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Posts Tagged ‘toxicology’


BioInformatic Resources at the Environmental Protection Agency: Tools and Webinars on Toxicity Prediction

Curator Stephen J. Williams Ph.D.

New GenRA Module in EPA’s CompTox Dashboard Will Help Predict Potential Chemical Toxicity

Published September 25, 2018

As part of its ongoing computational toxicology research, EPA is developing faster and improved approaches to evaluate chemicals for potential health effects.  One commonly applied approach is known as chemical read-across. Read-across uses information about how a chemical with known data behaves to make a prediction about the behavior of another chemical that is “similar” but does not have as much data. Current read-across, while cost-effective, relies on a subjective assessment, which leads to varying predictions and justifications depending on who undertakes and evaluates the assessment.

To reduce uncertainties and develop a more objective approach, EPA researchers have developed an automated read-across tool called Generalized Read-Across (GenRA), and added it to the newest version of the EPA Computational Toxicology Dashboard. The goal of GenRA is to encode as many expert considerations used within current read-across approaches as possible and combine these with data-driven approaches to transition read-across towards a more systematic and data-based method of making predictions.

EPA chemist Dr. Grace Patlewicz says it was this uncertainty that motivated the development of GenRA. “You don’t actually know if you’ve been successful at using read-across to help predict chemical toxicity because it’s a judgement call based on one person versus the next. That subjectivity is something we were trying to move away from.” Patlewicz says.

Since toxicologists and risk assessors are already familiar with read-across, EPA researchers saw value in creating a tool that that was aligned with the current read-across workflow but which addressed uncertainty using data analysis methods in what they call a “harmonized-hybrid workflow.”

In its current form, GenRA lets users find analogues, or chemicals that are similar to their target chemical, based on chemical structural similarity. The user can then select which analogues they want to carry forward into the GenRA prediction by exploring the consistency and concordance of the underlying experimental data for those analogues. Next, the tool predicts toxicity effects of specific repeated dose studies. Then, a plot with these outcomes is generated based on a similarity-weighted activity of the analogue chemicals the user selected. Finally, the user is presented with a data matrix view showing whether a chemical is predicted to be toxic (yes or no) for a chosen set of toxicity endpoints, with a quantitative measure of uncertainty.

The team is also comparing chemicals based on other similarity contexts, such as physicochemical characteristics or metabolic similarity, as well as extending the approach to make quantitative predictions of toxicity.

Patlewicz thinks incorporating other contexts and similarity measures will refine GenRA to make better toxicity predictions, fulfilling the goal of creating a read-across method capable of assessing thousands of chemicals that currently lack toxicity data.

“That’s the direction that we’re going in,” Patlewicz says. “Recognizing where we are and trying to move towards something a little bit more objective, showing how aspects of the current read-across workflow could be refined.”

Learn more at: https://comptox.epa.gov

 

A listing of EPA Tools for Air Quality Assessment

Tools

  • Atmospheric Model Evaluation Tool (AMET)
    AMET helps in the evaluation of meteorological and air quality simulations.
  • Benchmark Dose Software (BMDS)
    EPA developed the Benchmark Dose Software (BMDS) as a tool to help estimate dose or exposure of a chemical or chemical mixture associated with a given response level. The methodology is used by EPA risk assessors and is fast becoming the world’s standard for dose-response analysis for risk assessments, including air pollution risk assessments.
  • BenMAP
    BenMAP is a Windows-based computer program that uses a Geographic Information System (GIS)-based to estimate the health impacts and economic benefits occurring when populations experience changes in air quality.
  • Community-Focused Exposure and Risk Screening Tool (C-FERST)
    C-FERST is an online tool developed by EPA in collaboration with stakeholders to provide access to resources that can be used with communities to help identify and learn more about their environmental health issues and explore exposure and risk reduction options.
  • Community Health Vulnerability Index
    EPA scientists developed a Community Health Vulnerability Index that can be used to help identify communities at higher health risk from wildfire smoke. Breathing smoke from a nearby wildfire is a health threat, especially for people with lung or heart disease, diabetes and high blood pressure as well as older adults, and those living in communities with poverty, unemployment and other indicators of social stress. Health officials can use the tool, in combination with air quality models, to focus public health strategies on vulnerable populations living in areas where air quality is impaired, either by wildfire smoke or other sources of pollution. The work was published in Environmental Science & Technology.
  • Critical Loads Mapper Tool
    The Critical Loads Mapper Tool can be used to help protect terrestrial and aquatic ecosystems from atmospheric deposition of nitrogen and sulfur, two pollutants emitted from fossil fuel burning and agricultural emissions. The interactive tool provides easy access to information on deposition levels through time; critical loads, which identify thresholds when pollutants have reached harmful levels; and exceedances of these thresholds.
  • EnviroAtlas
    EnviroAtlas provides interactive tools and resources for exploring the benefits people receive from nature or “ecosystem goods and services”. Ecosystem goods and services are critically important to human health and well-being, but they are often overlooked due to lack of information. Using EnviroAtlas, many types of users can access, view, and analyze diverse information to better understand the potential impacts of various decisions.
  • EPA Air Sensor Toolbox for Citizen Scientists
    EPA’s Air Sensor Toolbox for Citizen Scientists provides information and guidance on new low-cost compact technologies for measuring air quality. Citizens are interested in learning more about local air quality where they live, work and play. EPA’s Toolbox includes information about: Sampling methodologies; Calibration and validation approaches; Measurement methods options; Data interpretation guidelines; Education and outreach; and Low cost sensor performance information.
  • ExpoFIRST
    The Exposure Factors Interactive Resource for Scenarios Tool (ExpoFIRST) brings data from EPA’s Exposure Factors Handbook: 2011 Edition (EFH) to an interactive tool that maximizes flexibility and transparency for exposure assessors. ExpoFIRST represents a significant advance for regional, state, and local scientists in performing and documenting calculations for community and site-specific exposure assessments, including air pollution exposure assessments.
  • EXPOsure toolbox (ExpoBox)
    This is a toolbox created to assist individuals from within government, industry, academia, and the general public with assessing exposure, including exposure to air contaminants, fate and transport processes of air pollutants and their potential exposure concentrations. It is a compendium of exposure assessment tools that links to guidance documents, databases, models, reference materials, and other related resources.
  • Federal Reference & Federal Equivalency Methods
    EPA scientists develop and evaluate Federal Reference Methods and Federal Equivalency Methods for accurately and reliably measuring six primary air pollutants in outdoor air. These methods are used by states and other organizations to assess implementation actions needed to attain National Ambient Air Quality Standards.
  • Fertilizer Emission Scenario Tool for CMAQ (FEST-C)
    FEST-C facilitates the definition and simulation of new cropland farm management system scenarios or editing of existing scenarios to drive Environmental Policy Integrated Climate model (EPIC) simulations.  For the standard 12km continental Community Multi-Scale Air Quality model (CMAQ) domain, this amounts to about 250,000 simulations for the U.S. alone. It also produces gridded daily EPIC weather input files from existing hourly Meteorology-Chemistry Interface Processor (MCIP) files, transforms EPIC output files to CMAQ-ready input files and links directly to Visual Environment for Rich Data Interpretation (VERDI) for spatial visualization of input and output files. The December 2012 release will perform all these functions for any CMAQ grid scale or domain.
  • Instruction Guide and Macro Analysis Tool for Community-led Air Monitoring 
    EPA has developed two tools for evaluating the performance of low-cost sensors and interpreting the data they collect to help citizen scientists, communities, and professionals learn about local air quality.
  • Integrated Climate and Land use Scenarios (ICLUS)
    Climate change and land-use change are global drivers of environmental change. Impact assessments frequently show that interactions between climate and land-use changes can create serious challenges for aquatic ecosystems, water quality, and air quality. Population projections to 2100 were used to model the distribution of new housing across the landscape. In addition, housing density was used to estimate changes in impervious surface cover.  A final report, datasets, the ICLUS+ Web Viewer and ArcGIS tools are available.
  • Indoor Semi-Volatile Organic Compound (i-SVOC)
    i-SVOC Version 1.0 is a general-purpose software application for dynamic modeling of the emission, transport, sorption, and distribution of semi-volatile organic compounds (SVOCs) in indoor environments. i-SVOC supports a variety of uses, including exposure assessment and the evaluation of mitigation options. SVOCs are a diverse group of organic chemicals that can be found in: Many are also present in indoor air, where they tend to bind to interior surfaces and particulate matter (dust).

