Abstract LB-122: Combinations of SHP2 inhibitor to overcome RAS activation by receptor tyrosine kinases in response to ERK inhibition

Introduction: The RTK-RAS-MAPK pathway is frequently activated in cancers due to a variety of mechanisms including mutations or amplifications in RTK, KRAS or BRAF. The effectiveness of inhibitors targeting those oncogenic drivers is often limited by the pathway feedback activation originated at the RTK level in response to ERK inhibition. The non-receptor protein tyrosine phosphatase SHP2 mediates RAS activation downstream of various receptor tyrosine kinases. Potent and selective allosteric SHP2 inhibitors such as TNO155 are in clinical development and offer an appealing one-size-fits-all approach to overcome RTK-mediated feedback activation of RAS and enhance the efficacy of inhibitors targeting RTK, BRAF or KRASG12C. We sought to study the combination efficacy and mechanism in pre-clinical models for prioritization in clinical trials. Experimental procedures: The combination efficacy and synergy of TNO155 with EGF816 (a 3rd generation EGFR inhibitor), dabrafenib+trametinib or a tool KRAS G12C inhibitor (G12Ci) were respectively assessed in a number of EGFR mutant lung cancer models, BRAFV600E colorectal cancer models and KRASG12C lung and colorectal cancer models. The effect of the combinations on ERK inhibition was also studied. Results: TNO155 has varying single agent activity in vitro in EGFR mutant lung cancer cell lines and is not affected by clinically relevant resistance mechanisms to EGFR inhibitors such as secondary mutations in EGFR (T790M and C797S) or MET amplification. In addition, the combination of TNO155 and EGF816 is synergistic across cell lines, coincident with sustained ERK inhibition. In BRAFV600E colorectal cancer cell lines with feedback activation of EGFR, MET or FGFR respectively in response to treatment with dabrafenib+trametinib, TNO155 synergistically enhanced the efficacy of dabrafenib+trametinib in all three cell lines, phenocopying respective RTK inhibitors. In KRASG12C lung cancer cell lines, quick rebound of p-ERK was observed as early as 24 hour post treatment with G12Ci and cannot be blocked by increasing concentrations of G12Ci, suggesting feedback activation of wild-type KRAS or other RAS isoforms. In contrast, TNO155 effectively blocked the p-ERK rebound and enhanced the efficacy of G12Ci. Similar observations were made in KRASG12C colorectal cancer cell lines. Conclusions: Our findings suggest that SHP2 inhibition is an effective strategy to block the feedback activation of wild type and G12C KRAS, as well as NRAS and HRAS, by a variety of RTKs, in response to ERK inhibition. Given the mutant selective properties of those inhibitors we studied, the tolerability of their combinations with TNO155 is highly expected. Our data provide pre-clinical rationale to explore those TNO155 combinations in the corresponding cancer indications in clinic.

Citation Format: Huaixiang Hao, Chen Liu, Hongyun Wang, Hengyu Lu, Scott Delach, Matthew LaMarche, Jeffrey Engelman, Peter Hammerman, Giordano Caponigro, Susan Moody, Morvarid Mohseni. Combinations of SHP2 inhibitor to overcome RAS activation by receptor tyrosine kinases in response to ERK inhibition [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr LB-122.

Phase II Study of AZD4547 in Patients With Tumors Harboring Aberrations in the FGFR Pathway: Results From the NCI-MATCH Trial (EAY131) Subprotocol W

PURPOSE

NCI-MATCH is a nationwide, histology-agnostic, signal-finding, molecular profile-driven trial for patients with refractory cancers, lymphomas, or myelomas. Patients with tumors harboring actionable aberration(s) in fibroblast growth factor receptor (FGFR) 1-3 were treated with AZD4547, an oral FGFR1-3 inhibitor.

METHODS

Patients' tumors were screened by next-generation sequencing for predefined FGFR amplification, activating mutations, or fusions. Patients were treated with AZD4547, 80 mg orally twice daily until progression of disease or drug intolerance. A response rate of 16% was considered promising.

