Discovery and Clinical Proof-of-Concept of RLY-2608, a First-in-Class Mutant-Selective Allosteric PI3Kα Inhibitor That Decouples Antitumor Activity from Hyperinsulinemia

PIK3CA (PI3Kα) is a lipid kinase commonly mutated in cancer, including ∼40% of hormone receptor-positive breast cancer. The most frequently observed mutants occur in the kinase and helical domains. Orthosteric PI3Kα inhibitors suffer from poor selectivity leading to undesirable side effects, most prominently hyperglycemia due to inhibition of wild-type (WT) PI3Kα. Here, we used molecular dynamics simulations and cryo-electron microscopy to identify an allosteric network that provides an explanation for how mutations favor PI3Kα activation. A DNA-encoded library screen leveraging electron microscopy-optimized constructs, differential enrichment, and an orthosteric-blocking compound led to the identification of RLY-2608, a first-in-class allosteric mutant-selective inhibitor of PI3Kα. RLY-2608 inhibited tumor growth in PIK3CA-mutant xenograft models with minimal impact on insulin, a marker of dysregulated glucose homeostasis. RLY-2608 elicited objective tumor responses in two patients diagnosed with advanced hormone receptor-positive breast cancer with kinase or helical domain PIK3CA mutations, with no observed WT PI3Kα-related toxicities.

SIGNIFICANCE

Treatments for PIK3CA-mutant cancers are limited by toxicities associated with the inhibition of WT PI3Kα. Molecular dynamics, cryo-electron microscopy, and DNA-encoded libraries were used to develop RLY-2608, a first-in-class inhibitor that demonstrates mutant selectivity in patients. This marks the advance of clinical mutant-selective inhibition that overcomes limitations of orthosteric PI3Kα inhibitors. See related commentary by Gong and Vanhaesebroeck, p. 204 . See related article by Varkaris et al., p. 227 . This article is featured in Selected Articles from This Issue, p. 201.

Allosteric PI3Kα Inhibition Overcomes On-target Resistance to Orthosteric Inhibitors Mediated by Secondary PIK3CA Mutations

PIK3CA mutations occur in ∼8% of cancers, including ∼40% of HR-positive breast cancers, where the PI3K-alpha (PI3Kα)-selective inhibitor alpelisib is FDA approved in combination with fulvestrant. Although prior studies have identified resistance mechanisms, such as PTEN loss, clinically acquired resistance to PI3Kα inhibitors remains poorly understood. Through serial liquid biopsies and rapid autopsies in 39 patients with advanced breast cancer developing acquired resistance to PI3Kα inhibitors, we observe that 50% of patients acquire genomic alterations within the PI3K pathway, including PTEN loss and activating AKT1 mutations. Notably, although secondary PIK3CA mutations were previously reported to increase sensitivity to PI3Kα inhibitors, we identified emergent secondary resistance mutations in PIK3CA that alter the inhibitor binding pocket. Some mutations had differential effects on PI3Kα-selective versus pan-PI3K inhibitors, but resistance induced by all mutations could be overcome by the novel allosteric pan-mutant-selective PI3Kα-inhibitor RLY-2608. Together, these findings provide insights to guide strategies to overcome resistance in PIK3CA-mutated cancers.

SIGNIFICANCE

In one of the largest patient cohorts analyzed to date, this study defines the clinical landscape of acquired resistance to PI3Kα inhibitors. Genomic alterations within the PI3K pathway represent a major mode of resistance and identify a novel class of secondary PIK3CA resistance mutations that can be overcome by an allosteric PI3Kα inhibitor. See related commentary by Gong and Vanhaesebroeck, p. 204 . See related article by Varkaris et al., p. 240 . This article is featured in Selected Articles from This Issue, p. 201.

Identification of GDC-1971 (RLY-1971), a SHP2 Inhibitor Designed for the Treatment of Solid Tumors

Protein tyrosine phosphatase SHP2 mediates RAS-driven MAPK signaling and has emerged in recent years as a target of interest in oncology, both for treating with a single agent and in combination with a KRAS inhibitor. We were drawn to the pharmacological potential of SHP2 inhibition, especially following the initial observation that drug-like compounds could bind an allosteric site and enforce a closed, inactive state of the enzyme. Here, we describe the identification and characterization of GDC-1971 (formerly RLY-1971), a SHP2 inhibitor currently in clinical trials in combination with KRAS G12C inhibitor divarasib (GDC-6036) for the treatment of solid tumors driven by a KRAS G12C mutation.

Abstract P5-16-10: RLY-2608: The first allosteric mutant- and isoform-selective inhibitor of PI3Kα, is efficacious as a single agent and drives regressions in combination with standard of care therapies in PIK3CA mutant breast cancer models

