Platform For Translational Research Research Articles

Ex Vivo Porcine Organ Perfusion Models as a Suitable Platform for Translational Transplant Research.

In transplantation surgery, extending the criteria for organ donation to include organs that may have otherwise been previously discarded has provided the impetus to improve organ preservation. The traditional method of cold static storage (CS) has been tried and tested and is suitable for organs meeting standard criteria donation. Ex vivo machine perfusion is, however, associated with evidence suggesting that it may be better than CS alone and may allow for organ donation criteria to be extended. Much of our knowledge of organ preservation is derived from animal studies. We review ex vivo porcine organ perfusion models and discuss the relevance to the field of transplantation surgery. Following a systematic literature search, only articles that reported on experimental studies with focus on any aspect(s) of ex vivo and porcine perfusion of organs yet limited to the context of organ transplantation surgery were included. The database search and inclusion/exclusion criteria identified 22 journal articles. All 22 articles discussed ex vivo porcine organ perfusion within the context of transplant preservation surgery: 8 liver, 3 kidney, 3 lung, 2 pancreas/islet, 4 discussed a combined liver-kidney multiorgan model, 1 small bowel, and 1 cardiac perfusion model systems. The ex vivo porcine perfusion model is a suitable, reliable, and safe translational research model. It has advantages to investigate organ preservation techniques in a reproducible fashion in order to improve our understanding and has implications to extend the criteria for organ donation.

Patient-Derived Xenograft Models of Epithelial Ovarian Cancer for Preclinical Studies.

PurposePatient-derived tumor xenografts (PDXs) can provide more reliable information about tumor biology than cell line models. We developed PDXs for epithelial ovarian cancer (EOC) that have histopathologic and genetic similarities to the primary patient tissues and evaluated their potential for use as a platform for translational EOC research.Materials and MethodsWe successfully established PDXs by subrenal capsule implantation of primary EOC tissues into female BALB/C-nude mice. The rate of successful PDX engraftment was 48.8% (22/45 cases). Hematoxylin and eosin staining and short tandem repeat analysis showed histopathological and genetic similarity between the PDX and primary patient tissues.ResultsPatients whose tumors were successfully engrafted in mice had significantly inferior overall survival when compared with those whose tumors failed to engraft (p=0.040). In preclinical tests of this model, we found that paclitaxel-carboplatin combination chemotherapy significantly deceased tumor weight in PDXs compared with the control treatment (p=0.013). Moreover, erlotinib treatment significantly decreased tumor weight in epidermal growth factor receptor–overexpressing PDX with clear cell histology (p=0.023).ConclusionPDXs for EOC with histopathological and genetic stability can be efficiently developed by subrenal capsule implantation and have the potential to provide a promising platform for future translational research and precision medicine for EOC.

The Use of Translational Research Platforms in Clinical and Biomedical Data Exploration.

The rise of precision medicine combined with the variety of biomedical data sources and their heterogeneous nature make the integration and exploration of information that they retain more complicated. In light of these issues, translational research platforms were developed as a promising solution. Research centers have used translational tools for the study of integrated data for hypothesis development and validation, cohort discovery and data-exploration. For this article, we reviewed the literature in order to determine the use of translational research platforms in precision medicine. These tools are used to support scientists in various domains regarding precision medicine research. We identified eight platforms: BRISK, iCOD, iDASH, tranSMART, the recently developed OncDRS, as well as caTRIP, cBio Cancer Portal and G-DOC. The last four platforms explore multidimensional data specifically for cancer research. We focused on tranSMART, for it is the most broadly used platform, since its development in 2012.

Exploring and visualizing multidimensional data in translational research platforms.

The unprecedented advances in technology and scientific research over the past few years have provided the scientific community with new and more complex forms of data. Large data sets collected from single groups or cross-institution consortiums containing hundreds of omic and clinical variables corresponding to thousands of patients are becoming increasingly commonplace in the research setting. Before any core analyses are performed, visualization often plays a key role in the initial phases of research, especially for projects where no initial hypotheses are dominant. Proper visualization of data at a high level facilitates researcher’s abilities to find trends, identify outliers and perform quality checks. In addition, research has uncovered the important role of visualization in data analysis and its implied benefits facilitating our understanding of disease and ultimately improving patient care. In this work, we present a review of the current landscape of existing tools designed to facilitate the visualization of multidimensional data in translational research platforms. Specifically, we reviewed the biomedical literature for translational platforms allowing the visualization and exploration of clinical and omics data, and identified 11 platforms: cBioPortal, interactive genomics patient stratification explorer, Igloo-Plot, The Georgetown Database of Cancer Plus, tranSMART, an unnamed data-cube-based model supporting heterogeneous data, Papilio, Caleydo Domino, Qlucore Omics, Oracle Health Sciences Translational Research Center and OmicsOffice® powered by TIBCO Spotfire. In a health sector continuously witnessing an increase in data from multifarious sources, visualization tools used to better grasp these data will grow in their importance, and we believe our work will be useful in guiding investigators in similar situations.