RESULTS

Between July 2016 and June 2017, 70 patients were assigned and 48 received protocol therapy and are eligible for analysis. Patients' tumors harbored FGFR1 or FGFR2 amplification (n = 20), FGFR2 or FGFR3 single-nucleotide variants (n = 19), or FGFR1 or FGFR3 fusions (n = 9). The most common primary tumors were breast (33.3%), urothelial (12.5%), and cervical cancer (10.4%).Grade 3 adverse events were consistent with those described in previous clinical trials. Confirmed partial responses were seen in 8% (90% CI, 3% to 18%) and were observed only in patients whose tumors harbored FGFR1-3 point mutations or fusions. Stable disease was observed in 37.5% (90% CI, 25.8% to 50.4%). The median progression-free survival (PFS) was 3.4 months, and the 6-month PFS rate was 15% (90% CI, 8% to 31%). For patients with tumors harboring FGFR fusions, the response rate was 22% (90% CI, 4.1% to 55%), and 6-month PFS rate was 56% (90% CI, 31% to 100%).

CONCLUSION

Preliminary signals of activity appeared to be limited to cancers harboring FGFR activating mutations and fusions, although AZD4547 did not meet the primary end point. Different FGFR somatic alterations may confer different levels of signaling potency and/or oncogene dependence.

Loss of PTEN Is Associated with Resistance to Anti-PD-1 Checkpoint Blockade Therapy in Metastatic Uterine Leiomyosarcoma

Response to immune checkpoint blockade in mesenchymal tumors is poorly characterized, but immunogenomic dissection of these cancers could inform immunotherapy mediators. We identified a treatment-naive patient who has metastatic uterine leiomyosarcoma and has experienced complete tumor remission for >2 years on anti-PD-1 (pembrolizumab) monotherapy. We analyzed the primary tumor, the sole treatment-resistant metastasis, and germline tissue to explore mechanisms of immunotherapy sensitivity and resistance. Both tumors stained diffusely for PD-L2 and showed sparse PD-L1 staining. PD-1⁺ cell infiltration significantly decreased in the resistant tumor (p = 0.039). Genomically, the treatment-resistant tumor uniquely harbored biallelic PTEN loss and had reduced expression of two neoantigens that demonstrated strong immunoreactivity with patient T cells in vitro, suggesting long-lasting immunological memory. In this near-complete response to PD-1 blockade in a mesenchymal tumor, we identified PTEN mutations and reduced expression of genes encoding neoantigens as potential mediators of resistance to immune checkpoint therapy.

Abstract 3682: Synergistic immunostimulatory effects and therapeutic benefit of combined histone deacetylase and bromodomain inhibition in non-small cell lung cancer

Effective therapies for non-small cell lung cancer (NSCLC) remain challenging despite an increasingly comprehensive understanding of somatically altered oncogenic pathways. It is now clear that therapeutic agents with potential to impact the tumor immune microenvironment potentiate immune-orchestrated therapeutic benefit. This study evaluated the immunoregulatory properties of two classes of drugs that modulate the epigenome, histone deacetylase (HDAC) and bromodomain inhibitors with a focus on key cell subsets that are engaged in an immune response. By evaluating human peripheral blood and NSCLC tumors, we show that the selective HDAC6 inhibitor ricolinostat promotes phenotypic changes associated with enhanced T-cell priming and function of antigen presenting cells. The bromodomain inhibitor JQ1 attenuated CD4+Foxp3+ T regulatory cell suppressive function and synergized with ricolinostat to facilitate immune-mediated tumor growth arrest, leading to prolonged survival of mice with lung adenocarcinomas. Collectively, our findings highlight immunomodulatory effects of two epigenetic modifiers that together promote T-cell-mediated anti-tumor immunity and demonstrate their therapeutic potential for NSCLC treatment.

Citation Format: Dennis O. Adeegbe, Yan Liu, Patrick Lizotte, Yusuke Kamihara, Mark Awad, David Barbie, Jerome Ritz, Simon Jones, Steven Quayle, Peter Hammerman, Kwok-Kin Wong. Synergistic immunostimulatory effects and therapeutic benefit of combined histone deacetylase and bromodomain inhibition in non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3682. doi:10.1158/1538-7445.AM2017-3682

Immune Profiling of Adenoid Cystic Carcinoma: PD-L2 Expression and Associations with Tumor-Infiltrating Lymphocytes

