High-throughput detection of clinically relevant mutations in archived tumor samples by multiplexed PCR and next-generation sequencing

PURPOSE

Tailoring cancer treatment to tumor molecular characteristics promises to make personalized medicine a reality. However, reliable genetic profiling of archived clinical specimens has been hindered by limited sensitivity and high false-positive rates. Here, we describe a novel methodology, MMP-seq, which enables sensitive and specific high-throughput, high-content genetic profiling in archived clinical samples.

EXPERIMENTAL DESIGN

We first validated the technical performance of MMP-seq in 66 cancer cell lines and a Latin square cross-dilution of known somatic mutations. We next characterized the performance of MMP-seq in 17 formalin-fixed paraffin-embedded (FFPE) clinical samples using matched fresh-frozen tissue from the same tumors as benchmarks. To demonstrate the potential clinical utility of our methodology, we profiled FFPE tumor samples from 73 patients with endometrial cancer.

RESULTS

We demonstrated that MMP-seq enabled rapid and simultaneous profiling of a panel of 88 cancer genes in 48 samples, and detected variants at frequencies as low as 0.4%. We identified DNA degradation and deamination as the main error sources and developed practical and robust strategies for mitigating these issues, and dramatically reduced the false-positive rate. Applying MMP-seq to a cohort of endometrial tumor samples identified extensive, potentially actionable alterations in the PI3K (phosphoinositide 3-kinase) and RAS pathways, including novel PIK3R1 hotspot mutations that may disrupt negative regulation of PIK3CA.

CONCLUSIONS

MMP-seq provides a robust solution for comprehensive, reliable, and high-throughput genetic profiling of clinical tumor samples, paving the way for the incorporation of genomic-based testing into clinical investigation and practice.

Developing biomarkers to predict benefit from HGF/MET pathway inhibitors

Activation of the MET signalling pathway is critical in regulating multiple cellular processes underlying tumourigenic growth and has represented an attractive target for therapeutic intervention in cancer. Early stage clinical studies of multiple agents targeting this pathway have been undertaken, frequently in unselected patient cohorts with variable results. Promising data in patient subgroups in these studies indicate the need for predictive biomarkers to identify the patients most likely to benefit from these therapies. In this review, we discuss the current knowledge of mechanisms of MET activation, the status of the clinical evaluation of MET-targeted therapies, the associated efforts to identify and validate biomarkers, and the considerations and challenges for potential development of companion diagnostics.

Pathology in drug discovery and development

The rapid pace of drug discovery and drug development in oncology, immunology and ophthalmology brings new challenges; the efficient and effective development of new targeted drugs will require more detailed molecular classifications of histologically homogeneous diseases that show heterogeneous clinical outcomes. To this end, single companion diagnostics for specific drugs will be replaced by multiplex diagnostics for entire therapeutic areas, preserving tissue and enabling rapid molecular taxonomy. The field will move away from the development of new molecular entities as single agents, to which resistance is common. Instead, a detailed understanding of the pathological mechanisms of resistance, in patients and in preclinical models, will be key to the validation of scientifically rational and clinically effective drug combinations. To remain at the heart of disease diagnosis and appropriate management, pathologists must evolve into translational biologists and biomarker scientists. Herein, we provide examples of where this metamorphosis has already taken place, in lung cancer and melanoma, where the transformation has yet to begin, in the use of immunotherapies for ophthalmology and oncology, and where there is fertile soil for a revolution in treatment, in efforts to classify glioblastoma and personalize treatment. The challenges of disease heterogeneity, the regulatory environment and adequate tissue are ever present, but these too are being overcome in dedicated academic centres. In summary, the tools necessary to overcome the 'whens' and 'ifs' of the molecular revolution are in the hands of pathologists today; it is a matter of standardization, training and leadership to bring these into routine practice and translate science into patient benefit. This Annual Review Issue of the Journal of Pathology highlights the central role for pathology in modern drug discovery and development.

Abstract P6-09-01: Central Ki67 analysis as a predictor for adjuvant capecitabine efficacy in early breast cancer (EBC) subtypes in US oncology trial 01062

Background: USON 01062 (O’Shaughnessy J, et al. Proc SABCS, 2010, abst S4-2) showed no improvement in the primary endpoint of disease-free survival (DFS) (median FU 5 yrs: HR 0.84, 95% CI: 0.67-1.05; p = 0.125) with the addition of capecitabine (X) to standard adjuvant chemotherapy, but showed improvement in OS (HR 0.68, 95% CI: 0.51-0.92; p = 0.011). Exploratory analysis of local pathology-assessed Ki67 suggested benefit from adjuvant X in pts with more highly proliferative cancers with Ki67 ≥ 10% (Pippen J et al. Proc ASCO, 2011, abst 500). The objective of this study is to determine whether centrally-performed Ki67 IHC results corroborate or refute this finding.

Methods: 2610 pts with resected high risk EBC were randomized to receive 4 cycles of AC (doxorubicin 60mg/m2 and cyclophosphamide 600mg/m2) IV every 3 wks for 4 cycles followed by either docetaxel 100mg/m2 IV or docetaxel 75mg/m2 IV plus X 825mg/m2 PO bid for 14 days every 3 wks for 4 cycles. Archival primary breast cancer tissue was collected on 2000 pts for predictive biomarker analyses. Central Ki67 IHC was performed using the anti-Ki67 monoclonal antibody SP6 and was read by one pathologist (HK) according to published recommendations (Dowsett M, et al. JNCI 103:1-9, 2011).