Inhibition of CDK4/6 combined with the estrogen receptor (ER) degrader fulvestrant significantly improves progression free survival and overall survival in advanced hormone receptor positive (HR+) breast cancer patients and is now the standard of care (SOC) in this disease. Up to 40% of HR+ breast cancers harbor PIK3CA mutations leading to activation of phosphoinositide 3-kinase alpha (PI3Kα), which has been associated with resistance to CDK4/6 inhibitors and fulvestrant. Therefore, PI3Kα inhibitor combinations with CDK4/6 inhibitors and/or fulvestrant are of high interest in HR+, PIK3CA mutant breast cancer. The therapeutic index of active site (orthosteric) inhibitors of PI3Kα has been limited by the dual issues of no clinically meaningful selectivity for mutant versus wild-type (WT) PI3Kα and off-isoform inhibitory activity. Alpelisib, the only approved orthosteric PI3Kα inhibitor, is emblematic of the class with toxicity related to inhibition of wild type PI3Kα and other PI3K isoforms resulting in sub-optimal inhibition of mutant PI3Kα, frequent discontinuation, and challenges in combining with CDK4/6 inhibitors. To overcome these limitations, we designed RLY-2608, the first allosteric, mutant, and isoform-selective inhibitor of PI3Kα. We solved the full-length cryo-EM structure of PI3Kα, performed long time-scale molecular dynamic simulations to elucidate conformational differences between WT and mutant PI3Kα, and leveraged these insights to enable the design of RLY-2608. RLY-2608 does not compete with orthosteric inhibitors for binding and associates 8x faster with mutant PI3Kα relative to WT PI3Kα. In biochemical assays, RLY-2608 inhibits kinase domain (H1047R) and helical domain (E542K, and E545K) mutant PI3Kα activity, demonstrating <10nM potency with 8-12x selectivity relative to WT. RLY-2608 is > 1000-fold selective over the β, δ, and γ PI3K isoforms in biochemical assays and demonstrates exquisite selectivity across a panel of 322 kinases, with no other kinases showing >50% inhibition. We performed in vitro combinations in two HR+ PIK3CA mutant cell lines (MCF7: E545K; T47D: H1047R) and observed synergy between RLY-2608 and fulvestrant or CDK4/6 inhibitors. In vivo, we tested combinations of RLY-2608 with fulvestrant and/or the CDK4/6 inhibitor abemaciclib in the MCF7 xenograft model. Oral administration of RLY-2608 in combination with fulvestrant led to improved efficacy compared to either agent alone in a dose-dependent manner, with regressions observed in the combination arms at all doses. Furthermore, the triple combination of RLY-2608, fulvestrant, and abemaciclib resulted in superior efficacy compared to either the RLY-2608 + fulvestrant or RLY-2608 + abemaciclib doublets, with deep regressions observed in the triple combination arm. In addition, in vivo combination efficacy with fulvestrant and CDK4/6 inhibitors (palbociclib or abemaciclib) was assessed in patient-derived xenografts harboring the PIK3CA H1047R or E545K mutation along with a second site PIK3CA minor mutation. In these studies, combination benefit was observed with doses of RLY-2608 significantly lower than the dose required for maximum efficacy as a single agent. RLY-2608 synergizes in vitro with both anti-estrogen and CDK4/6 inhibitors in cell models of HR+/PIK3CA mutant breast cancer. RLY-2608 can be combined with fulvestrant and CDK4/6 inhibitors in vivo with tumor regressions observed in both cell- and patient-derived xenograft models. The pre-clinical profile of RLY-2608 supports the clinical development of RLY-2608 both in single agent and combination clinical trials in patients with PIK3CA mutant tumors, including HR+/PIK3CA mutant breast cancer.

Citation Format: Ermira Pazolli, Randy Kipp, Alessandro Boezio, Hakan Gunaydin, Amanda Iskandar, Matthew Zubrowski, Bret Williams, Kelley Shortsleeves, Alexandre Larivee, Tom McLean, Klaus Michelsen, Hongtao Zeng, Jonathan LaRochelle, Joe Manna, Lucian DiPietro, Andre Lescarbeau, Mary Mader, Bindu Bennet, Jeremy Wilbur, Qi Wang, Levi Pierce, Iain Martin, James Watters, Pascal Fortin, Donald Bergstrom. RLY-2608: The first allosteric mutant- and isoform-selective inhibitor of PI3Kα, is efficacious as a single agent and drives regressions in combination with standard of care therapies in PIK3CA mutant breast cancer models [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 P5-16-10.

Abstract P251: Discovery and characterization of RLY-2608: The first allosteric, mutant, and isoform-selective inhibitor of PI3Kα

