Molecular Profiling Techniques Research Articles

54PD - Multidisciplinary molecular tumour board: a tool to improve clinical practice and selection accrual for clinical trials in cancer patients

Personalized medicine, based on the discovery of druggable targets through Next-Generation Sequencing (NGS) and other molecular profiling techniques, is changing the clinical practice in Oncology. In this setting, Molecular Tumour Board (MTB) became a crucial multidisciplinary tool for results interpretation in order to better select the treatment for our patients, including the inclusion in clinical trials. We analysed, retrospectively, a cohort of patients with several advanced solid tumours and no candidate for standard treatment consulted in Phase I – Early Clinical Trials Unit of the Antwerp University Hospital with molecular profile (MP) that were discussed in the MTB. Patients with in house and commercial NGS platforms were included. A subgroup of those patients were analysed also based in immunochemistry (IHC) and/or in situ hybridization (ISH). In this study, 141 tissue samples of 133 national and international patients were included. The median age was 59 years old (18 – 85). The majority of the patients were women (56%). A total of 75.9% samples (n = 107) had genomic alterations with an average of 3.44 alterations; of which 80.4% (n = 86) correspond to gene mutations in the NGS panel. About 58.1% (n = 50) had more than one mutated gene. TP53 (32%), KRAS (13%), PIK3CA (8%) and APC (7%) were the more frequent mutated genes. In the subgroup analysis of patients with additional MP information (IHC = X: CISH = 4: FISH = 6) the more common alterations were: TOPO1 (9%), TOP2A (9%), MGMT (8%) and PTEN (8%). By primary tumour site, lung (14.9%), colon (12.1%), pancreas (9.2%) and breast (7.8%) were the most frequent. In 55% (n = 78) of the cases MTB suggested treatment: 70.5% (n = 55) matched therapy and 29.5% (n = 23) non-matched therapy. Almost 37% (n = 29) were included in clinical trials and 6.4% (n = 5) with compassionate use. With Multidisciplinary MTB a considerable number of patients with advanced cancer could be offered targeted therapy or clinical trials based on molecular profiling. National programs for reimbursement and access to suitable target drugs and clinical trials are crucial to guarantee a step forward in cancer treatment.

The emergence of molecular profiling and omics techniques in seagrass biology; furthering our understanding of seagrasses.

Seagrass meadows are disappearing at alarming rates as a result of increasing coastal development and climate change. The emergence of omics and molecular profiling techniques in seagrass research is timely, providing a new opportunity to address such global issues. Whilst these applications have transformed terrestrial plant research, they have only emerged in seagrass research within the past decade; In this time frame we have observed a significant increase in the number of publications in this nascent field, and as of this year the first genome of a seagrass species has been sequenced. In this review, we focus on the development of omics and molecular profiling and the utilization of molecular markers in the field of seagrass biology. We highlight the advances, merits and pitfalls associated with such technology, and importantly we identify and address the knowledge gaps, which to this day prevent us from understanding seagrasses in a holistic manner. By utilizing the powers of omics and molecular profiling technologies in integrated strategies, we will gain a better understanding of how these unique plants function at the molecular level and how they respond to on-going disturbance and climate change events.

Abstract 3166: Querying, viewing and analyzing colorectal cancer translational research studies in tranSMART