Abstract IA13: The Patient-Derived Xenograft Program at The Jackson Laboratory

Abstract The Patient Derived Xenograft (PDX) Program at The Jackson Laboratory have as its focus, the development of quality surrogates of primary human tumors for the research community, the construction and optimization of murine hosts for human tumor xenografts, and the conduct of research into cancer biology using these PDX models. Begun in 2010, the PDX Program is based on the foundational murine host, the NOD-scid IL2rgnull or NSG (NOD.Cg-Prkdcscid IL2rgtm1wjl/SzJIL2rgtm1wjl) mouse, which lacks T, B, and NK cells and harbors deficiencies in innate immune response due to defects in multiple cytokine receptors including the IL2. 4, 7, 9, 15, and 21 receptors1,2. NSG mice have superior engraftment profiles as compared to other immunodeficient strains. These tumor xenografts in NSG hosts maintain the features of primary of engrafted human tumors including, tumor heterogeneity, three-dimensional architecture, and tumor biology including response to therapeutics. The engraftment rates vary according to tumor types with prostate cancers being among the lowest (3%), and colorectal cancers (66%), melanomas, and glioblastomas being among the best, according to whether the tumors are from metastatic sites, show a higher tumor grade, or have larger amounts of starting tumor material. We currently have 446 PDX models in stock with ~100 in the pipeline, and when coupled with 218 models from our Korean cooperative institution (Ewha University), our total collection is ~664 covering 15 tumor types with none beyond passage number 4 (P4). Most have genomic data available and the Korean PDXs have matching normal tissue and DNA sequence data. Importantly, the human immune system can be engrafted in NSG mice and in the presence of a human tumor, can be used to study tumor-immune cell interactions including response to immune therapeutics. In addition, our colleagues and we have developed genetic modifications of the NSG to provide unique engraftment options: MHC class I and II knockouts to reduce xenogeneic graft-vs.-host disease, expressing HLA-A2 and other HLA class I and II transgenes to develop HLA-restricted human cytotoxic T cells, and IL-6 and prolactin to support engraftment of tumors needing these factors. NSG mice expressing human IL3/GM-CSF/SCF supports the immune reconstitution of myeloid progenitors providing a more complete immune system and has been useful in testing cancer immune therapeutics. With 26 staff dedicated to PDX and NSG experimentation, we provide strains of NSG mice with or without human immune cell reconstitution, and conduct large-scale pharmacological studies in cohorts of PDX models. 1Hidalgo M, Amant F, Biankin AV, Budinská E, Byrne AT, Caldas C, Clarke RB, de Jong S, Jonkers J, Mælandsmo GM, Roman-Roman S, Seoane J, Trusolino L, Villanueva A. Patient-derived xenograft models: an emerging platform for translational cancer research. Cancer Discov. 2014 Sep;4(9):998-1013. 2Shultz LD, Goodwin N, Ishikawa F, Hosur V, Lyons BL, Greiner DL. Human cancer growth and therapy in immunodeficient mouse models. Cold Spring Harbor Protoc. 2014 Jul 1;2014(7):694-708. Citation Format: Edison T. Liu, James Keck, Susie Airhart, Lenny Shultz, Charles Lee, Carol Bult. The Patient-Derived Xenograft Program at The Jackson Laboratory. [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 IA13.

Patient-derived xenograft in zebrafish embryos: a new platform for translational research in neuroendocrine tumors.

Preclinical research on neuroendocrine tumors usually involves immortalized cell lines and few animal models. In the present study we described an in vivo model based on patient-derived xenografts of neuroendocrine tumor cells in zebrafish (Danio rerio) embryos, allowing a rapid analysis of the angiogenic and invasive potential. Patient-derived neuroendocrine tumor cells were transplanted in 48 hours post-fertilization Tg(fli1a:EGFP) y1 zebrafish embryos that express enhanced green fluorescent protein in the entire vasculature. Neuroendocrine tumor cells, stained with CM-Dil, were injected into the subperidermal (perivitelline) space, close to the developing subintestinal venous plexus. A proper control group, represented by zebrafish injected with only D-PBS, was included in this study. Angiogenic and invasive potentials of each patient-derived xenograft were evaluated by both epifluorescence and confocal microscopes. Six out of eight neuroendocrine tumor samples were successfully transplanted in zebrafish embryos. Although the implanted tumor mass had a limited size (about 100 cells for embryos), patient-derived xenografts showed pro-angiogenic (5 cases) and invasive (6 cases) behaviors within 48 hours post injection. Patient-derived xenograft in zebrafish embryos appears to be a reliable in vivo preclinical model for neuroendocrine tumors, tumors with often limited cell availability. The rapidity of this procedure makes our model a promising platform to perform preclinical drug screening and opens a new scenario for personalized treatment in patients with neuroendocrine tumors.