Phosphoinositide 3-kinase alpha (PI3Kα) is the most frequently mutated kinase in solid tumors. Traditionally, the development of PI3Kα inhibitors has focused on the active, or orthosteric site. The therapeutic index of orthosteric inhibitors is limited by the lack of clinically meaningful selectivity for mutant versus wild-type (WT) PI3Kα and off-isoform activity. Alpelisib, the only approved orthosteric PI3Kα inhibitor, is emblematic of the class with toxicity related to inhibition of WT PI3Kα and other PI3K isoforms resulting in sub-optimal inhibition of mutant PI3Kα with reductions in dose intensity and frequent discontinuation. To overcome these limitations, we designed RLY-2608, the first allosteric, mutant, and isoform-selective PI3Kα inhibitor. We solved the full-length cryo-EM structure of PI3Kα, performed long time-scale molecular dynamic simulations to elucidate conformational differences between WT and mutant PI3Kα, and leveraged these insights to enable the design of RLY-2608. RLY-2608 does not compete with orthosteric inhibitors for binding and associates 8x faster with mutant PI3Kα relative to WT. In biochemical assays, RLY-2608 inhibits both kinase domain (H1047R) and helical domain (E542K, and E545K) mutant PI3Kα activity with <10nM potency and 8-12x selectivity relative to WT PI3Kα. RLY-2608 is > 1000-fold selective over the β, δ, and γ PI3K isoforms in biochemical assays and demonstrates exquisite selectivity across a panel of 322 kinases, with no other kinases showing > 50% inhibition. In MCF10A cells engineered to express only mutant or WT PI3Kα, RLY-2608 inhibited phosphorylated AKT (pAKT) in a mutant-selective manner. Furthermore, pAKT and viability were significantly inhibited across a panel of cancer cell lines carrying hotspot PIK3CA mutations. RLY-2608 showed anti-tumor activity in both kinase and helical domain PIK3CA mutant in vivo xenograft models with marked regressions or stasis observed in all models. RLY-2608 was well tolerated, with pharmacodynamic modulation and efficacy observed in a dose dependent manner. Insulin levels measured as an indicator of glucose homeostasis were significantly lower when compared to orthosteric inhibitors, suggesting that RLY-2608 can achieve maximum efficacy by maintaining PI3Kα mutant target coverage throughout the dosing interval with significantly reduced impact on WT PI3Kα. In higher species, dosing of RLY-2608 for 28 days resulted in exposures exceeding mutant PI3Kα cellular PD IC90 throughout the dosing interval without elevated glucose levels or histopathological or ophthalmic findings associated with hyperglycemia. Compared to orthosteric inhibitors, RLY-2608 demonstrates preferential binding and inhibition of mutant PI3Kα, is highly selective across the kinome, and achieves in vivo efficacy without dysregulating glucose homeostasis. These results support clinical investigation of RLY-2608 as a differentiated mechanism for inhibition of oncogenic PI3Kα in patients with PIK3CA mutant tumors.

Citation Format: Ermira Pazolli, Randy Kipp, Alessandro Boezio, Hakan Gunaydin, Amanda Iskandar, Matthew Zubrowski, Bret Williams, Kelley Shortsleeves, Alexandre Larivee, Tom McLean, Klaus Michelsen, Hongtao Zeng, Jonathan LaRochelle, Joe Manna, Lucian DiPietro, Mary Mader, Bindu Bennet, Jeremy Wilbur, Qi Wang, Levi Pierce, Iain Martin, James Watters, Pascal Fortin, Donald Bergstrom. Discovery and characterization of RLY-2608: The first allosteric, mutant, and isoform-selective inhibitor of PI3Kα [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P251.

Abstract P5-15-02: Evaluating the cost of endocrine therapy vs. radiation therapy alone for low risk hormone positive early stage breast cancer in elderly patients

Objective: Elderly patients with low-risk hormone-positive breast cancer are at risk of over treatment. Avoidance of radiation therapy (RT) in favor of endocrine therapy alone was first heralded as the optimal conservative strategy due to logistical simplicity, low acute sequelae and a reduction of contralateral cancers not seen with RT. However, long-term use of aromatase inhibitors (AI) is not without costs and morbidity, often leading to low compliance and notable late effects. We therefore performed a cost-effectiveness analysis to compare the outcomes and costs between AI for five years without RT versus hypofractionated RT alone without endocrine therapy.

Materials and Methods: Using data from available phase III trials and meta-analyses, we constructed a patient-level microsimulation Markov decision model to replicate the comparative outcomes between the strategies above from the societal perspective among 200,000 simulated patients. Five years of anastrozole was compared to a 15-fraction hypofractionated whole breast RT course without boost in a cohort of patients with low-risk disease as defined by CALGB 9343 entry criteria. Noncompliance with AI was modeled from recent population-based data. Relative effectiveness on ipsilateral breast tumor recurrence and contralateral breast cancers were based off the NSABP B-21 trial, adjusted to match the modern outcomes demonstrated in CALGB 9343 and PRIME II with further adjustment for AI over tamoxifen (ATAC, EBCTCG meta-analysis). Indirect costs of travel were accounted for, as were the costs of common and serious side-effects from RT (dermatitis, fibrosis, second malignancy, heart disease) and AI (arthralgia, hot flashes, osteopenia, fracture, thrombosis). A 1-year cycle time and lifetime horizon were used, with all costs adjusted to 2018 US dollars and extracted primarily from Medicare reimbursement data. The primary measure of efficacy was the quality-adjusted life-year (QALY) with age-adjusted utilities extracted from the literature. Half-cycle correction and a 3% discount rate were applied. Probabilistic sensitivity analysis was used to vary all parameters simultaneously.

Results: On average, RT was approximately $3,981 more expensive than endocrine therapy over the lifetime horizon. Under a number of assumptions, RT appeared similar in long-term effectiveness to AI therapy, with a difference of less than 0.03 quality-adjusted life years. Given the low value of the denominator in the incremental cost-effectiveness ratio (ICER), RT did not meet the formally defined $100,000/QALY threshold. On one-way sensitivity analysis, the ICER was particularly sensitive to the incidence and impact of salvage strategies for recurrence, treatment of contralateral breast cancers, cardiac events and fracture rates.

Conclusions: Modeling with the available evidence suggests it is likely that quality-of-life after RT-alone is nearly identical to an AI-alone strategy but associated with a small increase in cost. These results suggest select patients at risk of noncompliance can safely be treated with RT-alone rather than AI alone. Given the relative pros and cons of each strategy, RT-alone should be considered for select elderly low-risk breast patients.