Results: Central Ki67 IHC has been performed on 1440 pts who had centrally-validated informed consents. The distribution of% Ki67-positive cells by locally-assessed ER/HER2 subtype is shown below. 45% of HR+ HER2- BCs had a Ki67 ≤ 10%, while 24% had a Ki67 11% to 20%, and 31% had a Ki67 > 20%. The concordance between the local vs central Ki67 results was low at 46% for Ki67 <10%, 49% for Ki67 10%-20%, and 76% for Ki67 > 20%. The central Ki67 results tended to be higher than the local testing results. Central mRNA classifiers were developed for ER, PR, HER2 and Ki67 using Fluidigm Microfluidics Dynamic Arrays and correlate highly with central IHC assessment of these markers.

Conclusions: HR+ HER2- EBC is enriched for cancers with a low proliferative rate, a group of pts unlikely to benefit from the cell cycle-specific cytotoxic agent, capecitabine. Analyses of the impact of adjuvant X added to AC/T in EBC pts according to ER status, and according to Ki67 (analyzed as a binary and continuous variable) will be performed prior to SABCS, 2013.

Number of Patients% Ki67 Pos CellsTotal *HR+TNHER2+/HR+HER2+/ HR-0-104163622222711-151391066151016-20126871615821-3018411539201031-1005751403423555Total144081042510790*Totals do not equal sum of subtype categories due to missing HER2 information

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P6-09-01.

Abstract B190: GDC-0068 is a novel and selective Akt inhibitor that enhances the efficacy of FOLFOX in primary gastric cancer models

Background: Akt, a serine/threonine protein kinase, is a key signaling node in the PI3K/Akt/mTOR pathway and plays an essential role in regulating tumor cell proliferation, migration and survival. PI3K/Akt signaling is up-regulated in gastric cancer, mainly due to loss of PTEN, and is associated with poor prognosis and chemoresistance. Chemotherapeutics such as doxorubicin and 5-FU/cisplatin have been shown to upregulate PI3K/Akt signaling in several solid cancers in response to DNA damage. We have previously reported on a potent highly selective ATP-competitive pan-Akt inhibitor, GDC-0068, which inhibits cell cycle progression and viability of cancer cell lines and xenografts driven by Akt signaling, including those with defects in the tumor suppressor PTEN, oncogenic mutations in PIK3CA, and amplification of HER2. Thus, we hypothesized that the combination of FOLFOX and GDC-0068 would induce anti-tumor activity in primary gastric cancer models.

Methods: Gastric cancer cell lines (n=11) were treated with increasing concentrations of GDC-0068 and FOLFOX and evaluated for combinational efficacy over single agent via cell viability assay. For in vivo studies, primary gastric cancer xenograft models were implanted in immuno-compromised mice and treated with GDC-0068 and FOLFOX as single agents or in combination.

Results: In vitro, the combination of GDC-0068 and FOLFOX results in enhanced inhibition of tumor cell viability in the cell lines with activation of the PI3K pathway compared to either single agent alone. These results were recapitulated in vivo, in the primary xenograft models STO#240 and STO#182, where the combination of GDC-0068 and FOLFOX resulted in increased tumor growth inhibition or regressions compared to single agents alone. All combinations tested were well tolerated in vivo based on minimal changes in body weights.

Conclusions: Our preclinical studies demonstrate improved anti-tumor efficacy when GDC-0068 is combined with FOLFOX in gastric cancer models in vitro and in vivo. The data supports the clinical development of GDC-0068 in combination with FOLFOX for the treatment of gastric cancer.

Citation Information: Mol Cancer Ther 2013;12(11 Suppl):B190.

Citation Format: Ellen Ingalla, Rebecca Hong, Heidi Savage, Elizabeth Punnoose, Sandra Rost, Hartmut Koeppen, Deepak Sampath, Michelle A. Nannini. GDC-0068 is a novel and selective Akt inhibitor that enhances the efficacy of FOLFOX in primary gastric cancer models. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr B190.

Loss of NAPRT1 expression by tumor-specific promoter methylation provides a novel predictive biomarker for NAMPT inhibitors

PURPOSE

We sought to identify predictive biomarkers for a novel nicotinamide phosphoribosyltransferase (NAMPT) inhibitor.

EXPERIMENTAL DESIGN

We use a NAMPT inhibitor, GNE-617, to evaluate nicotinic acid rescue status in a panel of more than 400 cancer cell lines. Using correlative analysis and RNA interference (RNAi), we identify a specific biomarker for nicotinic acid rescue status. We next determine the mechanism of regulation of expression of the biomarker. Finally, we develop immunohistochemical (IHC) and DNA methylation assays and evaluate cancer tissue for prevalence of the biomarker across indications.

RESULTS

Nicotinate phosphoribosyltransferase (NAPRT1) is necessary for nicotinic acid rescue and its expression is the major determinant of rescue status. We demonstrate that NAPRT1 promoter methylation accounts for NAPRT1 deficiency in cancer cells, and NAPRT1 methylation is predictive of rescue status in cancer cell lines. Bisulfite next-generation sequencing mapping of the NAPRT1 promoter identified tumor-specific sites of NAPRT1 DNA methylation and enabled the development of a quantitative methylation-specific PCR (QMSP) assay suitable for use on archival formalin-fixed paraffin-embedded tumor tissue.

