Invasive vs. conservative management of older patients with non-ST-elevation acute coronary syndrome: individual patient data meta-analysis

BACKGROUND AND AIMS

Older patients with non-ST-elevation acute coronary syndrome (NSTEACS) are less likely to receive guideline-recommended care including coronary angiography and revascularization. Evidence-based recommendations regarding interventional management strategies in this patient cohort are scarce. This meta-analysis aimed to assess the impact of routine invasive vs. conservative management of NSTEACS by using individual patient data (IPD) from all available randomized controlled trials (RCTs) including older patients.

METHODS

MEDLINE, Web of Science and Scopus were searched between 1 January 2010 and 11 September 2023. RCTs investigating routine invasive and conservative strategies in persons >70 years old with NSTEACS were included. Observational studies or trials involving populations outside the target range were excluded. The primary endpoint was a composite of all-cause mortality and myocardial infarction (MI) at 1 year. One-stage IPD meta-analyses were adopted by use of random-effects and fixed-effect Cox models. This meta-analysis is registered with PROSPERO (CRD42023379819).

RESULTS

Six eligible studies were identified including 1479 participants. The primary endpoint occurred in 181 of 736 (24.5%) participants in the invasive management group compared with 215 of 743 (28.9%) participants in the conservative management group with a hazard ratio (HR) from random-effects model of 0.87 (95% CI 0.63-1.22; P = .43). The hazard for MI at 1 year was significantly lower in the invasive group compared with the conservative group (HR from random-effects model 0.62, 95% CI 0.44-0.87; P = .006). Similar results were seen for urgent revascularization (HR from random-effects model 0.41, 95% CI 0.18-0.95; P = .037). There was no significant difference in mortality.

CONCLUSIONS

No evidence was found that routine invasive treatment for NSTEACS in older patients reduces the risk of a composite of all-cause mortality and MI within 1 year compared with conservative management. However, there is convincing evidence that invasive treatment significantly lowers the risk of repeat MI or urgent revascularisation. Further evidence is needed from ongoing larger clinical trials.

MiniBooNE and MicroBooNE Combined Fit to a 3+1 Sterile Neutrino Scenario

This Letter presents the results from the MiniBooNE experiment within a full "3+1" scenario where one sterile neutrino is introduced to the three-active-neutrino picture. In addition to electron-neutrino appearance at short baselines, this scenario also allows for disappearance of the muon-neutrino and electron-neutrino fluxes in the Booster Neutrino Beam, which is shared by the MicroBooNE experiment. We present the 3+1 fit to the MiniBooNE electron-(anti)neutrino and muon-(anti)neutrino data alone and in combination with MicroBooNE electron-neutrino data. The best-fit parameters of the combined fit with the exclusive charged-current quasielastic analysis (inclusive analysis) are Δm^{2}=0.209  eV^{2}(0.033  eV^{2}), |U_{e4}|^{2}=0.016(0.500), |U_{μ4}|^{2}=0.500(0.500), and sin^{2}(2θ_{μe})=0.0316(1.0). Comparing the no-oscillation scenario to the 3+1 model, the data prefer the 3+1 model with a Δχ^{2}/d.o.f.=24.7/3(17.3/3), a 4.3σ(3.4σ) preference assuming the asymptotic approximation given by Wilks's theorem.

Measurements of Nonsinglet Moments of the Nucleon Structure Functions and Comparison to Predictions from Lattice QCD for Q^{2}=4 GeV^{2}

We present extractions of the nucleon nonsinglet moments utilizing new precision data on the deuteron F_{2} structure function at large Bjorken-x determined via the Rosenbluth separation technique at Jefferson Lab Experimental Hall C. These new data are combined with a complementary set of data on the proton previously measured in Hall C at similar kinematics and world datasets on the proton and deuteron at lower x measured at SLAC and CERN. The new Jefferson Lab data provide coverage of the upper third of the x range, crucial for precision determination of the higher moments. In contrast to previous extractions, these moments have been corrected for nuclear effects in the deuteron using a new global fit to the deuteron and proton data. The obtained experimental moments represent an order of magnitude improvement in precision over previous extractions using high x data. Moreover, recent exciting developments in lattice QCD calculations provide a first ever comparison of these new experimental results with calculations of moments carried out at the physical pion mass, as well as a new approach that first calculates the quark distributions directly before determining moments.

Ultra-deep next-generation sequencing of plasma cell-free DNA in patients with advanced lung cancers: results from the Actionable Genome Consortium

BACKGROUND

Noninvasive genotyping using plasma cell-free DNA (cfDNA) has the potential to obviate the need for some invasive biopsies in cancer patients while also elucidating disease heterogeneity. We sought to develop an ultra-deep plasma next-generation sequencing (NGS) assay for patients with non-small-cell lung cancers (NSCLC) that could detect targetable oncogenic drivers and resistance mutations in patients where tissue biopsy failed to identify an actionable alteration.

PATIENTS AND METHODS

Plasma was prospectively collected from patients with advanced, progressive NSCLC. We carried out ultra-deep NGS using cfDNA extracted from plasma and matched white blood cells using a hybrid capture panel covering 37 lung cancer-related genes sequenced to 50 000× raw target coverage filtering somatic mutations attributable to clonal hematopoiesis. Clinical sensitivity and specificity for plasma detection of known oncogenic drivers were calculated and compared with tissue genotyping results. Orthogonal ddPCR validation was carried out in a subset of cases.

RESULTS

In 127 assessable patients, plasma NGS detected driver mutations with variant allele fractions ranging from 0.14% to 52%. Plasma ddPCR for EGFR or KRAS mutations revealed findings nearly identical to those of plasma NGS in 21 of 22 patients, with high concordance of variant allele fraction (r = 0.98). Blinded to tissue genotype, plasma NGS sensitivity for de novo plasma detection of known oncogenic drivers was 75% (68/91). Specificity of plasma NGS in those who were driver-negative by tissue NGS was 100% (19/19). In 17 patients with tumor tissue deemed insufficient for genotyping, plasma NGS identified four KRAS mutations. In 23 EGFR mutant cases with acquired resistance to targeted therapy, plasma NGS detected potential resistance mechanisms, including EGFR T790M and C797S mutations and ERBB2 amplification.

CONCLUSIONS

Ultra-deep plasma NGS with clonal hematopoiesis filtering resulted in de novo detection of targetable oncogenic drivers and resistance mechanisms in patients with NSCLC, including when tissue biopsy was inadequate for genotyping.

Correction: RCP induces Slug expression and cancer cell invasion by stabilizing β1 integrin

Following the publication of this article the authors noted that images were inadvertently duplicated in Fig. 1b. The corrected Fig. 1 can be found in the associated Correction. The conclusions of this paper are not affected. The authors sincerely apologize for this error. This error has not been corrected in the HTML or PDF of the original Article.

Significant Excess of Electronlike Events in the MiniBooNE Short-Baseline Neutrino Experiment

The MiniBooNE experiment at Fermilab reports results from an analysis of ν_{e} appearance data from 12.84×10^{20} protons on target in neutrino mode, an increase of approximately a factor of 2 over previously reported results. A ν_{e} charged-current quasielastic event excess of 381.2±85.2 events (4.5σ) is observed in the energy range 200<E_{ν}^{QE}<1250  MeV. Combining these data with the ν[over ¯]_{e} appearance data from 11.27×10^{20} protons on target in antineutrino mode, a total ν_{e} plus ν[over ¯]_{e} charged-current quasielastic event excess of 460.5±99.0 events (4.7σ) is observed. If interpreted in a two-neutrino oscillation model, ν_{μ}→ν_{e}, the best oscillation fit to the excess has a probability of 21.1%, while the background-only fit has a χ^{2} probability of 6×10^{-7} relative to the best fit. The MiniBooNE data are consistent in energy and magnitude with the excess of events reported by the Liquid Scintillator Neutrino Detector (LSND), and the significance of the combined LSND and MiniBooNE excesses is 6.0σ. A two-neutrino oscillation interpretation of the data would require at least four neutrino types and indicate physics beyond the three neutrino paradigm. Although the data are fit with a two-neutrino oscillation model, other models may provide better fits to the data.

First Measurement of Monoenergetic Muon Neutrino Charged Current Interactions

We report the first measurement of monoenergetic muon neutrino charged current interactions. MiniBooNE has isolated 236 MeV muon neutrino events originating from charged kaon decay at rest (K^{+}→μ^{+}ν_{μ}) at the NuMI beamline absorber. These signal ν_{μ}-carbon events are distinguished from primarily pion decay in flight ν_{μ} and ν[over ¯]_{μ} backgrounds produced at the target station and decay pipe using their arrival time and reconstructed muon energy. The significance of the signal observation is at the 3.9σ level. The muon kinetic energy, neutrino-nucleus energy transfer (ω=E_{ν}-E_{μ}), and total cross section for these events are extracted. This result is the first known-energy, weak-interaction-only probe of the nucleus to yield a measurement of ω using neutrinos, a quantity thus far only accessible through electron scattering.

CA 125: The past and the Future

Over the last 15 years, substantial progress has been made in understanding the potential and the limitations of the CA 125 assay. More than 2000 papers have been published concerning laboratory and clinical studies of CA 125. The original CA 125 assay utilized the OC 125 antibody that recognizes the CA 125 epitope on a high molecular weight glycoprotein. Despite repeated attempts, the gene encoding the peptide component has not yet been cloned. Monoclonal antibodies have been raised against other epitopes expressed by this molecule, leading to the development of the CA 125-II assay that exhibits less day-to-day variation. Using either assay, elevated levels of CA 125 are detected in a number of benign conditions, including endometriosis. CA 125 is most consistently elevated in epithelial ovarian cancer, but can be expressed in a number of gynecologic (endometrial, fallopian tube) and non-gynecologic (pancreatic, breast, colon and lung) cancers. The best established application of the CA 125 assay is in monitoring ovarian cancer. The rate of decline in CA 125 during primary chemotherapy has been an important independent prognostic factor in several multivariate analyses. Persistent elevation of CA 125 at the time of a second look surgical surveillance procedure predicts residual disease with >95% specif city. Rising CA 125 values have preceded clinical detection of recurrent disease by at least 3 months in most, but not all studies. Given the modest activity of salvage chemotherapy, this information has not yet impacted on survival. Rising CA 125 during subsequent chemotherapy has been associated with progressive disease in more than 90% of cases. CA 125 may serve as an effective surrogate marker for clinical response in phase II trials of new drugs. CA 125 levels can aid in distinguishing malignant from benign pelvic masses, permitting effective triage of patients for primary surgery. Early detection of ovarian cancer remains the most promising application of CA 125. An algorithm has been developed that estimates the risk of ovarian cancer (ROC) based upon the level and trend of CA 125 values. A major trial has been initiated that uses the ROC algorithm to trigger transvaginal sonography and/or subsequent laparotomy. Such a trial could demonstrate improvement in survival through early detection. This strategy should provide adequate specificity, but sensitivity for early stage disease may not be optimal. In the future, improved sensitivity may be attained using multiple markers and neural network analysis. Most serum tumor markers have been proteins or carbohydrates, but lipid markers such as lysophosphatidic acid deserve evaluation. Genomic and proteonomic technologies should identify additional novel markers.