Abstract All translational research projects basically share the same design, which is correlating variation in disease phenotype to variation in underlying biology. Typical questions to be addressed are: ‘Which (out of thousands) biomarkers predict good/bad outcome?’ and ‘Which (out of thousands) biomarkers predict whether a patient will benefit from a particular therapy?’. In line with this concept, many research teams have generated large amounts of experimental molecular data from patient samples, yet generally this information is inaccessible for examination due to local storage of both (meta)data and the data processing workflows used. Alternatively, data stored in central databases may only be available for exploration and interpretation by data specialists, provided that the processing workflow has been published and is available. Thus, if data is not recorded and easily retrievable, validation of obtained results (e.g. promising biomarkers) may be virtually impossible. Additionally, it will be difficult to query existing data sets to answer new questions, which may lead to experiments being unnecessarily repeated and biological materials being wasted. In the Netherlands, the Translational Research IT (TraIT) project initiated by the Center for Translational Molecular Medicine (CTMM, www.ctmm-trait.nl) aims to provide IT solutions to support translational research from start to end, including sustainable management and analysis of data. These data types involve the clinical, biomedical imaging, biobanking, (molecular) experimental data domains and their associated workflows. In addition to domain-specific solutions to manage these data types, the processed or ‘final’ data of these different domains will become available in the data-integration platform tranSMART for querying, visualization and analysis. To ensure sustainable data stewardship and provide easy access to existing data for the CTMM colorectal cancer project ‘Decrease in Colorectal Cancer Death (DeCoDe)’, data has been made available in tranSMART and more datasets are being added. The data encompasses both clinical and (molecular) experimental data from non-high-throughput molecular profiling (NHTMP) assays and array-based profiling techniques. It is now possible with tranSMART to explore the respective DeCoDe datasets and perform various analyses (survival, Fisher-exact tests, ANOVA, aCGH tests etc.), without needing deep bioinformatics expertise. Through metadata tags it is possible to trace back raw or pre-processed data in other tools (e.g. clinical data in OpenClinica, array-data in GEO, or histological images of tissue microarrays). Data can be examined in more detail by domain experts using tools they are familiar with or other tools provided by CTMM-TraIT. Thus, existing rich data are made findable, accessible, interoperable and reusable (FAIR) and source data can be traced back for customized processing. Citation Format: Mariska Bierkens, Wim van der Linden, Ward Weistra, Kees van Bochove, Jeroen A.M. Beliën, Remond J.A. Fijneman, Rita Azevedo, Jan-Willem Boiten, Gerrit A. Meijer. Querying, viewing and analyzing colorectal cancer translational research studies in tranSMART. [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 3166.

Prognostic factors, predictive markers and cancer biology: the triad for successful oral cancer chemoprevention.

Oral squamous cell carcinomas represent a significant cancer burden worldwide. Unfortunately, chemoprevention strategies investigated to date have failed to produce an agent considered standard of care to prevent oral cancers. Nonetheless, recent advances in clinical trial design may streamline drug development in this setting. In this manuscript, we review some of these improvements, including risk prediction tools based on molecular markers that help select patients most suitable for chemoprevention. We also discuss the opportunities that novel preclinical models and modern molecular profiling techniques will bring to the prevention field in the near future, and propose a clinical trials framework that incorporates molecular prognostic factors, predictive markers and cancer biology as a roadmap to improve chemoprevention strategies for oral cancers.

Evaluation of the methods to identify patients who may benefit from PARP inhibitor use.

The effectiveness of poly (ADP-ribose) polymerase inhibitors (PARPi) in treating cancers associated with BRCA1/2 mutations hinges upon the concept of synthetic lethality and exemplifies the principles of precision medicine. Currently, most clinical trials are recruiting patients based on pathological subtypes or have included BRCA mutation analysis (germ line and/or somatic) as part of the selection criteria. Mounting evidence, however, suggests that these drugs may also be efficacious in tumors with defects in other genes involved in the homologous recombination repair pathway. Advances in molecular profiling techniques together with increased research efforts have led to a better understanding of the molecular aberrations underlying this BRCA-like phenotype and helped broaden the concept of BRCAness. Hence, it is likely that the list of predictive biomarkers for PARPi therapy will increase in future. There is currently no gold standard method of testing for PARPi response and no universal guidelines are in place on how to incorporate biomarker testing into routine clinical diagnostics. In this review, we explore the concept of BRCAness and highlight the different methods that have been used to identify patients who may benefit from the use of these anticancer agents. The identification of predictive biomarkers is crucial in improving patient selection and expanding the clinical applications of PARPi therapy.

