Analysis of rare fusions in NSCLC: Genomic architecture and clinical implications

OBJECTIVES

Molecular diagnosis for targeted therapies has been improved significantly in non-small-cell lung cancer (NSCLC) patients in recent years. Here we report on the prevalence of rare fusions in NSCLC and dissect their genomic architecture and potential clinical implications.

MATERIALS AND METHODS

Overall, n = 5554 NSCLC patients underwent next-generation sequencing (NGS) for combined detection of oncogenic mutations and fusions either at primary diagnosis (n = 5246) or after therapy resistance (n = 308). Panels of different sizes were employed with closed amplicon-based, or open assays, i.e. anchored multiplex PCR (AMP) and hybrid capture-based, for detection of translocations, including "rare" fusions, defined as those beyond ALK, ROS1, RET and <0.5 % frequency in NSCLC.

RESULTS

Rare fusions involving EGFR, MET, HER2, BRAF and other potentially actionable oncogenes were detected in 0.5% (n = 26) of therapy-naive and 2% (n = 6) TKI-treated tumors. Detection was increased using open assays and/or larger panels, especially those covering >25 genes, by approximately 1-2% (p = 0.001 for both). Patient characteristics (age, gender, smoking, TP53 co-mutations (56%), or mean tumor mutational burden (TMB) (4.8 mut/Mb)) showed no association with presence of rare fusions. Non-functional alterations, i.e. out-of-frame or lacking kinase domains, comprised one-third of detected rare fusions and were significantly associated with simultaneous presence of classical oncogenic drivers, e.g. EGFR or KRAS mutations (p < 0.001), or use of larger panels (frequency of non-functional among the detected rare fusions 57% for 25+ gene- vs. 12% for smaller panels, p < 0.001). As many rare fusions were identified before availability of targeted therapy, mean survival for therapy-naïve patients was 23.8 months, comparable with wild-type tumors.

CONCLUSION

Approximately 1-2% of advanced NSCLC harbor rare fusions, which are potentially actionable and may support diagnosis. Routine adoption of broad NGS assays capable to identify exact fusion points and potentially retained protein domains can increase the yield of therapeutically relevant molecular information in advanced NSCLC.

Assigning evidence to actionability: An introduction to variant interpretation in precision cancer medicine

Modern concepts in precision cancer medicine are based on increasingly complex genomic analyses and require standardized criteria for the functional evaluation and reporting of detected genomic alterations in order to assess their clinical relevance. In this article, we propose and address the necessary steps in systematic variant evaluation consisting of bioinformatic analysis, functional annotation and clinical interpretation, focusing on the latter two aspects. We discuss the role and clinical application of current variant classification systems and point out their scope and limitations. Finally, we highlight the significance of the molecular tumor board as a platform for clinical decision-making based on genomic analyses.

Functional Precision Medicine Identifies New Therapeutic Candidates for Medulloblastoma

Medulloblastoma is among the most common malignant brain tumors in children. Recent studies have identified at least four subgroups of the disease that differ in terms of molecular characteristics and patient outcomes. Despite this heterogeneity, most patients with medulloblastoma receive similar therapies, including surgery, radiation, and intensive chemotherapy. Although these treatments prolong survival, many patients still die from the disease and survivors suffer severe long-term side effects from therapy. We hypothesize that each patient with medulloblastoma is sensitive to different therapies and that tailoring therapy based on the molecular and cellular characteristics of patients' tumors will improve outcomes. To test this, we assembled a panel of orthotopic patient-derived xenografts (PDX) and subjected them to DNA sequencing, gene expression profiling, and high-throughput drug screening. Analysis of DNA sequencing revealed that most medulloblastomas do not have actionable mutations that point to effective therapies. In contrast, gene expression and drug response data provided valuable information about potential therapies for every tumor. For example, drug screening demonstrated that actinomycin D, which is used for treatment of sarcoma but rarely for medulloblastoma, was active against PDXs representing Group 3 medulloblastoma, the most aggressive form of the disease. Functional analysis of tumor cells was successfully used in a clinical setting to identify more treatment options than sequencing alone. These studies suggest that it should be possible to move away from a one-size-fits-all approach and begin to treat each patient with therapies that are effective against their specific tumor. SIGNIFICANCE: These findings show that high-throughput drug screening identifies therapies for medulloblastoma that cannot be predicted by genomic or transcriptomic analysis.