CONCLUSIONS

Tumor-specific promoter hypermethylation of NAPRT1 inactivates one of two NAD salvage pathways, resulting in synthetic lethality with the coadministration of a NAMPT inhibitor. NAPRT1 expression is lost due to promoter hypermethylation in most cancer types evaluated at frequencies ranging from 5% to 65%. NAPRT1-specific immunohistochemical or DNA methylation assays can be used on archival formalin paraffin-embedded cancer tissue to identify patients likely to benefit from coadministration of a Nampt inhibitor and nicotinic acid.

Abstract A067: Targeting p21-activated kinases in breast cancer

Luminal breast cancer is the most commonly diagnosed cancer worldwide and mechanisms of innate and acquired resistance are not yet well understood. P21-activated kinases (PAKs) are members of the STE20 family of serine/threonine kinases that lie downstream of receptor tyrosine kinases and Rho family GTPases. PAKs regulate many cellular processes that are commonly perturbed in cancer, including migration, polarization and proliferation, and are therapeutic targets of interest. PAK1 is also overexpressed in several cancers and we recently showed that focal genomic amplification of PAK1 occurs in ~8% of luminal breast cancer (Proc Natl Acad Sci 2011; 108:7177). PAK1 amplification has also been associated with poor patient outcome and PAK1 is a putative mediator of resistance to anti-estrogen therapy (Nature 2012; 486:346). The aim of this study was to further characterize PAK family kinases in breast adenocarcinoma. Luminal breast cancer cells with PAK1 focal amplification rapidly underwent apoptosis following inhibition of this kinase. To identify potential mechanisms of acquired resistance we have derived PAK1-resistant cell lines and begun characterizing via genomic and proteomics approaches. Furthermore, in contrast to the role of PAK1 in luminal breast cancer, elevated expression of PAK4 was associated with poor outcome in basal-like breast cancer. We developed a novel small molecule inhibitor with high potency and selectivity of group II PAKs to delineate the role of PAK4 signaling in basal breast cancer. Together, our results provide evidence for dysregulation of PAK1 and PAK4 in differing subtypes of breast cancer and roles in for these kinases in cellular survival, proliferation and migration in this tumor indication.

Citation Format: Klaus Hoeflich, Christy Ong, Karen Lyle, Adrian Jubb, Wei Zhou, Adrian Harris, Marcia Belvin, Lori Friedman, Hartmut Koeppen, Joachim Rudolph, Steven Staben. Targeting p21-activated kinases in breast cancer. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research: Genetics, Biology, and Clinical Applications; Oct 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2013;11(10 Suppl):Abstract nr A067.

In situ validation of an intestinal stem cell signature in colorectal cancer

OBJECTIVE

Wnt/Tcf, Lgr5, Ascl2 and/or Bmi1 signalling is believed to define the mouse intestinal stem cell niche(s) from which adenomas arise. The aim of this study was to determine the relevance of these putative intestinal stem cell markers to human colorectal cancer.

DESIGN

19 putative intestinal stem cell markers, including Ascl2 and Lgr5, were identified from published data and an evaluation of a human colorectal gene expression database. Associations between these genes were assessed by isotopic in situ hybridisation (ISH) in 57 colorectal adenocarcinomas. Multiplex fluorescent ISH and chromogenic non-isotopic ISH were performed to confirm expression patterns. The prognostic significance of Lgr5 was assessed in 891 colorectal adenocarcinomas.

RESULTS

Ascl2 and Lgr5 were expressed in 85% and 74% of cancers respectively, and expression was positively correlated (p=0.003). Expression of Bmi1 was observed in 47% of cancers but was very weak in 98% of cases with expression. Both Ascl2 and/or Lgr5 were positively correlated with the majority of genes in the signature but neither was correlated with Cdk6, Gpx2, Olfm4 or Tnfrsf19. Lgr5 did not have prognostic significance.

CONCLUSION

These data suggest that 74-85% of colorectal cancers express a Lgr5/Ascl2 associated signature and support the hypothesis that they derive from Lgr5(+)/Ascl2(+) crypt stem cells, not Bmi1(+) stem cells. However, Olfm4 was not found to be a useful marker of Lgr5(+) cells in normal colon or tumours. In this large series, Lgr5 expression is not associated with increased tumour aggressiveness, as might be expected from a cancer stem cell marker.