Adenoid cystic carcinoma (ACC) is among the most lethal salivary gland tumors, with no treatments for metastatic disease that prolong survival. We examined tissue from 28 primary and metastatic ACC deposits obtained from 21 patients for infiltrating immune cells and PD-L1/PD-L2 expression and determined mRNA profiles of over 1,400 oncogenic and immune-related genes. We also assessed the effect of chemoradiation on immune mediators in a patient who had serial biopsies available. Most tumors expressed PD-L2 but had few infiltrating immune cells. Lack of immune-cell infiltrate was associated with expression of genes in the β-catenin/Wnt and PI3K pathways. Additionally, certain transcripts linked to growth and invasion were differentially expressed among primary and metastatic deposits. Chemoradiation appeared to increase CD8(+) effector T cells, decrease regulatory T cells, and promote a systemic humoral response. These data suggest a potential role for PD-L2 inhibition and immune modulation as treatment for patients with ACC. Cancer Immunol Res; 4(8); 679-87. ©2016 AACR.

Abstract 4184: Pre-clinical study using KRAS mutant mouse models for lung cancer immunotherapy together with MEK inhibition

Activating KRAS mutations are identified as the most common driver oncogene for lung adenocarcinomas, accounts for 20∼30% of lung cancer patients. The development of therapeutic strategy for KRAS mutant lung cancer patients remains to be an unmet need, due to poor prognosis and therapeutic resistance to conventional therapy. The purpose of our study is through utilizing different types of genetically engineered mouse models (GEMMs), to understand the molecular heterogeneity of KRAS mutant lung cancer, to define the immune microenvironment, and to determine the feasibility and strategy of using MEK inhibition in combination with immune checkpoint inhibitors for the treatment of KRAS mutant lung cancer.

We generated two different types of GEMMs with KRAS mutations that develop tumor in the lung: Kras with G12D mutation or KRAS with G12C mutation. Continuous treatment of either KrasG12D or KRASG12C mice with MEK inhibitor Selumetinib (AZD6244, ARRY-142886) shows short-term response followed by drug resistance to single regimen treatment. The immuno-profiling shows that Selumetinib can increase cytotoxic T cells percentage and decrease PD-L1 expression on both myeloid cells and lymphocytes. Prolonged treatment of Selumetinib on KRAS mutant mice will lead to down-regulation of the expression of immune-checkpoint inhibitory factors Ctla-4 and Pd-1 on both CD4+ and CD8+ T cells. When KRAS mutant mice are treated with Selumetinib intermittently, they show improved response comparing with continuous treatment. When combining MEK inhibition with immune checkpoint blockade by using Selumetinib together with Pd-1 antibody treatment, Tim3 and Ctla-4 expression on T cells is increased potentially leading to T cell exhaustion and immune suppression in lung cancer. These pre-clinical results provide molecular insight for the immune response to MEK inhibition in KRAS driven lung cancer. Furthermore, these data support our hypothesis that MEK inhibition combination with immune checkpoint blockade treatment will have better outcome for lung cancer patients that have KRAS mutation through activating T cell response.

Citation Format: Jiehui Deng, Shuai Li, Grit Herter-Sprie, Paul D. Smith, Gordon J. Freeman, Jeffrey A. Engelman, Peter Hammerman, Kwok-Kin Wong. Pre-clinical study using KRAS mutant mouse models for lung cancer immunotherapy together with MEK inhibition. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4184.

Abstract 3315: Functional genomic profiling of lung adenocarcinoma identifies BRAF mutations as novel therapeutic targets