    • Pesticides;
    • Ingredients in cleaning agents and personal care products;
    • Additives to vinyl flooring, furniture, clothing, cookware, food packaging, and electronics.
  • Municipal Solid Waste Decision Support Tool (MSW DST)EXIT
    This tool is designed to aid solid waste planners in evaluating the cost and environmental aspects of integrated municipal solid waste management strategies. The tool is the result of collaboration between EPA and RTI International and its partners.
  • Optical Noise-Reduction Averaging (ONA) Program Improves Black Carbon Particle Measurements Using Aethalometers
    ONA is a program that reduces noise in real-time black carbon data obtained using Aethalometers. Aethalometers optically measure the concentration of light absorbing or “black” particles that accumulate on a filter as air flows through it. These particles are produced by incomplete fossil fuel, biofuel and biomass combustion. Under polluted conditions, they appear as smoke or haze.
  • RETIGO tool
    Real Time Geospatial Data Viewer (RETIGO) is a free, web-based tool that shows air quality data that are collected while in motion (walking, biking or in a vehicle). The tool helps users overcome technical barriers to exploring air quality data. After collecting measurements, citizen scientists and other users can import their own data and explore the data on a map.
  • Remote Sensing Information Gateway (RSIG)
    RSIG offers a new way for users to get the multi-terabyte, environmental datasets they want via an interactive, Web browser-based application. A file download and parsing process that now takes months will be reduced via RSIG to minutes.
  • Simulation Tool Kit for Indoor Air Quality and Inhalation Exposure (IAQX)
    IAQX version 1.1 is an indoor air quality (IAQ) simulation software package that complements and supplements existing indoor air quality simulation (IAQ) programs. IAQX is for advanced users who have experience with exposure estimation, pollution control, risk assessment, and risk management. There are many sources of indoor air pollution, such as building materials, furnishings, and chemical cleaners. Since most people spend a large portion of their time indoors, it is important to be able to estimate exposure to these pollutants. IAQX helps users analyze the impact of pollutant sources and sinks, ventilation, and air cleaners. It performs conventional IAQ simulations to calculate the pollutant concentration and/or personal exposure as a function of time. It can also estimate adequate ventilation rates based on user-provided air quality criteria. This is a unique feature useful for product stewardship and risk management.
  • Spatial Allocator
    The Spatial Allocator provides tools that could be used by the air quality modeling community to perform commonly needed spatial tasks without requiring the use of a commercial Geographic Information System (GIS).
  • Traceability Protocol for Assay and Certification of Gaseous Calibration Standards
    This is used to certify calibration gases for ambient and continuous emission monitors. It specifies methods for assaying gases and establishing traceability to National Institute of Standards and Technology (NIST) reference standards. Traceability is required under EPA ambient and continuous emission monitoring regulations.
  • Watershed Deposition Mapping Tool (WDT)
    WDT provides an easy to use tool for mapping the deposition estimates from CMAQ to watersheds to provide the linkage of air and water needed for TMDL (Total Maximum Daily Load) and related nonpoint-source watershed analyses.
  • Visual Environment for Rich Data Interpretation (VERDI)
    VERDI is a flexible, modular, Java-based program for visualizing multivariate gridded meteorology, emissions, and air quality modeling data created by environmental modeling systems such as CMAQ and the Weather Research and Forecasting (WRF) model.

 

Databases

  • Air Quality Data for the CDC National Environmental Public Health Tracking Network 
    EPA’s Exposure Research scientists are collaborating with the Centers for Disease Control and Prevention (CDC) on a CDC initiative to build a National Environmental Public Health Tracking (EPHT) network. Working with state, local and federal air pollution and health agencies, the EPHT program is facilitating the collection, integration, analysis, interpretation, and dissemination of data from environmental hazard monitoring, and from human exposure and health effects surveillance. These data provide scientific information to develop surveillance indicators, and to investigate possible relationships between environmental exposures, chronic disease, and other diseases, that can lead to interventions to reduce the burden of theses illnesses. An important part of the initiative is air quality modeling estimates and air quality monitoring data, combined through Bayesian modeling that can be linked with health outcome data.
  • EPAUS9R – An Energy Systems Database for use with the Market Allocation (MARKAL) Model
    The EPAUS9r is a regional database representation of the United States energy system. The database uses the MARKAL model. MARKAL is an energy system optimization model used by local and federal governments, national and international communities and academia. EPAUS9r represents energy supply, technology, and demand throughout the major sectors of the U.S. energy system.
  • Fused Air Quality Surfaces Using Downscaling
    This database provides access to the most recent O3 and PM2.5 surfaces datasets using downscaling.
  • Health & Environmental Research Online (HERO)
    HERO provides access to scientific literature used to support EPA’s integrated science assessments, including the  Integrated Science Assessments (ISA) that feed into the National Ambient Air Quality (NAAQS) reviews.
  • SPECIATE 4.5 Database
    SPECIATE is a repository of volatile organic gas and particulate matter (PM) speciation profiles of air pollution sources.

A listing of EPA Tools and Databases for Water Contaminant Exposure Assessment

Exposure and Toxicity

  • EPA ExpoBox (A Toolbox for Exposure Assessors)
    This toolbox assists individuals from within government, industry, academia, and the general public with assessing exposure from multiple media, including water and sediment. It is a compendium of exposure assessment tools that links to guidance documents, databases, models, reference materials, and other related resources.