Abstract A30: RATHER: High-resolution molecular profiling of invasive lobular breast cancers

Abstract Introduction: RATHER (Rational Therapy for Breast Cancer) is an international multi-site collaborative effort that aims to use high resolution molecular profiling techniques to identify novel kinase targets for two subtypes of breast cancer, invasive lobular cancers (ILC) and triple negatives (TN) where no targeted therapies are available at present. Experiments: DNA, RNA and protein were extracted from 137 ILC and 155 TN samples with an average of 5 years clinical follow-up. A variety of high resolution molecular profiling methods were used such as copy number analysis (Affymetrix SNP6), gene expression profiling (Agilent 4x44K gene arrays), targeted sequencing (Agilent customized kinome panel & Illumina Nextera Custom Enrichment), whole transcriptomic sequencing and reverse phase protein lysate array (RPPA) analysis. Results: Combining copy number and gene expression data, we have classified the ILC tumors into the intergrative Cluster (IntClust) subgroups that we have previously identified from our large-scale breast cancer study, METABRIC (Molecular Taxonomy of Breast Cancer International Consortium). The ILC tumors were predominantly in IntClust3 (37.2%) and IntClust8 (21.2%). Only two genes were found to be frequently mutated (>10%) ie. CDH1 (40.8%) and PIK3CA (35%ILC). The PI3K pathway has been found to be frequently altered in ILCs by either mutations (PIK3CA and AKT1) or copy number alterations (PTEN). Integrating with transcriptomic and proteomic data, two main subtypes of ILCs were identified: (i) an immune responsive subtype with mRNA up-regulation of PDL1, PD1 and CTLA4 and greater sensitivity to DNA-damaging agents in representative cell line models; (ii) a hormone receptor signalling subtype, associated with Epithelial to Mesenchymal Transition (EMT), and gain of chromosomes 1q and 8q and loss of chromosome 11q. Using somatic mutation rate and eIF4B protein level, we identified three groups with different clinical outcomes, including a group with extremely good prognosis. Conclusion: We provide a comprehensive overview of the molecular alterations driving ILC and have explored links with therapy response. This molecular characterization will help to tailor treatment of ILC through the application of specific targeted, chemo- and/or immune-therapies. Citation Format: Suet-Feung Chin, Magali Michault, Ian Majewski, Tesa M. Severson, Tycho Bismeijer, Leanne De Korning, Justine Peeters, Phillip Schouten, Oscar M. Rueda, Astrid Bosma, Finbarr Tarrant, Yue Fan, BeiLei He, Bernard Pereira, Helen A. Bardwell, Elena Provenzano, Darran P. O'Connor, Sabine Linn, Thierry Dubois, Iris Simon, William Gallagher, Lodewyk Wessels, Rene Bernards, Carlos Caldas. RATHER: High-resolution molecular profiling of invasive lobular breast cancers. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research; Oct 17-20, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(2_Suppl):Abstract nr A30.

Cellular identity at the single-cell level

A single cell creates surprising heterogeneity in a multicellular organism. While every organismal cell shares almost an identical genome, molecular interactions in cells alter the use of DNA sequences to modulate the gene of interest for specialization of cellular functions. Each cell gains a unique identity through molecular coding across the DNA, RNA, and protein conversions. On the other hand, loss of cellular identity leads to critical diseases such as cancer. Most cell identity dissection studies are based on bulk molecular assays that mask differences in individual cells. To probe cell-to-cell variability in a population, we discuss single cell approaches to decode the genetic, epigenetic, transcriptional, and translational mechanisms for cell identity formation. In combination with molecular instructions, the physical principles behind cell identity determination are examined. Deciphering and reprogramming cellular types impact biology and medicine.

Clinical Insights into Pulmonary Exacerbations in Cystic Fibrosis from the Microbiome. What Are We Missing?

Pulmonary exacerbations account for much of the decrease in lung function and consequently most of the morbidity and mortality in patients with cystic fibrosis. These events are driven by an acute inflammatory response to infection. Recent technological advancements in molecular profiling techniques have allowed for a proliferation of microbiome studies of the lower airways of patients with cystic fibrosis. But these methods may not provide a comprehensive and unbiased measure of the lung microbiota in these patients and molecular profiles do not always translate to quantitative microbiology. Furthermore, these studies have not yet been able to provide much in the way of mechanistic insights into exacerbations or to guide patient therapy. We propose a model in which pulmonary exacerbations may be driven by an active subpopulation of the lung microbiota, which may represent only a small portion of the microbiota measured in a clinical sample. Methodology should be focused on the ultimate goal, which is to use the best available approaches to provide accurate quantitative measures of the microbiome to inform clinical decisions and provide rapid assessment of treatment efficacy. These strategies would be relevant to other chronic lung diseases such as chronic obstructive pulmonary disease and neutrophilic asthma.