Citation Format: Ward MC, Vicini F, Chadha M, Pierce L, Recht A, Hayman J, Thaker N, Khan A, Keisch M, Shah C. Evaluating the cost of endocrine therapy vs. radiation therapy alone for low risk hormone positive early stage breast cancer in elderly patients [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-15-02.

Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field

Designing tight-binding ligands is a primary objective of small-molecule drug discovery. Over the past few decades, free-energy calculations have benefited from improved force fields and sampling algorithms, as well as the advent of low-cost parallel computing. However, it has proven to be challenging to reliably achieve the level of accuracy that would be needed to guide lead optimization (∼5× in binding affinity) for a wide range of ligands and protein targets. Not surprisingly, widespread commercial application of free-energy simulations has been limited due to the lack of large-scale validation coupled with the technical challenges traditionally associated with running these types of calculations. Here, we report an approach that achieves an unprecedented level of accuracy across a broad range of target classes and ligands, with retrospective results encompassing 200 ligands and a wide variety of chemical perturbations, many of which involve significant changes in ligand chemical structures. In addition, we have applied the method in prospective drug discovery projects and found a significant improvement in the quality of the compounds synthesized that have been predicted to be potent. Compounds predicted to be potent by this approach have a substantial reduction in false positives relative to compounds synthesized on the basis of other computational or medicinal chemistry approaches. Furthermore, the results are consistent with those obtained from our retrospective studies, demonstrating the robustness and broad range of applicability of this approach, which can be used to drive decisions in lead optimization.

Trypsinogen activation as observed in accelerated molecular dynamics simulations

Serine proteases are involved in many fundamental physiological processes, and control of their activity mainly results from the fact that they are synthetized in an inactive form that becomes active upon cleavage. Three decades ago Martin Karplus's group performed the first molecular dynamics simulations of trypsin, the most studied member of the serine protease family, to address the transition from the zymogen to its active form. Based on the computational power available at the time, only high frequency fluctuations, but not the transition steps, could be observed. By performing accelerated molecular dynamics (aMD) simulations, an interesting approach that increases the configurational sampling of atomistic simulations, we were able to observe the N-terminal tail insertion, a crucial step of the transition mechanism. Our results also support the hypothesis that the hydrophobic effect is the main force guiding the insertion step, although substantial enthalpic contributions are important in the activation mechanism. As the N-terminal tail insertion is a conserved step in the activation of serine proteases, these results afford new perspective on the underlying thermodynamics of the transition from the zymogen to the active enzyme.

Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation

Accelerated molecular dynamics (aMD) simulations greatly improve the efficiency of conventional molecular dynamics (cMD) for sampling biomolecular conformations, but they require proper reweighting for free energy calculation. In this work, we systematically compare the accuracy of different reweighting algorithms including the exponential average, Maclaurin series, and cumulant expansion on three model systems: alanine dipeptide, chignolin, and Trp-cage. Exponential average reweighting can recover the original free energy profiles easily only when the distribution of the boost potential is narrow (e.g., the range ≤20k_BT) as found in dihedral-boost aMD simulation of alanine dipeptide. In dual-boost aMD simulations of the studied systems, exponential average generally leads to high energetic fluctuations, largely due to the fact that the Boltzmann reweighting factors are dominated by a very few high boost potential frames. In comparison, reweighting based on Maclaurin series expansion (equivalent to cumulant expansion on the first order) greatly suppresses the energetic noise but often gives incorrect energy minimum positions and significant errors at the energy barriers (∼2–3k_BT). Finally, reweighting using cumulant expansion to the second order is able to recover the most accurate free energy profiles within statistical errors of ∼k_BT, particularly when the distribution of the boost potential exhibits low anharmonicity (i.e., near-Gaussian distribution), and should be of wide applicability. A toolkit of Python scripts for aMD reweighting “PyReweighting” is distributed free of charge at http://mccammon.ucsd.edu/computing/amdReweighting/.

Abstract P6-06-05: RadiotypeDx: Identification and validation of a radiation sensitivity signature in human breast cancer

Purpose: An unmet clinical need in breast cancer (BC) management is the identification of which patients will respond to radiation therapy (RT). We hypothesized that the integration of post-RT clonogenic survival data with gene expression data across a large spectrum of BC cell lines would generate a BC-specific RT sensitivity signature predictive for RT response in BC patients and allow identification of patients with tumors refractive to conventional therapy.

Methods: Using clonogenic survival assays, we identified the range of surviving fraction (SF) after 2 Gy of RT across 21 BC cell lines. Using SF as a continuous variable, the RT sensitivity score (RSS) was correlated to gene expression using a Spearman correlation method on an individual gene basis. Genes were selected for the signature based on positive or negative correlation with a p-value <0.05 and FDR of <0.01. Unsupervised hierarchical clustering identified differences in gene expression across resistant and sensitive cell lines to generate a radiation sensitivity (RS) signature. This signature was trained and validated in a separate human breast tumor dataset (185 pts) containing early stage, node-negative patients treated with surgery and RT alone without adjuvant chemotherapy to assess the predictive effect of RS signature on recurrence risk after RT. Gene function and potentially actionable targets from the signature were validated using clongenic survival and DNA damage assays.