Abstract 1935: Molecular characterization of orthotopic patient-derived xenograft models of pediatric brain tumors

[Introduction: Solid tumors of the nervous system are the most common childhood cancers after leukemias. Even though we might be able to cure more and more patients, survivors still severely suffer long-term from the intensive treatments. Therefore, new treatment strategies are urgently needed. Orthotopic patient-derived xenograft (PDX) models are an excellent platform for biomarker and preclinical drug development. However, the rarity of pediatric brain tumors and the multitude of different sub entities hinder the generation of large collection of PDX models of specific entities within single institutions. In order to generate an overview about existing PDX models in the community, we started collecting established PDX models from various centers all over the world and performed extensive molecular characterization to precisely determine the distinct molecular subgroup and constellation of genetic alterations for each PDX model, and thus identify its targetable oncogenic drivers.

Material and Methods: PDX models were established and maintained by dissociating tumor material into a single cell suspension and then orthotopically injecting it into the brain of immunodeficient animals. All PDX models and matching primary tumors (if available) have been analyzed by whole-exome and low-coverage whole-genome sequencing, as well as DNA methylation and gene expression profiling at the German Cancer Research Center (DKFZ).

Results and Discussion: Thus far, we have collected and characterized 70 established PDX models from 6 ATRTs, 8 ependymomas, 16 high-grade gliomas, 38 medulloblastomas, and 2 CNS-PNETs. PDX models always retain their molecular subtype and in the vast majority of cases also the mutations and copy number alterations when compared to their primary tumors. Only in rare cases do we observe additional aberrations, which most likely represent outgrowths of subclones from the primary tumor. Analysis of our entire cohort identified an overrepresentation of the most aggressive tumor subtypes, but also subtypes which have not been available for preclinical testing before due to lack of genetically engineered mouse models or suitable cell lines, such as Group 4 medulloblastoma. Based on our current analysis, the PDX models within the community are not yet covering the entire heterogeneity within the patient population. As a follow up, we aim to make these models and data accessible in a user-friendly manner so that the community can use them for preclinical research.

Conclusion: PDX models of pediatric brain tumors are very rare. Our molecular characterization allows researchers all over the world to find the right models for their specific scientific question. Therefore, this work will provide an unprecedented resource to study tumor biology and pave the way for improving treatment strategies for children with malignant brain tumors.

Citation Format: Sebastian Brabetz, Susanne N. Gröbner, Huriye Seker-Cin, Florian Selt, Till Milde, David T. Jones, Madison T. Wise, Jessica M. Rusert, Kyle Pedro, Andy Strand, Olaf Witt, Sarah E. Leary, Xiao-Nan Li, Robert J. Wechsler-Reya, James M. Olson, Stefan M. Pfister, Marcel Kool. Molecular characterization of orthotopic patient-derived xenograft models of pediatric brain tumors [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 1935. doi:10.1158/1538-7445.AM2017-1935

Abstract B37: Chemi-genomic analysis of patient-derived xenografts to identify personalized therapies for medulloblastoma

Medulloblastoma (MB) is the most common malignant brain tumor in children. Even with an intensive regimen of surgery, radiation and chemotherapy, one-third of patients still die from their disease. Moreover, survivors suffer devastating side effects including cognitive deficits, endocrine disorders and an increased incidence of secondary cancers later in life. Thus, more effective and less toxic therapies are desperately needed. Recent genomic analyses have identified 4 major subgroups of MB—WNT, SHH, Group 3 and Group 4—that differ in terms of mutations, gene expression profiles and patient outcomes. Despite this heterogeneity, all MB patients currently receive the same therapy. To identify novel therapies for each subgroup of MB, we have assembled a diverse panel of patient-derived xenograft (PDX) lines. These lines, established by orthotopic transplantation of tumor cells obtained from surgery, recapitulate the properties of patients' tumors more accurately than cultured cell lines. We are using these PDX lines to screen small molecule libraries and identify compounds that can inhibit tumor growth and survival. To date we have completed screening of 18 lines, including 10 representing Group 3 MB, the most aggressive and lethal form of the disease. Among the ~7800 compounds tested, we have found 20 that are effective against the majority of Group 3 PDX lines. Ongoing studies are focused on validating the activity of these compounds against additional Group 3 lines and moving the most promising ones forward into in vivo efficacy studies. Similar approaches will be pursued for each of the other subgroups of MB. Drug response data will also be compared with genomic and epigenomic data (whole exome and low coverage whole genome DNA sequencing, DNA methylation analysis, and gene expression profiling) to identify biomarkers of drug responsiveness and key pathways that may be exploited for therapy. Based on these studies, we hope to move away from a one-size-fits-all approach, and begin to treat each patient with therapies that are likely to be effective against their tumor.