Comparison of DNA and RNA analyte extraction and melanin removal methods from formalin-fixed, paraffin-embedded (FFPE) melanoma.

e20002 Background: The increasing availability of molecular profiling techniques amenable to FFPE tissue presents a key opportunity to study the molecular basis of melanoma. In order to optimize ou...

Molecular characterization and targeted therapeutic approaches in breast cancer.

Despite the wide improvements in breast cancer (BC) detection and adjuvant treatment, BC is still responsible for approximately 40,000 deaths annually in the United States. Novel biomarkers are fundamental to assist clinicians in BC detection, risk stratification, disease subtyping, prediction of treatment response, and surveillance, allowing a more tailored approach to therapy in both primary and metastatic settings. In primary BC, the development of molecular profiling techniques has added prognostic and predictive information to conventional biomarkers - estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2. Moreover, the application of next-generation sequencing and reverse-phase protein microarray methods in the metastatic setting holds the promise to further advance toward a personalized management of cancer. The improvement in our understanding on BC biology associated with the study of the genomic aberrations characterizing the most common molecular subtypes allows us to explore new targets for drug development. Finally, the integration of cancer stem cell-targeted therapies and immune therapies in future combination regimens increases our chances to successfully treat a larger proportion of women with more aggressive and resistant metastatic disease. This article reviews the current state of novel biological markers for BC, the evidence to demonstrate their clinical validity and utility, and the implication for therapeutic targeting.

Understanding the rules of the road: proteomic approaches to interrogate the blood brain barrier

The blood brain barrier (BBB) is often regarded as a passive barrier that protects brain parenchyma from toxic substances, circulating leukocytes, while allowing the passage of selected molecules. Recently, a combination of molecular profiling techniques have characterized the constituents of the BBB based on in vitro models using isolated endothelial cells and ex vivo models analyzing isolated blood vessels. Characterization of gene expression profiles that are specific to the endothelium of brain blood vessels, and the identification of proteins, cells and multi-cellular structure that comprise the BBB have led to a emerging consensus that the BBB is not, in and of itself, a simple barrier of specialized endothelial cells. Instead, regulation of transcytosis, permeability, and drug translocation into the central nervous system is now viewed as a collection of neurovascular units (NVUs) that, together, give the BBB its unique biological properties. We will review recent technology advancing the understanding of the molecular basis of the BBB with a focus on proteomic approaches.

Abstract PR05: ERK pathway activation is associated with acquired resistance to AZD9291, a third-generation irreversible inhibitor targeting EGFR sensitizing (EGFRm+) and resistance (T790M) mutations in NSCLC