Chemical and Product Categories (CPCat) Database
CPCat is a database containing information mapping more than 43,000 chemicals to a set of terms categorizing their usage or function. The comprehensive list of chemicals with associated categories of chemical and product use was compiled from publically available sources. Unique use category taxonomies from each source are mapped onto a single common set of approximately 800 terms. Users can search for chemicals by chemical name, Chemical Abstracts Registry Number, or by CPCat terms associated with chemicals.

A listing of EPA Tools and Databases for Chemical Toxicity Prediction & Assessment

  • Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS)
    SeqAPASS is a fast, online screening tool that allows researchers and regulators to extrapolate toxicity information across species. For some species, such as humans, mice, rats, and zebrafish, the EPA has a large amount of data regarding their toxicological susceptibility to various chemicals. However, the toxicity data for numerous other plants and animals is very limited. SeqAPASS extrapolates from these data rich model organisms to thousands of other non-target species to evaluate their specific potential chemical susceptibility.

 

A listing of EPA Webinar and Literature on Bioinformatic Tools and Projects

Comparative Bioinformatics Applications for Developmental Toxicology

Discuss how the US EPA/NCCT is trying to solve the problem of too many chemicals, too high cost, and too much biological uncertainty Discuss the solution the ToxCast Program is proposing; a data-rich system to screen, classify and rank chemicals for further evaluation

https://cfpub.epa.gov/si/si_public_record_report.cfm?Lab=NCCT&dirEntryId=186844

CHEMOINFORMATIC AND BIOINFORMATIC CHALLENGES AT THE US ENVIRONMENTAL PROTECTION AGENCY.

This presentation will provide an overview of both the scientific program and the regulatory activities related to computational toxicology. This presentation will provide an overview of both the scientific program and the regulatory activities related to computational toxicology.

https://cfpub.epa.gov/si/si_public_record_report.cfm?Lab=NCCT&dirEntryId=154013

How Can We Use Bioinformatics to Predict Which Agents Will Cause Birth Defects?

The availability of genomic sequences from a growing number of human and model organisms has provided an explosion of data, information, and knowledge regarding biological systems and disease processes. High-throughput technologies such as DNA and protein microarray biochips are now standard tools for probing the cellular state and determining important cellular behaviors at the genomic/proteomic levels. While these newer technologies are beginning to provide important information on cellular reactions to toxicant exposure (toxicogenomics), a major challenge that remains is the formulation of a strategy to integrate transcript, protein, metabolite, and toxicity data. This integration will require new concepts and tools in bioinformatics. The U.S. National Library of Medicine’s Pubmed site includes 19 million citations and abstracts and continues to grow. The BDSM team is now working on assembling the literature’s unstructured data into a structured database and linking it to BDSM within a system that can then be used for testing and generating new hypotheses. This effort will generate data bases of entities (such as genes, proteins, metabolites, gene ontology processes) linked to PubMed identifiers/abstracts and providing information on the relationships between them. The end result will be an online/standalone tool that will help researchers to focus on the papers most relevant to their query and uncover hidden connections and obvious information gaps.

https://cfpub.epa.gov/si/si_public_record_report.cfm?Lab=NCCT&dirEntryId=227345

ADVANCED PROTEOMICS AND BIOINFORMATICS TOOLS IN TOXICOLOGY RESEARCH: OVERCOMING CHALLENGES TO PROVIDE SIGNIFICANT RESULTS

This presentation specifically addresses the advantages and limitations of state of the art gel, protein arrays and peptide-based labeling proteomic approaches to assess the effects of a suite of model T4 inhibitors on the thyroid axis of Xenopus laevis.

https://cfpub.epa.gov/si/si_public_record_report.cfm?Lab=NHEERL&dirEntryId=152823

Bioinformatic Integration of in vivo Data and Literature-based Gene Associations for Prioritization of Adverse Outcome Pathway Development

Adverse outcome pathways (AOPs) describe a sequence of events, beginning with a molecular initiating event (MIE), proceeding via key events (KEs), and culminating in an adverse outcome (AO). A challenge for use of AOPs in a safety evaluation context has been identification of MIEs and KEs relevant for AOs observed in regulatory toxicity studies. In this work, we implemented a bioinformatic approach that leverages mechanistic information in the literature and the AOs measured in regulatory toxicity studies to prioritize putative MIEs and/or early KEs for AOP development relevant to chemical safety evaluation. The US Environmental Protection Agency Toxicity Reference Database (ToxRefDB, v2.0) contains effect information for >1000 chemicals curated from >5000 studies or summaries from sources including data evaluation records from the US EPA Office of Pesticide Programs, the National Toxicology Program (NTP), peer-reviewed literature, and pharmaceutical preclinical studies. To increase ToxRefDB interoperability, endpoint and effect information were cross-referenced with codes from the United Medical Language System, which enabled mapping of in vivo pathological effects from ToxRefDB to PubMed (via Medical Subject Headings or MeSH). This enabled linkage to any resource that is also connected to PubMed or indexed with MeSH. A publicly available bioinformatic tool, the Entity-MeSH Co-occurrence Network (EMCON), uses multiple data sources and a measure of mutual information to identify genes most related to a MeSH term. Using EMCON, gene sets were generated for endpoints of toxicological relevance in ToxRefDB linking putative KEs and/or MIEs. The Comparative Toxicogenomics Database was used to further filter important associations. As a proof of concept, thyroid-related effects and their highly associated genes were examined, and demonstrated relevant MIEs and early KEs for AOPs to describe thyroid-related AOs. The ToxRefDB to gene mapping for thyroid resulted in >50 unique gene to chemical relationships. Integrated use of EMCON and ToxRefDB data provides a basis for rapid and robust putative AOP development, as well as a novel means to generate mechanistic hypotheses for specific chemicals. This abstract does not necessarily reflect U.S. EPA policy. Abstract and Poster for 2019 Society of Toxicology annual meeting in March 2019

https://cfpub.epa.gov/si/si_public_record_report.cfm?Lab=NCCT&dirEntryId=344452

Bioinformatic Integration of in vivo Data and Literature-based Gene Associations for Prioritization of Adverse Outcome Pathway Development