Results: Clonogenic survival identifies a range of radiation sensitivity in human BCC lines (SF 77%-17%) with no significant correlation (r value <0.3) to the intrinsic BC subtype. Using Spearmans correlation method, a total of 126 genes were identified as being associated with radiation sensitivity (72 positively correlated, 54 negatively correlated). Unsupervised hierarchical expression discriminates gene expression patterns in the RT resistant and RT sensitive cell lines and is enriched for genes involved in cell cycle arrest and DNA damage response (enrichment p-value 5.0 E-22). Knockdown of genes associated with the radioresistance signature identifies previously unreported radiation resistance genes, including TACC1 and RND3 with enhancement ratios of 1.25 and 1.37 in BCC lines. Application of this RS signature to an independent breast cancer dataset with clinical outcomes validates the signature and accurately identifies patients with decreased rates of recurrence compared to patients with high expression of the radioresistant signature (p-value <0.0001, misclassification error rate .31, 12/13 patients with locoregional recurrence accurately identified).

Conclusion: In this study, we derive a human BC-specific RT sensitivity signature (RadiotypeDx) with biologic relevance from preclinical studies and validate this signature for prediction of recurrence in an independent clinical dataset. The signature is not correlated to the intrinsic subtypes of human breast cancer and thus provides useful information beyond traditional breast cancer subtyping. By identifying patients with tumors refractory to standard RT, this signature has the potential to allow for personalization of radiotherapy, particularly in patients for whom treatment intensification is needed.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P6-06-05.

Abstract P6-04-04: Maternal embryonic leucine zipper kinase (MELK) is a novel radiosensitizing and therapeutic target and is independently prognostic in triple-negative breast cancer

Background: While effective targeted therapies exist for estrogen receptor (ER)-positive and HER2/neu-positive breast cancer, no such effective therapies exist for ER-negative, PR-negative, and HER2-negative (“triple negative”) cancers. Given the lack of targeted agents for triple negative (TN) disease and their relative radiation insensitivity, it is clear that additional targets for treatment are critically needed.

Our previous work identified one such novel molecular target as maternal embryonic leucine zipper kinase (MELK), and we sought to investigate the impact of MELK expression on radiation response and patient outcomes.

Methods: Using gene expression arrays, we interrogated the expression of MELK in 2,061 breast tumor samples as well as a panel of 51 breast cancer cell lines. We measured protein expression in TN cancers with western blotting and used clonogenic survival assays to quantitate radiosensitivity of BCC lines at baseline and after MELK inhibition. Multiple datasets were used to evaluate the prognostic import of MELK. Kaplan-Meier analysis using local control and survival data was performed. Chi squared scores were calculated to determine significance and hazard ratios (HR) and 95% confidence intervals (CI) were calculated. A Cox proportional hazards model was constructed to identify potential factors of survival.

Results: We demonstrate that MELK expression is significantly elevated in human TN breast cancers, including chemoradiation resistant tumors (305 tumors compared to 1756 non-TN breast tumors; p-value 7.5 e-21). MELK protein and RNA expression is induced by ionizing radiation (5.6-7.5 fold at 72 hours, p-value <0.01). We characterized the radiation sensitivity of BCC lines and demonstrated that MELK expression is significantly correlated with radioresistance (as measured by clonogenic survival) in 21 breast cancer cell lines (R: 0.62, p-value 0.003). Inhibition of MELK using both siRNA and small molecule inhibitors induces radiation sensitivity in vitro with and enhancement ratio (ER) of 1.5-1.6. We demonstrate that high MELK expression is strongly correlated with p53 mutation positive status (p-value <0.001). Finally, local control and survival analyses of patients with BC showed that those patients whose tumors have high expression of MELK have significantly higher rates of LR after radiation and an overall poorer prognosis than patients with low expression of MELK (HR for LR 1.89-2.23, p-value 0.001; HR for overall survival 1.46-3.3; p-value <0.001 in 3 independent datasets). In multivariate analysis of all patients, only MELK expression and grade were significantly associated with worse local recurrence free (LRF) survival with a HR of 1.35 (95% CI 1.05-1.72, p-value < 0.01).

Conclusion: Here, we identify MELK as a potential biomarker of radioresistance and target for radiosensitization in triple negative breast cancers. MELK overexpression was associated with local failure across multiple data sets. MVA identified MELK as the strongest factor associated with poor local control. Our results support the rationale for developing clinical strategies to inhibit MELK as a novel target in triple-negative breast cancer.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P6-04-04.

Structural insight into the separate roles of inositol tetraphosphate and deacetylase-activating domain in activation of histone deacetylase 3

Histone deacetylases (HDACs) repress transcription by deacetylating acetyllysines on specific histone tails. HDAC3 is implicated in neurodegenerative diseases, certain leukemias, and even in disrupting HIV-1 latency. A recent crystal structure of HDAC3 in complex with the deacetylase-activating domain (DAD) of its corepressor complex revealed an inositol tetraphosphate (IP4) molecule at the protein-protein interface. IP4 was shown to play an important, yet mechanistically ambiguous, role in the activity of HDAC3. The goal of this article is to explore the conformational ensemble of HDAC3 in its inactive apo state and in the presence of each or both of DAD and IP4. Using triplicate, 100 ns molecular dynamic simulations, we study the apo, ternary, and intermediate DAD-bound or IP4-bound HDAC3 states. We find that a population-shift effect is induced by the presence of each corepressor, and is most notable in the presence of both. Our results offer new insights into the change in dynamics necessary for the activation of HDAC3 and highlight the roles of IP4 and DAD in this process.

