Targetable Molecular Alterations Research Articles

EGFR mutations in lung adenocarcinoma: Epidemiology and clinical relevance of common versus rare mutations.

e19067 Background: In lung adenocarcinoma, oncogenic mutations of the epidermal growth factor receptor (EGFR) are the most frequent and biologically targetable molecular alterations. Classical acti...

Abstract B200: A new resource enabling the practical utility of targeted therapy in oncology clinics.

Abstract Academic oncology now recognizes that a cancer's genetic signature may be as important in clinical decision-making as its tissue of origin. However, the degree to which this revolution in thinking has penetrated the clinic is unknown. Our commercial platform, which operates at the point of contact between patients and their physicians, is ideally positioned to address this question. After clinical samples provided by oncologists are analyzed by any molecular diagnostic platform, our internal experts interpret the results using our knowledge integration platform and provide treatment-strategy roadmaps to guide future interventions. Since 2008, approximately 4000 patients have been assessed using this methodology. Overall, the practical utility of the platform has been high: over 70% of cases across all cancer types have revealed actionable results, defined as a molecular profile that suggests either rational on- or off-label use of an FDA-approved agent or enrollment into a clinical trial. Among the 130 patients for whom follow-up is available, use of this platform has resulted in a known effect on therapy selection in 35% of cases and a potential future effect on therapy in an additional 61% of cases. The utility of the approach has also been demonstrated through acceptance by oncologists; 36% of patients who have engaged the service were referred by their oncologists. Although not rising to the rigor of prospective randomized trial data, information in our database may be used in hypothesis generation. For example, while ERBB2 amplification is common in breast cancer, ERBB2 mutations have been documented in a small percentage of non-small cell lung cancer (NSCLC), and were detected in 4% (19/450) of NSCLC cases in our dataset. Mutations or copy number alterations in ERBB2 have also been identified in our dataset in 4% (7/195) of colorectal cancers, 6% (4/68) of urothelial carcinomas, and 10% (4/39) of endometrial carcinomas. In one case, a 61-year-old woman with Stage IV NSCLC presented with a secondary metastasis on the pleura, undergoing treatment with carboplatin and pemetrexed chemotherapy, following earlier treatment of a primary lung tumor with surgery and radiation. Multiplex sequencing identified a somatic exon 20 insertion (AYVM 771-774) in ERBB2, and subsequent treatment with trastuzumab resulted in nearly two years of progression-free survival. These results are consistent with published case studies in this patient population and suggest that clinical trials examining trastuzumab in NSCLC patients with ERBB2 exon 20 mutations may be warranted. In conclusion, our data demonstrate the increasing importance of targeted therapy in clinical oncology. They also demonstrate how databases such as ours, which document uncommon targetable molecular alterations, may have significant impact on real-time treatment decision-making and have potential as hypothesis-generating resources for future clinical trials. Citation Information: Mol Cancer Ther 2013;12(11 Suppl):B200. Citation Format: Sheryl K. Elkin, Linda Call, Jo-Ellen Murphy, Kelly Sullivan, Jennifer Carter. A new resource enabling the practical utility of targeted therapy in oncology clinics. [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 B200.

Abstract S3-6: Profiling of triple-negative breast cancers after neoadjuvant chemotherapy identifies targetable molecular alterations in the treatment-refractory residual disease