Patients with non-small cell lung cancer (NSCLC) display a wide spectrum of oncologic outcomes, suggesting significant underlying biologic diversity. Despite two notable exceptions in the cases of EGFR mutations and ALK rearrangements, current therapeutic management is largely homogeneous for a given stage. To advance genotype-directed therapy in NSCLC, we sought to identify genetic determinants of therapeutic resistance by leveraging cancer genomic data with a recently developed high-throughput platform for measuring radiation survival (Cancer Res. 2013. 73(20): 6289-98). To adequately represent the biologic spectrum of lung cancer and maximize power to detect clinically relevant genotypes, we profiled 104 lung cancer cell lines, including 89 NSCLC and 15 small cell lung cancer (SCLC) lines. We used our recently validated high-throughput proliferation assay to measure survival. Genomic correlates of radiosensitivity were explored by accessing Oncomap data from the Cancer Cell Line Encyclopedia, the COSMIC database of the Cancer Genome Project, and The Cancer Genome Atlas. Radiation survival across lineages reflected clinical experience and the literature regarding differential response to radiation, inasmuch as lung squamous cell carcinoma and adenocarcinoma (ACA) had similar radiosensitivity, whereas SCLC was less radiosensitive. Importantly, radiosensitivity varied more within a lineage than across lineages, with a 6-fold difference in integral survival among ACA lines. Correlation with cancer genomic data revealed clustering of BRAF mutations within the most resistant ACA lines (p = 0.035). When radiation survival distributions were compared by mutation status, BRAF-mutant ACA lines were significantly more resistant than BRAF wild-type ACA lines (p = 0.023). Some of the mutations identified by our analysis have been previously annotated by The Cancer Genome Atlas lung adenocarcinoma dataset and others appear to be novel. The identified BRAF mutations located in the highly conserved kinase domain enhanced kinase activity in a fashion analogous to the well-known BRAF V600E mutation. Integration of high-throughput radiation survival profiling with large-scale cancer genomic data suggests BRAF mutations are associated with therapeutic resistance in lung ACA. Our analysis nominates BRAF pathway inhibitors, which are commercially available, as therapeutic sensitizers in select BRAF-mutant lung ACA. Further investigation has the potential to yield an additional genotype-directed therapy that could impact up to 7% of patients with lung ACA, a prevalence comparable to that of ALK rearrangements (4%) or EGFR mutations (10%).

Citation Format: Mohamed Abazeed, Brian Yard, Drew Adams, Pablo Tamayo, Jason Hearn, Eui Kyu Chie, Stuart Schreiber, Matthew Meyerson, Craig Peacock, Peter Hammerman. Functional genomic profiling of lung adenocarcinoma identifies BRAF mutations as novel therapeutic targets. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3315. doi:10.1158/1538-7445.AM2015-3315

Abstract 4259: The radiogenomic landscape of cancer

Radiotherapy is the mainstay of treatment for many solid malignancies. Despite this, there have not been extensive systematic analyses of the correlation between therapeutic sensitivity and genomic parameters. To accelerate discovery of patient-matched radiotherapy, or precision radiotherapeutics, systematic approaches are needed to identify specific genetic features that confer radiotherapeutic resistance and target these features with small-molecule drugs. We have quantitatively measured the sensitivity of 533 genomically characterized cancer cell lines to radiation, uncovering novel and established genetic, lineage, chromosomal copy number, and gene-expression-based dependencies. We show that small molecules that target genetic alterations driving therapeutic resistance effect genotype selective radiosensitization, establishing a preclinical basis for personalized therapeutic regimens. This dataset is an important resource that can be used to develop novel therapeutic hypotheses and to accelerate discovery of drugs given concurrently with radiation matched to patients by their cancer genotype, thereby enhancing efficacy and limiting toxicity in the context of a new approach of precision radiotherapy.

Citation Format: Mohamed Abazeed, Drew Adams, Pablo Tamayo, Matthew Meyerson, Peter Hammerman, Stuart Schreiber. The radiogenomic landscape of cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4259. doi:10.1158/1538-7445.AM2014-4259

Abstract 4260: PTPRT mutation induces STAT3 activation in HNSCC preclinical models

Purpose: Head and neck squamous cell carcinoma (HNSCC) is an invasive malignancy with more than 40,000 cases diagnosed annually in the United States. Increased activation of signal transducer and activator of transcription 3 (STAT3) has been implicated in HNSCC tumorigenesis, although the mechanisms underlying aberrant STAT3 signaling are not fully elucidated. Activation of kinases upstream of STAT3 signaling, such as the epidermal growth factor receptor (EGFR), Janus kinase (JAK), and Src kinase, likely contribute, but downstream inactivators of STAT3 signaling, especially protein tyrosine phosphatases, remain incompletely understood. We recently elucidated the mutational profile of 74 HNSCC tumors and detected mutations in the receptor-like protein tyrosine phosphatase (PTPR) family in nearly one third of samples analyzed. Notably, known activating mutations of upstream kinases, including EGFR, JAK, and Src kinase, were not found. These findings were confirmed in an expanded cohort of 279 HNSCC tumors. High frequencies of PTPRT mutations have also been reported in other human cancers including colorectal cancer, lung carcinomas, and glioblastomas. Of these genes, PTPRT was mutated most frequently, with a total of 20 novel non-synonymous mutations detected in HNSCC tumors. Importantly, wild-type PTPRT was recently reported by others directly dephosphorylate STAT3. We therefore hypothesize that mutational inactivation of PTPRT contributes to HNSCC tumorigenesis via hyperphosphorylation of STAT3.