Dynamics and calcium association to the N-terminal regulatory domain of human cardiac troponin C: a multiscale computational study

Troponin C (TnC) is an important regulatory molecule in cardiomyocytes. Calcium binding to site II in TnC initiates a series of molecular events that result in muscle contraction. The most direct change upon Ca(2+) binding is an opening motion of the molecule that exposes a hydrophobic patch on the surface allowing for Troponin I to bind. Molecular dynamics simulations were used to elucidate the dynamics of this crucial protein in three different states: apo, Ca(2+)-bound, and Ca(2+)-TnI-bound. Dynamics between the states are compared, and the Ca(2+)-bound system is investigated for opening motions. On the basis of the simulations, NMR chemical shifts and order parameters are calculated and compared with experimental observables. Agreement indicates that the simulations sample the relevant dynamics of the system. Brownian dynamics simulations are used to investigate the calcium association of TnC. We find that calcium binding gives rise to correlative motions involving the EF hand and collective motions conducive of formation of the TnI-binding interface. We furthermore indicate the essential role of electrostatic steering in facilitating diffusion-limited binding of Ca(2+).

Effect of radiotherapy after breast-conserving surgery on 10-year recurrence and 15-year breast cancer death: meta-analysis of individual patient data for 10,801 women in 17 randomised trials

BACKGROUND

After breast-conserving surgery, radiotherapy reduces recurrence and breast cancer death, but it may do so more for some groups of women than for others. We describe the absolute magnitude of these reductions according to various prognostic and other patient characteristics, and relate the absolute reduction in 15-year risk of breast cancer death to the absolute reduction in 10-year recurrence risk.

METHODS

We undertook a meta-analysis of individual patient data for 10,801 women in 17 randomised trials of radiotherapy versus no radiotherapy after breast-conserving surgery, 8337 of whom had pathologically confirmed node-negative (pN0) or node-positive (pN+) disease.

FINDINGS

Overall, radiotherapy reduced the 10-year risk of any (ie, locoregional or distant) first recurrence from 35·0% to 19·3% (absolute reduction 15·7%, 95% CI 13·7-17·7, 2p<0·00001) and reduced the 15-year risk of breast cancer death from 25·2% to 21·4% (absolute reduction 3·8%, 1·6-6·0, 2p=0·00005). In women with pN0 disease (n=7287), radiotherapy reduced these risks from 31·0% to 15·6% (absolute recurrence reduction 15·4%, 13·2-17·6, 2p<0·00001) and from 20·5% to 17·2% (absolute mortality reduction 3·3%, 0·8-5·8, 2p=0·005), respectively. In these women with pN0 disease, the absolute recurrence reduction varied according to age, grade, oestrogen-receptor status, tamoxifen use, and extent of surgery, and these characteristics were used to predict large (≥20%), intermediate (10-19%), or lower (<10%) absolute reductions in the 10-year recurrence risk. Absolute reductions in 15-year risk of breast cancer death in these three prediction categories were 7·8% (95% CI 3·1-12·5), 1·1% (-2·0 to 4·2), and 0·1% (-7·5 to 7·7) respectively (trend in absolute mortality reduction 2p=0·03). In the few women with pN+ disease (n=1050), radiotherapy reduced the 10-year recurrence risk from 63·7% to 42·5% (absolute reduction 21·2%, 95% CI 14·5-27·9, 2p<0·00001) and the 15-year risk of breast cancer death from 51·3% to 42·8% (absolute reduction 8·5%, 1·8-15·2, 2p=0·01). Overall, about one breast cancer death was avoided by year 15 for every four recurrences avoided by year 10, and the mortality reduction did not differ significantly from this overall relationship in any of the three prediction categories for pN0 disease or for pN+ disease.

INTERPRETATION

After breast-conserving surgery, radiotherapy to the conserved breast halves the rate at which the disease recurs and reduces the breast cancer death rate by about a sixth. These proportional benefits vary little between different groups of women. By contrast, the absolute benefits from radiotherapy vary substantially according to the characteristics of the patient and they can be predicted at the time when treatment decisions need to be made.

FUNDING

Cancer Research UK, British Heart Foundation, and UK Medical Research Council.

Electron imaging of pyrrhotite superstructures

Natural pyrrhotites, when studied by high resolution electron microscopy, yield crystallographic information on a unit cell scale. Structural heterogeneity is prominent. The many reported superstructures are interpretable through an antiphase model. The 5C pyrrhotite superstructure results from an ordered sequence of antiphase domains while the higher temperature NC type results from a disordered sequence.