Abstract Background: Neoadjuvant chemotherapy (NAC) is increasingly used in patients with triple-negative breast cancer (TNBC). NAC can induce a pathologic complete response (pCR) in ∼30% of patients which portends a favorable prognosis. In contrast, patients with residual disease (RD) in the breast at surgical resection exhibit worse outcomes. Objective: We hypothesized that profiling residual TNBCs after NAC would identify molecularly targetable lesions in the chemotherapy-resistant component of the tumor and that the persistent tumor cells would mirror micro-metastases which ultimately recur in such patients. Methods: We utilized targeted next generation sequencing (NGS) for 182 oncogenes and tumor suppressors in a CLIA certified lab (Foundation Medicine, Cambridge, MA) and gene expression profiling (NanoString) of the RD after NAC in 102 patients with TNBC. The RD was stained for Ki67, which has been reported to predict outcome after NAC in unselected breast cancers. Results: Thirteen tumors were not evaluable due to low tumor cellularity. Of 89 evaluable post-NAC tumors, 57 (64%) were basal-like; 19% HER2-enriched; 6% luminal A; 6% luminal B and 5% normal-like. Mean depth of coverage was 635 (range: 135–1207). Of 81 tumors evaluated by NGS, 72/81 (89%) demonstrated mutations in TP53, 22 were MCL1-amplified (27%), and 17 were MYC-amplified (21%). Alterations in the PI3K/mTOR pathway (AKT1-3, PIK3CA, PIK3R1, RAPTOR, PTEN, and TSC1) were identified in 27 tumors (33%). Cell cycle genes were altered in 25 tumors (31%), including amplifications of CDK2, CDK4, and CDK6, CCND1-3, and CCNE1 as well as RB loss. Alterations in the DNA repair pathway (BRCA1/2, ATM; 16 tumors; 20%) and the Ras/MAPK pathway (KRAS, RAF1, NF1; 10 tumors; 12%) were also common. Sporadic growth factor receptor amplifications occurred in EGFR, KIT, PDGFRA, PDGFRB, MET, FGFR1, FGFR2, and IGF1R. NGS identified 7 patients with ERBB2 gene amplification in the RD which was confirmed by FISH in both the pre- and post-treatment tissue, suggesting NGS could assist in the identification of ERBB2-overexpressing tumors misclassified at the time of diagnosis. In general, the gene amplifications identified by NGS corresponded to enhanced gene expression levels. Amplifications of MYC were independently associated with poor recurrence-free survival (RFS) and overall survival (OS). An interaction effect on survival was observed between MEK activation (assayed by a gene expression signature) and MYC amplification, suggesting cooperation between these pathways. Alterations in DNA repair also identified a subgroup with poor RFS and OS. In contrast, high post-NAC Ki67 score did not predict poor RFS or OS in this predominantly TNBC cohort. Conclusions: The diversity of lesions in residual TNBCs after NAC underscores the need for powerful and broad molecular approaches to identify actionable molecular alterations and, in turn, better inform personalized therapy of this aggressive disease. Incorporation of this platform into clinical studies and eventually standards of care should aid in the prioritization of patients with RD after NAC into rational adjuvant studies. Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr S3-6.

Abstract 5074: Massively parallel DNA-sequencing of aggressive prostate cancer reveals disease heterogeneity and identifies targetable mutations

Abstract Background: Recent advances in our understanding of the mutational landscape of prostate cancer (PCa) have occurred through sequencing of primary prostate tumors. Highly aggressive PCa most often does not come to surgery preventing access to frozen sample for high-throughput studies. The purpose of this study is to determine the spectrum of mutations in a subgroup of highly aggressive PCa and to evaluate for targetable molecular alterations using a novel mutation analysis platform from archival formalin-fixed paraffin embedded (FFPE) samples. Methods: 21 PCa (of which 9 were Gleason 5, 8 metastatic), 18 Neuroendocrine PCa (NEPC), and 18 benign FFPE prostate samples from 35 unique cases were evaluated and 77 high-density foci were selected for DNA extraction and sequencing library construction. Hybridization-based capture of 3230 exons and 37 intronic intervals of 189 cancer-related genes was performed, followed by deep, massively-parallel sequencing. Sequence data were analyzed for single nucleotide variants (sub), small insertions and deletions (indels), significant copy number changes, and selected re-arrangements/fusion genes. Results: 5/8 biopsies and 62/65 (overall 93%) of prostate or metastatic foci yielded sufficient DNA (≥50 ng) for analysis from 40μ of FFPE tissue. Average uniquely-mapping sequence coverage was 885x. 133 mutations were identified in 30 genes with 58/67 samples containing at least one mutation. TMPRSS2-ERG fusion was present in 31% of cases. Recurrent high confidence cancer alterations included: gain of MYC (9%), gain or sub/indel of AR (43%), deletion or sub/indel of PTEN (23%), RB1 (20%), BRCA2 (11%), and sub/indel of TP53 (40%), CTNNB1 (11%), PIK3CA (6%), ATM (6%). Several novel mutations were identified, including in BRAF and BRCA2. AR alterations were more common in PCa compared to NEPC, and were present even in clinically localized PCa. There was high concordance between NEPC and PCa foci in mixed tumors, as well as between primary tumor and metastases. Conclusions: This study demonstrates feasibility of in-depth DNA analysis using FFPE tissue, and even biopsy material. The spectrum of driver mutations observed highlights potential value of comprehensive genomic profiling for targeted therapy selection in clinical care. These analyses have laid the foundation for ongoing comparison with indolent PCa, and have identified potential new drug targets (e.g., PARP inhibitors for ATM and BRCA2 mutations), with a goal towards better defining biomarkers that distinguish aggressive and indolent PCa and designing more effective treatment approaches for patients with lethal PCa. 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 5074. doi:1538-7445.AM2012-5074

Identifying cancer mutations in neuroendocrine prostate cancer (NEPC) through massively parallel DNA sequencing of formalin-fixed paraffin-embedded (FFPE) tissue.