Abstract 434: Rational molecular assessment and innovative drug selection (RAIDs): exome data from cervical cancer

Abstract Background Recent retrospective data1,2 identified major molecular alterations in cervical cancer (CC), but so far there has been no prospective assessment on patient outcome using a complete molecular profiling with quality control evaluation of treatment. The Cetuxicol (phase 2) clinical trial showed that the addition of Cetuximab over a 6 week period, did not improve DFS. PI3K pathway mutations in the tumor in the Cetuximab treatment arm led to a worse DFS3. We are lacking prognostic and predictive biomarkers for CC treatment and there is a growing need for the development of biomarkers to follow up the course of the disease. Methodology RAIDs (http://www.raids-fp7.eu) is a multidisciplinary co-operation between academic clinical centers, SMEs and translational research platforms in seven European countries. It includes: 1) a cognitive cohort study (BioRAIDs)4, one of the first prospective trials intended to define patient stratification for targeted therapies, 2) a targeted clinical trial using an HPV directed vaccine and 3) preclinical studies aiming at assessing new treatment strategies. Molecular analysis on quality controlled tumor and sera samples from 500 patients enrolled in BioRAIDs combine Next Generation Sequencing at SeqOmics (Hungary), PIK3CA mutations detection in circulating tumor (ct) DNA at ERASMUS (The Netherlands), Reverse Phase Protein array and HPV insertion sites analyses at Institut Curie (France). Bioinformatics pipelines to detect somatic mutations and clustering methods were developed in order to stratify the patients into different subtypes. Following quality control, the pharmacological profiling of a panel of 20 CC cell lines using a panel of drugs which may potentially synergize with “standard treatment” has been completed. Drugs were chosen so as to interfere with different signaling pathways. Results Molecular profiles including exome sequencing and ctDNA analyses on 48 quality controlled samples from the BioRAIDs patients and 20 CC cell lines will be presented. Preliminary results on HPV insertion sites in tumor and serum will be reported. Somatic and DNA copy number alterations from exome sequencing profiles confirm PI3K pathway mutations to be a dominant feature in CC. Stratifications of patients’ tumors based on their mutation profiles show that some cell lines cluster similarly to patients’ tumors, suggesting that they will be helpful for the prediction of response to drugs for patients within the same cluster. Conclusions The identification of predictive tumor/blood based biomarkers will permit the definition of new strategies for precision medicine in CC. A bioinformatics analysis which will assess drug responsiveness in CC cell lines in relation to specific genomic alterations is ongoing. Its results should permit to select treatments according to genetic “constellations” of the tumors. Citation Format: Suzy Scholl, Maud Kamal, Els Berns, Balzs Balint, Attila Kereszt, Leanne de Koning, Emmanuelle Jeannot, Windy Luscap-rondof, Vonick Sibut, Philippe Hupe, Gemma Kenter, Sanne Samuels, Katja Jordanova, Sandrine Blanchet, Laurence Lafanachere, Marc Billaud, RAIDs consortium. Rational molecular assessment and innovative drug selection (RAIDs): exome data from cervical cancer. [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 434.

Abstract 631: The mouse tumor biology database (MTB): An integrated data resource for mouse and patient derived xenograft (PDX) models of human cancer