Local Therapy in BRCA1/2 Carriers with Operable Breast Cancer: Comparison of Breast Conservation and Mastectomy

Background: Women with inherited germline BRCA1/2 mutations have a 55-85% cumulative risk of breast cancer (BC) by age 70. Thus, knowledge of expected outcomes following various treatments is needed to advise these patients should they be diagnosed with BC. It is unclear whether breast conservation (BCT) offers similar rates of tumor control as mastectomy (M) in BRCA1/2 carriers and it is doubtful whether a randomized trial comparing these options could be performed. Thus, this analysis compares the outcomes between similarly staged women with BRCA1/2 mutations treated with BCT vs. M.Methods: Women with deleterious BRCA1/2 mutations diagnosed with operable BC and who consented to longitudinal studies were identified at 10 institutions in the US, Australia, Spain and Israel. Patient, clinical and treatment characteristics were compared between those receiving BCT and those receiving M +/- RT. Time-to-event endpoints included first failure of treatment, diagnosis of contralateral breast cancer (CBC), and overall and BC-specific survival. Cox regression models were constructed to detect significant associations between patient and clinical characteristics and time-to-event endpoints.Results: Clinical characteristics and outcomes for 302 BCT and 353 M patients were compared. With a median F/U of 8.2 years for BCT patients and 8.9 years following M, 15-year local failure as first failure was significantly higher with BCT vs. M (23.5% vs. 5.5%, p&lt;0.0001). Multivariate analysis indicted choice of local therapy as the only factor significantly predicting local recurrence, with a 4.5-fold risk of local failure with BCT compared to M (p&lt;0.0001). Local failure analyses by cohort revealed the presence of a BRCA2 mutation (HR 2.8; p=0.024) and no use of adjuvant chemotherapy (HR 5.4; p=0.0001) as significant predictors within the BCT group; presence of invasive lobular cancer (HR 9.9; p=0.004) was the only significant predictor within the M cohort. No significant differences were seen in distant failure, BC-specific or overall survival by local therapy. 15-year estimates of CBC were 52.1% with BCT; 41.4% with M; and 37.9% with M+RT (p=0.44). Analyses of BCT vs. M +/- RT and surgery +/- RT did not reveal significant differences in CBC by cohort.Conclusions: The higher risk of local failure in BRCA1/2-associated BC treated with BCT compared to M did not translate into an increased risk of distant failure or mortality. RT did not result in a detectable increase in CBC at 15 years above baseline elevated rates. These results at both the involved and contralateral breasts should be discussed when patients with BRCA1/2-associated BC are considering local treatment options.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 959.

Workshop on Partial Breast Irradiation: State of the Art and the Science, Bethesda, MD, December 8-10, 2002

Breast conserving surgery followed by radiation therapy has been accepted as an alternative to mastectomy in the management of patients with early-stage breast cancer. Over the past decade there has been increasing interest in a variety of radiation techniques designed to treat only the portion of the breast deemed to be at high risk for local recurrence (partial-breast irradiation [PBI]) and to shorten the duration of treatment (accelerated partial-breast irradiation [APBI]). To consider issues regarding the equivalency of the various radiation therapy approaches and to address future needs for research, quality assurance, and training, the National Cancer Institute, Division of Cancer Treatment and Diagnosis, Radiation Research Program, hosted a Workshop on PBI in December 2002. Although 5- to 7-year outcome data on patients treated with PBI and APBI are now becoming available, many issues remain unresolved, including clinical and pathologic selection criteria, radiation dose and fractionation and how they relate to the standard fractionation for whole breast irradiation, appropriate target volume, local control within the untreated ipsilateral breast tissue, and overall survival. This Workshop report defines the issues in relation to PBI and APBI, recommends parameters for consideration in clinical trials and for reporting of results, serves to enhance dialogue among the advocates of the various radiation techniques, and emphasizes the importance of education and training in regard to results of PBI and APBI as they become emerging clinical treatments.

Protection of mice against challenge with homologous and heterologous serovars of Actinobacillus pleuropneumoniae after live vaccination

Protective immune responses and the virulence of Actinobacillus pleuropneumoniae (APP) have been attributed, in part, to toxins (Apx) produced by the bacterium. A mutant of the serovar 7 strain HS93 (HS93Tox-), lacking the genes encoding the structural toxin ApxA and the post-translational activating protein ApxC, but retaining the genes required for secretion ApxB and ApxD, was isolated and shown to be attenuated in a mouse model. A plasmid vector system was developed and used to express the ApxA gene from within the HS93Tox- strain. The resulting strain, HS93Tox-/pIG-T1K, expresses the Apx structural protein in a non-activated form. HS93Tox-/pIG-T1K was shown to be attenuated in a mouse model and to be capable of inducing Apx-specific antibodies, which were boosted on re-inoculation. Live vaccination of mice with HS93Tox-/pIG-T1K offered protection against homologous wild-type serovar 7 challenge, and also heterologous challenge with a serovar 1 strain. This is in contrast to vaccination with the HS93Tox- strain, which failed to protect mice against a heterologous challenge.