Abstract PD8-11: APOBEC3 contributes to mutational load in breast cancer

Breast cancer results in large part from the accumulation of multiple mutations in premalignant cells, which provide a molecular basis for genetic diversity. This genetic diversity in premalignant cells allows selection for increased proliferation and survival and ultimately leads to invasion, metastasis, and therapeutic resistance. Recent genome-wide sequencing data showed that APOBEC3B (A3B) contributes to mutational load in breast cancer. A3B, a DNA cytosine deaminase, is overexpressed in more than 50% of breast tumors and more than 75% of breast cancer cell lines. Its overexpression and aberrant activation lead to unexpected clusters of mutations in the majority of breast cancers. This phenomenon of clustered mutations, termed kataegis (shower in Greek) forms a unique mutation signature in breast cancer. On the basis of the finding that A3B is a key molecular determinant of the mutator phenotype in breast cancer, the goal of our research is to utilize informatics tools to systematically characterize genetic alterations of APOBEC3 family proteins in breast cancer genomic data and define the molecular impact of altered APOBEC3 family proteins on mutability and anti-tumor immunity.

Our data showed that the mutation rate and copy number amplification/deletion of APOBEC3 genes are low. The levels of APOBEC3A (A3A) and A3B are highly correlated and are highest in Basal subtype and lowest in Luminal A tumors, in concordance with the proliferation of subtypes. Additionally, A3A and A3B are significantly correlated with total mutational load as well as with TP53 mutation, and with somatic copy number alterations (SCNA), especially focal SCNA. Among APOBEC3 genes, A3B is significantly associated DNA replication, DNA damage repair, cell cycle and proteasome signatures, and shows predictive and prognostic capacity in ER-positive patients. Interestingly, A3G expression is strongly associated with immune response signature genes in all breast tumors. Consequently, A3G is highly associated with tumor-infiltrating lymphocytes in breast and several other disease types.

In summary, our data demonstrate distinct expression pattern of APOBEC3 genes in different breast cancer subpopulations. Overexpression of different APOBEC3 family members leads to distinct molecular consequences. These data provide new molecular insights into pathophysiological functions of APOBEC3 genes in breast cancer and provide therapeutic opportunities for the breast cancer patients whose tumors have altered APOBEC3 expression levels and potentially are driven by APOBEC3 genes. Importantly, APOBEC3G is associated with evidence of immune activation that may signal responsiveness to immune checkpoint inhibitors.

Citation Format: Zhao W, Peng Y, Mills GB, Peng G. APOBEC3 contributes to mutational load in breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr PD8-11.

Abstract P3-04-01: Molecular determinants of post-mastectomy breast cancer recurrence

Introduction

The management of breast cancer (BC) patients who undergo mastectomy in the setting of 1-3 positive lymph nodes has been controversial. This retrospective Translational Breast Cancer Research Consortium study evaluated the molecular aberrations associated with locoregional recurrence (LRR) or distant metastasis (DM) compared to controls in an effort to identify molecular predictors associated with recurrence.

Methods/Materials

We identified 115 HER2 negative, therapy naïve, T 1-3 and N 0-1 BC patients treated with mastectomy and no post mastectomy radiation therapy from 1997 to present with available FFPE tissue blocks. The cohort included 32 patients with LRR, 34 with DM, and 49 controls (without recurrence) who were matched for stage, grade, hormone receptor status, age ≤ or &gt; 50, chemotherapy receipt, and margin status. Matched primary and recurrent LRR samples were available for 3 patients. Hybrid capture next generation sequencing (NGS) of 142 cancer related genes and RNAseq were performed to identify DNA/RNA alterations associated with LRR or DM. The frequency of common alterations on NGS was compared with Fisher's exact test. Expression of each gene from mRNA-Seq was treated as an explanatory variable. Immunohistochemistry (IHC) was performed for PTEN, Ki-67 and cleaved caspase 3 (CC3). PTEN loss and percentage of Ki-67 and CC3 positive cells were compared between groups with Fisher's exact test and nonparametric methods, respectively.

Results

RNAseq was performed on 115 patients; there was no difference in RNA expression levels between the groups. DNA analysis was performed on 57 patients (17 LRR, 15 DM and 25 controls), NF1 mutation rate was significantly elevated in both the LRR (24%) and DM (27%) samples compared to controls 0%; (p=0.0070). The mitogen activated protein kinase (MAPK) pathway was significantly mutated in both LRR (47%) and DM (40%) samples compared to the controls 0%; (p&lt;0.0001). There was no significant difference in the rate of alterations of the PI3K/Akt/mTOR pathway among the three groups. Of three patients with matched primary vs LRR samples, one had concordant mutations. The second patient had additional mutations in the LRR, including gain of a NF1 mutation. The third patient had complete discordance of mutations identified in primary and LRR and had gain of HER2 amplification, suggestive of a new primary. There was no significant association between the groups and the loss of PTEN expression or CC3 expression. There was a significant difference between Ki 67 positive cells in patients with LRR (mean 29%), DM (mean 26%) versus controls (mean 14%, p= 0.0011). HR+ patients were significantly more likely to have a positive PTEN, lower Ki-67 and lower CC3 expression, p=0.0004, p&lt;0.0001, and p&lt;0.0001 respectively.

Conclusions

In this matched cohort analysis, mutations in the MAPK pathway, specifically NF1, were associated with both LRR and DM, suggesting that alterations in this pathway are associated with a more aggressive tumor phenotype. However, there were no molecular features that discriminated between those likely to recur locally alone versus distantly. Further study is needed to validate these findings, and to determine whether targeting alterations in this pathway could decrease the risk of recurrence.

Citation Format: Keene KS, King T, Hwang ES, Peng B, McGuire K, Tapia C, Zhang H, Bae S, Nakhlis F, Klauber-Demore N, Meszoely I, Sabel MS, Willey SC, Eterovic KA, Hudis C, Wolff A, De Los Santos J, Thompson A, Mills GB, Meric-Bernstam F. Molecular determinants of post-mastectomy breast cancer recurrence [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P3-04-01.

A feasibility study of neoadjuvant talazoparib for operable breast cancer patients with a germline BRCA mutation demonstrates marked activity

This study was undertaken to determine the feasibility of enrolling breast cancer patients on a single-agent-targeted therapy trial before neoadjuvant chemotherapy. Specifically, we evaluated talazoparib in patients harboring a deleterious BRCA mutation (BRCA+). Patients with a germline BRCA mutation and ≥1 cm, HER2-negative primary tumors were eligible. Study participants underwent a pretreatment biopsy, 2 months of talazoparib, off-study core biopsy, anthracycline, and taxane-based chemotherapy ± carboplatin, followed by surgery. Volumetric changes in tumor size were determined by ultrasound at 1 and 2 months of therapy. Success was defined as 20 patients accrued within 2 years and <33% experienced a grade 4 toxicity. The study was stopped early after 13 patients (BRCA1 + n = 10; BRCA2 + n = 3) were accrued within 8 months with no grade 4 toxicities and only one patient requiring dose reduction due to grade 3 neutropenia. The median age was 40 years (range 25–55) and clinical stage included I (n = 2), II (n = 9), and III (n = 2). Most tumors (n = 9) were hormone receptor-negative, and one of these was metaplastic. Decreases in tumor volume occurred in all patients following 2 months of talazoparib; the median was 88% (range 30–98%). Common toxicities were neutropenia, anemia, thrombocytopenia, nausea, dizziness, and fatigue. Single-agent-targeted therapy trials are feasible in BRCA+ patients. Given the rapid rate of accrual, profound response and favorable toxicity profile, the feasibility study was modified into a phase II study to determine pathologic complete response rates after 4–6 months of single-agent talazoparib.

An investigational PARP inhibitor seems safe and possibly effective when given ahead of surgery to women with BRCA-mutated breast cancer. Jennifer Litton and colleagues from the University of Texas MD Anderson Cancer Center in Houston, USA, conducted a small feasibility study to see if patients with stage I-III breast cancer and inherited mutations in BRCA1 or BRCA2 would put off their standard course of chemotherapy ahead of surgery to first receive two months of talazoparib, an experimental inhibitor of poly ADP ribose polymerase (PARP), an enzyme involved in DNA damage repair. The trial was a resounding success. In fact, owing to rapid patient enrollment, decreases in tumor volume among all 13 participants and few signs of serious side effects, the researchers amended the study protocol to give talazoparib for longer and test for therapeutic efficacy.

Abstract P1-07-01: A pan-cancer perspective of functional proteomics provides novel information content for uncommon breast cancer subtypes

Cancer cell lines (CCLs) serve as models to study the functional consequences of the genomic lesions in patients and as screening platforms for prediction of drug response. While genomic and transcriptomic data have proven to be useful predictors, the ability of these omics platforms to predict protein level and function is limited. Furthermore, since proteins are the targets of the majority of the targeted therapies, protein levels and importantly protein function would be expected to provide more powerful predictions than DNA or RNA data. While large scale genomic and transcriptomic data linked to drug sensitivity are available for over a thousand CCLs, proteomic data is available for only a small subset of lines. Here we performed proteomic profiling of 736 cell lines using reverse-phase protein arrays (RPPAs) with approximately 300 antibodies providing an unbiased sparse representation of the majority of signaling pathways.

The functional proteomic analysis revealed 10 protein-based clusters across all cell lines. Similar to human tumors, the breast cell lines fell into three major clusters representing basal-like, luminal/Her2-amplified and claudin-low breast cancer subtypes. The basal-like and claudin-low clusters contained all of the representative breast cancer cell lines as well as a much larger number of other CCLs. For example, the 6 claudin-low breast cancers analyzed reside in an EMT cluster, in which only 8/126 are breast cell lines. However, the complete cluster including multiple non-breast cancer cell lines recapitulated mRNA and protein features of claudin-low breast tumors, including a high EMT signature and low level of hormone receptor pathway activity. We thus explored whether we could gain power for linking the limited number of basal and claudin-low breast cancer cell lines to therapeutic sensitivity by assessing patterns of drug sensitivity in each cluster for both the breast and non-breast cancer cell lines in the cluster. We explored drug sensitivity of 481 therapeutic compounds from the Cancer Therapeutic Response Portal (CTRP v2) and demonstrated that the non- breast cancer and breast cancer cell lines in each cluster provided similar patterns of drug sensitivity. For example, Claudin-low/EMT cell lines of both breast cancer and non-breast cancer origin showed decreased sensitivity to PI3K/mTOR inhibitors compared to luminal breast cancers (p&lt;0.05 for 4 mTOR inhibitors) and drugs targeting EGFR family compared to basal cell lines (p&lt;0.05 for 7 EGFR/ERBB2 inhibitors). Thus it is possible to gain information by characterizing cell lines with similar patterns of protein expression and provide important information related to drug sensitivity of uncommon breast cancer lineages. The functional proteomic analysis provides a wealth of information that complements the genomic and transciptomic studies of cancer cell lines, and demonstrates the opportunity to leverage cell line 'pan-cancer' proteomic patterns to improve characterization of specific breast cancer subtypes. To facilitate broad access to these data, we developed a user-friendly data portal, the MD Anderson Cell Lines Project (MCLP), that provides both data analysis and download (http://ibl.mdanderson.org/mclp/).

Citation Format: Zhao W, Li J, Lu Y, Akbani R, Liang H, Mills GB. A pan-cancer perspective of functional proteomics provides novel information content for uncommon breast cancer subtypes [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-07-01.

Abstract P1-05-11: Comprehensive comparison of breast cancer molecular portraits by African and European ancestry in the cancer genome atlas

Background: African American breast cancer patients have worse survival rates than European American patients. Although racial differences in the distribution of breast cancer intrinsic subtype are known, it is unclear if there are other inherent genomic differences contributing to this racial outcome disparity.