Biomarkers and associations with the clinical activity of PD-L1 blockade in a MPDL3280A study

3001

Background: PD-L1, which is highly expressed on tumors, is a ligand of PD-1, an inhibitory receptor present on activated T cells. PD-L1 expression is regulated by intrinsic (mutations) and adaptive (tumor infiltrating T cells) mechanisms. MPDL3280A, a human monoclonal antibody containing an engineered Fc-domain designed to optimize efficacy and safety, targets PD-L1, blocking PD-L1 from binding its receptors, including PD-1 and B7.1. Methods: A Ph I study was conducted with MPDL3280A administered IV q3w in pts with locally advanced or metastatic solid tumors. The expansion cohort required available tumor tissue. In addition, the study included a serial biopsy cohort with tumor sampling prior to and during treatment. Tumor samples were analyzed by IHC and a Genentech immunochip measuring ≈90 immune-related genes to characterize the tumor immune microenvironment at baseline (BL) and/or during MPDL3280A treatment. Further, blood-based biomarkers and circulating immune cell subsets were serially measured. Results: Pretreatment tumor samples were available for IHC from 112 pts and for immunochip from 96 pts.In addition, 23 pts had paired BL and on-treatment samples. Blood-based biomarkers were evaluated in 76 pts. Elevated BL PD-L1 expression by IHC was associated with response to MPDL3280A, and coordinated expression of PD-L1 and CD8+ T-cells was observed. Furthermore, a T-cell gene signature (including CD8, IFNg and Granzyme-A) was associated with treatment response. On treatment, responding tumors showed increasing PD-L1 expression and a Th1-dominant immune infiltrate, providing evidence for adaptive PD-L1 upregulation. Nonresponders showed minimal tumor CD8+ T-cell infiltration and an absence of T-cell activation (measured by Granzyme-A and Perforin expression). Additionally, a subpopulation of pts exhibited changes in circulating cytokines (IFNg) and activated T-cell subsets (HLADR+Ki67+). Conclusions: PD-L1 tumor expression and T-cell gene signature correlate with response to MPDL3280A. MPDL3280A therapy led to T-cell reactivation and restored antitumor immunity. These data provide mechanistic insights into immunotherapy and support pt selection for treatment with MPDL3280A monotherapy. Clinical trial information: NCT01375842.

Identification and analysis of in vivo VEGF downstream markers link VEGF pathway activity with efficacy of anti-VEGF therapies

PURPOSE

The aim of this study was to identify conserved pharmacodynamic and potential predictive biomarkers of response to anti-VEGF therapy using gene expression profiling in preclinical tumor models and in patients.

EXPERIMENTAL DESIGN

Surrogate markers of VEGF inhibition [VEGF-dependent genes or VEGF-dependent vasculature (VDV)] were identified by profiling gene expression changes induced in response to VEGF blockade in preclinical tumor models and in human biopsies from patients treated with anti-VEGF monoclonal antibodies. The potential value of VDV genes as candidate predictive biomarkers was tested by correlating high or low VDV gene expression levels in pretreatment clinical samples with the subsequent clinical efficacy of bevacizumab (anti-VEGF)-containing therapy.

RESULTS

We show that VDV genes, including direct and more distal VEGF downstream endothelial targets, enable detection of VEGF signaling inhibition in mouse tumor models and human tumor biopsies. Retrospective analyses of clinical trial data indicate that patients with higher VDV expression in pretreatment tumor samples exhibited improved clinical outcome when treated with bevacizumab-containing therapies.

CONCLUSIONS

In this work, we identified surrogate markers (VDV genes) for in vivo VEGF signaling in tumors and showed clinical data supporting a correlation between pretreatment VEGF bioactivity and the subsequent efficacy of anti-VEGF therapy. We propose that VDV genes are candidate biomarkers with the potential to aid the selection of novel indications as well as patients likely to respond to anti-VEGF therapy. The data presented here define a diagnostic biomarker hypothesis based on translational research that warrants further evaluation in additional retrospective and prospective trials.

Systems-wide analysis of K-Ras, Cdc42, and PAK4 signaling by quantitative phosphoproteomics

Although K-Ras, Cdc42, and PAK4 signaling are commonly deregulated in cancer, only a few studies have sought to comprehensively examine the spectrum of phosphorylation-mediated signaling downstream of each of these key signaling nodes. In this study, we completed a label-free quantitative analysis of oncogenic K-Ras, activated Cdc42, and PAK4-mediated phosphorylation signaling, and report relative quantitation of 2152 phosphorylated peptides on 1062 proteins. We define the overlap in phosphopeptides regulated by K-Ras, Cdc42, and PAK4, and find that perturbation of these signaling components affects phosphoproteins associated with microtubule depolymerization, cytoskeletal organization, and the cell cycle. These findings provide a resource for future studies to characterize novel targets of oncogenic K-Ras signaling and validate biomarkers of PAK4 inhibition.

Abstract 3479: Sensitivity of endometrial cancer cells to inhibitors targeting different nodes of the PI3K pathway and their combination with a MEK inhibitor

Activation of the PI3K pathway has been reported in endometrial cancers, and there are a number of inhibitors targeting different nodes of the PI3K pathway currently in clinical trials, including the PI3K/mTOR dual inhibitor GDC-0980 that is in a phase II trial for endometrial cancer (NCT01455493). In this study, we set to examine the prevalence of overlapping mutational activation of the PI3K pathway with other pathways, such as MAPK. We also tested whether targeting different nodes of PI3K pathway, such as PI3K, AKT, or PI3K/mTOR could exert differential effects on endometrial cancer cells, and whether combination with a MEK inhibitor could provide an additional benefit in inhibiting endometrial cancer cell growth.

