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610 Background: This large randomized open-label phase 2 trial compared the efficacy and safety of Neratinib (N), the irreversible pan-HER tyrosine kinase inhibitor, + Paclitaxel (P) vs Trastuzumab...

The Drug-Gene Interaction database (DGIdb) mines existing resources that generate hypotheses about how mutated genes might be targeted therapeutically or prioritized for drug development. It provides an interface for searching lists of genes against a compendium of drug-gene interactions and potentially 'druggable' genes. DGIdb can be accessed at http://dgidb.org/.

Background: Breast cancer genome sequencing projects, performed by the genome sequencing centers in the U.S., Canada, and the U.K., are elucidating the somatic mutations and other genomic alterations that occur in human breast cancer. These studies recently identified somatic HER2 mutations in breast cancers lacking HER2 gene amplification. Results: Compilation of data from seven sequencing studies documented 22 patients with somatic HER2 mutations. These mutations clustered in three regions. The first cluster was at amino acid (aa) 309–310 (exon 8), located in the extracellular domain. These aa residues form part of the HER2 dimerization interface. The second cluster was at aa 755–781, located in the kinase domain (exons 19–20). This was the most common location for HER2 mutations, with 17 out of 22 patients having somatic mutations here. The third region was at aa 835–896, also in the kinase domain (exons 21–22). Using multiple experimental approaches (cell line experiments, in vitro kinase assays, protein structure modeling, and xenograft experiments), we tested seven of these HER2 mutations and showed that 4 of them are activating mutations that are sensitive to lapatinib and trastuzumab. Another 2 mutations were found to be lapatinib resistant and we determined their sensitivity to neratinib, canertinib, and gefitinib. Conclusions: These findings biologically validate somatic HER2 mutations as good targets for breast cancer treatment, but the appropriate choice of targeted drug is dependent on the precise mutation present. This study is among the first to functionally characterize mutations identified by breast cancer genome sequencing. A prospective, multi-institutional clinical trial has been launched to screen for HER2 mutation positive patients and determine the clinical outcome of treatment with HER2 targeted drugs. Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr S5-6.

The Reaper (Rpr) gene encodes a 65-amino acid protein that induces apoptosis in Drosophila by an unknown mechanism. A previous study reported that Rpr expression induced generation of the lipid second messenger ceramide and through use of the peptide caspase inhibitor N-benzyloxycarbonyl-VAD-fluoromethylketone(zVAD.fmk ) ordered ceramide generation downstream of caspases in SL2 cells (Pronk, G. J. , Ramer, K., Amiri, P., and Williams, L. T. (1996) Science 271, 808-810). The present study re-evaluates these events in SL2 cells transfected with cDNA for Rpr, with or without the baculovirus caspase inhibitor p35, under the control of the metallothionein promoter. Following copper addition, Rpr protein was detected at 1.5 h and maximal at 2.5 h. Ceramide generation and caspase activation occurred nearly simultaneously, each detectable at 2-2.5 h and maximal at 6 h. Ceramide levels increased from a base line of 5 pmol/nmol lipid phosphorus to a maximum of 10 pmol/nmol lipid phosphorus. Identical increases in ceramide were detected using the enzymatic 1,2-diacylglycerol kinase assay or the non-enzymatic o-phthalaldehyde derivatization high pressure liquid chromatography assay. In contrast, diacylglycerol levels were not increased by Rpr expression. Apoptosis, first detected at 4 h, was maximal at 16 h. Co-expression of p35 did not affect Rpr-induced ceramide generation, whereas caspase activation and apoptosis were abolished. In contrast, zVAD.fmk inhibited ceramide generation and apoptosis. These data show that Rpr-induced ceramide generation is upstream or independent of p35-inhibitable caspases and demonstrate differences in the actions of peptide and p35 caspase inhibitors.