Methods: We defined patient race based on genomic ancestry and compared multiple molecular features of breast cancer between 154 black and 776 white patients in The Cancer Genome Atlas (TCGA). We examined the contribution of these molecular features to survival outcomes using Cox proportional hazards models. We also estimated the heritability of breast cancer subtypes using a mixed effect model.

Results: Compared to whites, black patients had higher odds of basal-like (odds ratio=3.80, p&lt;0.001) and HER2-enriched (odds ratio=2.22, p=0.027) breast cancers in reference to luminal A subtype. Beyond differences in relative frequency of intrinsic subtypes, black and white patients had distinct gene expression, protein expression, and somatic mutation landscapes. However, the majority of these molecular differences were eliminated after adjusting for subtype; in the subtype-adjusted models, we found 142 genes, 16 methylation probes, 4 copy number segments, 1 protein, and no somatic mutation were differentially expressed or present between black and white patients. Using the top 40 differentially expressed genes, we built a race-enriched gene signature, which had excellent capacity of distinguishing breast tumors from black versus white patients (c-index=0.852 in the validation dataset). We also estimated the heritability of breast cancer subtype (basal vs. non-basal) to be 0.436 (p=1.5x10-14) and showed that two genetic variants (rs1078806 in FGFR2, rs34084277 in BABAM1) were associated with intrinsic subtype and can partially explain racial differences in subtype frequencies.

Conclusion: On the molecular level, once intrinsic subtype frequency differences are accounted for, there are few genomic or proteomic differences observed between blacks and whites. More than 40% of breast cancer subtype frequency differences may be due to genetic ancestry. These results suggest that future studies are warranted to investigate genetic and non-genetic factors that contribute to the development and progression of breast cancer subtypes in order to reduce racial disparity.

Citation Format: Huo D, Hu H, Rhie SK, Gamazon ER, Cherniack AD, Liu J, Yoshimatsu TF, Pitt JJ, Hoadley KA, Troester M, Ru Y, Lichtenberg T, Sturtz LA, Shelley CS, Mills GB, Laird PW, Shriver CD, Perou CM, Olopade OI. Comprehensive comparison of breast cancer molecular portraits by African and European ancestry in the cancer genome atlas [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-05-11.

Abstract P6-13-01: Proteomic response in breast cancer treated with neoadjuvant chemotherapy with and without bevacizumab: Reverse phase protein array (RPPA) results from NeoAva - A randomized phase II study

BACKGROUND: Patients with HER2 negative primary tumors of ≥25 mm were treated with neoadjuvant chemotherapy (4 x FEC100 + 12 weeks of taxane-based therapy) and randomized (1:1) to receive bevacizumab or not. Mammography, ultrasound and MR imaging were used for response evaluation, in addition to the final pathology assessment after surgery.

HYPOTHESIS: RPPA proteomic analyses support identification of molecular mechanisms associated with clinical response to bevacizumab treatment.

METHODS: Tumor responses were evaluable in 132 patients; of which 66 received bevacizumab. Ratio of the tumor size at final pathology assessment, and at inclusion was calculated to obtain a continuous scale of response reflecting the percentage of tumor shrinkage in response to therapy. Tumor material was obtained at screening, 12 weeks into treatment and at surgical removal of tumors at 25 weeks. Lysates from each sample was analyzed on reverse phase protein arrays (RPPA) for expression levels of 210 proteins of which 54 were phospho-specific.

RESULTS: Several proteins were found for which expression prior to treatment reflected a better response on tumor shrinkage in the combination treatment arm (chemotherapy+bevacizumab). The proteomic response from week 0 to 12 in both treatment arms had an overall similar profile regarding up- and down-regulated proteins; however, the combination treatment (FEC100 + bevacizumab) induced a more pronounced effect on regulation of each protein. This might reflect the capability of bevacizumab therapy to potentiate the effects of the anthracyclin based chemotherapy from week 0 to 12. Conversely, from week 12-25 (taxane-based therapy + bevacizumab) this effect was lost or even reversed, except for certain phosphoproteins where potentiation imposed by bevacizumab was sustained throughout the whole treatment period. We are in the process of analyzing the impact of phosphorylation and thus protein activation states on treatment response. Furthermore, tumors with low hormone receptor pathway score demonstrated a better response in the combination treatment (chemotherapy+bevacizumab). Additionally, in these good responders the hormone signaling pathway was significantly upregulated during treatment. Further investigations are conducted to determine if this was due to selective ablation of hormone receptor negative tumor cells, or a re-programming of the molecular phenotype of cells present prior to treatment. The above mentioned results have potentially important clinical relevance and will be further investigated with respect to subtypes and the biological pathways affected by antiangiogenic therapy.

Citation Format: Haugen MH, Lindgjærde OC, Krohn M, Zhao W, Lindholm EM, Silwal-Pandit L, Borgen E, Garred Ø, Fangberget A, Holmen MM, Schlichting E, Skjerven H, Lundgren S, Wist E, Naume B, Mælandsmo GM, Lu Y, Børresen-Dale A-L, Mills GB, Engebråten O. Proteomic response in breast cancer treated with neoadjuvant chemotherapy with and without bevacizumab: Reverse phase protein array (RPPA) results from NeoAva - A randomized phase II study [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P6-13-01.

Neomorphic mutations create therapeutic challenges in cancer

Oncogenesis is a pathologic process driven by genomic aberrations, including changes in nucleotide sequences. The majority of these mutational events fall into two broad categories: inactivation of tumor suppressor genes (hypomorph, antimorph or amorph) or activation of oncogenes (hypermorph). The recent surge in genome sequence data and functional genomics research has ushered in the discovery of aberrations in a third category: gain-of-novel-function mutation (neomorph). These neomorphic mutations, which can be found in both tumor suppressor genes and oncogenes, produce proteins with entirely different functions from their respective wild-type (WT) proteins and the other morphs. The unanticipated phenotypic outcomes elicited by neomorphic mutations imply that tumors with the neomorphic mutations may not respond to therapies designed to target the WT protein. Therefore, understanding the functional activities of each genomic aberration to be targeted is crucial in devising effective treatment strategies that will benefit specific cancer patients.

Phosphorylation-dependent cleavage regulates von Hippel Lindau proteostasis and function

Loss of von Hippel Lindau (VHL) protein function is a key driver of VHL diseases, including sporadic and inherited clear cell renal cell carcinoma. Modulation of the proteostasis of VHL, especially missense point-mutated VHL, is a promising approach to augmenting VHL levels and function. VHL proteostasis is regulated by multiple mechanisms including folding, chaperone binding, complex formation and phosphorylation. Nevertheless, many details underlying the regulations of VHL proteostasis are unknown. VHL is expressed as two variants, VHL30 and VHL19. Furthermore, the long-form variant of VHL was often detected as multiple bands by western blotting. However, how these multiple species of VHL are generated and whether the process regulates VHL proteostasis and function are unknown. We hypothesized that the two major species are generated by VHL protein cleavage, and the cleavage regulates VHL proteostasis and subsequent function. We characterized VHL species using genetical and pharmacological approaches and showed that VHL was first cleaved at the N-terminus by chymotrypsin C before being directed for proteasomal degradation. Casein kinase 2-mediated phosphorylation at VHL N-terminus was required for the cleavage. Furthermore, inhibition of cleavage stabilized VHL protein and thereby promoted HIF downregulation. Our study reveals a novel mechanism regulating VHL proteostasis and function, which is significant for identifying new drug targets and developing new therapeutic approaches targeting VHL deficiency in VHL diseases.

Utility of a molecular prescreening program in advanced colorectal cancer for enrollment on biomarker-selected clinical trials

BACKGROUND

Incorporation of multiple enrichment biomarkers into prospective clinical trials is an active area of investigation, but the factors that determine clinical trial enrollment following a molecular prescreening program have not been assessed.

PATIENTS AND METHODS

Patients with 5-fluorouracil-refractory metastatic colorectal cancer at the MD Anderson Cancer Center were offered screening in the Assessment of Targeted Therapies Against Colorectal Cancer (ATTACC) program to identify eligibility for companion phase I or II clinical trials with a therapy targeted to an aberration detected in the patient, based on testing by immunohistochemistry, targeted gene sequencing panels, and CpG island methylation phenotype assays.

RESULTS

Between August 2010 and December 2013, 484 patients were enrolled, 458 (95%) had a biomarker result, and 157 (32%) were enrolled on a clinical trial (92 on biomarker-selected and 65 on nonbiomarker selected). Of the 458 patients with a biomarker result, enrollment on biomarker-selected clinical trials was ninefold higher for predefined ATTACC-companion clinical trials as opposed to nonpredefined biomarker-selected clinical trials, 17.9% versus 2%, P < 0.001. Factors that correlated positively with trial enrollment in multivariate analysis were higher performance status, older age, lack of standard of care therapy, established patient at MD Anderson, and the presence of an eligible biomarker for an ATTACC-companion study. Early molecular screening did result in a higher rate of patients with remaining standard of care therapy enrolling on ATTACC-companion clinical trials, 45.1%, in contrast to nonpredefined clinical trials, 22.7%; odds ratio 3.1, P = 0.002.

CONCLUSIONS

Though early molecular prescreening for predefined clinical trials resulted in an increase rate of trial enrollment of nonrefractory patients, the majority of patients enrolled on clinical trials were refractory to standard of care therapy. Within molecular prescreening programs, tailoring screening for preidentified and open clinical trials, temporally linking screening to treatment and optimizing both patient and physician engagement are efforts likely to improve enrollment on biomarker-selected clinical trials.

CLINICAL TRIALS NUMBER

The study NCT number is NCT01196130.

Mitochondrial oligomers boost glycolysis in cancer stem cells to facilitate blebbishield-mediated transformation after apoptosis

Apoptosis culminates in secondary necrosis due to lack of ATP. Cancer stem cells form spheres after apoptosis by evoking the blebbishield emergency program. Hence, determining how blebbishields avoid secondary necrosis is crucial. Here we demonstrate that N-Myc and VEGFR2 control transformation from blebbishields, during which oligomers of K-Ras, p27, BAD, Bax, and Bak boost glycolysis to avoid secondary necrosis. Non-apoptotic cancer cells also utilize oligomers to boost glycolysis, which differentiates the glycolytic function of oligomers from their apoptotic action. Smac mimetic in combination with TNF-α or TRAIL but not in combination with FasL abrogates transformation from blebbishields by inducing secondary necrosis. Thus blebbishield-mediated transformation is dependent on glycolysis, and Smac mimetics represent potential candidates to abrogate the blebbishield emergency program.

Incidental germline variants in 1000 advanced cancers on a prospective somatic genomic profiling protocol

BACKGROUND

Next-generation sequencing in cancer research may reveal germline variants of clinical significance. We report patient preferences for return of results and the prevalence of incidental pathogenic germline variants (PGVs).

PATIENTS AND METHODS

Targeted exome sequencing of 202 genes was carried out in 1000 advanced cancers using tumor and normal DNA in a research laboratory. Pathogenic variants in 18 genes, recommended for return by The American College of Medical Genetics and Genomics, as well as PALB2, were considered actionable. Patient preferences of return of incidental germline results were collected. Return of results was initiated with genetic counseling and repeat CLIA testing.

RESULTS

Of the 1000 patients who underwent sequencing, 43 had likely PGVs: APC (1), BRCA1 (11), BRCA2 (10), TP53 (10), MSH2 (1), MSH6 (4), PALB2 (2), PTEN (2), TSC2 (1), and RB1 (1). Twenty (47%) of 43 variants were previously known based on clinical genetic testing. Of the 1167 patients who consented for a germline testing protocol, 1157 (99%) desired to be informed of incidental results. Twenty-three previously unrecognized mutations identified in the research environment were confirmed with an orthogonal CLIA platform. All patients approached decided to proceed with formal genetic counseling; in all cases where formal genetic testing was carried out, the germline variant of concern validated with clinical genetic testing.