Alteration of oncogenes and tumor suppressor genes were profiled in 80 endometrial cancer samples by qRT-PCR, targeted deep sequencing, and IHC staining. Multiple PI3K inhibitors, including GDC-0941 (PI3K), GDC-0068 (AKT), GDC-0980 (PI3K/mTOR), and the MEK inhibitor GDC-0973 were tested in a panel of 27 endometrial cancer cell lines for their effects on cell growth. Cell signaling status at baseline and on-treatment was profiled by reverse phase protein array. Mutations and copy number variations of relevant oncogenes and tumor suppressor genes were examined in these cells by targeted deep sequencing.

In the 80 endometrial tumor tissues we profiled, there were multiple instances of PI3K pathway alteration including 31% PIK3CA mutations, 9% AKT1 mutations, 16% MET mutations, and 38% PTEN null. In addition, KRAS mutations significantly overlapped with PTEN null or PIK3CA mutation in the same specimen. Endometrial cancer cell lines had distinct patterns of sensitivity to inhibitors targeting different nodes of the PI3K pathway. Preliminary results showed that GDC-0068 was more effective in cell lines with PTEN mutations, while GDC-0941 had a greater effect on those with PIK3CA mutations, and the cell lines were broadly sensitive to GDC-0980. In spite of the widespread activation of the PI3K pathway in endometrial cancer cells, synergistic inhibition of cell growth was observed when GDC-0973 was combined with either GDC-0068 or GDC-0941 in most of the cell lines tested. We will seek to identify genomic and/or proteomic features that will allow better selection as to which node of the PI3K pathway to target, and when to combine with a MEK inhibitor.

Citation Format: Matthew J. Wongchenko, Yinghui Guan, Marie-Claire Wagle, Lisa Ryner, Shan Lu, Hartmut Koeppen, Garret Hampton, Mark Lackner, Yulei Wang, Yibing Yan. Sensitivity of endometrial cancer cells to inhibitors targeting different nodes of the PI3K pathway and their combination with a MEK inhibitor. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3479. doi:10.1158/1538-7445.AM2013-3479

Abstract 4567: Biomarker evaluation in phase I clinical trials of selective PI3K and PI3K/mTOR inhibitors

Background: The PI3K/Akt pathway is frequently activated in cancer by multiple mechanisms including PI3K activating mutations, PTEN loss, RTK activation, and other means. GDC-0941 and GDC-0980 are selective PI3K and dual PI3K/mTOR inhibitors, respectively, which are currently in phase II clinical development. Assays for candidate predictive and pharmacodynamic biomarkers were conducted on patient samples collected from phase I studies of GDC-0941 and GDC-0980. The purpose was to confirm pathway inhibition at tolerable doses, as well as look for association between anti-tumor activity and candidate predictive biomarkers.

Methods: Archival tumor tissue samples were analyzed using a 6 gene qPCR mutation assay (PIK3CA, EGFR, KRAS, BRAF, NRAS, AKT1), an immunohistochemistry assay for PTEN, and a fluorescence in situ hybridization (FISH) assay for PIK3CA. Select samples were analyzed for an expanded qPCR mutation panel and subjected to targeted next-generation sequencing (Illumina). For pharmacodynamic biomarker assays, pre- and post-treatment biopsies were collected from a subset of patients. In addition to previously described pS6 analysis, samples were analyzed for phospho-AKT, phospho-PRAS40, and CyclinD1 by immunohistochemistry.

Results: Predictive biomarker assays were conducted on over 200 samples from the phase I studies. Overall we found a prevalence of 7% PIK3CA mutations and 12% loss of PTEN in these samples. PIK3CA amplification was observed in several samples from ovarian cancer patients. Based on several means of evaluating tumor response (FDG-PET, RECIST, time on study), activity was seen at or below clinically relevant doses in several different tumor types, including breast, ovarian, and mesothelioma. We report here the predictive biomarker status in all patients from whom tissue was available, and analysis of the extent to which these alterations are associated clinical outcome, to the extent such associations can be determined from a phase I dose escalation study designed to look a safety and tolerability.

Conclusions: Pharmacodynamic assays confirmed effective pathway knockdown at safe and tolerated clinical doses of GDC-0941 and GDC-0980. Anti-tumor activity was observed in patients with PIK3CA mutations, as well as some patients whose tumors did not harbor pathway alterations. These data support patient stratification in phase II clinical studies to determine whether predictive biomarkers will be useful in identifying responsive patients.

Citation Format: Jill Spoerke, Rupal Desai, Rajesh Patel, Jill Fredrickson, Yulei Wang, Gallia Levy, Steve Gendreau, Jennifer Lauchle, Mika Derynck, Rajiv Raja, Hartmut Koeppen, Garret Hampton, Yibing Yan, Mark R. Lackner. Biomarker evaluation in phase I clinical trials of selective PI3K and PI3K/mTOR inhibitors. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4567. doi:10.1158/1538-7445.AM2013-4567

Abstract 3462: High-throughput qRT-PCR expression profiling of estrogen receptor positive breast tumors

The class I phosphatidylinositol 3’ kinases (PI3K) play a major role in proliferation and survival in a wide variety of human cancers, and activation of the PI3K pathway is thought to be an important driver in estrogen receptor positive (ER+) breast cancer. A key factor in successful development of drugs targeting this pathway will be development in appropriate molecular subsets. Important questions relevant to PI3K inhibitor development in ER+ breast cancers are whether these inhibitors will work equally well in luminal A compared to luminal B tumors, and whether gene expression signatures of pathway activation may have additional utility in patient stratification beyond PIK3CA mutation status alone.