Adverse outcome pathways (AOPs) describe a sequence of events, beginning with a molecular initiating event (MIE), proceeding via key events (KEs), and culminating in an adverse outcome (AO). A challenge for use of AOPs in a safety evaluation context has been identification of MIEs and KEs relevant for AOs observed in regulatory toxicity studies. In this work, we implemented a bioinformatic approach that leverages mechanistic information in the literature and the AOs measured in regulatory toxicity studies to prioritize putative MIEs and/or early KEs for AOP development relevant to chemical safety evaluation. The US Environmental Protection Agency Toxicity Reference Database (ToxRefDB, v2.0) contains effect information for >1000 chemicals curated from >5000 studies or summaries from sources including data evaluation records from the US EPA Office of Pesticide Programs, the National Toxicology Program (NTP), peer-reviewed literature, and pharmaceutical preclinical studies. To increase ToxRefDB interoperability, endpoint and effect information were cross-referenced with codes from the United Medical Language System, which enabled mapping of in vivo pathological effects from ToxRefDB to PubMed (via Medical Subject Headings or MeSH). This enabled linkage to any resource that is also connected to PubMed or indexed with MeSH. A publicly available bioinformatic tool, the Entity-MeSH Co-occurrence Network (EMCON), uses multiple data sources and a measure of mutual information to identify genes most related to a MeSH term. Using EMCON, gene sets were generated for endpoints of toxicological relevance in ToxRefDB linking putative KEs and/or MIEs. The Comparative Toxicogenomics Database was used to further filter important associations. As a proof of concept, thyroid-related effects and their highly associated genes were examined, and demonstrated relevant MIEs and early KEs for AOPs to describe thyroid-related AOs. The ToxRefDB to gene mapping for thyroid resulted in >50 unique gene to chemical relationships. Integrated use of EMCON and ToxRefDB data provides a basis for rapid and robust putative AOP development, as well as a novel means to generate mechanistic hypotheses for specific chemicals. This abstract does not necessarily reflect U.S. EPA policy. Abstract and Poster for 2019 Society of Toxicology annual meeting in March 2019

https://cfpub.epa.gov/si/si_public_record_report.cfm?Lab=NCCT&dateBeginPublishedPresented=03%2F26%2F2014&dateEndPublishedPresented=03%2F26%2F2019&dirEntryId=344452&keyword=Chemical+Safety&showCriteria=2&sortBy=pubDateYear&subject=Chemical+Safety+Research

Bioinformatic Integration of in vivo Data and Literature-based Gene Associations for Prioritization of Adverse Outcome Pathway Development

Adverse outcome pathways (AOPs) describe a sequence of events, beginning with a molecular initiating event (MIE), proceeding via key events (KEs), and culminating in an adverse outcome (AO). A challenge for use of AOPs in a safety evaluation context has been identification of MIEs and KEs relevant for AOs observed in regulatory toxicity studies. In this work, we implemented a bioinformatic approach that leverages mechanistic information in the literature and the AOs measured in regulatory toxicity studies to prioritize putative MIEs and/or early KEs for AOP development relevant to chemical safety evaluation. The US Environmental Protection Agency Toxicity Reference Database (ToxRefDB, v2.0) contains effect information for >1000 chemicals curated from >5000 studies or summaries from sources including data evaluation records from the US EPA Office of Pesticide Programs, the National Toxicology Program (NTP), peer-reviewed literature, and pharmaceutical preclinical studies. To increase ToxRefDB interoperability, endpoint and effect information were cross-referenced with codes from the United Medical Language System, which enabled mapping of in vivo pathological effects from ToxRefDB to PubMed (via Medical Subject Headings or MeSH). This enabled linkage to any resource that is also connected to PubMed or indexed with MeSH. A publicly available bioinformatic tool, the Entity-MeSH Co-occurrence Network (EMCON), uses multiple data sources and a measure of mutual information to identify genes most related to a MeSH term. Using EMCON, gene sets were generated for endpoints of toxicological relevance in ToxRefDB linking putative KEs and/or MIEs. The Comparative Toxicogenomics Database was used to further filter important associations. As a proof of concept, thyroid-related effects and their highly associated genes were examined, and demonstrated relevant MIEs and early KEs for AOPs to describe thyroid-related AOs. The ToxRefDB to gene mapping for thyroid resulted in >50 unique gene to chemical relationships. Integrated use of EMCON and ToxRefDB data provides a basis for rapid and robust putative AOP development, as well as a novel means to generate mechanistic hypotheses for specific chemicals. This abstract does not necessarily reflect U.S. EPA policy. Abstract and Poster for 2019 Society of Toxicology annual meeting in March 2019

https://cfpub.epa.gov/si/si_public_record_report.cfm?Lab=NCCT&dateBeginPublishedPresented=04%2F02%2F2014&dateEndPublishedPresented=04%2F02%2F2019&dirEntryId=344452&keyword=Chemical+Safety&showCriteria=2&sortBy=pubDateYear&subject=Chemical+Safety+Research

Bioinformatic Integration of in vivo Data and Literature-based Gene Associations for Prioritization of Adverse Outcome Pathway Development

Adverse outcome pathways (AOPs) describe a sequence of events, beginning with a molecular initiating event (MIE), proceeding via key events (KEs), and culminating in an adverse outcome (AO). A challenge for use of AOPs in a safety evaluation context has been identification of MIEs and KEs relevant for AOs observed in regulatory toxicity studies. In this work, we implemented a bioinformatic approach that leverages mechanistic information in the literature and the AOs measured in regulatory toxicity studies to prioritize putative MIEs and/or early KEs for AOP development relevant to chemical safety evaluation. The US Environmental Protection Agency Toxicity Reference Database (ToxRefDB, v2.0) contains effect information for >1000 chemicals curated from >5000 studies or summaries from sources including data evaluation records from the US EPA Office of Pesticide Programs, the National Toxicology Program (NTP), peer-reviewed literature, and pharmaceutical preclinical studies. To increase ToxRefDB interoperability, endpoint and effect information were cross-referenced with codes from the United Medical Language System, which enabled mapping of in vivo pathological effects from ToxRefDB to PubMed (via Medical Subject Headings or MeSH). This enabled linkage to any resource that is also connected to PubMed or indexed with MeSH. A publicly available bioinformatic tool, the Entity-MeSH Co-occurrence Network (EMCON), uses multiple data sources and a measure of mutual information to identify genes most related to a MeSH term. Using EMCON, gene sets were generated for endpoints of toxicological relevance in ToxRefDB linking putative KEs and/or MIEs. The Comparative Toxicogenomics Database was used to further filter important associations. As a proof of concept, thyroid-related effects and their highly associated genes were examined, and demonstrated relevant MIEs and early KEs for AOPs to describe thyroid-related AOs. The ToxRefDB to gene mapping for thyroid resulted in >50 unique gene to chemical relationships. Integrated use of EMCON and ToxRefDB data provides a basis for rapid and robust putative AOP development, as well as a novel means to generate mechanistic hypotheses for specific chemicals. This abstract does not necessarily reflect U.S. EPA policy. Abstract and Poster for 2019 Society of Toxicology annual meeting in March 2019

https://cfpub.epa.gov/si/si_public_record_report.cfm?Lab=NCCT&dateBeginPublishedPresented=04%2F02%2F2014&dateEndPublishedPresented=04%2F02%2F2019&dirEntryId=344452&fed_org_id=111&keyword=Chemical+Safety&showCriteria=2&sortBy=pubDateYear&subject=Chemical+Safety+Research

Bioinformatic Integration of in vivo Data and Literature-based Gene Associations for Prioritization of Adverse Outcome Pathway Development