Abstract The laboratory mouse is the premier model organism for understanding the genetic basis of human cancer and is a powerful platform for investigating novel targets for therapeutic intervention. Research using genetically engineered mouse models has led to key insights into the genetics of cancer susceptibility, the function of tumor suppressors and oncogenes, and therapy responses in pre-clinical and co-clinical studies. Patient Derived Xenografts (PDX) models are another model system for in vivo cancer studies. PDX models are created by implanting patient tumors into immunodeficient or humanized mouse hosts. PDX models are a powerful translational research platform for pre-clinical and co-clinical studies. The number of mouse models and the volume and heterogeneity of data related to the characterization of these models has increased dramatically in recent years, making integrated searches of these data and identifying relevant models a significant barrier to their effective use. The Mouse Tumor Biology database (MTB) (http://tumor.informatics.jax.org) provides on-line query tools to facilitate cohesive searches and visualization of these varied data, thus enabling the identification of novel mouse models of human cancer and potential therapeutic treatments. The Mouse Tumor Biology database is an expertly curated resource for information and data about genetically modified mouse strains and PDX models of human cancer. Enforcement of standard gene and strain nomenclature and use of controlled vocabularies within MTB enables complete and accurate searching of the published literature for relevant mouse models. MTB contains data from spontaneous or endogenously induced tumors from genetically defined mice including tumor classification, incidence and latency, tumor associated QTLs, pathology reports, images and genetic changes in the tumor (somatic) and background strain (germline) genomes. The PDX resource enables searches based on tumor type, cancer diagnosis, and genomic properties of the engrafted tumors. Information in MTB is obtained from curation of peer-reviewed scientific publications and from direct data submissions from individual investigators and large-scale programs. MTB contains over 71,000 Tumor Frequencies, and over 2,080 Pathology Reports with over 5,800 images from over 3,600 references. MTB also provides access to detailed clinical, pathological, expression and genomics data from over 450 PDX models. Information in MTB is integrated with cancer models data from other bioinformatics resources including PathBase, the Gene Expression Omnibus (GEO), and ArrayExpress. MTB is supported by NCI grant CA089713. Citation Format: Dale A. Begley, Debbie M. Krupke, Steven B. Neuhauser, Joel E. Richardson, John P. Sundberg, Janan T. Eppig, Carol J. Bult. The mouse tumor biology database (MTB): An integrated data resource for mouse and patient derived xenograft (PDX) models of human cancer. [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 631.

Abstract CT076: Women's triple-negative, first-line treatment: Improving outcomes in triple-negative breast cancer using molecular triaging and diagnostic imaging to guide neoadjuvant therapy

Abstract BACKGROUND: Triple negative breast cancer (TNBC) is a heterogeneous disease with identified biologically diverse subtypes. There are known differences in response to neoadjuvant chemotherapy (NACT) in TNBC patients with 50% having excellent response to treatment (pCR/Residual cancer burden [RCB]-I) and good survival prognosis, while 50% demonstrate marked residual disease (RCB-II-III) with significantly worse prognosis. Lack of response early into NACT indicates a low chance (5%) of achieving pCR. Thus, it is important to develop diagnostic platforms predictive of pCR, in order to direct patients with responsive disease toward standard NACT and non-responsive disease toward experimental therapies within clinical trials. METHODS: All patients will undergo biopsy of the primary tumor for molecular analyses, but will then be randomized 2:1 to know these results versus not (control). An algorithm that incorporates pre-defined genomic signatures will determine predicted sensitivity to NACT, which contains anthracyclines and taxanes. All patients will begin standard of care anthracycline based NACT with diagnostic imaging to assess response after 4 cycles. Patients who fit molecular/imaging criteria for non-responsive disease will undergo a second biopsy to confirm tumor cellularity and be offered a clinical trial based upon the initial molecular profiling (if known) or based upon physician/patient choice if randomized to the control arm. Patients who fit criteria for responsive disease in either arm will be recommended to continue with taxane-based NACT. Rates of excellent therapy response (pCR/RCB-I) will be compared between the randomized arms. One additional core and two FNAs will be obtained at the time of each planned biopsy and used to generate cell lines and PDX models for study of therapy resistance. Inclusion criteria include: Tumor size ?1.5 cm diameter; TNBC by standard assays; ?18 years of age; LVEF ?50%; adequate organ and bone marrow function. Exclusion criteria include: Stage IV disease; history of invasive cancer within 5 years; excisional biopsy of the primary tumor; biopsy site changes that limit response assessment; medically unfit for chemotherapy; prior anthracycline; >grade II neuropathy; Zubrod performance status of >2; history of serious cardiac event. The study was activated on 11/09/2015. To date, 10 patients have been enrolled. PRIMARY AIM: Prospectively determine the impact of a molecular diagnostic/imaging platform to guide neoadjuvant therapy in patients with localized invasive TNBC. SECONDARY AIMS: -Determine the impact of targeted therapy to improve pathological response in chemotherapy resistant disease in patients who are selected for clinical trials based upon molecular features of their tumors. -Generate a translational research platform to facilitate molecular diagnostic development, study mechanisms of acquired resistance, and inform the next generation of clinical trials. STATISTICAL METHODS: A maximum of 360 patients will be randomized (2:1)using a group sequential design with one-sided O’Brien-Fleming boundaries, with two equally spaced binding interim tests for futility and superiority and one final test, having an overall Type I error .05 and power .80 to detect an improvement in pCR/RCB-I from 50% to 64%. Citation Format: Zahi Mitri, Naoto T. Ueno, Wei Yang, Vicente Valero, Jennifer K. Litton, Rashmi Murthy, Bora Lim, Nuhad K. Ibrahim, Banu K. Arun, Elizabeth A. Mittendorf, Kelly K. Hunt, Funda Meric-Bernstam, Alastair Thompson, Michael Gilcrease, Helen Piwnica-Worms, Debasish Tripathy, William Fraser Symmans, Stacy Moulder-Thompson. Women's triple-negative, first-line treatment: Improving outcomes in triple-negative breast cancer using molecular triaging and diagnostic imaging to guide neoadjuvant therapy. [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 CT076.