The goal of this study was to develop a methodology for high throughput profiling of ER+ breast cancers, in order to enable molecular subtyping of patients enrolled in clinical studies. To accomplish this, we developed an analysis platform to measure the relative expression of 90 breast cancer and PI3K pathway specific genes in formalin-fixed paraffin-embedded (FFPE) tissue. The content for this panel consists of genes known to be important for epithelial-mesenchymal biology, proliferation rate, and transcriptional output of the PI3K pathway. The 96 assay panel (including 6 housekeeping genes) was developed on the Fluidigm Biomark microfluidics platform and was extensively validated using well-characterized breast cancer cell lines and FFPE breast cancer samples of known subtypes based on immunohistochemistry for HER2, ER, and PR. All assays showed high levels of inter-and intra-chip reproducibility and were sensitive on standard curves down to 3ng RNA input.

Using this method we were able to separate breast cancers into distinct molecular subtypes, as well as identify more proliferative luminal B type tumors. In addition, PIK3CA mutation status, a potential biomarker, was determined using a highly specific and sensitive qRT-PCR mutation assay, in order to allow comparison with the PI3K pathway activation signature. We extended these analyses to a small cohort of patient samples consisting of matched primary and metastatic tumor tissues, and report here the correlation of primary and matched metastatic ER+ breast cancer FFPE tumor samples at both the gene expression and mutational levels. We found that the majority of matched pairs were concordant for both mutation status and gene expression, though a subset did show differences. Future studies will examine the prognostic significance and clinical relevance of this gene signature.

Citation Format: Erica B. Schleifman, Rupal M. Desai, Jill Spoerke, Cheryl Victoria Wong, Ilma Abbas, Carol O'Brien, Garret Hampton, Timothy Wilson, Hartmut Koeppen, Rajesh Patel, Teiko Sumiyoshi, Ling Fu, Rachel Tam, Rajiv Raja, Mark Lackner. High-throughput qRT-PCR expression profiling of estrogen receptor positive breast tumors. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3462. doi:10.1158/1538-7445.AM2013-3462

Abstract 2849: Pharmacodynamic biomarkers of anti-PD-L1 activity in pre-clinical mouse tumor models

Programmed cell death 1 ligand 1 (PD-L1, CD274, B7-H1) is an immune checkpoint molecule expressed in various tissues, including multiple peripheral blood mononuclear cells and placenta. PD-L1 binds its receptor PD-1 on activated T cells to negatively regulate their function in both physiological and pathological conditions. PD-L1 also binds B7.1 (CD80), further down modulating immune responses. Importantly, numerous cancers resist T-cell mediated cytotoxic activity by over-expressing PD-L1.

The goal of this study was to identify pharmacodynamic biomarkers of response to agents blocking PD-L1/PD-1 pathway in pre-clinical models. CT-26 and MC-38 murine mouse tumor models were selected for this analysis, based on their PD-L1 expression and in-vivo sensitivity to anti-PD-L1 treatment. Tumors have been collected at various time points following treatment with an antibody blocking PD-L1 binding to PD-1 and B7.1. Subsequently, FACS, IHC, qPCR and a multiplex qPCR-based expression assay measuring a panel of ∼90 immune-related biomarkers have been used to evaluate changes in major immune cell subtypes and their activation status. We show that the intra-tumoral immune environment undergoes a time-sensitive dynamic modulation in response to PD-L1 pathway blockade, including an early and potent Th1 driven CTL response, as measured by relevant markers. Additionally, our findings show that targeting PD-L1 in pre-clinical tumor models can reinvigorate the host immune responses against the tumor and lead to T-cell mediated tumor killing. Our data also support identification of potential pharmacodynamic biomarkers that can be used to monitor activity of agents targeting the PD-L1 pathway in the clinic.

Citation Format: Marigold Boe, Mahrukh Huseni, Brittany Jiang, Hartmut Koeppen, Heather Maecker, Bryan Irving, Priti Hegde, Marcin Kowanetz. Pharmacodynamic biomarkers of anti-PD-L1 activity in pre-clinical mouse tumor models. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2849. doi:10.1158/1538-7445.AM2013-2849

Targeting activated Akt with GDC-0068, a novel selective Akt inhibitor that is efficacious in multiple tumor models

PURPOSE

We describe the preclinical pharmacology and antitumor activity of GDC-0068, a novel highly selective ATP-competitive pan-Akt inhibitor currently in clinical trials for the treatment of human cancers.

EXPERIMENTAL DESIGN

The effect of GDC-0068 on Akt signaling was characterized using specific biomarkers of the Akt pathway, and response to GDC-0068 was evaluated in human cancer cell lines and xenograft models with various genetic backgrounds, either as a single agent or in combination with chemotherapeutic agents.

RESULTS

GDC-0068 blocked Akt signaling both in cultured human cancer cell lines and in tumor xenograft models as evidenced by dose-dependent decrease in phosphorylation of downstream targets. Inhibition of Akt activity by GDC-0068 resulted in blockade of cell-cycle progression and reduced viability of cancer cell lines. Markers of Akt activation, including high-basal phospho-Akt levels, PTEN loss, and PIK3CA kinase domain mutations, correlate with sensitivity to GDC-0068. Isogenic PTEN knockout also sensitized MCF10A cells to GDC-0068. In multiple tumor xenograft models, oral administration of GDC-0068 resulted in antitumor activity ranging from tumor growth delay to regression. Consistent with the role of Akt in a survival pathway, GDC-0068 also enhanced antitumor activity of classic chemotherapeutic agents.