Adverse outcome pathways (AOPs) describe a sequence of events, beginning with a molecular initiating event (MIE), proceeding via key events (KEs), and culminating in an adverse outcome (AO). A challenge for use of AOPs in a safety evaluation context has been identification of MIEs and KEs relevant for AOs observed in regulatory toxicity studies. In this work, we implemented a bioinformatic approach that leverages mechanistic information in the literature and the AOs measured in regulatory toxicity studies to prioritize putative MIEs and/or early KEs for AOP development relevant to chemical safety evaluation. The US Environmental Protection Agency Toxicity Reference Database (ToxRefDB, v2.0) contains effect information for >1000 chemicals curated from >5000 studies or summaries from sources including data evaluation records from the US EPA Office of Pesticide Programs, the National Toxicology Program (NTP), peer-reviewed literature, and pharmaceutical preclinical studies. To increase ToxRefDB interoperability, endpoint and effect information were cross-referenced with codes from the United Medical Language System, which enabled mapping of in vivo pathological effects from ToxRefDB to PubMed (via Medical Subject Headings or MeSH). This enabled linkage to any resource that is also connected to PubMed or indexed with MeSH. A publicly available bioinformatic tool, the Entity-MeSH Co-occurrence Network (EMCON), uses multiple data sources and a measure of mutual information to identify genes most related to a MeSH term. Using EMCON, gene sets were generated for endpoints of toxicological relevance in ToxRefDB linking putative KEs and/or MIEs. The Comparative Toxicogenomics Database was used to further filter important associations. As a proof of concept, thyroid-related effects and their highly associated genes were examined, and demonstrated relevant MIEs and early KEs for AOPs to describe thyroid-related AOs. The ToxRefDB to gene mapping for thyroid resulted in >50 unique gene to chemical relationships. Integrated use of EMCON and ToxRefDB data provides a basis for rapid and robust putative AOP development, as well as a novel means to generate mechanistic hypotheses for specific chemicals. This abstract does not necessarily reflect U.S. EPA policy. Abstract and Poster for 2019 Society of Toxicology annual meeting in March 2019

https://cfpub.epa.gov/si/si_public_record_report.cfm?Lab=NCCT&dirEntryId=344452&fed_org_id=111&keyword=Chemical+Safety&showCriteria=2&sortBy=pubDateYear&subject=Chemical+Safety+Research

 

Bioinformatic Integration of in vivo Data and Literature-based Gene Associations for Prioritization of Adverse Outcome Pathway Development

Adverse outcome pathways (AOPs) describe a sequence of events, beginning with a molecular initiating event (MIE), proceeding via key events (KEs), and culminating in an adverse outcome (AO). A challenge for use of AOPs in a safety evaluation context has been identification of MIEs and KEs relevant for AOs observed in regulatory toxicity studies. In this work, we implemented a bioinformatic approach that leverages mechanistic information in the literature and the AOs measured in regulatory toxicity studies to prioritize putative MIEs and/or early KEs for AOP development relevant to chemical safety evaluation. The US Environmental Protection Agency Toxicity Reference Database (ToxRefDB, v2.0) contains effect information for >1000 chemicals curated from >5000 studies or summaries from sources including data evaluation records from the US EPA Office of Pesticide Programs, the National Toxicology Program (NTP), peer-reviewed literature, and pharmaceutical preclinical studies. To increase ToxRefDB interoperability, endpoint and effect information were cross-referenced with codes from the United Medical Language System, which enabled mapping of in vivo pathological effects from ToxRefDB to PubMed (via Medical Subject Headings or MeSH). This enabled linkage to any resource that is also connected to PubMed or indexed with MeSH. A publicly available bioinformatic tool, the Entity-MeSH Co-occurrence Network (EMCON), uses multiple data sources and a measure of mutual information to identify genes most related to a MeSH term. Using EMCON, gene sets were generated for endpoints of toxicological relevance in ToxRefDB linking putative KEs and/or MIEs. The Comparative Toxicogenomics Database was used to further filter important associations. As a proof of concept, thyroid-related effects and their highly associated genes were examined, and demonstrated relevant MIEs and early KEs for AOPs to describe thyroid-related AOs. The ToxRefDB to gene mapping for thyroid resulted in >50 unique gene to chemical relationships. Integrated use of EMCON and ToxRefDB data provides a basis for rapid and robust putative AOP development, as well as a novel means to generate mechanistic hypotheses for specific chemicals. This abstract does not necessarily reflect U.S. EPA policy. Abstract and Poster for 2019 Society of Toxicology annual meeting in March 2019

https://cfpub.epa.gov/si/si_public_record_report.cfm?Lab=NCCT&dateBeginPublishedPresented=03%2F26%2F2014&dateEndPublishedPresented=03%2F26%2F2019&dirEntryId=344452&fed_org_id=111&keyword=Chemical+Safety&showCriteria=2&sortBy=pubDateYear&subject=Chemical+Safety+Research

Bioinformatic Integration of in vivo Data and Literature-based Gene Associations for Prioritization of Adverse Outcome Pathway Development

Adverse outcome pathways (AOPs) describe a sequence of events, beginning with a molecular initiating event (MIE), proceeding via key events (KEs), and culminating in an adverse outcome (AO). A challenge for use of AOPs in a safety evaluation context has been identification of MIEs and KEs relevant for AOs observed in regulatory toxicity studies. In this work, we implemented a bioinformatic approach that leverages mechanistic information in the literature and the AOs measured in regulatory toxicity studies to prioritize putative MIEs and/or early KEs for AOP development relevant to chemical safety evaluation. The US Environmental Protection Agency Toxicity Reference Database (ToxRefDB, v2.0) contains effect information for >1000 chemicals curated from >5000 studies or summaries from sources including data evaluation records from the US EPA Office of Pesticide Programs, the National Toxicology Program (NTP), peer-reviewed literature, and pharmaceutical preclinical studies. To increase ToxRefDB interoperability, endpoint and effect information were cross-referenced with codes from the United Medical Language System, which enabled mapping of in vivo pathological effects from ToxRefDB to PubMed (via Medical Subject Headings or MeSH). This enabled linkage to any resource that is also connected to PubMed or indexed with MeSH. A publicly available bioinformatic tool, the Entity-MeSH Co-occurrence Network (EMCON), uses multiple data sources and a measure of mutual information to identify genes most related to a MeSH term. Using EMCON, gene sets were generated for endpoints of toxicological relevance in ToxRefDB linking putative KEs and/or MIEs. The Comparative Toxicogenomics Database was used to further filter important associations. As a proof of concept, thyroid-related effects and their highly associated genes were examined, and demonstrated relevant MIEs and early KEs for AOPs to describe thyroid-related AOs. The ToxRefDB to gene mapping for thyroid resulted in >50 unique gene to chemical relationships. Integrated use of EMCON and ToxRefDB data provides a basis for rapid and robust putative AOP development, as well as a novel means to generate mechanistic hypotheses for specific chemicals. This abstract does not necessarily reflect U.S. EPA policy. Abstract and Poster for 2019 Society of Toxicology annual meeting in March 2019

https://cfpub.epa.gov/si/si_public_record_report.cfm?Lab=NCCT&dirEntryId=344452&fed_org_id=111&keyword=Chemical+Safety&showCriteria=2&sortBy=pubDateYear&subject=Chemical+Safety+Research