Development and validation of a comprehensive genomic diagnostic tool for myeloid malignancies

AbstractThe diagnosis of hematologic malignancies relies on multidisciplinary workflows involving morphology, flow cytometry, cytogenetic, and molecular genetic analyses. Advances in cancer genomics have identified numerous recurrent mutations with clear prognostic and/or therapeutic significance to different cancers. In myeloid malignancies, there is a clinical imperative to test for such mutations in mainstream diagnosis; however, progress toward this has been slow and piecemeal. Here we describe Karyogene, an integrated targeted resequencing/analytical platform that detects nucleotide substitutions, insertions/deletions, chromosomal translocations, copy number abnormalities, and zygosity changes in a single assay. We validate the approach against 62 acute myeloid leukemia, 50 myelodysplastic syndrome, and 40 blood DNA samples from individuals without evidence of clonal blood disorders. We demonstrate robust detection of sequence changes in 49 genes, including difficult-to-detect mutations such as FLT3 internal-tandem and mixed-lineage leukemia (MLL) partial-tandem duplications, and clinically significant chromosomal rearrangements including MLL translocations to known and unknown partners, identifying the novel fusion gene MLL-DIAPH2 in the process. Additionally, we identify most significant chromosomal gains and losses, and several copy neutral loss-of-heterozygosity mutations at a genome-wide level, including previously unreported changes such as homozygosity for DNMT3A R882 mutations. Karyogene represents a dependable genomic diagnosis platform for translational research and for the clinical management of myeloid malignancies, which can be readily adapted for use in other cancers.

Patient-Derived Xenograft (PDX) Models: An Emerging Platform for Cancer Drug Development and Translational Research

Patient-Derived Xenograft (PDX) Models: An Emerging Platform for Cancer Drug Development and Translational Research

Development of a translational model to screen medications for cocaine use disorder II: Choice between intravenous cocaine and money in humans

BackgroundA medication for treating cocaine use disorder has yet to be approved. Laboratory-based evaluation of candidate medications in animals and humans is a valuable means to demonstrate safety, tolerability and initial efficacy of potential medications. However, animal-to-human translation has been hampered by a lack of coordination. Therefore, we designed homologous cocaine self-administration studies in rhesus monkeys (see companion article) and human subjects in an attempt to develop linked, functionally equivalent procedures for research on candidate medications for cocaine use disorder. MethodsEight (N=8) subjects with cocaine use disorder completed 12 experimental sessions in which they responded to receive money ($0.01, $1.00 and $3.00) or intravenous cocaine (0, 3, 10 and 30mg/70kg) under independent, concurrent progressive-ratio schedules. Prior to the completion of 9 choice trials, subjects sampled the cocaine dose available during that session and were informed of the monetary alternative value. ResultsThe allocation of behavior varied systematically as a function of cocaine dose and money value. Moreover, a similar pattern of cocaine choice was demonstrated in rhesus monkeys and humans across different cocaine doses and magnitudes of the species-specific alternative reinforcers. The subjective and cardiovascular responses to IV cocaine were an orderly function of dose, although heart rate and blood pressure remained within safe limits. ConclusionsThese coordinated studies successfully established drug versus non-drug choice procedures in humans and rhesus monkeys that yielded similar cocaine choice behavior across species. This translational research platform will be used in future research to enhance the efficiency of developing interventions to reduce cocaine use.