Abstract First- and second-generation EGFR tyrosine kinase inhibitors (TKIs) are established first line therapies for patients with advanced NSCLC with activating/sensitising mutations in EGFR. Unfortunately, patients ultimately develop disease progression with acquisition of a second-site EGFR T790M mutation in more than half of cases. This has led to the development of third generation EGFR TKIs such as AZD9291 which inhibit both the EGFRm+ and T790M mutations in preclinical models, and are showing activity in patients with TKI-resistant tumors harbouring T790M in Phase I studies. Despite the potential improvements brought by third generation EGFR-TKIs, advanced EGFRm+ tumor cells will still remain highly adaptable, and the inevitability of further resistance will potentially limit the effectiveness of these drugs. As such, the identification of resistance mechanisms to these agents is essential to guide future therapeutic strategies and identify novel:novel combinations. To interrogate resistance to AZD9291, we have generated panels of EGFRm+ cell populations resistant to gefitinib (first generation TKI), and EGFRm+ and EGFRm+/T790M cell populations resistant to afatinib (second generation TKI) and WZ4002 or AZD9291 (third generation TKIs). Subsequently, we have characterized the cell lines using a phenotypic screen to compare the sensitivity of small molecule inhibitors of canonical signaling pathways between the resistant and parental cell populations. In addition we have used a variety of molecular profiling techniques to determine the DNA mutation and copy number status and mRNA expression profile of a panel of cancer associated genes within the resistant cell populations. The effects on cell survival across the range of resistant models by a panel of pathway inhibitors, in combination with the originating TKI, indicated that resistance to the EGFR inhibitors was frequently associated with increased sensitivity to selumetinib (AZD6244; ARRY-142886) (MEK1/2 inhibitor), suggesting that ERK signaling is commonly reactivated to circumvent inhibition of the EGFR pathway. Further, molecular analysis indicated the presence of mutations in NRAS, including a novel E63K mutation, or increased copy number of NRAS or KRAS within 12/25 and 3/9 resistant cell populations representing resistance in EGFRm+ and EGFRm+/T790M settings respectively. Analysis of the functional consequence of the observed RAS modifications confirmed their role in driving the survival of EGFR pathway addicted cells when EGFR signaling is inhibited. Collectively, these data suggest that ERK pathway activation, in particular as a result of increased RAS activation, is frequently associated with acquired resistance to AZD9291 and other EGFR TKI inhibitors. In addition the data suggests that combining AZD9291 with selumetinib could prevent or delay resistance, and therefore potentially drive superior duration of benefit compared to TKI alone. Citation Format: Cath Eberlein, Katie Al-Kadhimi, Sarah Ross, Henry Brown, Paul Fisher, Daniel Stetson, Zhongwu Lai, Kenneth Thress, Brian Dougherty, William Pao, Darren Cross. ERK pathway activation is associated with acquired resistance to AZD9291, a third-generation irreversible inhibitor targeting EGFR sensitizing (EGFRm+) and resistance (T790M) mutations in NSCLC. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Drug Sensitivity and Resistance: Improving Cancer Therapy; Jun 18-21, 2014; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(4 Suppl): Abstract nr PR05.

Label free quantification of time evolving morphologies using time-lapse video microscopy enables identity control of cell lines and discovery of chemically induced differential activity in iso-genic cell line pairs

Label free time-lapse video microscopy based monitoring of time evolving cell population morphology has potential to offer a simple and cost effective method for identity control of cell lines. Such morphology monitoring also has potential to offer discovery of chemically induced differential changes between pairs of cell lines of interest, for example where one in a pair of cell lines is normal/sensitive and the other malignant/resistant. A new simple algorithm, pixel histogram hierarchy comparison (PHHC), for comparison of time evolving morphologies (TEM) in phase contrast time-lapse microscopy movies was applied to a set of 10 different cell lines and three different iso-genic colon cancer cell line pairs, each pair being genetically identical except for a single mutation. PHHC quantifies differences in morphology by comparing pixel histogram intensities at six different resolutions. Unsupervised clustering and machine learning based classification methods were found to accurately identify cell lines, including their respective iso-genic variants, through time-evolving morphology. Using this experimental setting, drugs with differential activity in iso-genic cell line pairs were likewise identified. Thus, this is a cost effective and expedient alternative to conventional molecular profiling techniques and might be useful as part of the quality control in research incorporating cell line models, e.g. in any cell/tumor biology or toxicology project involving drug/agent differential activity in pairs of cell line models.

Effect of stacking insecticidal cry and herbicide tolerance epsps transgenes on transgenic maize proteome.