Bioinformatic Integration of in vivo Data and Literature-based Gene Associations for Prioritization of Adverse Outcome Pathway Development

Adverse outcome pathways (AOPs) describe a sequence of events, beginning with a molecular initiating event (MIE), proceeding via key events (KEs), and culminating in an adverse outcome (AO). A challenge for use of AOPs in a safety evaluation context has been identification of MIEs and KEs relevant for AOs observed in regulatory toxicity studies. In this work, we implemented a bioinformatic approach that leverages mechanistic information in the literature and the AOs measured in regulatory toxicity studies to prioritize putative MIEs and/or early KEs for AOP development relevant to chemical safety evaluation. The US Environmental Protection Agency Toxicity Reference Database (ToxRefDB, v2.0) contains effect information for >1000 chemicals curated from >5000 studies or summaries from sources including data evaluation records from the US EPA Office of Pesticide Programs, the National Toxicology Program (NTP), peer-reviewed literature, and pharmaceutical preclinical studies. To increase ToxRefDB interoperability, endpoint and effect information were cross-referenced with codes from the United Medical Language System, which enabled mapping of in vivo pathological effects from ToxRefDB to PubMed (via Medical Subject Headings or MeSH). This enabled linkage to any resource that is also connected to PubMed or indexed with MeSH. A publicly available bioinformatic tool, the Entity-MeSH Co-occurrence Network (EMCON), uses multiple data sources and a measure of mutual information to identify genes most related to a MeSH term. Using EMCON, gene sets were generated for endpoints of toxicological relevance in ToxRefDB linking putative KEs and/or MIEs. The Comparative Toxicogenomics Database was used to further filter important associations. As a proof of concept, thyroid-related effects and their highly associated genes were examined, and demonstrated relevant MIEs and early KEs for AOPs to describe thyroid-related AOs. The ToxRefDB to gene mapping for thyroid resulted in >50 unique gene to chemical relationships. Integrated use of EMCON and ToxRefDB data provides a basis for rapid and robust putative AOP development, as well as a novel means to generate mechanistic hypotheses for specific chemicals. This abstract does not necessarily reflect U.S. EPA policy. Abstract and Poster for 2019 Society of Toxicology annual meeting in March 2019

https://cfpub.epa.gov/si/si_public_record_report.cfm?Lab=NCCT&dateBeginPublishedPresented=04%2F11%2F2014&dateEndPublishedPresented=04%2F11%2F2019&dirEntryId=344452&fed_org_id=111&keyword=Chemical+Safety&showCriteria=2&sortBy=pubDateYear&subject=Chemical+Safety+Research

Bioinformatic Integration of in vivo Data and Literature-based Gene Associations for Prioritization of Adverse Outcome Pathway Development

Adverse outcome pathways (AOPs) describe a sequence of events, beginning with a molecular initiating event (MIE), proceeding via key events (KEs), and culminating in an adverse outcome (AO). A challenge for use of AOPs in a safety evaluation context has been identification of MIEs and KEs relevant for AOs observed in regulatory toxicity studies. In this work, we implemented a bioinformatic approach that leverages mechanistic information in the literature and the AOs measured in regulatory toxicity studies to prioritize putative MIEs and/or early KEs for AOP development relevant to chemical safety evaluation. The US Environmental Protection Agency Toxicity Reference Database (ToxRefDB, v2.0) contains effect information for >1000 chemicals curated from >5000 studies or summaries from sources including data evaluation records from the US EPA Office of Pesticide Programs, the National Toxicology Program (NTP), peer-reviewed literature, and pharmaceutical preclinical studies. To increase ToxRefDB interoperability, endpoint and effect information were cross-referenced with codes from the United Medical Language System, which enabled mapping of in vivo pathological effects from ToxRefDB to PubMed (via Medical Subject Headings or MeSH). This enabled linkage to any resource that is also connected to PubMed or indexed with MeSH. A publicly available bioinformatic tool, the Entity-MeSH Co-occurrence Network (EMCON), uses multiple data sources and a measure of mutual information to identify genes most related to a MeSH term. Using EMCON, gene sets were generated for endpoints of toxicological relevance in ToxRefDB linking putative KEs and/or MIEs. The Comparative Toxicogenomics Database was used to further filter important associations. As a proof of concept, thyroid-related effects and their highly associated genes were examined, and demonstrated relevant MIEs and early KEs for AOPs to describe thyroid-related AOs. The ToxRefDB to gene mapping for thyroid resulted in >50 unique gene to chemical relationships. Integrated use of EMCON and ToxRefDB data provides a basis for rapid and robust putative AOP development, as well as a novel means to generate mechanistic hypotheses for specific chemicals. This abstract does not necessarily reflect U.S. EPA policy. Abstract and Poster for 2019 Society of Toxicology annual meeting in March 2019

https://cfpub.epa.gov/si/si_public_record_report.cfm?Lab=NCCT&dateBeginPublishedPresented=04%2F11%2F2014&dateEndPublishedPresented=04%2F11%2F2019&dirEntryId=344452&keyword=Chemical+Safety&showCriteria=2&sortBy=pubDateYear&subject=Chemical+Safety+Research

A Web-Hosted R Workflow to Simplify and Automate the Analysis of 16S NGS Data

Next-Generation Sequencing (NGS) produces large data sets that include tens-of-thousands of sequence reads per sample. For analysis of bacterial diversity, 16S NGS sequences are typically analyzed in a workflow that containing best-of-breed bioinformatics packages that may leverage multiple programming languages (e.g., Python, R, Java, etc.). The process totransform raw NGS data to usable operational taxonomic units (OTUs) can be tedious due tothe number of quality control (QC) steps used in QIIME and other software packages forsample processing. Therefore, the purpose of this work was to simplify the analysis of 16SNGS data from a large number of samples by integrating QC, demultiplexing, and QIIME(Quantitative Insights Into Microbial Ecology) analysis in an accessible R project. User command line operations for each of the pipeline steps were automated into a workflow. In addition, the R server allows multi-user access to the automated pipeline via separate useraccounts while providing access to the same large set of underlying data. We demonstratethe applicability of this pipeline automation using 16S NGS data from approximately 100 stormwater runoff samples collected in a mixed-land use watershed in northeast Georgia. OTU tables were generated for each sample and the relative taxonomic abundances were compared for different periods over storm hydrographs to determine how the microbial ecology of a stream changes with rise and fall of stream stage. Our approach simplifies the pipeline analysis of multiple 16S NGS samples by automating multiple preprocessing, QC, analysis and post-processing command line steps that are called by a sequence of R scripts. Presented at ASM 2015 Rapid NGS Bioinformatic Pipelines for Enhanced Molecular Epidemiologic Investigation of Pathogens

https://cfpub.epa.gov/si/si_public_record_report.cfm?Lab=NERL&dirEntryId=309890

DEVELOPING COMPUTATIONAL TOOLS NECESSARY FOR APPLYING TOXICOGENOMICS TO RISK ASSESSMENT AND REGULATORY DECISION MAKING.