A limitation of recent genome studies is that they have almost exclusively focused on early stage untreated samples. Consequently the genomic landscape of advanced and treatment-resistant disease is poorly documented, even though Stage 4 patients stand to benefit most from new therapeutic approaches. To address this issue we developed a panel of patient-derived xenografts (PDX) from Stage 3 and 4 patients with treatment-resistant disease to create a platform for detailed molecular and pharmacological investigation. Recently we reported a whole genome sequencing study of a single example of a breast cancer primary, brain metastasis and PDX “trio” demonstrating that the PDX model efficiently captured almost all of the genome-wide variants observed in the tumor and was enriched for mutations present in the metastatic sample (Ding, Ellis et al., Nature 2010). We now extend these findings by conducting massively parallel sequencing of 13 additional PDX models from a diverse set of locally- advanced or Stage 4 breast cancers, all of whom subsequently died from their disease. Structural variants (deletions, inversions and translocations) were remarkably stable and although new single nucleotide variants were observed post-engraftment, most were either non-coding or not expressed and only one had established functionality (K-RAS). PDX models are therefore high-fidelity genomic models for the biological and pharmacological study of complex, often tumor-unique somatic events responsible for lethal drug-resistant advanced breast cancer. Citation Format: Shunqiang Li, Dong Shen, Ding Li, Tao Yu, Jingqin Luo, Jeremy Hoog, Joshua McMichael, Chris Miller, Dave Larson, Ron Bose, Bob Fulton, Rick Wilson, Charles Perou, Elaine Mardis, Matthew Ellis. Patient derived xenografts as high-fidelity genomic models for advanced breast cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-236. doi:10.1158/1538-7445.AM2013-LB-236

Deeper understanding the mechanisms by which luminal-type breast cancer develops resistance to endocrine therapy and development of novel strategies to treat these patients requires model systems recapitulate human breast cancer as accurately as possible. An increasing body of work suggests patient derived xenografts (PDX) may represent an informative model for development of novel therapeutics. We therefore established seven xenograft tumor lines from late-stage breast cancer patients with estrogen positive (ER+) disease. To date five ER+ PDX lines have been tested for responses to estradiol treatment in overiectomized NOD/SCID mice. Three showed estradiol independent-growth, one estrogen-stimulated growth and in one estradiol-induced a regression. These patterns mimicked the clinical phenotypes of each patient, tracking survival and responses to serial endocrine treatments. To define new mechanisms for resistance, whole genome DNA sequencing, RNA sequencing and Reverse Phase Protein Assay analysis was conducted. These studies identified an ESR1/YAP1 balanced translocation in a PDX model and tumor of origin showing low levels of ER, paradoxical high level expression form luminal genes and extreme ET resistance. The ESR1 YAP1 fusion maintained the N terminal DNA binding motif of ESR1, but the hormone binding and AF2 motifs were replaced with the C terminal transactivation domain of YAP1. Expression ESR1 YAP1 in ER+ breast cancer models down-regulated ER and induced estrogen independent growth. PDX endocrine phenotypes parallel tumor of origin responses to endocrine therapy and revel novel mechanism for endocrine therapy resistance. Citation Format: Matthew J. Ellis, Shunqiang Li, Dong Shen, Li Ding, Robert Crowder, Jeiya Shao, Rodrigo Goncalves, Yu Tao, Jingqin Luo, Aleix Prat, Wenbin Liu, Ana Maria Gonzalez-Angulo, Shuying Liu, Joshua F. McMichael, Chris Miller, Dave Larson, Robert S. Fulton, Tom Mooney, Jeremy Hoog, Li Lin, Therese Giuntoli, Caroline Bumb, Crystal Cooper, Rebecca Aft, Robert T. Kitchens, Stephen N. Johnson, Chanpheng Phommaly, Megha Shiyam Kavuri, Katherine DeSchryver, Austin Lin, YiYu Dong, Cynthia X. Ma, Timothy Pluard, Michael Naughton, Ron Bose, Rama Suresh, Reida G. McDowell, Loren Michel, Richard Wilson, Shaomeng Wang, Christopher Maher, Gordon B. Mills, Charles Perou, Elaine R. Mardis. Patient-derived xenografts from advanced luminal-type breast cancer: insights into endocrine therapy resistance. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-265. doi:10.1158/1538-7445.AM2013-LB-265