Citation Format: Jessica M. Rusert, Alexandra Garancher, Yoko T. Udaka, Sebastian Brabetz, Lourdes A. Esparza, Huriye Seker-Cin, Lin Qi, Mari Kogiso, Simone Schubert, Till Milde, Yoon-Jae Cho, Xiao-Nan Li, James M. Olson, John R. Crawford, Michael L. Levy, Marcel Kool, Stefan M. Pfister, Robert J. Wechsler-Reya. Chemi-genomic analysis of patient-derived xenografts to identify personalized therapies for medulloblastoma. [abstract]. In: Proceedings of the AACR Special Conference: Patient-Derived Cancer Models: Present and Future Applications from Basic Science to the Clinic; Feb 11-14, 2016; New Orleans, LA. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(16_Suppl):Abstract nr B37.

Abstract A07: Molecular characterization of patient-derived xenograft models of pediatric brain tumors

Recent genomic studies have revealed multiple molecular subtypes of pediatric brain cancers that are not only biologically but also clinically distinct. In order to develop novel treatment strategies for these often fatal diseases we need more preclinical models like orthotopic patient-derived xenograft (PDX) models that correctly reflect the many different tumor types. Prior to drug selection and testing, extensive molecular characterizations are needed to precisely assign a distinct molecular subgroup to each PDX model and to learn about its targetable oncogenic drivers.

In an international effort we aim to characterize a large repertoire of PDX models reflecting the many different molecular subtypes of pediatric brain cancer. Thus far, we have collected and characterized 64 established PDX models from 6 atypical teratoid rhabdoid tumors (AT/RT), 7 ependymomas (EPN), 16 high-grade gliomas (HGG), 32 medulloblastomas (MB), and 3 primitive neuroectodermal tumors (PNET). All PDX models and their matching primary tumors (if available) are analyzed by whole-exome and low-coverage whole-genome sequencing, as well as DNA methylation and gene expression profiling.

The DNA methylation and gene expression data showed that PDX models always cluster together with their respective brain tumor reference samples and in most cases very close to their matching primary tumor. Tumor subtype-specific oncogenic lesions could be detected by both sequencing technologies. By comparing PDX models to their primary tumor, we showed that they retain the molecular subtype, mutations and copy number alterations. Only in rare cases we observed additional aberrations in PDX models such as chromothriptic events in one MB (Group 3) or chromosome 1q gain in one EPN (posterior fossa subtype A). However, these additional aberrations are typical for this tumor subtype and were therefore most likely already present in the primary lesion at a subclonal level.

Analysis of our entire cohort identified a overrepresentation of the most aggressive tumor subtypes, but also subtypes which have not been available for preclinical testing before due to lack of genetically engineered mouse models or suitable cell lines, such as Group 4 MBs. Our molecular characterizations of PDX models provide an unprecedented resource to study tumor biology and pave the way for improving treatment strategies of malignant pediatric brain tumors.

Citation Format: Sebastian Brabetz, Huriye Seker-Cin, Susanne N. Gröbner, Norman L. Mack, Volker Hovestadt, David T. W. Jones, Till Milde, Madison T. Wise, Jessica M. Rusert, Kyle Pedro, Karina Bloom, Xiao-Nan Li, Robert J. Wechsler-Reya, James M. Olson, Stefan M. Pfister, Marcel Kool. Molecular characterization of patient-derived xenograft models of pediatric brain tumors. [abstract]. In: Proceedings of the AACR Special Conference: Patient-Derived Cancer Models: Present and Future Applications from Basic Science to the Clinic; Feb 11-14, 2016; New Orleans, LA. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(16_Suppl):Abstract nr A07.