GENOMICS, PROTEOMICS & METABOLOMICS CAN PROVIDE USEFUL WEIGHT-OF-EVIDENCE DATA ALONG THE SOURCE-TO-OUTCOME CONTINUUM, WHEN APPROPRIATE BIOINFORMATIC AND COMPUTATIONAL METHODS ARE APPLIED TOWARDS INTEGRATING MOLECULAR, CHEMICAL AND TOXICOGICAL INFORMATION. GENOMICS, PROTEOMICS & METABOLOMICS CAN PROVIDE USEFUL WEIGHT-OF-EVIDENCE DATA ALONG THE SOURCE-TO-OUTCOME CONTINUUM, WHEN APPROPRIATE BIOINFORMATIC AND COMPUTATIONAL METHODS ARE APPLIED TOWARDS INTEGRATING MOLECULAR, CHEMICAL AND TOXICOGICAL INFORMATION.

https://cfpub.epa.gov/si/si_public_record_report.cfm?Lab=NCCT&dirEntryId=156264

The Human Toxome Project

The Human Toxome project, funded as an NIH Transformative Research grant 2011–‐ 2016, is focused on developing the concepts and the means for deducing, validating, and sharing molecular Pathways of Toxicity (PoT). Using the test case of estrogenic endocrine disruption, the responses of MCF–‐7 human breast cancer cells are being phenotyped by transcriptomics and mass–‐spectroscopy–‐based metabolomics. The bioinformatics tools for PoT deduction represent a core deliverable. A number of challenges for quality and standardization of cell systems, omics technologies, and bioinformatics are being addressed. In parallel, concepts for annotation, validation, and sharing of PoT information, as well as their link to adverse outcomes, are being developed. A reasonably comprehensive public database of PoT, the Human Toxome Knowledge–‐base, could become a point of reference for toxicological research and regulatory tests strategies. A reasonably comprehensive public database of PoT, the Human Toxome Knowledge–‐base, could become a point of reference for toxicological research and regulatory tests strategies.

https://cfpub.epa.gov/si/si_public_record_report.cfm?Lab=NCCT&dirEntryId=309453

High-Resolution Metabolomics for Environmental Chemical Surveillance and Bioeffect Monitoring

High-Resolution Metabolomics for Environmental Chemical Surveillance and Bioeffect Monitoring (Presented by: Dean Jones, PhD, Department of Medicine, Emory University) (2/28/2013)

https://www.epa.gov/chemical-research/high-resolution-metabolomics-environmental-chemical-surveillance-and-bioeffect

Identification of Absorption, Distribution, Metabolism, and Excretion (ADME) Genes Relevant to Steatosis Using a Gene Expression Approach

Absorption, distribution, metabolism, and excretion (ADME) impact chemical concentration and activation of molecular initiating events of Adverse Outcome Pathways (AOPs) in cellular, tissue, and organ level targets. In order to better describe ADME parameters and how they modulate potential hazards posed by chemical exposure, our goal is to investigate the relationship between AOPs and ADME related genes and functional information. Given the scope of this task, we began using hepatic steatosis as a case study. To identify ADME genes related to steatosis, we used the publicly available toxicogenomics database, Open TG-GATEsTM. This database contains standardized rodent chemical exposure data from 170 chemicals (mostly drugs), along with differential gene expression data and corresponding associated pathological changes. We examined the chemical exposure microarray data set gathered from 9 chemical exposure treatments resulting in pathologically confirmed (minimal, moderate and severe) incidences of hepatic steatosis. From this differential gene expression data set, we utilized differential expression analyses to identify gene changes resulting from the chemical exposures leading to hepatic steatosis. We then selected differentially expressed genes (DEGs) related to ADME by filtering all genes based on their ADME functional identities. These DEGs include enzymes such as cytochrome p450, UDP glucuronosyltransferase, flavin-containing monooxygenase and transporter genes such as solute carriers and ATP-binding cassette transporter families. The up and downregulated genes were identified across these treatments. Total of 61 genes were upregulated and 68 genes were down regulated in all treatments. Meanwhile, 25 genes were both up regulated and downregulated across all the treatments. This work highlights the application of bioinformatics in linking AOPs with gene modulations specifically in relationships to ADME and exposures to chemicals. This abstract does not necessarily reflect U.S. EPA policy. This work highlights the application of bioinformatics tools to identify genes that are modulated by adverse outcomes. Specifically, we delineate a method to identify genes that are related to ADME and can impact target tissue dose in response to chemical exposures. The computational method outlined in this work is applicable to any adverse outcome pathway, and provide a linkage between chemical exposure, target tissue dose, and adverse outcomes. Application of this method will allow for the rapid screening of chemicals for their impact on ADME-related genes using available gene data bases in literature.

https://cfpub.epa.gov/si/si_public_record_report.cfm?Lab=NHEERL&dirEntryId=341273

Development of Environmental Fate and Metabolic Simulators

Presented at Bioinformatics Open Source Conference (BOSC), Detroit, MI, June 23-24, 2005. see description

https://cfpub.epa.gov/si/si_public_record_report.cfm?Lab=NERL&dirEntryId=257172

 

Useful Webinars on EPA Computational Tools and Informatics

 

Computational Toxicology Communities of Practice

Computational Toxicology Research

EPA’s Computational Toxicology Communities of Practice is composed of hundreds of stakeholders from over 50 public and private sector organizations (ranging from EPA, other federal agencies, industry, academic institutions, professional societies, nongovernmental organizations, environmental non-profit groups, state environmental agencies and more) who have an interest in using advances in computational toxicology and exposure science to evaluate the safety of chemicals.

The Communities of Practice is open to the public. Monthly webinars are held at EPA’s RTP campus, on the fourth Thursday of the month (occasionally rescheduled in November and December to accommodate holiday schedules), from 11am-Noon EST/EDT. Remote participation is available. For more information or to be added to the meeting email list, contact: Monica Linnenbrink (linnenbrink.monica@epa.gov).