503 Background: To correlate clinical features of estrogen receptor positive breast cancer with somatic mutations, massively parallel sequencing (MPS) was applied to tumor and normal DNAs accrued from patients treated with neoadjuvant aromatase inhibitors (AI). Methods: MPS was applied to 77 baseline tumor biopsy samples from the preoperative letrozole trial (JACS 2009: 208, 906) and the Z1031 trial (JCO 2011: 29, 2342) followed by targeted sequencing in another 240 trial samples. Standard statistical approaches were used to compare mutation status and clinical parameters and pathway-based correlation was used to assess interactions between signaling perturbations induced by gene mutations and response to neoadjuvant AI. Results: Eighteen genes were significantly mutated above background. Aside from PIK3CA mutations, the list is dominated by loss-of-function mutations in tumor suppressor genes. Five (RUNX1, CBFP, MYH9, MLL3 and SF3B1) have been previously linked to benign and malignant hematopoietic disorders. Clinical correlation revealed that TP53 mutation was associated with PAM50 LumB status, high-grade histology and high proliferation rates whereas loss-of-function mutations in MAP3K1 associate with PAM50 lumA status, low proliferation rates, and low grade histology. Mutations in GATA3 were associated with greater suppression of proliferation upon AI treatment suggesting mutGATA3 may predict endocrine response. Notably, mutations in MAP3K1 were more common in PIK3CA mutant cases, suggesting cooperation. Pathway analysis demonstrated that rare MAP2K4 mutations produce similar pathway perturbations as MAP3K1 mutation, a logical finding since MAP2K4 is a substrate for MAP3K1. Signaling network patterns driven by lncRNA MALAT1 mutations were associated with multiple poor clinical outcome features. Rare mutations in druggable kinases included two in the kinase domain of HER2. Conclusions: Tumor heterogeneity in luminal-type breast cancer is driven by specific patterns of somatic mutations, however most druggable or potentially prognostic mutations are infrequent. Prospective clinical trials based on these findings will require comprehensive genome sequencing approaches and large scale investigations.

Background: Estrogen receptors are over-expressed in around 70% of breast cancer cases. The genetic changes that occur during aromatase inhibitor (AI) treatment are not well understood and may differ depending upon the patient's response phenotype. Methods: We performed whole genome sequencing (WGS) of matched blood, pre-treatment, and post-treatment biopsy samples from 22 estrogen receptor positive breast cancer patients treated with neoadjuvant aromatase inhibitors. For 5 cases, we performed the whole genome sequencing (WGS) on patients’ matched normal, two pre AI-treatment, and two post AI-treatment DNA isolates from biopsy samples. We validated all putative coding and non-coding somatic mutations using deep sequencing. By comparing the validated somatic mutations from pre- and post- AI treatment biopsy samples, we were able to determine the alterations in the tumor genomes. In every case we defined the clonal architecture of each pair of pre-treatment and post-treatment biopsy samples by comparing the variant allele frequencies from thousands of validated somatic mutations. Results: Comparisons of the two pre AI-treatment biopsy samples from the same patient indicates that the variant allele frequencies of mutations showed high concordances in all 5 cases, 0.74 to 0.95 range of correlation coefficient. Only a small percentage of somatic mutations were detected in one pre-treatment sample and not the other (4.65% overall). In comparing the somatic variations between pre-treatment and matched post-treatment biopsy samples in 22 cases, we found that patients with good clinical response to AI treatment retained known driver mutations only in their pre-treatment tumors. Conversely, those patients with poor clinical response presented new driver mutations in their post-treatment samples. Furthermore, the variant allele frequency for most mutated genes decreased in post AI treatment samples for patients with good AI treatment response; on the contrary, the variant allele frequency increased for patients with poor clinical response. Conclusions: From WGS of matched normal, pre-treatment, and post-treatment biopsy samples, we identified new driver genes mutated in patients with poor clinical response, while patients with good clinical response had lost mutated driver genes in their post-treatment biopsy samples. The genetic landscape revealed by WGS of pre-treatment and post-treatment biopsy samples reveals mutational repertoires are remodeled by AI therapy. This finding suggests deep sequencing of AI treated samples will be necessary to reveal the complete complement of mutations present in a patient's tumor. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-423. doi:1538-7445.AM2012-LB-423