BackgroundThe safe use of stacked transgenic crops in agriculture requires their environmental and health risk assessment, through which unintended adverse effects are examined prior to their release in the environment. Molecular profiling techniques can be considered useful tools to address emerging biosafety gaps. Here we report the first results of a proteomic profiling coupled to transgene transcript expression analysis of a stacked commercial maize hybrid containing insecticidal and herbicide tolerant traits in comparison to the single event hybrids in the same genetic background.ResultsOur results show that stacked genetically modified (GM) genotypes were clustered together and distant from other genotypes analyzed by PCA. Twenty-two proteins were shown to be differentially modulated in stacked and single GM events versus non-GM isogenic maize and a landrace variety with Brazilian genetic background. Enrichment analysis of these proteins provided insight into two major metabolic pathway alterations: energy/carbohydrate and detoxification metabolism. Furthermore, stacked transgene transcript levels had a significant reduction of about 34% when compared to single event hybrid varieties.ConclusionsStacking two transgenic inserts into the genome of one GM maize hybrid variety may impact the overall expression of endogenous genes. Observed protein changes differ significantly from those of single event lines and a conventional counterpart. Some of the protein modulation did not fall within the range of the natural variability for the landrace used in this study. Higher expression levels of proteins related to the energy/carbohydrate metabolism suggest that the energetic homeostasis in stacked versus single event hybrid varieties also differ. Upcoming global databases on outputs from “omics” analyses could provide a highly desirable benchmark for the safety assessment of stacked transgenic crop events. Accordingly, further studies should be conducted in order to address the biological relevance and implications of such changes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-014-0346-8) contains supplementary material, which is available to authorized users.

Abstract 1722: Investigating resistance to AZD9291

Abstract First- and second-generation EGFR TKIs are established first line therapy for patients with NSCLC with activating mutations in EGFR. Unfortunately, patients ultimately develop disease progression with acquisition of a second-site EGFR T790M mutation in more than half of cases. This has led to the development of third generation EGFR TKIs which inhibit both the EGFRm+ and T790M mutations in preclinical models and are showing activity in TKI-resistant patients in Phase I studies. Despite the potential improvements brought by third generation EGFR-TKIs, advanced EGFRm+ tumor cells will still remain highly adaptable and the inevitability of further resistance will limit the effectiveness of these drugs. As such, the identification of resistance mechanisms to these agents is essential to guide future therapeutic strategies and identify novel:novel combinations. To interrogate resistance to AZD9291, we have generated panels of EGFRm+ cell lines resistant to gefitinib (first generation TKI) and EGFRm+ and EGFRm+/T790M cell lines resistant to afatinib and AZD9291 (second and third generation TKIs, respectively). Subsequently, we characterised the cell lines using a variety of molecular profiling techniques including Next Generation Sequencing (NGS), Affymetrix gene expression analysis, and phenotypic profiling following pharmacological modulation by small molecule inhibitors of canonical signaling pathways. The effects on cell survival across the range of resistant models by a panel of pathway inhibitors indicated that resistance to the EGFR inhibitors, in particular AZD9291, is frequently associated with increased sensitivity to selumetinib (AZD6244; ARRY-142886) (MEK1/2 inhibitor), suggesting that ERK signaling is commonly reactivated to circumvent inhibition of the EGFR pathway. Molecular characterisation of the panel of cell lines suggests a range of different resistance mechanisms may be responsible for reactivation of ERK signaling, including a decrease in negative regulators of ERK such as DUSP6 or an epithelial to mesenchymal transition consistent with previous observations. Collectively, these data suggest that combining an EGFR TKI with a MEK inhibitor could prevent or delay resistance and drive superior duration of benefit from these agents. Citation Format: Cath Eberlein, Laura Ratcliffe, Lucy O'Brien, Katie Al-Khadimi, Henry Brown, Paul Fisher, Daniel Stetson, Zhongwu Lai, Gayle Marshall, Claire Barnes, Kenneth Thress, Brian Dougherty, William Pao, Darren Cross. Investigating resistance to AZD9291. [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 1722. doi:10.1158/1538-7445.AM2014-1722

