chem. 268:23585-23592, 1993). One such mutation, Y586F (a Y-to-F change at position 586), reduced RNase H activity, as assayed by in situ gel analysis, to about 5% of the wild-type level and prevented viral replication. We have now recovered a revertant virus with near-normal infectivity and in vitro enzymatic activity. The revertant contains a single substitution, N613H, distant in the primary sequence of the protein, but modeling with the Escherichia coli RNase H structure suggests that the reverted residue is close in space to the original substituted residue. Examination of the structure permits some suggestions as to how this second-site revertant restores enzyme activity.

Effects on DNA synthesis and translocation caused by mutations in the RNase H domain of Moloney murine leukemia virus reverse transcriptase

To determine the various roles of RNase H in reverse transcription, we generated a panel of mutations in the RNase H domain of Moloney murine leukemia virus reverse transcriptase based on sequence alignments and the crystal structures of Escherichia coli and human immunodeficiency virus type 1 RNases H (S. W. Blain and S. P. Goff, J. Biol. Chem. 268:23585-23592, 1993). These mutations were introduced into a full-length provirus, and the resulting genomes were tested for infectivity by transient transfection assays or after generation of stable producer lines. Several of the mutant viruses replicated normally, some showed significant delays in infectivity, and others were noninfectious. Virions were collected, and the products of the endogenous reverse transcription reaction were examined to determine which steps might be affected by these mutations. Some mutants left their minus-strand strong-stop DNA in RNA-DNA hybrid form, in a manner similar to that of RNase H null mutants. Some mutants showed increased polymerase pausing. Others were impaired in first-strand translocation, independently of their wild-type ability to degrade genomic RNA, suggesting a new role for RNase H in strand transfer. DNA products synthesized in vivo by the wild-type and mutant viruses were also examined. Whereas wild-type virus did not accumulate detectable levels of minus-strand strong-stop DNA, several mutants were blocked in translocation and did accumulate this intermediate. These results suggest that in vivo wild-type virus normally translocates minus-strand strong-stop DNA efficiently.

Nuclease activities of Moloney murine leukemia virus reverse transcriptase. Mutants with altered substrate specificities

RNases H are traditionally thought to degrade RNA only in RNA-DNA hybrid form. We found that the wild-type Moloney murine leukemia virus (M-MuLV) reverse transcriptase (RT) was capable of degrading RNA in RNA-RNA duplexes as well as in RNA-DNA hybrids, as assayed by in situ gel techniques. Escherichia coli RNase H does not degrade the RNA-RNA duplex in this assay, while E. coli RNase III, a double-strand-specific ribonuclease, does. The apparent specific activity of M-MuLV RT on RNA-RNA duplexes is similar to that on RNA-DNA hybrids. Neither the DNA polymerase domain nor the RNase H domain of RT expressed individually exhibited this RNA-RNA activity. We have generated a series of mutations in the RNase H domain of M-MuLV RT, expressed the mutant enzymes in E. coli, and assayed these mutants for various activities. All RTs were as active as the wild type in the oligo(dT):poly(rA) DNA polymerase assay, and many retained both nuclease activities. Two enzymes with mutations at the carboxyl terminus of the RNase H domain retained RNA-DNA activity, but not RNA-RNA activity. Another mutant enzyme showed the opposite phenotype, retaining RNA-RNA, but not RNA-DNA, nuclease activity. Thus, we were able to genetically separate the two activities. These results may be helpful in defining enzyme-substrate interactions.

Defects in Moloney murine leukemia virus replication caused by a reverse transcriptase mutation modeled on the structure of Escherichia coli RNase H

We have studied a mutant Moloney murine leukemia virus with a deletion in reverse transcriptase (RT) which is predicted to make its RNase H domain resemble structurally that of human immunodeficiency virus RT. This deletion was based on improved RNase H homology alignments made possible by the recently solved three-dimensional structure for Escherichia coli RNase H. This mutant Moloney murine leukemia virus RT was fully active in the oligo(dT)-poly(rA) DNA polymerase assay and retained nearly all of wild-type RT's RNase H activity in an in situ RNase H gel assay. However, proviruses reconstructed to include this deletion were noninfectious. Minus-strand strong-stop DNA was made by the deletion mutant, but the amount of minus-strand translocation was intermediate to the very low level measured with RNase H-null virions and the high level seen with wild-type RT. The average length of translocated minus-strand DNA was shorter for the deletion mutant than for wild type, suggesting that mutations in the RNase H domain of RT also affect DNA polymerase activity.