CONCLUSIONS

GDC-0068 is a highly selective, orally bioavailable Akt kinase inhibitor that shows pharmacodynamic inhibition of Akt signaling and robust antitumor activity in human cancer cells in vitro and in vivo. Our preclinical data provide a strong mechanistic rationale to evaluate GDC-0068 in cancers with activated Akt signaling.

P21-activated kinase 1 (PAK1) as a therapeutic target in BRAF wild-type melanoma

BACKGROUND

Although remarkable clinical response rates in melanoma have been observed using vemurafenib or dabrafenib in patients with tumors carrying oncogenic mutations in BRAF, a substantial unmet medical need remains for the subset of patients with wild-type BRAF tumors.

METHODS

To investigate the role of p21-activated kinases (PAKs) in melanoma, we determined PAK1 genomic copy number and protein expression for a panel of human melanoma tissues. PAK1 was inhibited in vitro and in vivo using RNA interference or PF-3758309 inhibitor treatment in a panel of melanoma cell lines with known BRAF and RAS (rat sarcoma) genotype to better understand its role in melanoma cell proliferation and migration. Tumorigenesis was assessed in vivo in female NCR nude mice and analyzed with cubic spline regression and area under the curve analyses. All statistical tests were two-sided.

RESULTS

Strong cytoplasmic PAK1 protein expression was prevalent in melanomas (27%) and negatively associated with activating mutation of the BRAF oncogene (P < .001). Focal copy number gain of PAK1 at 11q13 was also observed in 9% of melanomas (n = 87; copy number ≥ 2.5) and was mutually exclusive with BRAF mutation (P < .005). Selective PAK1 inhibition attenuated signaling through mitogen-activated protein kinase (MAPK) as well as cytoskeleton-regulating pathways to modulate the proliferation and migration of BRAF wild-type melanoma cells. Treatment of BRAF wild-type melanomas with PF-3758309 PAK inhibitor decreased tumor growth for SK-MEL23 and 537MEL xenografts (91% and 63% inhibition, respectively; P < .001) and MAPK pathway activation in vivo.

CONCLUSIONS

Taken together, our results provide evidence for a functional role of PAK1 in BRAF wild-type melanoma and therapeutic use of PAK inhibitors in this indication.

Evaluation of PTEN status in circulating tumor cells (CTCs) and matched tumor tissue from patients with castrate-resistant prostate cancer (CRPC)

62

Background: PTEN loss occurs frequently in prostate cancer and may trigger progression to CRPC through activation of the PI3K/AKT pathway. A blood-based assay that determines PTEN status in CRPC patients could enable informed treatment decisions such as the use of a PI3K-targeted therapy. We evaluated PTEN status in archived tissue, metastatic bone biopsies, and CTCs from CRPC patients. Here we report the results of PTEN evaluation in CTCs from 42 CRPC patients and matched tissue from 6 patients with more underway. Methods: Nucleated cells from CRPC patient blood were plated onto glass slides and subjected to IF staining and CTC identification by high-speed fluorescent scanners at Epic Sciences. CTCs were identified as CK+/CD45- cells with intact DAPI nuclei, and samples with ≥5 CTCs per 2 slides (74%) were then tested for PTEN by FISH. Partial loss was defined as a decrease in PTEN copies (PTEN < CEP10) and total loss as zero PTEN copies. PTEN IHC in tissue was stained using CST clone 138G6 and H-scores ≤ 200 counted as loss. Results: Partial or total loss of PTEN by FISH was observed in 15 of 31 patients (48%) by CTC analysis. Changes in ploidy were frequently observed and broad heterogeneity seen both within and between patients. Weighted across patients, the most frequently observed abnormal genotypes in CTCs were 2 CEP10/0 PTEN (total loss, diploid, 5.8%), 3 CEP10/0 PTEN (total loss, triploid, 4.5%), and 3 CEP10/3 PTEN (PTEN-normal, triploid, 4.2%). These genotypes were not observed in over 1,000 white blood cells evaluated evenly across 31 patients, demonstrating that cells identified as CTCs on the Epic platform show malignant features not observed in normal cells. PTEN loss was detected by IHC in 6 of 8 (75%) archived patient samples and 7 of 8 (87%) of matched bone biopsies. Where CTCs were available (6 cases), PTEN status was correctly determined as lost in 4 cases, normal in 1 case and borderline in one case. Conclusions: Our results illustrate the high percentage of PTEN loss in CRPC patients and the potential for using CTCs as a non-invasive, real-time biopsy to determine a patient’s PTEN status. PTEN status will be determined using these assays in an upcoming AKT inhibitor Phase II trial.