110 Background: NEPC is an aggressive and lethal variant of prostate cancer that most commonly arises from existing prostate adenocarcinoma (PCA). Little is known about the underlying biology of NEPC, as metastases are rarely biopsied. The purpose of this study is to determine the spectrum of somatic mutations in NEPC by using a novel DNA sequencing platform and to evaluate for targetable molecular alterations. Methods: 44 NEPC and mixed NEPC/PCA were evaluated and 77 high density foci of NEPC, PCA, and benign areas were selected for DNA extraction. Massively parallel sequencing via HiSeq2000 was performed using indexed seq libraries constructed by adapter ligation followed by hybridization with optimized capture probes. Data was processed using publicly available and newly validated software tools to make mutation assignments for base alterations, indels, and CNAs in 182 cancer associated genes and common sites of rearrangement for 15 genes. Results: 5/8 biopsies and 62/65 (overall 93%) of prostate foci yielded sufficient DNA (>50 ng) for analysis from 40m of FFPE tissue. Average median sequence coverage was 934x. TMPRSS2-ERG fusion was present in 28% of NEPC. Recurrent homozygous deletions involving PTEN and RB1 were seen, and 1 tumor with BRCA2 loss. Several high confidence non-synonymous mutations were identified including TP53 (40%), CTNNB1 (12%), and less frequently mutations involving PTEN, PIK3CA, AR, as well as other novel mutations/fusions. There was high concordance between NEPC and PCA foci in mixed tumors, as well as between primary tumor and metastases. High confidence lesions were validated with exome sequencing and FISH. Conclusions: This study shows feasibility of an in-depth DNA analysis using FFPE tissue, and even biopsy material. Comprehensive genome sequencing has nominated novel biologic pathways and provides insight into disease progression from PCA to NEPC, as well as potential new drug targets for a tumor that is currently lethal. This is a useful and comprehensive sequencing tool to evaluate tumors such as NEPC and other metastatic tumors, where obtaining tissue is challenging.

Abstract C22: Massively parallel DNA-sequencing of aggressive prostate cancer reveals disease heterogeneity and identifies targetable mutations

Abstract Background: Recent advances in our understanding of the mutational landscape of prostate cancer (PCa) have occurred through sequencing of primary prostate tumors. Highly aggressive PCa most often does not come to surgery preventing access to frozen sample for high-throughput studies. The purpose of this study is to determine the spectrum of mutations in a subgroup of highly aggressive PCa and to evaluate for targetable molecular alterations using a novel mutation analysis platform from archival formalin-fixed paraffin embedded (FFPE) samples. Methods: 21 PCa (of which 9 were Gleason 5, 8 metastatic), 18 neuroendocrine PCa (NEPC), and 18 benign FFPE prostate samples from 35 unique cases were evaluated and 77 high-density foci were selected for DNA extraction and sequencing library construction. Hybridization-based capture of 3230 exons and 37 intronic intervals of 189 cancer-related genes was performed, followed by deep, massively-parallel sequencing. Sequence data were analyzed for single nucleotide variants (sub), small insertions and deletions (indels), significant copy number changes, and selected re-arrangements/fusion genes. Results: 5/8 biopsies and 62/65 (overall 93%) of prostate or metastatic foci yielded sufficient DNA (≥50 ng) for analysis from 40μ of FFPE tissue. Average uniquely-mapping sequence coverage was 885×. 133 mutations were identified in 30 genes with 58/67 samples containing at least one mutation. TMPRSS2-ERG fusion was present in 31% of cases. Recurrent high confidence cancer alterations included: gain of MYC (9%), gain or sub/indel of AR (43%), deletion or sub/indel of PTEN (23%), RB1 (20%), BRCA2 (11%), and sub/indel of TP53 (40%), CTNNB1 (11%), PIK3CA (6%), ATM (6%). Several novel mutations were identified, including in BRAF and BRCA2. AR alterations were more common in PCa compared to NEPC, and were present even in clinically localized PCa. There was high concordance between NEPC and PCa foci in mixed tumors, as well as between primary tumor and metastases. Conclusions: This study demonstrates feasibility of in-depth DNA analysis using FFPE tissue, and even biopsy material. The spectrum of driver mutations observed highlights potential value of comprehensive genomic profiling for targeted therapy selection in clinical care. These analyses have laid the foundation for ongoing comparison with indolent PCa, and have identified potential new drug targets (e.g., PARP inhibitors for ATM and BRCA2 mutations), with a goal towards better defining biomarkers that distinguish aggressive and indolent PCa and designing more effective treatment approaches for patients with lethal PCa. Citation Format: Himisha Beltran, Philip J. Stephens, Juan Miguel Mosquera, Maureen T. Cronin, Mark A. Rubin, Roman Yelensky, Garrett Frampton, Kyung Park, Sean Downing, Theresa Y. MacDonald, Doron Lipson, Scott T. Tagawa, David M. Nanus. Massively parallel DNA-sequencing of aggressive prostate cancer reveals disease heterogeneity and identifies targetable mutations [abstract]. In: Proceedings of the AACR Special Conference on Advances in Prostate Cancer Research; 2012 Feb 6-9; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(4 Suppl):Abstract nr C22.