New Therapies in T-cell Lymphoma

T-cell lymphomas represent 10–12% of all patients with non-Hodgkin lymphoma (NHL) in the Western world. When cutaneous T-cell lymphoma (CTCL) is excluded, peripheral T-cell lymphoma—not otherwise specified (PTCL-NOS), anaplastic large-cell lymphoma (ALCL), and angioimmunoblastic T-cell lymphoma (AITL) represent the overwhelming majority of patients in this population. These diseases remain a great challenge to treat. They are characterized by an aggressive presentation, extranodal disease, paraneoplastic phenomena, and resistance to standard chemotherapeutics. With the rapid development of new molecular gene profiling techniques, it is highly likely that these diseases will be subclassified by molecular abnormalities in the future. An evolving understanding of the tumor molecular pathogenesis will undoubtedly lead to further novel targeted therapies. Immunoconjugates, such as brentuximab vedotin (BV), have provided outstanding responses in relapsed, refractory CD30-positive ALCL. Histone deacetylase (HDAC) inhibitors have shown activity in PTCL and are potentially synergistic with proteasome inhibitors. Denileukin diftitox is an interesting recombinant DNA fusion protein linking fragments of the diphtheria toxin to interleukin-2 (IL-2) that is tested in clinical trials. Crizotinib, a highly specific anaplastic lymphoma kinase (ALK) inhibitor, has shown great promise in small number of patients with ALK-positive ALCL; the future of patients with this disorder looks very promising. Biomarker-driven chemotherapeutics is becoming a critical part of the state-of-the-art treatment in early- and late-phase clinical trials. It is crucial that future trials include sensible biomarker-based designs when future treatments are used in these challenging disorders.

Management of hepatoblastoma: an update.

To summarize the current standards and guidelines for the diagnosis and management of hepatoblastoma, a rare pediatric liver tumor. Hepatoblastoma is the most common malignant liver tumor in childhood. International collaborative efforts have led to uniform implementation of the pretreatment extent of disease (PRETEXT) staging system as a means to establish consensus classification and assess upfront resectability. Additionally, current histopathological classification, in light of more advanced molecular profiling and immunohistochemical techniques and integration of tumor biomarkers into risk stratification, is reviewed. Multimodal therapy is composed of chemotherapy and surgical intervention. Achievement of complete surgical resection plays a key role in successful treatment for hepatoblastoma. Overall, outcomes have greatly improved over the past four decades because of advances in chemotherapeutic agents and administration protocols as well as innovations of surgical approach, including the use of vascular exclusion, ultrasonic dissection techniques, and liver transplantation. Challenges remain in management of high-risk patients as well as patients with recurrent or metastatic disease. Eventually, a more individualized approach to treating the different types of the heterogeneous spectrum of hepatoblastoma, in terms of different chemotherapeutic protocols and timing as well as type and extent of surgery, may become the basis of successful treatment in the more complex or advanced types of hepatoblastoma.

One mouse, one patient paradigm: New avatars of personalized cancer therapy

Over the last few decades, study of cancer in mouse models has gained popularity. Sophisticated genetic manipulation technologies and commercialization of these murine systems have made it possible to generate mice to study human disease. Given the large socio-economic burden of cancer, both on academic research and the health care industry, there is a need for in vivo animal cancer models that can provide a rationale that is translatable to the clinic. Such a bench-to-bedside transition will facilitate a long term robust strategy that is economically feasible and clinically effective to manage cancer. The major hurdles in considering mouse models as a translational platform are the lack of tumor heterogeneity and genetic diversity, which are a hallmark of human cancers. The present review, while critical of these pitfalls, discusses two newly emerging concepts of personalized mouse models called “Mouse Avatars” and Co-clinical Trials. Development of “Mouse Avatars” entails implantation of patient tumor samples in mice for subsequent use in drug efficacy studies. These avatars allow for each patient to have their own tumor growing in an in vivo system, thereby allowing the identification of a personalized therapeutic regimen, eliminating the cost and toxicity associated with non-targeted chemotherapeutic measures. In Co-clinical Trials, genetically engineered mouse models (GEMMs) are used to guide therapy in an ongoing human patient trial. Murine and patient trials are conducted concurrently, and information obtained from the murine system is applied towards future clinical management of the patient’s tumor. The concurrent trials allow for a real-time integration of the murine and human tumor data. In combination with several molecular profiling techniques, the “Mouse Avatar” and Co-clinical Trial concepts have the potential to revolutionize the drug development and health care process. The present review outlines the current status, challenges and the future potential of these two new in vivo approaches in the field of personalized oncology.