CONCLUSIONS

In this series, 2.3% patients had previously unrecognized pathogenic germline mutations in 19 cancer-related genes. Thus, genomic sequencing must be accompanied by a plan for return of germline results, in partnership with genetic counseling.

Open-label randomized clinical trial of standard neoadjuvant chemotherapy with paclitaxel followed by FEC versus the combination of paclitaxel and everolimus followed by FEC in women with triple receptor-negative breast cancer†

BACKGROUND

Everolimus synergistically enhances taxane-induced cytotoxicity in breast cancer cells in vitro and in vivo in addition to demonstrating a direct antiproliferative activity. We aim to determine pharmacodynamics changes and response of adding everolimus to standard neoadjuvant chemotherapy in triple-negative breast cancer (TNBC).

PATIENTS AND METHODS

Phase II study in patients with primary TNBC randomized to T-FEC (paclitaxel 80 mg/m(2) i.v. weekly for 12 weeks, followed by 5-fluorouracil 500 mg/m(2), epirubicin 100 mg/m(2), and cyclophosphamide 500 mg/m(2) every 3 weeks for four cycles) versus TR-FEC (paclitaxel 80 mg/m(2) i.v. and everolimus 30 mg PO weekly for 12 weeks, followed by FEC). Tumor samples were collected to assess molecular changes in the PI3K/AKT/mTOR pathway, at baseline, 48 h, 12 weeks, and at surgery by reverse phase protein arrays (RPPA). Clinical end points included 12-week clinical response rate (12-week RR), pathological complete response (pCR), and toxicity.

RESULTS

Sixty-two patients were registered, and 50 were randomized, 27 received T-FEC, and 23 received TR-FEC. Median age was 48 (range 31-75). There was downregulation of the mTOR pathway at 48 h in the TR-FEC arm. Twelve-week RR by ultrasound were 29.6% versus 47.8%, (P = 0.075), and pCR were 25.9% versus 30.4% (P = 0.76) for T-FEC and TR-FEC, respectively. mTOR downregulation at 48 h did not correlate with 12-week RR in the TR-FEC group (P = 0.58). Main NCI grade 3/4 toxicities included anemia, neutropenia, rash/desquamation, and vomiting in both arms. There was one case of grade 3 pneumonitis in the TR-FEC arm. No grade 3/4 stomatitis occurred.

CONCLUSION

The addition of everolimus to paclitaxel was well tolerated. Everolimus downregulated mTOR signaling but downregulation of mTOR at 48 h did not correlate with 12-week RR in the TR-FEC group.

CLINICAL TRIAL NUMBER

NCT00499603.

Abstract P4-06-01: Expression and DNA copy number profiling suggest novel therapeutic approaches for triple negative breast cancer subtypes

The aggressive triple negative breast cancers (TNBCs), which lack ER, PR and HER2, comprise a high-risk subset of human breast cancers which remain poorly characterized and lack effective treatments. While recent meta-analyses indicate the complexity of these tumors, no robust independently validated phenotypes have been defined. We have identified four distinct molecular subtypes through independent non-negative matrix factorization of expression data from 84 Discovery and 114 Validation Set TNBCs profiled at a single institution, with matching CNV data (SNP array). We then classified 485 publically available TNBCs via a centroid signature of only 80 genes. All three sets supported stratification of tumors by cell cycle, DNA repair, and immunological signaling pathways that have significantly different clinical outcomes. The first subtype, composed of intermediate grade tumors, resembles the “Molecular Apocrine” or “Luminal AR” subtype described previously and was defined by enrichment of prolactin, aryl hydrocarbon receptor, and ERBB4 signaling with activated downstream expression patterns of ESR1 signaling. Large deletions of chromosome 6 were specific to this subtype. While focal deletions at 14q21.2 and 12q13.13 were present in &gt;60% of tumors of the other subtypes, the genes at these loci (FOXA1 and ERBB3) were overexpressed in the first subtype. Inhibitors of AR and MUC1, both overexpressed, may prove effective for these tumors. A second subtype defined as “Claudin-Low” or “Mesenchymal Stem-Like” showed overexpression of markers of mesenchymal lineage (ADIPOQ and OGN). Targets responsive to beta-blockers (ADRB2), and targetable molecules associated with platelet and endothelial function (EDNRB, PLA2G2A, PTGER3/4, PTGFR, PTGFRA) were also upregulated. Two basal-like subtypes were found with significant differences in DFS and OS, even after correction for available clinical covariates. The high-risk (31% 5-year DFS), low immune function subtype was regulated by SOX 10, 8, and 6 and had unique copy-number driven expression of FGFR2. The second, low-risk (78% 5-year DFS) basal-like subtype was enriched for overexpression of many immune pathways, regulated by increased STAT1 and activated STAT downstream signaling, as well as exclusive upregulation of CTLA4. This subtype also had the lowest tumor cell fraction as calculated by allele specific copy number analysis of tumors (ASCAT). Both basal-like subtypes expressed TTK, CHEK1, TOP2A, and AURKA. CDK1 was correlated with copy number variation at 10q21.1. We proposed and validated four molecular subtypes of TNBC before applying the resulting gene signature to 7 external expression sets. The described subtypes vary by clinical behavior and inferred biology. Each subtype appears to have specific gene expression regulated by copy number variation and a set of genes targetable by currently available agents. These findings further define the heterogeneity of TNBCs and suggest potential therapeutic targets for each subtype.

This work was supported by a Promise grant from the Susan G. Komen for the Cure Foundation (KG081694).

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-06-01.

Abstract PD1-9: P-REX1 employs a positive feedback loop to activate growth factor receptor/PI3K signaling

A mass spectrometry-based proteomic screen in ER+ breast cancer cells revealed that levels of P-REX1 are decreased upon PTEN loss, and increased upon PI3K inhibition. P-REX1 integrates signaling inputs from receptor tyrosine kinases (RTKs)/PI3K (via the PI3K phospholipid product PIP3) and G protein-coupled receptors (via Gbg subunits) to drive guanine exchange factor (GEF) activity on Rac1. RNAi knockdown of PREX1 and overexpression of exogenous PREX1 in ER+ breast cancer cells respectively decreased and increased activation of insulin-like growth factor receptor-1 (IGF-1R)/insulin receptor (InsR), PI3K/AKT/SGK3, and MEK/Erk under steady-state and growth factor (IGF-1, Heregulin)-stimulated conditions. While the P-REX1 homologue P-REX2a was previously shown to inhibit PTEN phosphatase activity to activate the PI3K/AKT pathway, we did not detect an effect of P-REX1 on PTEN activity. PREX1 knockdown suppressed PI3K/AKT signaling in PTEN-null breast cancer cells; therefore, P-REX1 and P-REX2a may not be functionally redundant. Knockdown and overexpression of PREX1 respectively increased and decreased doxorubicin-induced apoptosis in ER+ breast cancer cells, linking PREX1 with a pro-survival phenotype. Inhibition of signaling nodes downstream of PI3K (AKT, mTOR) derepresses feedback to activate RTKs and PI3K; knockdown of PREX1 abrogated the PI3K activation induced by inhibition of mTORC1/mTORC2. Structural analysis of P-REX1 revealed that the DH domain (which binds Gβγ and is required for GEF activity) is dispensable for P-REX1 effects on PI3K signaling, while the PH domain [which binds PIP3 and PI(3,4)P2] is required. These data place P-REX1 in a positive feedback loop, whereby PI3K generates PIP3 and PI(3,4)P2, and P-REX1 binds these phospholipids at the plasma membrane. In turn, P-REX1 promotes RTK activation, and RTKs activate PI3K/AKT and MEK/Erk signaling.

Gene expression profiling of diverse types of solid tumors (n = 2,009) and cancer cell lines (n = 807) revealed that PREX1 mRNA is most abundant in ER+ breast tumors compared to other subtypes. Reverse-phase protein array (RPPA) analysis of lysates from 712 breast tumors showed that P-REX1 levels are inversely correlated with markers of PI3K/AKT/mTOR pathway activation. Further, P-REX1 levels are higher in ER+ tumors than ER- tumors. In another series of 1,293 carcinomas, PREX1 was genetically amplified or mutated in 6.2% of cases, and in 5% of breast cancers. We then tested whether PREX1 lesions co-exist with other PI3K pathway-activating lesions. Among genes encoding proteins implicated in RTK/PI3K signaling and phosphatidylinositol metabolism, we found a significant enrichment for PREX1 mutation/amplification in 54/79 (68%) genes across 1,523 carcinomas. We tested the effects of 7 PREX1 mutants found in breast tumors on PI3K signaling in vitro. A G344R mutation in the PREX1 PH domain conferred increased affinity for PIP3 and PI(3,4)P2, and increased the levels of phospho-AKT. These findings suggest that P-REX1 is an ER+ breast tumor-specific oncogene, and PREX1 mutations increase its oncogenic effects in breast cancer. We propose that neutralizing P-REX1 function is a novel therapeutic approach to selectively abrogate oncogenic signaling in ER+ breast cancers while sparing normal tissues.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr PD1-9.

Functional proteomics characterization of residual triple-negative breast cancer after standard neoadjuvant chemotherapy

BACKGROUND

In this study, we used functional proteomics to determine the molecular characteristics of residual triple receptor-negative breast cancer (TNBC) patients after neoadjuvant systemic chemotherapy (NCT) and their relationship with patient outcomes in order to identify potential targets for therapy.

PATIENTS AND METHODS

Protein was extracted from 54 residual TNBCs, and 76 proteins related to breast cancer signaling were measured by reverse phase protein arrays (RPPAs). Univariable and multivariable Cox proportional hazard models were fitted for each protein. Survival outcomes were estimated by the Kaplan-Meier product limit method. Training and cross validation were carried out. The coefficients estimated from the multivariable Cox model were used to calculate a risk score (RS) for each sample.

RESULTS

Multivariable analysis using the top 25 proteins from univariable analysis at a false discovery rate (FDR) of 0.3 showed that AKT, IGFBP2, LKB1, S6 and Stathmin were predictors of recurrence-free survival (RFS). The cross-validation model was reproducible. The RS model calculated based on the multivariable analysis was -1.1086 × AKT + 0.2501 × IGFBP2 - 0.6745 × LKB1+1.0692 × S6 + 1.4086 × stathmin with a corresponding area under the curve, AUC = 0.856. The RS was an independent predictor of RFS (HR = 3.28, 95%CI = 2.07-5.20, P < 0.001).

CONCLUSIONS

We found a five-protein model that independently predicted RFS risk in patients with residual TNBC disease. The PI3 K pathway may represent potential therapeutic targets in this resistant disease.