Associations of CYP1A1, GSTM1, and CYP2E1 polymorphisms with lung cancer suggest cell type specificities to tobacco carcinogens

The dramatic shift in the pathological presentation of lung cancer [the proportional decrease in squamous cell carcinoma (SCC) and increase in adenocarcinoma (AC)] observed in the United States after the 1950s may have taken place as the result of the reduction in polycyclic aromatic hydrocarbons (PAHs) and the increase in N-nitrosamines in inhaled smoke from filtered low-yield cigarettes. The predominant mutation patterns of these tumors also suggest differences in their etiology. We tested the hypothesis that genetic susceptibility to PAHs, as determined by polymorphisms in CYP1A1 and GSTM1, predominantly causes lung SCCs, and susceptibility to nitrosamines, as determined by polymorphisms in CYP2E1, predominantly causes lung ACs. CYP1A1 and GSTM1 play a major role in the metabolic activation and detoxification of PAHs, respectively, and CYP2E1 plays a major role in the metabolic activation of nitrosamines. We conducted a population-based case-control study among 341 incident lung cancer cases and 456 controls of Caucasian, Japanese, or Hawaiian origin. In-person interviews collected detailed information on lifestyle risk factors, and DNA extracted from peripheral leukocytes was used in PCR-based genotyping assays. Logistic regression analyses were used to compute odds ratios and 95% confidence intervals (CIs) for each cell type, adjusting for smoking and dietary variables. The presence of at least one copy of the CYP1A1 MspI variant allele was found to be associated with a 2.4-fold (95% CI, 1.2-4.7) increase in the risk of SCC when this gene was considered singly and a 3.1-fold (95% CI, 1.2-7.9) increase in the risk of SCC when combined with a GSTM1 deletion. No significant association was found between MspI and all lung cancers or other cell types or with the CYP1A1 exon 7 polymorphism. In contrast, the CYP2E1 RsaI and DraI polymorphisms were not clearly related to SCC risk, but these homozygous variant genotypes were associated with a 10-fold (95% CI, 0.0-0.5) decrease in the risk of overall lung cancer (RsaI variant) and AC (DraI variant) compared to the homozygous wild-type genotypes. Inverse associations with these two closely linked CYP2E1 polymorphisms were also suggested for small cell carcinoma. In agreement with past experimental and epidemiological data, the associations found in this study between CYP1A1 and lung SCC and between CYP2E1 and lung AC suggest a certain specificity of tobacco smoke PAHs for lung SCC and tobacco-specific nitrosamines for lung ACs.

The lived experience of aloneness for older women currently being treated for depression

A phenomenological study was conducted to answer the following question: What is the lived experience of aloneness for older women currently being treated for depression? Eight women from Northern Ohio composed the purposively selected sample. Transcriptions of each 1-hr interview were reviewed by use of Colaizzi's (1978) method of data analysis. The analysis identified two major experiences of self for all participants: aloneness in depression and aloneness in recovery. Five paired, and somewhat dichotomous, themes defined the essence of aloneness: (a) vulnerability versus self-reliance, (b) fear versus hope, (c) helplessness versus resourcefulness, (d) loss of self-control versus self-determination, and (e) identity confusion versus self-reflection. All the participants expressed profound feelings of moving between the five paired themes as they gained clarity of insight into their experiences of depression and recovery. Results of this study make a valuable contribution by providing important insights into the lived experience of aloneness among older women currently being treated for depression, offer direction in the assessment and treatment of these women, and serve as an impetus for further research.

The use of mammography in breast preservation in locally advanced breast cancer

PURPOSE

As the feasibility of breast preservation in locally advanced breast cancer is currently under evaluation, little information is available correlating mammographic changes to chemotherapy with local outcome. To evaluate the role of mammography in selecting candidates with locally advanced breast cancer for conservative local therapy, we analyzed mammographic changes in the breast to induction chemotherapy and correlated the radiologic appearance with pathologic outcome.

METHODS AND MATERIALS

From 1985 through 1993, 91 patients with Stage III breast cancer were enrolled on a multimodality clinical trial using chemohormonal therapy followed by local treatment and maintenance therapy. Induction therapy consisted of cyclophosphamide, doxorubicin, methotrexate,and 5-fluorouracil with hormonal synchronization using tamoxifen and conjugated estrogens. After nine cycles, surgical biopsies of the breast were performed. Through 1988, clinical examination alone directed the site for postinduction biopsy; for patients treated after 1988, mammography, in addition to physical examination, determined the biopsy location. Local treatment was determined by biopsy result. Patients with a pathologic complete response received radiation only to the breast adn regional nodes, while those with pathologically proven residual disease underwent mastectomy and postoperative radiotherapy. Nine additional cycles of maintenance chemotherapy were administered.

RESULTS

Fifty-five of 91 patients (58%) obtained a clinical complete response (CR) to induction chemotherapy. Twenty-eight of the 53 women with a clinical CR had both pre- and postinduction mammograms. Of these 28 women, 9 obtained a pathologic CR and 19 obtained a pathologic partial response (PR). Fifty-five percent of the pathologic complete responders had resolution of mammographic abnormalities on the postinduction mammograms. Sixty-eight percent (13) of the pathologic partial responders had abnormal mammographic findings. The positive predictive value for residual cancer using physical examination was 92%, while the negative predictive value was only 36%. Among patients with a clinical complete response, the positive and negative predictive values for residual cancer using postinduction mammography were 79% and 56%, respectively. Limitations of mammography included uncertain significance of residual microcalcifications and residual masses on postinduction chemotherapy mammograms.

CONCLUSIONS

Although mammography improved the accuracy of noninvasive evaluations in patients with a clinical complete response, pathologic assessment was still required to determine appropriate local therapy. More sensitive imaging modalities or modifications of film-screen mammography may improve noninvasive detection of residual disease following induction chemotherapy.