Experimental Design: We assessed the contribution of mutant PTPRT to STAT3 phosphorylation and cell proliferation in preclinical HNSCC models. Cell lines expressing wild-type or mutant PTPRT either transiently or stably by retroviral infection were generated. Levels of pSTAT3 were determined by Western blot and cell proliferation determined by trypan blue exclusion assay.

Results: PTPRT was shown in pre-clinical models to regulate STAT3 phosphorylation. Cells expressing HNSCC tumor-derived mutants of PTPRT exhibited elevated levels of pSTAT3 and increased cell proliferation.

Conclusion: Our results indicate that STAT3 is regulated by PTPRT in HNSCC and that mutation of PTPRT leads to an increase in STAT3 activation and cell proliferation. These findings suggest that PTPRT mutations may contribute to HNSCC tumor growth and progression via loss of function and subsequent hyperphosphorylation of STAT3. In the future, mutation of PTPRT may serve as a biomarker for a subset of tumors that are sensitive to treatment with STAT3 inhibitors.

Citation Format: Vivian Lui, Noah Peyser, Patrick Kwok Shing NG, Malabika Sen, Hua Li, Yan Zeng, Sonali Joyce, Zhenghe John Wang, Peter Hammerman, Gordon Mills, Jennifer R. Grandis. PTPRT mutation induces STAT3 activation in HNSCC preclinical 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 4260. doi:10.1158/1538-7445.AM2013-4260

Abstract 2011: The PI3K pathway is the most frequently mutated mitogenic pathway in HNSCC

The genomic heterogeneity of HNSCC presents a major obstacle to broadly effective targeted therapy. We and others previously reported genomic mutational profiles of over 100 HNSCC tumors. To date, there has been a major translational gap between genomic findings and patient treatment selection in HNSCC. Mitogenic pathways are vital to cancer development and progression. Genetic mutations in mitogenic pathways have been shown to result in pathway activation, increased proliferation of tumor cells, and increased sensitivity to agents targeting the specific pathway. Here, we performed a bioinformatics analysis of 151 HNSCC to examine the mutational profiles of major mitogenic pathways previously shown to be important in HNSCC tumor biology, including MAPK, JAK/STAT and PI3K, and found that the PI3K pathway is the most frequently mutated mitogenic pathway (30.46% cases; 46/151 tumors) followed by JAK/STAT and MAPK, (9.27% cases; 14/151 tumors) and (7.95% cases; 12/151 tumors), respectively.

HNSCC tumors with mutations in PI3K harbored 2.3 times more non-synonymous mutations (165.50 ± 24.08 vs 72.05 ± 6.63 mutations, P<0.0001) and twice as many cancer gene mutations than the HNSCC tumors without any PI3K pathway mutations (7.15 ± 0.75 vs 3.56 ± 0.29 mutations, P<0.0001), including multiple mutational events of genes in the PI3K pathway, suggesting that PI3K pathway mutations may promote the expansion of HNSCC tumor cells that are already genetically unstable. Interestingly however, in a small subset of HPV-positive HNSCC tumors (3 out of 45), PIK3CA was the only cancer gene found to be mutated, suggesting that the PI3K pathway alone may be sufficient to drive some HPV-positive HNSCC. The observed frequency of PIK3CA mutation in our 151 HNSCC cohort (12.58%; 19 mutations total) is higher than that reported previously in other smoking-related cancers such as lung cancer and esophageal cancer, where the respective PIK3CA mutation rates are not greater than 3-5%, suggesting a likely enrichment of PIK3CA mutations in HNSCC. Other components of the PI3K pathway were mutated in <2 - 3.97% of HNSCC tumors sequenced. Major downstream effectors of the PI3K pathway, including PDK1, AKT1 were not mutated, while AKT2 and mTOR were mutated in just 1.29% (2 mutations) of HNSCC tumors.

Importantly, PIK3CA and the PI3K pathway are currently targetable in human cancers, with several agents in various stages of clinical development. The growth of HNSCC xenografts derived from a cell line with a PIK3CA(H1047R) mutation, treated with the mTOR/PI3K inhibitor BEZ-235, was significantly inhibited. These findings suggest that PIK3CA, and potentially other PI3K pathway, mutations may serve as predictive biomarkers in HNSCC to guide treatment selection.