Coordinate phosphorylation of multiple residues on single AKT1 and AKT2 molecules

Aberrant AKT activation is prevalent across multiple human cancer lineages providing an important new target for therapy. Twenty-two independent phosphorylation sites have been identified on specific AKT isoforms likely contributing to differential isoform regulation. However, the mechanisms regulating phosphorylation of individual AKT isoform molecules have not been elucidated because of the lack of robust approaches able to assess phosphorylation of multiple sites on a single AKT molecule. Using a nanofluidic proteomic immunoassay (NIA), consisting of isoelectric focusing followed by sensitive chemiluminescence detection, we demonstrate that under basal and ligand-induced conditions that the pattern of phosphorylation events is markedly different between AKT1 and AKT2. Indeed, there are at least 12 AKT1 peaks and at least 5 AKT2 peaks consistent with complex combinations of phosphorylation of different sites on individual AKT molecules. Following insulin stimulation, AKT1 was phosphorylated at Thr308 in the T-loop and Ser473 in the hydrophobic domain. In contrast, AKT2 was only phosphorylated at the equivalent sites (Thr309 and Ser474) at low levels. Further, Thr308 and Ser473 phosphorylation occurred predominantly on the same AKT1 molecules, whereas Thr309 and Ser474 were phosphorylated primarily on different AKT2 molecules. Although basal AKT2 phosphorylation was sensitive to inhibition of phosphatidylinositol 3-kinase (PI3K), basal AKT1 phosphorylation was essentially resistant. PI3K inhibition decreased pThr451 on AKT2 but not pThr450 on AKT1. Thus, NIA technology provides an ability to characterize coordinate phosphorylation of individual AKT molecules providing important information about AKT isoform-specific phosphorylation, which is required for optimal development and implementation of drugs targeting aberrant AKT activation.

Improved search for ν¯(μ)→ν¯(e) oscillations in the MiniBooNE experiment

The MiniBooNE experiment at Fermilab reports results from an analysis of ν[over ¯](e) appearance data from 11.27×10(20) protons on target in the antineutrino mode, an increase of approximately a factor of 2 over the previously reported results. An event excess of 78.4±28.5 events (2.8σ) is observed in the energy range 200<E(ν)(QE)<1250 MeV. If interpreted in a two-neutrino oscillation model, ν[over ¯](μ)→ν[over ¯](e), the best oscillation fit to the excess has a probability of 66% while the background-only fit has a χ(2) probability of 0.5% relative to the best fit. The data are consistent with antineutrino oscillations in the 0.01<Δm(2)<1.0 eV(2) range and have some overlap with the evidence for antineutrino oscillations from the Liquid Scintillator Neutrino Detector. All of the major backgrounds are constrained by in situ event measurements so nonoscillation explanations would need to invoke new anomalous background processes. The neutrino mode running also shows an excess at low energy of 162.0±47.8 events (3.4σ) but the energy distribution of the excess is marginally compatible with a simple two neutrino oscillation formalism. Expanded models with several sterile neutrinos can reduce the incompatibility by allowing for CP violating effects between neutrino and antineutrino oscillations.

Abstract P4-08-05: Basement membrane localized tumor cells are protected from HER2-targeted therapy in vivo

Drug resistance compromises the efficacy of HER2-targeted therapy. Results from our laboratory, and previous reports from others, indicate that tumor cell attachment to basement membrane (BM) and other extracellular matrix (ECM) proteins may confer drug resistance. We have discovered a differential drug response between the outer, matrix-attached cells and inner matrix-deprived cells comprising 3D tumor spheroids grown in reconstituted BM (Muranen 2012). The outer matrix-attached cells are resistant to multiple drug therapies due to upregulation of a multi-factor survival program including anti-apoptotic proteins and growth factor receptors. To address whether these observations are relevant in vivo, we utilized a previously described model of human-in-mouse HER2+ ductal carcinoma in situ, which involves the intraductal transplantation of human HER2+ SUM225 tumor cells directly into the ductal network of the mouse mammary gland. The tumors are characterized by organized nests of noninvasive cells confined within a BM surrounded by ECM. We focused on the tumor cell response to short-term lapatinib monotherapy in vivo. A close examination of the tumor architecture revealed that cells closest to the BM, and nearest to the vasculature, display a striking insensitivity to lapatinib whereas the remainder of the tumor undergoes extensive cell death in response to treatment. Further characterization also revealed that cells closest to the BM largely maintain proliferative capacity despite an overall reduction in the total Ki67+ cell population. To further explore the response to treatment, we performed reverse phase protein array (RPPA) analysis on protein lysates prepared from tumor fragments following lapatinib monotherapy. RPPA profile analysis revealed a lapatinib-induced adaptive response program characterized by upregulation of multiple receptor tyrosine kinases, reactivation of AKT and ERK pathway components, and the upregulation of prosurvival BCL2 family proteins. Evaluation of BCL2 in matched SUM225 tumor sections revealed selective upregulation within the BM-localized tumor cells. We predict BCL2 upregulation in the BM-localized tumor cells may represent the critical adaptive response mechanism by which these cell populations would escape lapatinib treatment. BCL2 therefore represents a target for designing combined therapeutic approaches capable of abrogating the protected BM-localized tumor cells. Under 3D culture, lapatinib combined with the BCL2 antagonist ABT737 resulted in greater SUM225 tumor cell synthetic lethality compared to single agent treatment. The combination treatment is currently being explored in vivo. We evaluated the translational relevance of our preclinical observations within the context of HER2+ clinical disease. Patient biopsy samples collected as part of an ongoing clinical trial were assayed for BCL2 before and after short-term HER2-targeted therapy. BCL2 was clearly upregulated post-treatment in a subset of patient samples and largely correlated with a poor response to treatment. Our results suggest that resistant populations may be a source of residual disease post-therapy, therefore identifying and characterizing these cells will be crucial to the prevention of disease recurrence in the clinic.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P4-08-05.

Abstract P5-10-03: OncomiR-569 deregulate p53 pathway and initiate breast oncogenesis

Background: The 3q26.2 chromosomal loci is highly amplified in large set of breast cancers, primarily in aggressive basal tumors are difficult to treat in the clinic. Our amplicon data suggests that 3q26.2 is a large structurally complex amplicon and multiple components in the amplicon contribute to tumor initiation and progression either alone or through cooperative activity. Detailed mapping of the 3q26.2 amplicon by us demonstrated a microRNA, miR569 is highly amplified as a part of 3q26.2 amplicon in breast cancer patient's samples. The role of microRNAs amplified at 3q26 loci is not well studied and their molecular functions and targets were not well known. Thus our studies provide novel mechanism underlying miR569 oncogenesis.

Methods: Following the Institutional Review Board approval, tissues obtained from MD Anderson Cancer Center tumor bank were used to exatract DNA and RNA. Human miR-569 was cloned into pEZX-MR06 lentiviral vector used for the production of amphotropic viruses to infect the target cells. The miRIDIAN microRNA mimics were used to overexpress miRs and the antimiRs were used to knock down the miRNAs. All the transfections were performed using Oligofectamine. Trypsinized cells were grown in 5% matrigel for the 3D morphogenesis of epithelial cells.

Results: Our results demonstrated a strong correlation between 3q26.2 amplification and expression of miR569 in patient samples of breast cancer. We subsequently demonstrated that overexpression and knockdown of miR569 in the breast epithelial cells altered their growth, proliferation, and lumen filling in 3-dimensional cultures grown in Matrigel. Importantly ectopic expression of miR569 in breast epithelial cells promoted tumor growth and increased metastatic potential in mouse xenograft models. Seed match based analysis of the microRNA targets, in silico studies and in vitro experiments showed that miR-569 directly target Tumor protein 53-induced nuclear protein1 (TP53INP1) and inhibited the expression of a tumor suppressor gene TP53INP1 expression. Loss of TP53INP1 expression mediated by miR569 altered normal cell growth cycle and subsequently promoted the survival and growth of tumor cells. Our in vitro results showed that knockdown of miR-569 and subsequent increase in TP53INP1 expression enhanced the sensitivity of cancer cell lines to cisplatin. Our immunohistochemical analysis showed that TP53INP1 protein levels were higher in normal tissues compared to cancer tissues. Further, reduced expression of TP53INP1 was observed in invasive cancers as compared to low malignant potential tumors, and decreased TP53INP1 protein levels were associated with worsened outcomes in breast cancer patients.

Disscussion: TP53INP1 had previously been identified as a combined target of p53 and p73; however our studies indicate that miR-569 regulates TP53INP1 levels independently of p53 and p73 expression. Based on our preclinical results of antimiR-569 on cell survival, tumor growth and cisplatin sensitivity, inhibiting miR-569 activity or increasing TP53INP1 expression may be valid therapeutic approaches to treat breast cancer.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P5-10-03.

Abstract P3-06-06: Lactate dehydrogenase B in breast cancer contributes to glycolytic phenotype and predicts response to neoadjuvant chemotherapy

Purpose: Although breast cancers are known to be molecularly heterogeneous, their metabolic heterogeneity is less well understood. This study aimed to identify and evaluate metabolic biomarkers in breast cancers and determine their ability to predict outcomes.

Methods: mRNA microarray data from breast cancer cell lines were used to identify bimodal genes, those with the highest potential for robust high/low classification in a clinical setting. Using a panel of breast cancer cell lines, expression and activity of the highest scoring bimodal metabolism gene, lactate dehydrogenase B (LDHB), was quantified and associated with glycolytic phenotype. The contribution of LDHB to glycolysis was evaluated using MDA-MB-231 and HCC1937 cell lines with stable lentiviral knockdown of LDHB. mRNA expression of LDHB was evaluated for association with neoadjuvant chemotherapy response within clinical and PAM50-derived subtypes.

Results: LDHB was highly expressed in cell lines with glycolytic, basal-like phenotypes. Knockdown of LDHB in cell lines reduced glycolytic dependence, linking LDHB expression directly to metabolic function. Using four independent patient datasets, LDHB mRNA expression was positively associated with basal subtype and negatively associated with luminal and HER2 subtypes. Furthermore, LDHB predicted basal phenotype independently of hormone-receptor (HR) clinical status (OR = 21.6 for HR-positive/HER2-negative and OR = 18.2 for triple-negative). While LDHB expression could predict basal phenotype, high LDHB expression identified aggressive breast cancer tumors that were primarily but not exclusively basal. Importantly, high LDHB expression predicted pathological complete response to neoadjuvant chemotherapy for both hormone receptor (HR) positive/HER2-negative (OR = 4.0, P = .0002) and triple-negative (OR = 3.0, P = .003) cancers. Consistent with increased response to chemotherapy, LDHB expression in basal cancers within the triple-negative group was associated with the proliferative marker CCNB1 (P &lt; .0001).

Conclusion: mRNA expression of LDHB as a single marker predicted glycolytic phenotype in cell lines and response to neoadjuvant chemotherapy in breast cancers independently of HR status. These observations support prospective clinical evaluation of LDHB as a predictive marker of response for breast cancer patients treated with neoadjuvant chemotherapy.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P3-06-06.

Abstract PD01-01: Overcoming endocrine therapy resistance related to PTEN loss by strategic combinations with mTOR, AKT, or MEK inhibitors

Background: Hyperactive PI3K signaling is associated with a more aggressive subtype of estrogen receptor (ER) positive breast cancer (BC) and with endocrine resistance. Loss or downregulation of PI3K's inhibitor PTEN is more common in basal and luminal B vs. luminal A BC. However, the role of PTEN in modulating response to various endocrine therapies is unclear. Here we investigated the effects of PTEN knockdown (KD) on endocrine sensitivity and the potential of multiple kinase inhibitors to restore and improve responses.

Methods: Nude mice bearing ER+ BC xenograft tumors of MCF7 cells stably expressing a doxycycline (Dox)-inducible PTEN-shRNA were randomized to four endocrine treatment groups [continued estrogen (E2) supplementation, or E2-deprivation (ED) alone or in combination with tamoxifen (Tam) or fulvestrant (Ful)]; all -/+ Dox. The effects of single or combined kinase inhibitors on these endocrine treatments -/+ Dox were studied in vitro using inhibitors (i) to mTOR (AZD2014, 0.2 μM), AKT (AZD5363, 1 μM), or MEK (Selumetinib/ARRY-142886, 1 μM). Cell growth, apoptosis, and ER and progesterone receptor (PR) signaling were analyzed using cell cytometry, qRT/PCR, and Western blotting. Synergism tests were used to examine the growth effects of the most promising combinatorial therapy with multiple kinase inhibitors in different endocrine settings.