Development of a translational model to screen medications for cocaine use disorder I: Choice between cocaine and food in rhesus monkeys

BackgroundHomologous cocaine self-administration procedures in laboratory animals and humans may facilitate translational research for medications development to treat cocaine dependence. This study, therefore, sought to establish choice between cocaine and an alternative reinforcer in rhesus monkeys responding under a procedure back-translated from previous human studies and homologous to a human laboratory procedure described in a companion paper. MethodsFour rhesus monkeys with chronic indwelling intravenous catheters had access to cocaine injections (0, 0.043, 0.14, or 0.43mg/kg/injection) and food (0, 1, 3, or 10 1g banana-flavored food pellets). During daily 5h sessions, a single cocaine dose and a single food-reinforcer magnitude were available in 10 30-min trials. During the initial “sample” trial, the available cocaine and food reinforcer were delivered non-contingently. During each of the subsequent nine “choice” trials, responding could produce either the cocaine or food reinforcer under an independent concurrent progressive-ratio schedule. ResultsPreference was governed by the cocaine dose and food-reinforcer magnitude, and increasing cocaine doses produced dose-dependent increases in cocaine choice at all food-reinforcer magnitudes. Effects of the candidate medication lisdexamfetamine (0.32–3.2mg/kg/day) were then examined on choice between 0.14mg/kg/injection cocaine and 10 pellets. Under baseline conditions, this reinforcer pair maintained an average of approximately 6 cocaine and 3 food choices. Lisdexamfetamine dose-dependently decreased cocaine choice in all monkeys, but food choice was not significantly altered. ConclusionsThese results support utility of this procedure in rhesus monkeys as one component of a platform for translational research on medications development to treat cocaine use disorder.

Integrating Heterogeneous Biomedical Data for Cancer Research: the CARPEM infrastructure.

SummaryCancer research involves numerous disciplines. The multiplicity of data sources and their heterogeneous nature render the integration and the exploration of the data more and more complex. Translational research platforms are a promising way to assist scientists in these tasks. In this article, we identify a set of scientific and technical principles needed to build a translational research platform compatible with ethical requirements, data protection and data-integration problems. We describe the solution adopted by the CARPEM cancer research program to design and deploy a platform able to integrate retrospective, prospective, and day-to-day care data. We designed a three-layer architecture composed of a data collection layer, a data integration layer and a data access layer. We leverage a set of open-source resources including i2b2 and tranSMART.

Standardized echocardiographic assessment of cardiac function in normal adult zebrafish and heart disease models.

ABSTRACTThe zebrafish (Danio rerio) is an increasingly popular model organism in cardiovascular research. Major insights into cardiac developmental processes have been gained by studies of embryonic zebrafish. However, the utility of zebrafish for modeling adult-onset heart disease has been limited by a lack of robust methods for in vivo evaluation of cardiac function. We established a physiological protocol for underwater zebrafish echocardiography using high frequency ultrasound, and evaluated its reliability in detecting altered cardiac function in two disease models. Serial assessment of cardiac function was performed in wild-type zebrafish aged 3 to 12 months and the effects of anesthetic agents, age, sex and background strain were evaluated. There was a varying extent of bradycardia and ventricular contractile impairment with different anesthetic drugs and doses, with tricaine 0.75 mmol l−1 having a relatively more favorable profile. When compared with males, female fish were larger and had more measurement variability. Although age-related increments in ventricular chamber size were greater in females than males, there were no sex differences when data were normalized to body size. Systolic ventricular function was similar in both sexes at all time points, but differences in diastolic function were evident from 6 months onwards. Wild-type fish of both sexes showed a reliance on atrial contraction for ventricular diastolic filling. Echocardiographic evaluation of adult zebrafish with diphtheria toxin-induced myocarditis or anemia-induced volume overload accurately identified ventricular dilation and altered contraction, with suites of B-mode, ventricular strain, pulsed-wave Doppler and tissue Doppler indices showing concordant changes indicative of myocardial hypocontractility or hypercontractility, respectively. Repeatability, intra-observer and inter-observer correlations for echocardiographic measurements were high. We demonstrate that high frequency echocardiography allows reliable in vivo cardiac assessment in adult zebrafish and make recommendations for optimizing data acquisition and analysis. This enabling technology reveals new insights into zebrafish cardiac physiology and provides an imaging platform for zebrafish-based translational research.

The Canadian Registry for Pulmonary Fibrosis: Design and Rationale of a National Pulmonary Fibrosis Registry.

Background. The relative rarity and diversity of fibrotic interstitial lung disease (ILD) have made it challenging to study these diseases in single-centre cohorts. Here we describe formation of a multicentre Canadian registry that is needed to describe the outcomes of fibrotic ILD and to enable detailed healthcare utilization analyses that will be the cornerstone for future healthcare planning. Methods. The Canadian Registry for Pulmonary Fibrosis (CARE-PF) is a prospective cohort anticipated to consist of at least 2,800 patients with fibrotic ILD. CARE-PF will be used to (1) describe the natural history of fibrotic ILD, specifically determining the incidence and outcomes of acute exacerbations of ILD subtypes and (2) determine the impact of ILD and acute exacerbations of ILD on health services use and healthcare costs in the Canadian population. Consecutive patients with fibrotic ILD will be recruited from five Canadian ILD centres over a period of five years. Patients will be followed up as clinically indicated and will complete standardized questionnaires at each clinic visit. Prespecified outcomes and health services use will be measured based on self-report and linkage to provincial health administrative databases. Conclusion. CARE-PF will be among the largest prospective multicentre ILD registries in the world, providing detailed data on the natural history of fibrotic ILD and the healthcare resources used by these patients. As the largest and most comprehensive cohort of Canadian ILD patients, CARE-PF establishes a network for future clinical research and early phase clinical trials and provides a platform for translational and basic science research.