Role of Genotyping in Non-Small Cell Lung Cancer Treatment

Non-small cell lung cancer (NSCLC) is a common malignant disease with an extremely poor prognosis. Chemotherapeutic treatment for advanced disease is currently based on histological subtyping, but recent discoveries of genetic alterations in subsets of NSCLC have already changed clinical practice with regard to Egfr mutations as predictive markers of response to gefitinib and erlotinib. This has also paved the way for the integration of molecular analyses into early phase clinical trials, as demonstrated by the clinical development of crizotinib, effective in lung cancer harbouring Alk rearrangements. Similarly, other subgroups of NSCLC carry potentially targetable molecular alterations and their study has the potential to change the diagnostic and therapeutic approach to lung cancer in the near future. In contrast to a wealth of knowledge surrounding genomic alterations in lung adenocarcinomas, fewer data are available concerning squamous cell lung cancer (SCC), although recent data demonstrate that genotyping can provide new therapeutic perspectives in SCC treatment. Moreover, the study of molecular predictive markers of response to chemotherapy aims to improve chemotherapeutic treatment, increasing efficacy and limiting toxicity.

Targeted Therapy in Lung Cancer; Lessons Learned from Past Experiences

Targeted Therapy in Lung Cancer; Lessons Learned from Past Experiences

Report from the Fifth National Cancer Institute Mouse Models of Human Cancers Consortium Nervous System Tumors Workshop

Cancers of the nervous system are clinically challenging tumors that present with varied histopathologies and genetic etiologies. While the prognosis for the most malignant of these tumors is essentially unchanged despite decades of basic and translational science research, the past few years have witnessed the identification of numerous targetable molecular alterations in these cancers. With the advent of advanced genomic sequencing methodologies and the development of accurate small-animal models of these nervous system cancers, we are now ideally positioned to develop personalized therapies that target the unique cellular and molecular changes that define their formation and drive their continued growth. Recently, the National Cancer Institute convened a workshop to advance our understanding of nervous system cancer mouse models and to inform clinical trials by reconsidering these neoplasms as complex biological systems characterized by heterogeneity at all levels.

Phase II study of sunitinib malate, a multitargeted tyrosine kinase inhibitor in patients with relapsed or refractory soft tissue sarcomas. Focus on three prevalent histologies: Leiomyosarcoma, liposarcoma and malignant fibrous histiocytoma

Soft tissue sarcomas (STS) represent a diverse group of histologic subtypes with targetable molecular alterations, often treated as a single disease. Sunitinib malate is a multitargeted receptor tyrosine kinase inhibitor active in other solid tumors carrying similar alterations (i.e., imatinib mesylate-refractory gastrointestinal stromal tumors). This single-institution phase II study investigated the safety and efficacy of sunitinib malate in three common STS subtypes. Patients with documented unresectable or metastatic STS (liposarcoma, leiomyosarcoma and malignant fibrous histiocytoma [MFH]), measurable disease, and 3 or less prior lines of therapy were eligible. Treatment consisted of sunitinib malate, 50 mg daily, for 4 weeks every 6 weeks. Forty-eight patients were enrolled, and 35% were heavily pretreated (≥ 2 prior lines of chemotherapy). The safety profile resembled previously known sunitinib malate toxicities. Median progression-free and overall survivals for liposarcoma, leiomyosarcoma, and MFH were 3.9 and 18.6, 4.2 and 10.1 and 2.5 and 13.6 months, respectively. The 3-month progression-free rates in the untreated and pretreated (chemotherapy) patients with liposarcoma, leiomyosarcoma and MFH were 75% and 69.2%, 60%, and 62.5% and 25% and 44.4%, respectively. With the caveats that a minority of patients with potentially indolent or low-grade disease could have been included and the small numbers, a 3-month progression-free rate of >40% suggests activity for sunitinib malate at least in liposarcomas and leiomyosarcomas. Thus, we believe that further investigation in these susceptible STS subtypes is warranted.