Results: In wild-type (WT) PTEN xenograft tumors, endocrine therapies were very effective, inducing frequent tumor regression. In PTEN KD tumors endocrine therapies were less effective — PTEN KD delayed tumor regression in all endocrine regimens and accelerated tumor progression in the Tam treated group. Furthermore, at day 250, only 1/8 and 0/7 tumors had developed resistance in the ED and the Ful (−Dox) groups, respectively, while with PTEN KD (+Dox), 7/15 and 5/15 tumors developed resistance to ED and to Ful. In vitro PTEN KD also induced resistance to all endocrine therapies. mRNA and/or protein levels of ER and PR were suppressed by PTEN KD and restored by mTORi and AKTi. In cells with WT PTEN, mTORi was highly effective with or without endocrine therapy. However, AKTi and MEKi were more effective in combination with endocrine therapy. All three inhibitors were less effective upon PTEN KD. The mTORi plus AKTi combination resulted in a potent synergistic inhibition in PTEN KD cells in the presence of E2 or with ED. In contrast, in the presence of Tam, AKTi plus MEKi, independent of PTEN status, was the most effective combination at the doses chosen. Finally, these inhibitors and combinations were more effective in the presence of Ful than ED or Tam in WT PTEN cells. AKTi combined with Ful was still highly effective even in PTEN KD cells, but mTORi and MEKi were less effective.

Conclusions: Our results suggest that PTEN loss renders endocrine therapy less effective in in vitro and in vivo experimental models. Single AKT/MEK kinase inhibitors are more potent in the presence of endocrine therapy. In PTEN KD cells, the activity of all three kinase inhibitors is largely diminished, except for AKTi in the presence of fulvestrant. Kinase inhibitor combinations are generally more effective, but the optimal combinations vary by PTEN status and type of endocrine therapy.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr PD01-01.

Functional proteomics characterization of residual breast cancer after neoadjuvant systemic chemotherapy

BACKGROUND

The purpose of this study was to determine the functional proteomic characteristics of residual breast cancer and hormone receptor (HR)-positive breast cancer after neoadjuvant systemic chemotherapy, and their relationship with patient outcomes.

METHODS

Reverse phase protein arrays of 76 proteins were carried out. A boosting approach in conjunction with a Cox proportional hazard model defined relapse predictors. A risk score (RS) was calculated with the sum of the coefficients from the final model. Survival outcomes and associations of the RS with relapse were estimated. An independent test set was used to validate the results.

RESULTS

Test (n = 99) and validation sets (n = 79) were comparable. CoxBoost revealed a three-biomarker (CHK1pS345, Caveolin1, and RAB25) and a two-biomarker (CD31 and Cyclin E1) model that correlated with recurrence-free survival (RFS) in all residual breast cancers and in HR-positive disease, respectively. Unsupervised clustering split patients into high- and low risk of relapse groups with different 3-year RFS (P ≤ 0.001 both). RS was a substantial predictor of RFS (P = 0.0008 and 0.0083) after adjustment for other substantial characteristics. Similar results were found in validation sets.

CONCLUSIONS

We found models that independently predicted RFS in all residual breast cancer and in residual HR-positive disease that may represent potential targets of therapy in this resistant disease.

MKNK1 is a YB-1 target gene responsible for imparting trastuzumab resistance and can be blocked by RSK inhibition

Trastuzumab (Herceptin) resistance is a major obstacle in the treatment of patients with HER2-positive breast cancers. We recently reported that the transcription factor Y-box binding protein-1 (YB-1) leads to acquisition of resistance to trastuzumab in a phosphorylation-dependent manner that relies on p90 ribosomal S6 kinase (RSK). To explore how this may occur we compared YB-1 target genes between trastuzumab-sensitive cells (BT474) and those with acquired resistance (HR5 and HR6) using genome-wide chromatin immunoprecipitation sequencing (ChIP-sequencing), which identified 1391 genes uniquely bound by YB-1 in the resistant cell lines. We then examined differences in protein expression and phosphorylation between these cell lines using the Kinexus Kinex antibody microarrays. Cross-referencing these two data sets identified the mitogen-activated protein kinase-interacting kinase (MNK) family as potentially being involved in acquired resistance downstream from YB-1. MNK1 and MNK2 were subsequently shown to be overexpressed in the resistant cell lines; however, only the former was a YB-1 target based on ChIP-PCR and small interfering RNA (siRNA) studies. Importantly, loss of MNK1 expression using siRNA enhanced sensitivity to trastuzumab. Further, MNK1 overexpression was sufficient to confer resistance to trastuzumab in cells that were previously sensitive. We then developed a de novo model of acquired resistance by exposing BT474 cells to trastuzumab for 60 days (BT474LT). Similar to the HR5/HR6 cells, the BT474LT cells had elevated MNK1 levels and were dependent on it for survival. In addition, we demonstrated that RSK phosphorylated MNK1, and that this phosphorylation was required for ability of MNK1 to mediate resistance to trastuzumab. Furthermore, inhibition of RSK with the small molecule BI-D1870 repressed the MNK1-mediated trastuzumab resistance. In conclusion, this unbiased integrated approach identified MNK1 as a player in mediating trastuzumab resistance as a consequence of YB-1 activation, and demonstrated RSK inhibition as a means to overcome recalcitrance to trastuzumab.

P4-09-09: Expression of c-MET and Phospho c-MET in Breast Cancers by Subtype and Its Impact on Survival Outcomes

Background

cMET is a tyrosine-kinase membrane receptor and its dysregulation is involved in tumor proliferation, survival, angiogenesis, and migration. High levels of cMET have been observed in various tumor types and correlate with adverse outcome. The purpose of this study was to evaluate levels of total cMET and phospho-cMET (p-cMET) in breast cancer and their impact on survival outcomes.

Materials and Methods: We measured quantitative expression of cMET and p-cMET in a cohort of 257 breast cancer primary tumor samples using reverse phase protein array. The level of cMET/p-cMET in each sample was expressed as a log-mean centered value after correction for protein loading with the use of the average expression levels of &gt; 50 proteins. The regression tree method and Martingale residual plots were applied to find the best cutoff point for high and low levels of each protein. Linear regression models were used to determine if mean expression was different among breast cancer subtypes. The Kaplan-Meier method was used to estimate relapse-free survival (RFS) and overall survival (OS) by cMET and p-cMET levels. Cox proportional hazards models were fit to determine the association of cMET and p-cMET levels with the risk of recurrence and death after adjustment for other patient and disease characteristics.

Results: Median age was 51, (range 23–85) years. There were 140 (54.5%) hormone receptor (ER/PR)-positive, 53 (20.6%) HER2−positive, and 64 (24.9%) triple-negative tumors. Using the selected cutoffs, a total of 181 (70.4%) and 123 (47.9%) patients had high expression of cMET and p-cMET, respectively.

There were no significant differences in the mean expression of cMET (P&lt;0.128) and p-cMET (P&lt;0.088) by breast cancer subtype. Dichotomized cMET and p-cMET expression was a significant prognostic factor of RFS (HR: 0.41, 95% CI: 0.23−0.75, P=0.004, and HR: 0.61, 95% CI:0.38−0.96, P=0.033, respectively) and OS (HR: 0.31, 95% CI:0.14−0.70, P=0.005, and HR: 0.52, 95% CI:0.29−0.93, P=0.025, respectively). Within breast cancer subtypes, high cMET expression was associated with worse RFS (P=0.02) and OS (P=0.01) in ER/PR-positive tumors, and high p-cMET expression was associated with worse RFS (P=0.03) and OS (P=0.03) for patients with HER2−positive breast cancer. Multivariable model after adjustment for patient and tumor characteristics showed that patients with tumors with high cMET levels had a significant higher risk of recurrence (HR 0.28; 95% CI, 0.36−0.80) and death (HR 0.24; 95% CI, 0.09−0.65). Similarly, patients with tumors with high p-cMET levels had a significant higher risk of recurrence (HR 0.53; 95% CI, 0.29−0.97).

Conclusion: In this cohort of patients, high expression of cMET and p-cMET was seen in all subtypes of breast cancer. High levels of cMET and p-cMET had a significant impact on breast cancers survival outcomes. cMET inhibition may a be promising novel target for therapy in breast cancer and deserves investigation.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P4-09-09.

P5-01-05: Activating Mutations in PIK3CA or AKT1 in the I-SPY 1 Trial (CALGB 150007/150012; ACRIN 6657)

Background

Mutations in the catalytic domain of phosphatidylinositol 3-kinase (PIK3CA) are among the most frequently observed activating mutations in breast cancer. We used the I SPY 1 TRIAL, a group of biologically and clinically high risk patients molecularly profiled and treated with neoadjuvant chemotherapy, to determine the frequency of mutations and their relationship to pathologic complete response (pCR) and outcomes, within the entire cohort and within subtypes defined by growth and hormone receptor (HR) expression.

Methods: Patients enrolled in the I-SPY 1 TRIAL had a tumor size ≥3.0cm and were administered a doxorubicin-containing regimen, followed by a taxane, prior to surgery. Sequenom single nucleotide polymorphism (SNP) profiling was performed on breast tumor genomic DNA isolated from a subset of patients (n=152). A total of 149 SNPs covering 16 genes (including PIK3CA and AKT1/2/3) were analyzed. Mutations were tested for association with estrogen receptor (ER), progesterone receptor (PgR), and HER2 status, as well as pCR, using Fisher's exact test; associations between mutations and recurrence-free survival (RFS) were measured by log-rank tests. pCR was defined as no invasive tumor present in either the breast or axillary lymph nodes following neoadjuvant treatment.

Results: Of 149 mutations profiled in the cohort, 13 of the SNPs were observed. PIK3CA mutations were the most frequently observed in the panel (15.1%), followed by AKT1(E17K; 2.7%), CTNNB1 (D32; 1.4%), NRAS(Q61; 0.7%), and FGFR2(N549; 0.7%). Mutations in PIK3CA or AKT1 was associated with ER-positivity (p=0.0047) and PgR-positivity (p=0.044). Within receptor subtypes, the frequencies of PIK3CA/AKT1 mutations were also significantly different (HR+HER2−: 27%:(18/68); HER2+ 20% (8/40) [HR+HER2+: 26%, HR-HER2+: 14%]; HR-HER2−: 0% (0/36), p&lt;0.0008). Unlike previous reports (Loi et al, PNAS 2010), no significant association between PIK3CA/AKT mutation status and RFS was observed when we restricted our analysis to the adjuvant endocrine treated subset of the HR+HER2− patients (n=49; log rank p = 0.369). In contrast, and similar to cell line reports (Junttila et al, Cancer Cell 2009), PIK3CA mutations appears to associate with worse RFS within the small subset of trastuzumab treated HER2+ patients (n=22, 13 HR-HER2+, 9 HR+HER2−; log rank p=0.001), suggesting mutations may influence response. Similar analyses of a larger cohort are planned to confirm these observations.

Conclusions: Within the I-SPY 1 TRIAL cohort, PIK3CA and AKT1 mutations are much more frequent in the HR+ and HER2 subsets but are not predictive of response to therapy or outcome except potentially within the HER2+ subset. The potential link observed between activating PIK3CA/AKT mutations and trastuzumab resistance merits further investigation, as it may provide a clinical rationale for testing PIK3CA mutation status in HER2+ patients and investigating combinational therapies targeting this pathway, particularly in the HER2+HR+ subset which have an elevated risk for recurrence despite pCR and trastuzumab therapy.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P5-01-05.