Review of Cohort Studies for Mood Disorders.

This paper aimed to review currently available cohort studies of subjects with mood disorders such as major depressive disorder (MDD) and bipolar disorder (BD). Using the PubMed and KoreaMed databases, we reviewed eight major cohort studies. Most studies recruited participants with MDD and BD separately, so direct comparison of factors associated with diagnostic changes was difficult. Regular and frequent follow-up evaluations utilizing objective mood ratings and standardized evaluation methods in a naturalistic fashion are necessary to determine detailed clinical courses of mood disorders. Further, biological samples should also be collected to incorporate clinical findings in the development of new diagnostic and therapeutic approaches. An innovative cohort study that can serve as a platform for translational research for treatment and prevention of mood disorders is critical in determining clinical, psychosocial, neurobiological and genetic factors associated with long-term courses and consequences of mood disorders in Korean patients.

Establishment and Characterization of a Panel of Patient-Derived Acute Leukemia Mouse Models As Emerging Platform for Translational Research

Many efforts are made to treat acute leukemia effectively, but still; new treatment options are urgently needed. In the past, mainly chemically induced and cell line-derived mouse models were used to evaluate the efficacy of new drugs. The high failure rate of 96% in early clinical development illustrates the urgent need for more predictive preclinical models as a major prerequisite for rapid bench-to-bedside translation of investigational anticancer therapies. Transplantable patient-derived xenograft (PDX) models of leukemia offer a strong preclinical tool for drug screening and biomarker development as they represent the complex clinical tumor heterogeneity and molecular diversity of human cancer.Between 2011 and 2015 we collected 91 samples of peripheral blood (PB) or bone marrow (BM) from patients diagnosed with acute myeloid or lymphoblastic leukemia (AML, ALL) and injected them intratibially (i.t.) into NOG (NOD/Shi-scid/IL-2Rγnull) mice (n=1-5/patient sample). Infiltration of human leukemic cells was determined by flow cytometry in murine PB, BM and spleen. If more than 5% of hCD45+, hCD33+, hCD34+, hCD38+, and/or HLA-ABC+ cells were detectable in one sample, it was classified as engrafted. Results were confirmed by histo-pathological examination. FISH analyses confirmed the cytogenetical concordance with the donor patient where available. 8 models were treated with cytarabine and results were compared to patient´s outcome and treatment experiments using cell line derived models of AML. Whole exome sequencing analyses of the transplantable models are underway for a deeper characterization of the respective leukemic clone which adapted to the murine microenvironment.Specimens of 44 female and 47 male patients (median age: 59 years, median BM infiltration: 39%) were collected. The donor patient cohort covered a broad range of different molecular subtypes: amongst others 5 MLL-rearrangements, 1 MLL-Deletion, 2 t(8;21) translocations, 20 cytogenetically normal and 7 complex karyotypes were included. Up to now 12 PDX models were in passage (P) 5 and higher, where P1 represents first implantation of human cells into the murine BM. 15 PDX models grew in P3 - P4, 21 in P2, 36 in P1 and 7 samples showed no engraftment. Engraftment capacity of the leukemic cells did not correlate significantly with any of the patient characteristics. BM engraftment ranged from 30% - 80%. Spleen and PB depicted 5 - 30% of leukemic cells. Infiltration rate in different organs and immuno-phenotypic characteristics of the human cells were specific for a defined model and preserved during serial transplantation. Take rates within one mouse cohort in serial transplantation were ≥98% for all transplantable PDX, similar to cell line derived models thereby qualifying the PDX approach as a suitable preclinical platform. Overall survival (OS) in P1 ranged from 52 to > 310 days (d). Models which could be serially transplanted showed model specific median OS ranging from 32 - 150 d. Comparable cell line derived models depicted median OS of 13 - 45 d. Of note, cell line derived models (KG-1, NOMO-1, MOLM-13, THP-1, MV4-11 or HL60, n ≥ 10 mice/cell line) induced hind limb paresis in all recipient mice. These symptoms could not be observed in PDX and most important are not part of the clinical picture. Cytarabine induced a significantly prolonged OS in 8/8 tested PDX models. Respective donor patients showed hematologic response under cytarabine based therapy highlighting the excellent predictivity of the in vivo platform. In contrast none of the investigated cell line derived models showed sensitivity towards cytarabine, although representing similar subtypes of AML as the investigated PDX models.Taken together a constantly expanding panel of well characterized AML/ALL PDX covering a broad range of different subtypes of the disease is available for drug development and tumorbiology studies. The comparison with cell line derived in vivo models revealed significant advantages of the PDX approach as the latter represents the molecular diversity more in detail, mimics the clinical signs of leukemia more realistic and most important mirrors sensitivity towards standard of care in a direct comparison with the donor patient´s clinical outcome. Therefore, we strongly believe that the AML/ALL PDX platform is a robust and predictive tool to address translational challenges in oncology research. DisclosuresOswald:Oncotest GmbH: Employment. Klingner:Oncotest GmbH: Employment. Lenhard:Oncotest GmbH: Employment. Schueler:Oncotest GmbH: Employment.