Citation Format: Matthew L. Hedberg, Vivian Lui, Hua Li, Bhavana Vangara, Kelsey Pendleton, Yan Zeng, Breean Gilbert, Maria Freilino, Sam Sauerwein, Noah Peyser, Brenda Diergaarde, Peter Hammerman, Levi Garraway, Gordon Mills, Jennifer Grandis. The PI3K pathway is the most frequently mutated mitogenic pathway in HNSCC. [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 2011. doi:10.1158/1538-7445.AM2013-2011

Abstract 3960: Rapid and efficient large-scale somatic mutation validation approaches for cancer genome sequencing

The landscape of somatic alterations in cancer is being rapidly uncovered by large-scale cancer genome sequencing projects in individual laboratories as well as consortia such as The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC). The decreasing cost of sequencing has resulted in an increase in the number of cancer genomes that are being sequenced, and thus the numbers of candidate somatic mutations being identified are rapidly expanding. A single cancer genome from a cancer with an average mutation background rate, such as ovarian or breast cancer, will have 3000-6000 mutations. A high mutation rate cancer such as melanoma or colon cancer can have as many as 100,000 mutations/genome. Multiplying these numbers by the dozens of sequenced genomes and hundreds of sequenced exomes across a wide spectrum of tumor types yields a staggering number of candidate mutations. However, approaches for rapidly validating these findings at scale have been lagging behind. Current approaches, such as custom designed hybrid capture arrays followed by sequencing, can take months to complete and cannot begin until the initial sequencing is complete and mutations are called. This can lead to long delays in the interpretation and publication of biological findings. Here we describe the results of several approaches for rapid and efficient validation on large-scale projects, such as TCGA. We will share our approach and results using Fluidigm and PacBio sequencing for validation and sample extension at a small scale with rapid turnaround where we have validated PIK3CA and TP53 mutations in breast cancer samples of varying purity as well as significantly mutated genes in medulloblastoma. Ideally one could validate mutations and gene fusions concurrent with their discovery. To that end, we will also describe our validation results using RNA-Seq data, commonly produced concurrently with genome and exome sequencing, in lung squamous and renal cancer. Finally, we will explore an approach for instant-validation through simultaneous sequencing of barcoded discovery and cross-validation libraries.

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 3960. doi:1538-7445.AM2012-3960

Abstract 1682: Uncovering signals of somatic selection through whole exome and whole genome sequencing of lung adenocarcinoma

We have sequenced the exomes of over 100 and the genomes of over 20 lung adenocarcinoma tumor-normal specimen pairs. We performed hybrid capture exome sequencing of nearly 18,000 genes to >100X median per-sample coverage with 76bp paired-end reads. We performed whole genome sequencing achieving 60X median tumor and 20X median normal coverage with 350bp median insert size and 101bp paired-end reads. Our exome analysis yielded over 50,000 substitution and small indel coding events, with a mean somatic mutation rate of 10-11 events / MB. This resulted in over 300 non-synonymous coding events per patient, most of which were presumed to be passenger mutations unrelated to tumorigenesis. This high mutational load required us to develop novel statistical approaches (MutSig, Lawrence et al, in preparation) to identify putative lung adenocarcinoma driver genes under positive somatic selection. We constructed a complex neutral mutation model that considered sequence context and several additional genomic covariates shown to mediate gene to gene inhomogeneities of passenger mutation rates. Identification of significant deviations from this background model allowed us to recover almost all known frequently mutated lung adenocarcinoma genes, including TP53, KRAS, STK11, PIK3CA, EGFR, ERBB2, RB1, SMARCA4, and KEAP1, as well as a host of novel putative driver genes. We applied similar principles to identify pathways and sub-networks of genes undergoing apparent positive selection in lung adenocarcinoma. Whole genome analysis yielded several high-confidence in-frame protein fusion and promoter-gene fusion events enriched in tumor vs normal specimens. We also found large numbers of somatic substitution and indel events in promoters, enhancers, and non-coding DNA elements and identified putative sites of somatic retrotransposition in our whole genome data. Overall, our study eclipses previous large-scale characterization of somatic sequence variation (Refs. 1-3) in lung adenocarcinoma by at least an order of magnitude. Using novel methods adapted to the analysis of high-mutation rate tumor types (lung squamous cell carcinoma, melanoma, colorectal cancer), we are able to recover signals of selection in both known and novel genes and pathways. Our results illuminate novel lung adenocarcinoma tumor biology and provide targets for therapeutic and diagnostic investigation. References 1. Ding et al. Somatic mutations affect key pathways in lung adenocarcinoma. Nature (2008) vol. 455 (7216) pp. 1069-75 2. Kan et al. Diverse somatic mutation patterns and pathway alterations in human cancers. Nature (2010) vol. 466 (7308) pp. 869-73 3. Lee et al. The mutation spectrum revealed by paired genome sequences from a lung cancer patient. Nature (2010) vol. 465 (7297) pp. 473-7