HDAC and PI3K Antagonists Cooperate to Inhibit Growth of MYC-Driven Medulloblastoma

Medulloblastoma (MB) is a highly malignant pediatric brain tumor. Despite aggressive therapy, many patients succumb to the disease, and survivors experience severe side effects from treatment. MYC-driven MB has a particularly poor prognosis and would greatly benefit from more effective therapies. We used an animal model of MYC-driven MB to screen for drugs that decrease viability of tumor cells. Among the most effective compounds were histone deacetylase inhibitors (HDACIs). HDACIs potently inhibit survival of MYC-driven MB cells in vitro, in part by inducing expression of the FOXO1 tumor suppressor gene. HDACIs also synergize with phosphatidylinositol 3-kinase inhibitors to inhibit tumor growth in vivo. These studies identify an effective combination therapy for the most aggressive form of MB.

Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma

Medulloblastoma is a highly malignant paediatric brain tumour currently treated with a combination of surgery, radiation and chemotherapy, posing a considerable burden of toxicity to the developing child. Genomics has illuminated the extensive intertumoral heterogeneity of medulloblastoma, identifying four distinct molecular subgroups. Group 3 and group 4 subgroup medulloblastomas account for most paediatric cases; yet, oncogenic drivers for these subtypes remain largely unidentified. Here we describe a series of prevalent, highly disparate genomic structural variants, restricted to groups 3 and 4, resulting in specific and mutually exclusive activation of the growth factor independent 1 family proto-oncogenes, GFI1 and GFI1B. Somatic structural variants juxtapose GFI1 or GFI1B coding sequences proximal to active enhancer elements, including super-enhancers, instigating oncogenic activity. Our results, supported by evidence from mouse models, identify GFI1 and GFI1B as prominent medulloblastoma oncogenes and implicate 'enhancer hijacking' as an efficient mechanism driving oncogene activation in a childhood cancer.

Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibition

Smoothened (SMO) inhibitors recently entered clinical trials for sonic-hedgehog-driven medulloblastoma (SHH-MB). Clinical response is highly variable. To understand the mechanism(s) of primary resistance and identify pathways cooperating with aberrant SHH signaling, we sequenced and profiled a large cohort of SHH-MBs (n = 133). SHH pathway mutations involved PTCH1 (across all age groups), SUFU (infants, including germline), and SMO (adults). Children >3 years old harbored an excess of downstream MYCN and GLI2 amplifications and frequent TP53 mutations, often in the germline, all of which were rare in infants and adults. Functional assays in different SHH-MB xenograft models demonstrated that SHH-MBs harboring a PTCH1 mutation were responsive to SMO inhibition, whereas tumors harboring an SUFU mutation or MYCN amplification were primarily resistant.

Reduced H3K27me3 and DNA hypomethylation are major drivers of gene expression in K27M mutant pediatric high-grade gliomas

Two recurrent mutations, K27M and G34R/V, within histone variant H3.3 were recently identified in ∼50% of pHGGs. Both mutations define clinically and biologically distinct subgroups of pHGGs. Here, we provide further insight about the dominant-negative effect of K27M mutant H3.3, leading to a global reduction of the repressive histone mark H3K27me3. We demonstrate that this is caused by aberrant recruitment of the PRC2 complex to K27M mutant H3.3 and enzymatic inhibition of the H3K27me3-establishing methyltransferase EZH2. By performing chromatin immunoprecipitation followed by next-generation sequencing and whole-genome bisulfite sequencing in primary pHGGs, we show that reduced H3K27me3 levels and DNA hypomethylation act in concert to activate gene expression in K27M mutant pHGGs.

Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma

Pilocytic astrocytoma, the most common childhood brain tumor, is typically associated with mitogen-activated protein kinase (MAPK) pathway alterations. Surgically inaccessible midline tumors are therapeutically challenging, showing sustained tendency for progression and often becoming a chronic disease with substantial morbidities. Here we describe whole-genome sequencing of 96 pilocytic astrocytomas, with matched RNA sequencing (n = 73), conducted by the International Cancer Genome Consortium (ICGC) PedBrain Tumor Project. We identified recurrent activating mutations in FGFR1 and PTPN11 and new NTRK2 fusion genes in non-cerebellar tumors. New BRAF-activating changes were also observed. MAPK pathway alterations affected all tumors analyzed, with no other significant mutations identified, indicating that pilocytic astrocytoma is predominantly a single-pathway disease. Notably, we identified the same FGFR1 mutations in a subset of H3F3A-mutated pediatric glioblastoma with additional alterations in the NF1 gene. Our findings thus identify new potential therapeutic targets in distinct subsets of pilocytic astrocytoma and childhood glioblastoma.