Abstract 5139: Cell sorting strategies for the isolation of cancer cells and associated fibroblasts from tumor biopsies, surgical resections, and patient-derived xenografts

Abstract The ability of early passage patient-derived tumor xenografts (PDXs) to recapitulate human tumor biology makes them invaluable tools for pre-clinical drug development (1, 2). Similarly, clinically-annotated human tumor cell lines of low passage have potential as scalable biosimilar reagents for in vitro study. Here, we describe an integrated platform for the purification, expansion, and quality control of tumor cells and cancer-associated fibroblasts (CAFs) from patient biopsies, surgical resections, and mouse PDX models. Following dissociation of solid tumors, cells are cultured on Matrigel® in fibroblast conditioned media containing Y-27632 (a Rho-associated kinase inhibitor). Cells are then analyzed by FACS using a panel of species- or cell type-specific antibodies. This panel (anti-mCD9, hCD9, hCD24, hCD90, MHC, HLA, and hEPCAM) permits quantitation of the percentage of mouse/human cells, and the percentages of tumor cells and CAFs in each patient specimen. From these data, a cell sorting strategy can be selected (e.g. mCD9 and hCD90 with hEpCAM or CD24) that will permit purification of both tumor cells and CAFs, along with removal of any mouse fibroblast contamination (for PDX tumors). Samples are sorted multiple times until target populations reach 99.99% purity (typically 2-3 rounds). Purified cells are then returned to culture, expanded over several weeks, and frozen at low passage. The purity and identity of these cultures is quality-assured using 1) mouse-specific QPCR, 2) a cDNA array designed to differentiate fibroblasts from tumor cells, and 3) STR genotyping. Tumor lines and CAFs are then scaled and re-qualified at passages 10 and 20, an essential step given the propensity of low-frequency mouse and human fibroblasts to ‘overtake’ impure cultures with time. Lastly, cancer lines and CAF cultures undergo genomic characterization and are evaluated for in vivo tumorigenicity (or the lack thereof for CAFs). To date, the platform has been used to generate a growing number of purified cancer and CAF pairs from patient materials. In conclusion, our goal is to provide useful reagents to the extramural community that will accompany current efforts within the Division of Cancer Treatment and Diagnosis (DCTD, NCI) aimed at generating a large and extensively characterized repository of PDX models. Funded by NCI Contract No. HHSN261200800001E.

Genomic characterization of a large panel of patient-derived hepatocellular carcinoma xenograft tumor models for preclinical development.

Lack of clinically relevant tumor models dramatically hampers development of effective therapies for hepatocellular carcinoma (HCC). Establishment of patient-derived xenograft (PDX) models that faithfully recapitulate the genetic and phenotypic features of HCC becomes important. In this study, we first established a cohort of 65 stable PDX models of HCC from corresponding Chinese patients. Then we showed that the histology and gene expression patterns of PDX models were highly consistent between xenografts and case-matched original tumors. Genetic alterations, including mutations and DNA copy number alterations (CNAs), of the xenografts correlated well with the published data of HCC patient specimens. Furthermore, differential responses to sorafenib, the standard-of-care agent, in randomly chosen xenografts were unveiled. Finally, in the models expressing high levels of FGFR1 gene according to the genomic data, FGFR1 inhibitor lenvatinib showed greater efficacy than sorafenib. Taken together, our data indicate that PDX models resemble histopathological and genomic characteristics of clinical HCC tumors, as well as recapitulate the differential responses of HCC patients to the standard-of-care treatment. Overall, this large collection of PDX models becomes a clinically relevant platform for drug screening, biomarker discovery and translational research in preclinical setting.