Abstract P4-07-01: The Class I Selective PI3K Inhibitor GDC-0941 Enhances the Efficacy of Docetaxel in Human Breast Cancer Models by Increasing the Rate of Apoptosis

Docetaxel (DTX) is commonly used as a front-line treatment option for breast cancer but many patients ultimately relapse and succumb to disease progression. Phosphatidylinositol 3-kinases (PI3K) are lipid kinases that regulate breast tumor cell growth, migration and survival. Given that phosphatidylinositol 3-kinase (PI3K) is frequently activated in breast cancer and induces chemo-resistance, it is an attractive target for combination therapy with standard of care drugs such as DTX. The current study was intended to determine if GDC-0941, an orally bioavailable class I selective PI3K inhibitor, enhances the anti-tumor activity of DTX in human breast cancer models in vitro and in vivo. A panel of 25 breast tumor cell lines representing luminal, HER2+ and basal sub-types were treated with GDC-0941, DTX or the combination of both drugs and assayed for cellular viability, modulation of PI3K pathway markers and apoptosis induction. The combination of GDC-0941 and DTX decreased the cellular viability of breast tumor cell lines in vitro but with variable drug synergy. The addition of both drugs resulted in stronger synergistic effects in a sub-set of tumor cell lines that was not predicted by breast cancer sub-type or mutations within the PI3K pathway. Human xenografts of breast cancer cell lines and patient-derived tumors were utilized to assess efficacy of GDC-0941 and DTX in vivo. In these models, the best combination efficacy was detected when the two drugs were dosed within 1 hour of each other. We also observed that GDC-0941 increased the rate of apoptosis in cells arrested in mitosis upon co-treatment with DTX. Our data provides a preclinical rationale for evaluating GDC-0941 in combination with DTX for breast cancer treatment.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P4-07-01.

Phosphoinositide 3-kinase (PI3K) pathway alterations are associated with histologic subtypes and are predictive of sensitivity to PI3K inhibitors in lung cancer preclinical models

PURPOSE

Class 1 phosphatidylinositol 3-kinase (PI3K) plays a major role in cell proliferation and survival in a wide variety of human cancers. Here, we investigated biomarker strategies for PI3K pathway inhibitors in non-small-cell lung cancer (NSCLC).

EXPERIMENTAL DESIGN

Molecular profiling for candidate PI3K predictive biomarkers was conducted on a collection of NSCLC tumor samples. Assays included comparative genomic hybridization, reverse-transcription polymerase chain reaction gene expression, mutation detection for PIK3CA and other oncogenes, PTEN immunohistochemistry, and FISH for PIK3CA copy number. In addition, a panel of NSCLC cell lines characterized for alterations in the PI3K pathway was screened with PI3K and dual PI3K/mTOR inhibitors to assess the preclinical predictive value of candidate biomarkers.

RESULTS

PIK3CA amplification was detected in 37% of squamous tumors and 5% of adenocarcinomas, whereas PIK3CA mutations were found in 9% of squamous and 0% of adenocarcinomas. Total loss of PTEN immunostaining was found in 21% of squamous tumors and 4% of adenocarcinomas. Cell lines harboring pathway alterations (receptor tyrosine kinase activation, PI3K mutation or amplification, and PTEN loss) were exquisitely sensitive to the PI3K inhibitor GDC-0941. A dual PI3K/mTOR inhibitor had broader activity across the cell line panel and in tumor xenografts. The combination of GDC-0941 with paclitaxel, erlotinib, or a mitogen-activated protein-extracellular signal-regulated kinase inhibitor had greater effects on cell viability than PI3K inhibition alone.

CONCLUSIONS

Candidate biomarkers for PI3K inhibitors have predictive value in preclinical models and show histology-specific alterations in primary tumors, suggesting that distinct biomarker strategies may be required in squamous compared with nonsquamous NSCLC patient populations.

Targeting the PI3K pathway in the brain--efficacy of a PI3K inhibitor optimized to cross the blood-brain barrier

PURPOSE

Glioblastoma (GBM), the most common primary brain tumor in adults, presents a high frequency of alteration in the PI3K pathway. Our objectives were to identify a dual PI3K/mTOR inhibitor optimized to cross the blood-brain barrier (BBB) and characterize its brain penetration, pathway modulation in the brain and efficacy in orthotopic xenograft models of GBM.

EXPERIMENTAL DESIGN

Physicochemical properties of PI3K inhibitors were optimized using in silico tools, leading to the identification of GNE-317. This compound was tested in cells overexpressing P-glycoprotein (P-gp) or breast cancer resistance protein (BCRP). Following administration to mice, GNE-317 plasma and brain concentrations were determined, and phosphorylated biomarkers (pAkt, p4EBP1, and pS6) were measured to assess PI3K pathway suppression in the brain. GNE-317 efficacy was evaluated in the U87, GS2, and GBM10 orthotopic models of GBM.

RESULTS

GNE-317 was identified as having physicochemical properties predictive of low efflux by P-gp and BCRP. Studies in transfected MDCK cells showed that GNE-317 was not a substrate of either transporter. GNE-317 markedly inhibited the PI3K pathway in mouse brain, causing 40% to 90% suppression of the pAkt and pS6 signals up to 6-hour postdose. GNE-317 was efficacious in the U87, GS2, and GBM10 orthotopic models, achieving tumor growth inhibition of 90% and 50%, and survival benefit, respectively.

CONCLUSIONS

These results indicated that specific optimization of PI3K inhibitors to cross the BBB led to potent suppression of the PI3K pathway in healthy brain. The efficacy of GNE-317 in 3 intracranial models of GBM suggested that this compound could be effective in the treatment of GBM.