Her2 is a receptor tyrosine kinase that is overexpressed in approximately 20-30% of human breast cancers and affects clinical prognosis and outcome of these cancers. Treatment of Her2-positive breast cancer with the monoclonal antibody, trastuzumab, has improved the outcomes and prognosis for patients with this breast cancer subtype. However, development of resistance to trastuzumab is a major clinical problem in metastatic Her2-positive breast cancer. Many of the known mechanisms of trastuzumab resistance cause changes in protein phosphorylation patterns and therefore we have employed quantitative phosphoproteomics to further study trastuzumab resistance. Quantitative phosphoproteomics is a powerful method to comparatively identify phosphorylated proteins between different samples. Using electrospray tandem-mass spectrometry coupled with immunoaffinity purification and titanium dioxide (TiO2) phosphoenrichment, we wanted to identify differentially phosphorylated proteins in a pair of trastuzumab sensitive and resistant cells. We used stable isotope labeling of amino acids in cell culture (SILAC) to obtain quantitative information on the proteins identified by mass spectrometry. We have obtained quantitative data on two trastuzumab sensitive and resistant pairs of Her2 overexpressing human breast cancer cell lines (BT474 and SKBR3). 275 proteins were identified in the phosphoenriched fraction from the SKBR3 pair with 83 proteins reporting a ratio. 769 proteins were identified in the phosphoenriched fraction from the BT474 pair with 683 proteins reporting a ratio. Treatment of the trastuzumab resistant cells with Her2 siRNA drastically resulted in cell death indicating the sustained dependence of these cells on Her2 despite the resistance to Her2 targeted therapy. RNAi experiments, in combination with trastuzumab exposure, of candidate proteins expressing an increase in phosphorylation will be tested further to determine if trastuzumab resistance can be reversed. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 5126. doi:10.1158/1538-7445.AM2011-5126

Background: Endocrine-therapy resistant HER2 negative luminal-type breast cancer is the commonest cause of breast cancer death but the molecular basis for aggressive clinical behavior is poorly understood. Endocrine therapy resistant cases can be identified early in the course of the disease though the persistant expression of the cell cycle biomarker Ki67 despite neoadjuvant treatment with a potent aromatase inhibitor (JNCI 2008:100;159–61). Methods: Massively parallel DNA sequencing (Nature 2010; 464:999–1005) was applied to samples from two neoadjuvant endocrine trials (“POL” J Am Coll Surg. 2009; 208: 906–14 and “ACOSOG Z1031” JCO in press) to define the whole genome sequence of 50 luminal-type breast cancers (PAM50 definition, JCO 2009;27:1160–7) with an average 30 fold coverage. Of these, 24 were defined as resistant (surgical specimen Ki67 > 10%) and 26 sensitive (Ki67 ≤ 10%). Approximately 10 trillion base pairs of sequence were analyzed. Putative somatic mutations were confirmed through targeted sequence analysis and the absence of the variant in matched normal DNA. Results: The mean number of single nucleotide non-silent variants (SNV) and small deletions (indels) was greater in the resistant group (49 per case) than sensitive cases (23) (p=0.02). The significantly mutated gene list included PIK3CA, TP53, ATR, RUNX1, MYST3, PRSS8, ZNHIT2 and MAP3K1. A large number of structural variations have also been identified with greater than 800 events from 28 patients orthogonally validated to date, mostly deletions but also translocations, although no recurrent translocations have been seen. About 25% of these deletions were paired with an SNV suggesting multiple novel double-hit tumor suppressor events. Extension analysis in 121 POL/Z1031 samples produced the following mutation incidence data PIK3CA (43%), TP53 (15.2%) and MAP3K1 (9.3%). The MAP3K1 mutations were most frequently frame-shift or nonsense, disrupting the C terminal kinase domain, a logical finding in a kinase activated by caspase 7 to promote apoptosis. Only 1 MAP3K1 mutation was observed in 60 basal-like breast cancers (luminal versus basal MAP3K1 mutation frequency p=0.04). Conclusions: MAP3K1is a novel breast cancer tumor suppressor gene more frequently lost in luminal-type than basal-like breast cancer. Further data analysis will be presented including pathway analyses that place less common mutations into a variety of cancer pathways, including phosphoinositol-3-kinase signaling, cell cycle regulation, metabolism, mitotic spindle regulation and DNA mismatch repair. These analyses suggest a classification of the disease that is not based on individual gene abnormalities but common cancer pathway activation events that ultimately determine outcome for patients with luminal-type disease. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr LB-87. doi:10.1158/1538-7445.AM2011-LB-87