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 1682. doi:1538-7445.AM2012-1682

Abstract 2: FGFR3 as a therapeutic target in squamous cell lung carcinoma

Squamous cell lung carcinoma (lung SCC) is the second most common subtype of non-small cell lung cancer with, 40,000 new cases diagnosed every year in the United States. Unlike lung adenocarcinoma, few targetable genomic events are known drivers of lung SCC, and therefore, therapeutic options are limited for patients with this disease. As part of The Cancer Genome Atlas (TCGA) project, we have analyzed the entire coding sequence of 196 lung SCCs for mutated genes which may be amenable to targeted therapeutics. In the 108 patient samples analyzed to date, we have observed mutations in the Fibroblast Growth Factor Receptor 3 (FGFR3) kinase gene in six cases at four sites, or 3% of samples. The observed FGFR3 mutations are present in both the extracellular domain and the kinase domain of the protein, an observation that is consistent with activating mutations in FGFR3 that are known to drive bladder cancer, and in fact, two of the observed mutations are at sites previously observed in bladder cancer. We therefore hypothesized that these mutations are oncogenic and may be driving transformation in a subset of lung SCC patients. Expression of mutated FGFR3 in NIH-3T3 cells led to anchorage-independent colony formation, which was inhibited by treatment with a pan-FGFR inhibitor. A known mechanism of FGFR3 activation is the constitutive dimerization of receptors with mutated extracellular domains via intermolecular disulfide bond formation, and we have observed this phenomenon in our ECD mutants as well. These data suggest that mutations in the FGFR3 gene are sufficient to transform cells. This finding, along with recently published data suggesting that FGFR1 amplification is also able to drive lung SCC development, demonstrates that the FGFR family may be a promising therapeutic target in lung SCC.

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 2. doi:1538-7445.AM2012-2

Abstract B13: FGFR2 as a therapeutic target in squamous cell lung carcinoma

Squamous cell lung carcinoma (lung SCC)) is the second most common subtype of non-small cell lung cancer, with 40,000 new cases diagnosed every year in the United States. Unlike lung adenocarcinoma, few targetable genomic events are known drivers of lung SCC, and therefore, therapeutic options are limited for patients with this disease. As part of The Cancer Genome Atlas (TCGA) project, we have analyzed the entire coding sequence of 196 lung SCCs for mutated genes which may be amenable to targeted therapeutics. In the 196 patient samples analyzed to date, we have observed mutations in the Fibroblast Growth Factor Receptor 2 (FGFR2) kinase gene in ten cases, or 5% of samples. The observed FGFR2 mutations are present in both the extracellular domain and the kinase domain of the protein, an observation that is consistent with activating mutations in FGFR2 that are known to drive endometrial cancer. We therefore hypothesized that these mutations are oncogenic and may be driving transformation in a subset of lung SCC patients. Expression of mutated FGFR2 in NIH-3T3 cells led to anchorage-independent colony formation, which was inhibited by treatment with the pan-FGFR inhibitor FIIN-1. A known mechanism of FGFR2 activation is the constitutive dimerization of receptors with mutated extracellular domains via intermolecular disulfide bond formation, and we have observed this phenomenon in two of our ECD mutants as well. These data suggest that both ECD and kinase mutations in the FGFR2 gene are sufficient to transform cells. This finding, along with recently published data suggesting that FGFR1 amplification is also able to drive lung SCC development, demonstrates that the FGFR family may be a promising therapeutic target in lung SCC.