Molecular models of the cardiorenal syndrome

Molecular profiling techniques have provided extensive sets of molecular features characterizing clinical phenotypes, but further extrapolation to mechanistic molecular models of disease pathophysiology faces major challenges. Here, we describe a computational procedure for delineating molecular disease models utilizing omics profiles, and exemplify the methodology on aspects of the cardiorenal syndrome describing the clinical association of declining kidney function and increased cardiovascular event rates. Individual molecular features as well as selected molecular processes were identified as linking cardiovascular and renal pathology as a combination of cross-organ mediators and common pathophysiology. The molecular characterization of the disease presents as a set of molecular processes together with their interactions, composing a molecular disease model of the cardiorenal syndrome. Integrating omics profiles describing aspects of cardiovascular disease and respective profiles for advanced chronic kidney disease on molecular interaction networks, computation of disease term-specific subgraphs, and complemented by subgraph segmentation allowed delineation of disease term-specific molecular models, at their intersection providing contributors to cardiorenal pathology. Building such molecular disease models allows in a generic way to integrate multi-omics sources for generating comprehensive sets of molecular processes, on such basis providing rationale for biomarker panel selection for further characterizing clinical phenotypes.

Abstract LB-160: A feasibility trial using molecular-guided therapy for the treatment of patients with refractory or recurrent neuroblastoma.

Abstract Background: Neuroblastoma is the most common extracranial solid tumor in children, and treatment options for recurrent neuroblastoma are limited. Using molecular profiling to target the molecular vulnerabilities of individual patient tumors with existing therapeutic agents may result in a rational, data-driven approach to treatment with potential to improve clinical outcomes. Methods: This was a multicenter study through the Neuroblastoma and Medulloblastoma Translational Research Consortium. The primary objective of this study was to evaluate the feasibility of supporting real-time treatment decisions through predictive modeling of genome-wide mRNA gene expression data from neuroblastoma tumor biopsies. Feasibility was defined as completion of tumor biopsy, histopathological evaluation, RNA extraction and quality control, gene expression profiling within a CLIA-certified laboratory, bioinformatic analysis, generation of a drug prediction report, molecular tumor board review yielding a formulated treatment plan, independent medical monitor review, treatment initiation within a 2-week period and completion of one cycle of therapy. The secondary objectives included a reproducibility study of patient biopsies, safety and response to therapy. Research validation in cell culture models of patient tumors was performed. Results: Fourteen patients with multiply relapsed neuroblastoma were enrolled between July 2011 and November 2012. All biopsies passed histopathology and RNA quality control. Generation of gene expression data and its analysis (3-8 days), reports which linked this data into medically actionable drug candidates (0-3 days), molecular tumor board (1-6 days) and independent medical monitor review (1 -4 days) were all completed in real-time. The average time was 12.4 days from biopsy to initiation of treatment. There were no unexpected serious adverse events on study and patients tolerated therapy well. Clinical benefit was seen 50% of patients. Triplicate biopsies showed reproducible sets of drugs and the comparatively large differences in drug lists between patients show that the drug lists are tailored to patients. Comparison of RNA expression profiles with RNA sequencing from each patient showed strong correlation. Conclusion: This study shows that it is feasible to create therapeutic treatment plans based on genomic profiling in real time and that patients are able to be treated safely on a tumor board derived molecular guided therapy using existing medications. Incorporation of further genomic studies to evaluate additional molecular profiling techniques in order to make more informed individual therapeutic treatment plans will be evaluated in future studies. Citation Format: Giselle L. Sholler, Genevieve Bergendahl, Alyssa VanderWerff, William Ferguson, William Roberts, Don Eslin, Jacqueline Kraveka, Joel Kaplan, Deanna Mitchell, Nehal Parikh, Kathleen Neville, Takamaru Ashikaga, Jeffrey Bond, Gina Hanna, Melinda Merchant, Matt Huentelman, Jason Corneveaux, Jeffrey Trent. A feasibility trial using molecular-guided therapy for the treatment of patients with refractory or recurrent neuroblastoma. [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-160. doi:10.1158/1538-7445.AM2013-LB-160