Her4 (ErbB-4) and Her2/neu (ErbB-2) are receptor tyrosine kinases belonging to the Epidermal Growth Factor Receptor (EGFR) family. Crystal structures of EGFR and Her4 kinase domains have demonstrated kinase dimerization and activation through an allosteric mechanism. The kinase domains form an asymmetric dimer, where the C-lobe surface of one monomer contacts the N-lobe of the other monomer. In vitro studies of EGFR tyrosine kinase dimerization and activation were previously reported using a nickel-chelating lipid - liposome system, and we now demonstrate this system can be broadly applied to all other members of the EGFR family. Polyhistidine tagged-Her4, Her2/neu, and Her3 kinase domains are bound to these nickel-chelating lipid containing liposomes and are brought to a high local concentration, mimicking what happens to the full-length receptors in vivo following ligand binding. Addition of Nickel-liposomes to Her4 kinase domain results in a 40-fold activation in kinase specific activity and a marked enhancement in C-terminal tail autophosphorylation. Activation of Her4 shows a sigmoidal dependence on kinase concentration, consistent with a cooperative process that requires kinase dimerization. Her2/neu kinase activity is also activated by Nickel-liposomes, and further increases in Her2/neu activity are achieved by heterodimerization with either Her3 or Her4. The ability of Her3 and Her4 to heterodimerize and activate other family members is studied in vitro. Her3 kinase domain readily activates Her2/neu but is a poor activator of Her4, which differs from the prediction made by the asymmetric dimer model, and suggests that the mode of dimerization of Her3 needs to be further studied. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3122.

The Saccharomyces cerevisiae SIS2 gene was identified by its ability, when present on a high copy number plasmid, to increase dramatically the growth rate of sit4 mutants. SIT4 encodes a type 2A-related protein phosphatase that is required in late G1 for normal G1 cyclin expression and for bud initiation. Overexpression of SIS2, which contains an extremely acidic carboxyl terminal region, stimulated the rate of CLN1, CLN2, SWI4 and CLB5 expression in sit4 mutants. Also, overexpression of SIS2 in a CLN1 cln2 cln3 strain stimulated the growth rate and the rate of CLN1 and CLB5 RNA accumulation during late G1. The SIS2 protein fractionated with nuclei and was released from the nuclear fraction by treatment with either DNase I or micrococcal nuclease, but not by RNase A. This result, combined with the finding that overexpression of SIS2 is extremely to a strain containing lower than normal levels of histones H2A and H2B, suggests that SIS2 might function to stimulate transcription via an interaction with chromatin.

We analysed primary breast cancers by genomic DNA copy number arrays, DNA methylation, exome sequencing, messenger RNA arrays, microRNA sequencing and reverse-phase protein arrays. Our ability to integrate information across platforms provided key insights into previously defined gene expression subtypes and demonstrated the existence of four main breast cancer classes when combining data from five platforms, each of which shows significant molecular heterogeneity. Somatic mutations in only three genes (TP53, PIK3CA and GATA3) occurred at >10% incidence across all breast cancers; however, there were numerous subtype-associated and novel gene mutations including the enrichment of specific mutations in GATA3, PIK3CA and MAP3K1 with the luminal A subtype. We identified two novel protein-expression-defined subgroups, possibly produced by stromal/microenvironmental elements, and integrated analyses identified specific signalling pathways dominant in each molecular subtype including a HER2/phosphorylated HER2/EGFR/phosphorylated EGFR signature within the HER2-enriched expression subtype. Comparison of basal-like breast tumours with high-grade serous ovarian tumours showed many molecular commonalities, indicating a related aetiology and similar therapeutic opportunities. The biological finding of the four main breast cancer subtypes caused by different subsets of genetic and epigenetic abnormalities raises the hypothesis that much of the clinically observable plasticity and heterogeneity occurs within, and not across, these major biological subtypes of breast cancer.

SummaryTo characterize patient-derived xenografts (PDXs) for functional studies, we made whole-genome comparisons with originating breast cancers representative of the major intrinsic subtypes. Structural and copy number aberrations were found to be retained with high fidelity. However, at the single-nucleotide level, variable numbers of PDX-specific somatic events were documented, although they were only rarely functionally significant. Variant allele frequencies were often preserved in the PDXs, demonstrating that clonal representation can be transplantable. Estrogen-receptor-positive PDXs were associated with ESR1 ligand-binding-domain mutations, gene amplification, or an ESR1/YAP1 translocation. These events produced different endocrine-therapy-response phenotypes in human, cell line, and PDX endocrine-response studies. Hence, deeply sequenced PDX models are an important resource for the search for genome-forward treatment options and capture endocrine-drug-resistance etiologies that are not observed in standard cell lines. The originating tumor genome provides a benchmark for assessing genetic drift and clonal representation after transplantation.