Abstract PR1: Integrating expression data improves mutational significance analysis of lung squamous carcinoma

In contrast to lung adenocarcinoma in which a driving and potentially targetable genetic aberration can be identified in excess of 50% of tumors, only 10% can be found in squamous cell lung cancer, the second most common type of lung cancer, none of which are druggable by an approved targeted therapy. Our limited knowledge regarding targetable genetic alterations in squamous cell lung cancer is the result of a lack of detailed genomic study of this disease and the lack of experimental validation of identified putative therapeutic targets. We have analyzed exome sequencing data to identify novel driving mutations in 184 lung squamous cell carcinomas using previously successful methods (Integrated genomic analyses of ovarian carcinoma, Nature 2011), but these analyses are confounded by an unusually high mutation rate, 8-9/Mb on average, some reaching as many as 80/Mb. Many of the most significantly mutated genes in the analysis are unlikely related to the pathogenesis of the disease based on a lack of expression in lung and known role in cancer, suggesting that genes which are not expressed (or minimally expressed) escape negative selection and result in a higher mutation density as compared with expressed genes.

Here, we present a method integrating expression and mutation data in order to more accurately determine the significance of a mutated gene based on the expression subclass in which it falls and the frequency at which it's mutated relative to our expectation; unexpressed genes are likely much more tolerant of mutations and should therefore have a higher expected background mutation rate. Analyses of this kind have removed many of the genes putatively irrelevant in this cancer type and have identified many biologically plausible novel genes that to date are unlinked with lung squamous cell carcinoma. We believe this method refines an already powerful analysis for identifying significantly mutated genes in cancer with a particularly high potential for separating signal and noise in the most highly mutated cancer types.

This abstract is also presented as Poster A17.

Busulfan and cyclophosphamide (Bu/Cy) as a preparative regimen for autologous stem cell transplantation in patients with non-Hodgkin lymphoma: a single-institution experience

High-dose chemotherapy with autologous stem cell transplantation (ASCT) has been established as a standard form of therapy for patients with non-Hodgkin lymphoma (NHL). While many high-dose chemotherapy combinations are used, no single regimen has proved superior over another. Here, we report our single center's experience in patients with NHL undergoing ASCT with the combination of busulfan and cyclophosphamide (Bu/Cy). This study is a retrospective analysis of 78 consecutive patients with NHL who underwent ASCT with Bu/Cy at Massachusetts General Hospital Cancer Center. Data were collected through review of electronic medical records. A total of 78 patients with NHL underwent ASCT with Bu/Cy preparative therapy between 1996 and 2006. Median follow-up for survivors was 5.0 years (range, 6 months to 12 years). Significant transplantation-associated complications included 9 documented bacterial infections, 4 cases of engraftment syndrome, 3 cases of hepatic veno-occlusive disease (VOD), 6 cases of cardiac complications, and 2 cases of pulmonary fibrosis. The 100-day treatment-related mortality (TRM) was 1%. At 3 years, progression-free survival (PFS) was 48% (95% confidence interval [CI]=37% to 59%) and overall survival (OS) was 65% (95% CI=53% to 74%). Our data indicate that in patients with NHL undergoing ASCT, Bu/Cy has efficacy and toxicity comparable to that of other reported regimens.

Evidence for an ATP-dependent bile acid transport protein other than the canalicular liver ecto-ATPase in rats

BACKGROUND & AIMS

Canalicular secretion is rate limiting in overall blood-to-bile transport of bile acids. Studies using transfected cells have implicated the canalicular ecto-adenosine triphosphatase (ecto-ATPase) in adenosine triphosphate (ATP)-dependent bile acid transport. However, the structural features of this ecto-ATPase are not those anticipated for an in-to-out ATP-dependent transporter. The aim of this study was to explore the possible existence of an ATP-dependent bile acid transport mechanism distinct from ecto-ATPase.

METHODS

Bile acid transport activity and ecto-ATPase expression were analyzed in primary rat hepatocytes, rat hepatoma HTC cells, and specially adapted HTC (HTC-R) cells using plasma membrane vesicles and Northern blot, slot blot, ribonuclease protection assay, and Western blot analyses.

RESULTS

Plasma membranes isolated from HTC-R cells exhibited ATP-dependent taurocholate transport, which was many-fold greater than that in HTC cells. Hepatocytes showed the highest transport rates. Protein and RNA analyses showed very low expression of ecto-ATPase in HTC and HTC-R cells compared with hepatocytes. There was no difference between the two cell types at both the RNA and protein level.

CONCLUSIONS

These findings show the presence in HTC-R cells and, apparently in hepatocytes, of one or more proteins other than the ecto-ATPase that mediate ATP-dependent transport of bile acids.