P4-05-01: Rab25 Alters Cellular Energetics and Growth Signaling during Breast Oncogenesis

Background: Conservation and consumption of cellular energy is centrally regulated by growth and metabolism of the whole organism. The cancer cell gains autonomy from this regulation to become an organism with indeterminate growth potential. Plasma membrane receptors including growth factors and nutrient receptors are sensors for microenvironmental cues that dictate the intracellular energetic pathways to recalibrate ATP production based on available resources. So altercations in both growth and metabolic pathways are common features of cancers. A unifying component between receptor mediated growth signaling and metabolic pathways within a cell could be the vesicular trafficking system that imports, transports and exports a wide array of cargo from both these pathways.

In fact, derailed endocytosis is a hallmark of cancer. The endocytic pathway, as demonstrated by our laboratory, is a frequent target of genomic aberrations in cancer, and plays a critical role in maintenance of cellular polarity, stem cell fnction, bioenergetics, proliferation, motility, invasion, metastasis, apoptosis and autophagy. The Rab GTPases along with their effectors are critical regulators of this endocytic machinary and can have a huge impact on the cellular iterinary of growth and metabolism.

Methods and results: A broad spectrum analysis of distribution of all the Rab family members across 52 breast cancer cell lines reflected a dichotomous distribution of Rab25, with higher mRNA and protein expression in ER+ cell lines. Rab 25 is of immense interest to us because of its unique substitution of leucine for glutamine at position 71which typically decreases the intrinsic GTPase activity, resulting in a dominant, constitutively active protein, akin to a transforming RAS mutation.

Using high throughput mRNA data analysis, we report that Rab25 and its effector Rab Coupling Protein (RCP) are frequently coamplified and coordinately elevated in ER +ve breast cancers. Specifically in the luminal B subtypes, they are significantly associated with a markedly worsened outcome. In vitro, in MCF7 cell line, we observe an increased EGFR stability and MAPK signaling in Rab25 overexpressing stable clones which could be reversed with shRNA knockdown of Rab25. Loss of either Rab25 or RCP inhibited survival and growth of MCF7 lines under serum free conditions suggesting that Rab25 can potentially facilitate growth factor independence in cancer cells. Most importantly, we report that Rab25 enhances mitochondrial ATP production in breast and ***ovarian cancer cells and significantly reduces acidification of the ECM. Our ongoing experiments are directed towards understanding the mechanistic link between Rab25 mediated effects on EGFR/pERK signaling and its effects on cellular metabolism.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P4-05-01.

P2-03-04: Novel Pathways Underlying the Initiation and Transition of DCIS to IDC of HER2−Overexpressing Breast Cancer Model

Background: The HER2/Neu -oncogene is amplified in 20–25% percent of human primary breast cancers and this alteration is associated with disease behaviour. The HER2/neu oncogene encodes a receptor-like tyrosine kinase, whose overexpression in breast cancer predicts poor prognosis and resistance to conventional therapies. Whereas signalling pathways emanating from HER2 have been characterized, much less is known about the transcriptionally regulated genes controlled by HER2 that contribute to the initiation of Ductal Carcinoma Insitu (DCIS) and their transition to an invasive ductal carcinoma (IDC).

Materials and Methods: Normal and HER2 overexpressing mammary epithelial cells (MCF10A) were grown in extracellular matrix to form 3D structures, When grown in extracellular matrix as 3-dimensional spheroids, control cells developed a hollow lumen, but HER2−overexpressing cells populated the lumen by evading apoptosis. On the next step, uopon the growth factror stimulation HER2−overexpressing cells grown in extracellular matrix, which protruded invasive outgrowths. Highly variable genes were selected from the described phenotypes using RNA isolated from the 3D structures and hybridized to an Affymetrix HuGene 1.0 ST oligonucleotide array. Results: Using microarrays we analysed transcriptional events responsible for the morphological changes and found several novel sets of genes such as integral proteins, transcription factors, matrix proteases, Notch genes and chemokines were highly altered in the HER2 overexpressing group which were not appreciated before. Using gene annotation we defined molecular-pathways responsible for the phenotypical changes. More specifically, our study proposes a two hit model describes the pathways involved in the initiation of the Ductal Carcinoma Insitu and their transition to Invasive Cancer underlying the HER2 transcriptional network.

Discussion: According to the proposed model, expansion of ductal hyperplasia is limited by intraluminal apoptosis, unless they overexpress HER2, which drives proliferation and forms DCIS due to HER2 induced Notch pathways genes. Secondly, results obtained with the 3D system and their reflection in clinical outcome, we propose that neither HER2 amplification, nor the presence of GFs, is sufficient for development of IDC, but their co-occurrence can instigate metastasis by the activation of genes of integrin-adhesion signaling. The more virulent scenario combines HER2 amplification with GFs, thereby switching a robust, auto-stimulatory program.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P2-03-04.

P5-21-01: A Renewable Tissue Resource of Phenotypically Stable Human Breast Cancer Xenografts for Preclinical Studies

Introduction Translational breast cancer research is hampered severely by difficulties in obtaining and studying primary human breast tissue, and by the lack of in vivo preclinical models that accurately reflect patient tumor biology. These limitations are due, in part, to the fact that traditional immunocompromised mouse models are not generally permissive for growth. We sought to circumvent some of these limitations by transplanting and growing human mammary tumors in the mammary fat pad of SCID/Beige immunocompromised mice in the absence of exogenous human fibroblasts.

Aims and Methods To establish a set of stable human breast cancer xenografts for preclinical studies. Human breast cancer biopsies were received, minced into small fragments and then transplanted directly into “cleared” fat pads of recipient SCID/Beige immunocompromised mice. Transplanted fat pads were checked weekly. After initial tumor was palpated and harvested, tumor fragments were transplanted into new SCID/Beige hosts for subsequent transplant generations. Serial immunohistochemical evaluations were performed to confirm human origin and biomarker status. Analytical flow cytometry for evaluating expression of proposed “cancer stem cell” markers, and gene and protein expression analysis were carried out on all stable lines.

Results and Conclusions Xenograft lines were established directly from breast cancer patient samples, without intervening culture in vitro, using the epithelium-free mammary fat pad as the transplantation site. Of the conditions tested, xenograft take rate was highest in the presence of a low-dose estradiol pellet without exogenous human fibroblasts. Thirty six stably transplantable xenograft lines representing 27 patients were established, using pre-treatment, mid-treatment, and/or post-treatment samples. Most patients yielding xenografts were “triple-negative” (ER-PR-HER2−) (n=21), we were able to establish lines from three ER-PR-HER2+ patients, one ER+PR+HER2−, one ER+PR-HER2−and one “triple-positive” (ER+PR+HER2+) patients. Serially passaged xenografts show phenotypic consistency with the tumor of origin at the histopathology level, and remarkable stability across multiple transplant generations at both the genomic, transcriptomic, and proteomic levels. Of 27 lines evaluated fully, thirteen xenografts showed metastasis to the mouse lung. These models thus serve as a renewable, quality-controlled tissue resource, and should prove useful for preclinical evaluation of experimental therapeutics.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P5-21-01.

S5-3: Basement Membrane Localized Tumor Cells Are Protected from HER2−Targeted Therapy In Vivo

Drug resistance compromises the efficacy of HER2−targeted therapy. Results from our laboratory, and previous reports from others, indicate that tumor cell attachment to basement membrane (BM) and other extracellular matrix (ECM) proteins may confer drug resistance. We have discovered a differential drug response between the outer, matrix-attached cells and inner matrix-deprived cells comprising 3-dimensional (3D) tumor spheroids grown in reconstituted basement membrane (T. Muranen and J. Brugge, unpublished data). The outer matrix-attached cells are resistant to multiple drug therapies. To address whether these observations are relevant in vivo, we utilized a previously described model of human-in-mouse HER2−positive ductal carcinoma in situ (DCIS), which involves the intraductal transplantation of human HER2−positive SUM225 tumor cells directly into the ductal network of the mouse mammary gland. The intraductal tumors generated are histologically indistinguishable from human DCIS lesions and recapitulate the architecture of the 3D tumor spheroids. The tumors are characterized by organized nests of noninvasive cells confined within a BM surrounded by ECM. These features permit a direct assessment of differential drug response within the tumor. We focused on the tumor cell response to short-term lapatinib monotherapy in vivo. A close examination of the tumor architecture revealed that cells closest to the basement membrane, and nearest to the vasculature, display a striking insensitivity to lapatinib whereas the remainder of the tumor undergoes extensive cell death in response to treatment. Further characterization also revealed that cells closest to the basement membrane largely maintain proliferative capacity despite an overall significant reduction in the total Ki67-positive cell population. These results provide in vivo evidence that basement membrane-attached tumor cells are protected from lapatinib. We confirmed that these cells maintain HER2 status and also observed an overall reduction in pHER2, pAKT and pERK throughout the tumor suggestive of adaptive response mechanisms, which support the proliferation and survival of these cell populations despite inhibition of the HER2 pathway. To further explore potential mechanisms of the adaptive response, we performed reverse phase protein array (RPPA) analysis on protein lysates prepared from tumor biopsy fragments following lapatinib monotherapy. RPPA profile analysis revealed an adaptive response composed of upregulation of multiple RTKs (HER2, IGFI-R) and altered apoptotic protein levels (Bcl-2, Bim, Bcl-xL) in addition to activation of AKT/S6K and ERK/p38 pathway components. These observations suggest that basement membrane-attached tumor cells may escape from lapatinib response via compensatory activation of these survival mechanisms. Each of these components will serve as targets for designing combined therapeutic approaches capable of targeting the protected basement membrane-attached tumor cells. Our results suggest that resistant populations may be a source of residual disease post-therapy, therefore identifying and characterizing these cells will be crucial to the prevention of disease recurrence in the clinic.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr S5-3.

Modeling ductal carcinoma in situ: a HER2-Notch3 collaboration enables luminal filling

A large fraction of ductal carcinoma in situ (DCIS), a non-invasive precursor lesion of invasive breast cancer, overexpresses the HER2/neu oncogene. The ducts of DCIS are abnormally filled with cells that evade apoptosis, but the underlying mechanisms remain incompletely understood. We overexpressed HER2 in mammary epithelial cells and observed growth factor-independent proliferation. When grown in extracellular matrix as three-dimensional spheroids, control cells developed a hollow lumen, but HER2-overexpressing cells populated the lumen by evading apoptosis. We demonstrate that HER2 overexpression in this cellular model of DCIS drives transcriptional upregulation of multiple components of the Notch survival pathway. Importantly, luminal filling required upregulation of a signaling pathway comprising Notch3, its cleaved intracellular domain and the transcriptional regulator HES1, resulting in elevated levels of c-MYC and cyclin D1. In line with HER2-Notch3 collaboration, drugs intercepting either arm reverted the DCIS-like phenotype. In addition, we report upregulation of Notch3 in hyperplastic lesions of HER2 transgenic animals, as well as an association between HER2 levels and expression levels of components of the Notch pathway in tumor specimens of breast cancer patients. Therefore, it is conceivable that the integration of the Notch and HER2 signaling pathways contributes to the pathophysiology of DCIS.

Kinome siRNA-phosphoproteomic screen identifies networks regulating AKT signaling

To identify regulators of intracellular signaling we targeted 541 kinases and kinase-related molecules with siRNAs and determined their effects on signaling with a functional proteomics reverse phase protein array (RPPA) platform assessing 42 phospho and total proteins. The kinome wide screen demonstrated a strong inverse correlation between phosphorylation of AKT and MAPK with 115 genes that when targeted by siRNAs demonstrated opposite effects on MAPK and AKT phosphorylation. Network based analysis identified the MAPK subnetwork of genes along with p70S6K and FRAP1 as the most prominent targets that increased phosphorylation of AKT, a key regulator of cell survival. The regulatory loops induced by the MAPK pathway are dependent on TSC2 but demonstrate a lesser dependence on p70S6K than the previously identified FRAP1 feedback loop. The siRNA screen also revealed novel bi-directionality in the AKT and GSK3 interaction, whereby genetic ablation of GSK3 significantly blocks AKT phosphorylation, an unexpected observation as GSK3 has only been predicted to be downstream of AKT. This method uncovered novel modulators of AKT phosphorylation and facilitated the mapping of regulatory loops.

Quantitative proteomic analysis in breast cancer

Much progress has recently been made in the genomic and transcriptional characterization of tumors. However, historically the characterization of cells at the protein level has suffered limitations in reproducibility, scalability and robustness. Recent technological advances have made it possible to accurately and reproducibly portray the global levels and active states of cellular proteins. Protein microarrays examine the native post-translational conformations of proteins including activated phosphorylated states, in a comprehensive high-throughput mode, and can map activated pathways and networks of proteins inside the cells. The reverse-phase protein microarray (RPPA) offers a unique opportunity to study signal transduction networks in small biological samples such as human biopsy material and can provide critical information for therapeutic decision-making and the monitoring of patients for targeted molecular medicine. By providing the key missing link to the story generated from genomic and gene expression characterization efforts, functional proteomics offer the promise of a comprehensive understanding of cancer. Several initial successes in breast cancer are showing that such information is clinically relevant.

Drosophila in cancer research: to boldly go where no one has gone before

Transformation and metastasis are complex processes that depend on integration of effects from multiple mutations. Modeling this complexity requires manipulating multiple genes in particular sub-populations of cells in vivo. This is technically challenging in mammalian model systems and has limited the rate of progress in understanding the effects of the complex aberrations present in cancer cells. In contrast, powerful genetic methods in the fruit fly Drosophila allow efficient generation and analysis of complex genotypes in defined cell populations. These methods are already fruitful in exploring the interactions among cancer mutations, and between cell populations that mimic the tumor microenvironment. In this issue of Oncogene, Willecke et al. (2011) describe the implementation of a novel genetic screen in Drosophila to identify genes required for tumor growth in vivo. This report illustrates the power of using Drosophila to perform systematic genome-wide genetic screens in complex genetic backgrounds and for the resulting data to inform our understanding of transformation and metastasis in human systems.

Abstract P3-10-23: Caveolin 1 and Patient Outcomes in Breast Cancer

Introduction: Caveolin 1 (Cav1) protein is a structural component of caveolae in cell membranes and is also present in the cell cytoplasm, nucleus and extracellular milieu. It regulates multiple cellular processes and has been reported to both positively and negatively effect tumour progression. In normal and malignant breast tissue Cav1 is immunohistochemically expressed in myoepithelial and stromal cells but rarely in luminal epithelial or breast cancer cells. Recent reports have correlated Cav1 expression in the stromal tumour microenvironment with lower tumor stage, grade and improved prognosis. This suggests a separate role for Cav 1 in influencing tumour behaviour by regulating the tumour microenvironment. Our aim was to further investigate the role of Cav1 in breast cancer by for the first time analysing its expression by reverse phase protein array(RPPA). Methods: We examined expression levels of Cav1 in 52 breast cancer cell lines and a large human early breast cancer cohort(n=712) with cancer cells composing 70% of the macrodissected breast cancer specimens used. Data was recorded when available for each case on standard clinical, pathological and survival endpoints. We examined the effect of Cav1 expression on tumour biology and patient survival. Results: High levels of Cav1 expression in breast cancer cell lines was strongly correlated with a TN phenotype (P&lt;0.001). Cav 1 expression was more strongly associated with the stromal subtype rather than basal subtype of TN cell lines (p=0.02).

In contrast, in human tumour tissue high levels of Cav1 correlated with the hormone receptor positive(ER) phenotype. There was also an association between Cav 1 expression and lower grade (P&lt;0.001), lower T stage (P&lt;0.001) and lower N stage (P&lt;0.001).

Cav 1 was significantly associated with improved relapse-free (RFS) and overall survival (OS) in the human cohort. On multivariate(MV) analysis Cav1 was associated with OS(HR 0.91/95% CI 0.82-1/p=0.05) but not RFS. In the subset of ER patients who only received adjuvant tamoxifen (n=199) Cav1 was also significantly associated with improved RFS and OS. MV analysis again showed this correlation to remain for OS (HR 0.81/95% CI 0.65-1/p=0.05) but not for RFS. In the TN subset (n=161) Cav1 expression did not have any survival impact. Discussion: Our results show different expression patterns of Cav1 in vitro and in vivo. TN tumors are thought to originate from the myoepithelial or stromal component of breast tissue which may explain the high levels of Cav1 in this subgroup of breast cancer cell lines. On the other hand, human tumour tissue showed an association between high Cav1 levels and ER tumours. Analysis of these macrodissected samples likely included stromal tissue surrounding the epithelial tumour cells which may explain this discrepancy.

Our data also show a correlation between high in vivo levels of Cav1 and less aggressive tumours with improved prognosis. On MV analysis Cav1 was an independent predictor of outcome in the whole cohort and in the ER subset treated with adjuvant tamoxifen only. Expression of stromal Cav1 measured by RPPA may again partly explain these findings. Further analysis with fully microdissected human breast tissue and immunohistochemical analysis of both stromal and cancer cell Cav1 expression is planned.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P3-10-23.

Lysophosphatidic acid augments human hepatocellular carcinoma cell invasion through LPA1 receptor and MMP-9 expression

Lysophosphatidic acid (LPA), produced extracellularly by autotaxin (ATX), has diverse biological activities implicated in tumor initiation and progression, including increasing cell survival, angiogenesis, invasion and metastasis. ATX, LPA and the matrix metalloproteinase (MMP)-9 have all been implicated in hepatocellular carcinoma (HCC) invasion and metastasis. We, thus sought to determine whether ATX with subsequent LPA production and action, including induction of MMP-9 could provide a unifying mechanism. ATX transcripts and LPA receptor type 1 (LPA1) protein are elevated in HCC compared with normal tissues. Silencing or pharmacological inhibition of LPA1 significantly attenuated LPA-induced MMP-9 expression and HCC cell invasion. Further, reducing MMP-9 activity or expression significantly inhibits LPA-induced HCC cell invasion, demonstrating that MMP-9 is downstream of LPA1. Inhibition of phosphoinositide-3 kinase (PI3K) signaling or dominant-negative mutants of protein kinase Cδ and p38 mitogen-activated protein kinase (MAPK) abrogated LPA-induced MMP-9 expression and subsequent invasion. We thus demonstrate a mechanistic cascade of ATX-producing LPA with LPA activating LPA1 and inducing MMP-9 through coordinate activation of the PI3K and the p38 MPAK signaling cascades, providing novel biomarkers and potential therapeutic targets for HCC.

Event excess in the MiniBooNE search for ¯νμ→¯νe oscillations

The MiniBooNE experiment at Fermilab reports results from a search for ¯ν_{μ}→¯ν_{e} oscillations, using a data sample corresponding to 5.66×10²⁰ protons on target. An excess of 20.9±14.0 events is observed in the energy range 475<E_{ν}^{QE}<1250  MeV, which, when constrained by the observed ¯ν_{μ} events, has a probability for consistency with the background-only hypothesis of 0.5%. On the other hand, fitting for ¯ν_{μ}→¯ν_{e} oscillations, the best-fit point has a χ² probability of 8.7%. The data are consistent with ¯ν_{μ}→¯ν_{e} oscillations in the 0.1 to 1.0  eV² Δm² range and with the evidence for antineutrino oscillations from the Liquid Scintillator Neutrino Detector at Los Alamos National Laboratory.

Integrin-linked kinase has a critical role in ErbB2 mammary tumor progression: implications for human breast cancer

Elevated expression of the integrin-linked kinase (ILK) has been observed in a variety of cancers and has been further correlated with poor clinical outcome. Here, we show that mammary epithelial disruption of ILK results in a profound block in mammary tumor induction. Consistent with these observations, inhibition of ILK function in ErbB2-expressing cells with small molecule inhibitor or RNA interference resulted in profound block in their in vitro invasive properties due to the induction of apoptotic cell death. The rare ILK-deficient tumors that eventually arose overcame this block in tumor induction by an upregulation of ErB3 phosphorylation. These observations provide direct evidence that ILK has a critical role in the initiation phase of ErbB2 tumor induction.

Gene and protein expression markers of response to combined antiangiogenic and epidermal growth factor targeted therapy in renal cell carcinoma

BACKGROUND

Metastatic renal cell carcinoma (mRCC) patients treated with anti-vascular endothelial growth factor (VEGF) therapies demonstrate promising outcomes but not all patients benefit. Factors that predict response remain to be elucidated.

PATIENTS AND METHODS

Nephrectomy material from 37 patients with mRCC receiving bevacizumab +/- erlotinib was used for protein and gene expression assessment. Protein lysates were subjected to reverse-phase protein array profiling. RNA extracts were used to carry out gene expression microarray-based profiling. Normalized protein and gene expression data were correlated with overall survival (OS) and progression-free survival (PFS) using univariate Cox hazard model and linear regression. Immunoblotting was carried out to validate the results.

RESULTS

High protein levels of AMP-activated protein kinase and low levels of cyclin B1 (CCNB1) were associated with longer OS and PFS. Further validation revealed reduced expression and activation of phosphoinositide 3-kinase (PI3K) pathway components and cell cycle factors in patients with prolonged survival after therapy. Gene expression analysis revealed up-regulation of PI3K- and cell cycle-related pathways in patients with shorter PFS.

CONCLUSIONS

The OS and PFS of bevacizumab +/- erlotinib-treated patients with renal cell carcinoma were associated with changes in expression of protein and gene expression markers related to PI3K pathway and cell cycle signaling.

Search for electron antineutrino appearance at the deltam(2) approximately 1 eV(2) Scale

The MiniBooNE Collaboration reports initial results from a search for nu(mu)-->nu(e) oscillations. A signal-blind analysis was performed using a data sample corresponding to 3.39x10(20) protons on target. The data are consistent with background prediction across the full range of neutrino energy reconstructed assuming quasielastic scattering, 200<E(nu)(QE)<3000 MeV: 144 electronlike events have been observed in this energy range, compared to an expectation of 139.2+/-17.6 events. No significant excess of events has been observed, both at low energy, 200-475 MeV, and at high energy, 475-1250 MeV. The data are inconclusive with respect to antineutrino oscillations suggested by data from the Liquid Scintillator Neutrino Detector at Los Alamos National Laboratory.

Measurement of the ratio of the numu charged-current single-pion production to quasielastic scattering with a 0.8 GeV neutrino beam on mineral oil

Using high statistics samples of charged-current numu interactions, the MiniBooNE [corrected] Collaboration reports a measurement of the single-charged-pion production to quasielastic cross section ratio on mineral oil (CH2), both with and without corrections for hadron reinteractions in the target nucleus. The result is provided as a function of neutrino energy in the range 0.4 GeV<Enu<2.4 GeV with 11% precision in the region of highest statistics. The results are consistent with previous measurements and the prediction from historical neutrino calculations.