Related Links

Past Webinar Presentations

Presentation File Presented By Date
OPEn structure-activity Relationship App (OPERA) Powerpoint(VideoEXIT) Dr. Kamel Mansouri, Lead Computational Chemist contractor for Integrated Laboratory Systems in the National Institute of Environmental Health Sciences 2019/4/25
CompTox Chemicals Dashboard and InVitroDB V3 (VideoEXIT) Dr. Antony Williams, Chemist in EPA’s National Center for Computational Toxicology and Dr. Katie Paul-Friedman, Toxicologist in EPA’s National Center for Computational Toxicology 2019/3/28
The Systematic Empirical Evaluation of Models (SEEM) framework (VideoEXIT) Dr. John Wambaugh, Physical Scientist in EPA’s National Center for Computational Toxicology 2019/2/28
ToxValDB: A comprehensive database of quantitative in vivo study results from over 25,000 chemicals (VideoEXIT) Dr. Richard Judson, Research Chemist in EPA’s National Center for Computational Toxicology 2018/12/20
Sequence Alignment to Predict Across Species Susceptibility (seqAPASS) (VideoEXIT) Dr. Carlie LaLone, Bioinformaticist, EPA’s National Health and Environmental Effects Research Laboratory 2018/11/29
Chemicals and Products Database (VideoEXIT) Dr. Kathie Dionisio, Environmental Health Scientist, EPA’s National Exposure Research Laboratory 2018/10/25
CompTox Chemicals Dashboard V3 (VideoEXIT) Dr. Antony Williams, Chemist, EPA National Center for Computational Toxicology (NCCT). 2018/09/27
Generalised Read-Across (GenRA) (VideoEXIT) Dr. Grace Patlewicz, Chemist, EPA National Center for Computational Toxicology (NCCT). 2018/08/23
EPA’S ToxCast Owner’s Manual  (VideoEXIT) Monica Linnenbrink, Strategic Outreach and Communication lead, EPA National Center for Computational Toxicology (NCCT). 2018/07/26
EPA’s Non-Targeted Analysis Collaborative Trial (ENTACT)      (VideoEXIT) Elin Ulrich, Research Chemist in the Public Health Chemistry Branch, EPA National Exposure Research Laboratory (NERL). 2018/06/28
ECOTOX Knowledgebase: New Tools and Data Visualizations(VideoEXIT) Colleen Elonen, Translational Toxicology Branch, and Dr. Jennifer Olker, Systems Toxicology Branch, in the Mid-Continent Ecology Division of EPA’s National Health & Environmental Effects Research Laboratory (NHEERL) 2018/05/24
Investigating Chemical-Microbiota Interactions in Zebrafish (VideoEXIT) Tamara Tal, Biologist in the Systems Biology Branch, Integrated Systems Toxicology Division, EPA’s National Health & Environmental Effects Research Laboratory (NHEERL) 2018/04/26
The CompTox Chemistry Dashboard v2.6: Delivering Improved Access to Data and Real Time Predictions (VideoEXIT) Tony Williams, Computational Chemist, EPA’s National Center for Computational Toxicology (NCCT) 2018/03/29
mRNA Transfection Retrofits Cell-Based Assays with Xenobiotic Metabolism (VideoEXIT* Audio starts at 10:17) Steve Simmons, Research Toxicologist, EPA’s National Center for Computational Toxicology (NCCT) 2018/02/22
Development and Distribution of ToxCast and Tox21 High-Throughput Chemical Screening Assay Method Description(VideoEXIT) Stacie Flood, National Student Services Contractor, EPA’s National Center for Computational Toxicology (NCCT) 2018/01/25
High-throughput H295R steroidogenesis assay: utility as an alternative and a statistical approach to characterize effects on steroidogenesis (VideoEXIT) Derik Haggard, ORISE Postdoctoral Fellow, EPA’s National Center for Computational Toxicology (NCCT) 2017/12/14
Systematic Review for Chemical Assessments: Core Elements and Considerations for Rapid Response (VideoEXIT) Kris Thayer, Director, Integrated Risk Information System (IRIS) Division of EPA’s National Center for Environmental Assessment (NCEA) 2017/11/16
High Throughput Transcriptomics (HTTr) Concentration-Response Screening in MCF7 Cells (VideoEXIT) Joshua Harrill, Toxicologist, EPA’s National Center for Computational Toxicology (NCCT) 2017/10/26
Learning Boolean Networks from ToxCast High-Content Imaging Data Todor Antonijevic, ORISE Postdoc, EPA’s National Center for Computational Toxicology (NCCT) 2017/09/28
Suspect Screening of Chemicals in Consumer Products Katherine Phillips, Research Chemist, Human Exposure and Dose Modeling Branch, Computational Exposure Division, EPA’s National Exposure Research Laboratory (NERHL) 2017/08/31
The EPA CompTox Chemistry Dashboard: A Centralized Hub for Integrating Data for the Environmental Sciences (VideoEXIT) Antony Williams, Chemist, EPA’s National Center for Computational Toxicology (NCCT) 2017/07/27
Navigating Through the Minefield of Read-Across Tools and Frameworks: An Update on Generalized Read-Across (GenRA)(VideoEXIT)

 

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Use of 3D Bioprinting for Development of Toxicity Prediction Models

Curator: Stephen J. Williams, PhD

SOT FDA Colloquium on 3D Bioprinted Tissue Models: Tuesday, April 9, 2019

The Society of Toxicology (SOT) and the U.S. Food and Drug Administration (FDA) will hold a workshop on “Alternative Methods for Predictive Safety Testing: 3D Bioprinted Tissue Models” on Tuesday, April 9, at the FDA Center for Food Safety and Applied Nutrition in College Park, Maryland. This workshop is the latest in the series, “SOT FDA Colloquia on Emerging Toxicological Science: Challenges in Food and Ingredient Safety.”

Human 3D bioprinted tissues represent a valuable in vitro approach for chemical, personal care product, cosmetic, and preclinical toxicity/safety testing. Bioprinting of skin, liver, and kidney is already appearing in toxicity testing applications for chemical exposures and disease modeling. The use of 3D bioprinted tissues and organs may provide future alternative approaches for testing that may more closely resemble and simulate intact human tissues to more accurately predict human responses to chemical and drug exposures.

A synopsis of the schedule and related works from the speakers is given below:

 

8:40 AM–9:20 AM Overview and Challenges of Bioprinting
Sharon Presnell, Amnion Foundation, Winston-Salem, NC
9:20 AM–10:00 AM Putting 3D Bioprinting to the Use of Tissue Model Fabrication
Y. Shrike Zhang, Brigham and Women’s Hospital, Harvard Medical School and Harvard-MIT Division of Health Sciences and Technology, Boston, MA
10:00 AM–10:20 AM Break
10:20 AM–11:00 AM Uses of Bioprinted Liver Tissue in Drug Development
Jean-Louis Klein, GlaxoSmithKline, Collegeville, PA
11:00 AM–11:40 AM Biofabrication of 3D Tissue Models for Disease Modeling and Chemical Screening
Marc Ferrer, National Center for Advancing Translational Sciences, NIH, Rockville, MD

Sharon Presnell, Ph.D. President, Amnion Foundation

Dr. Sharon Presnell was most recently the Chief Scientific Officer at Organovo, Inc., and the President of their wholly-owned subsidiary, Samsara Sciences. She received a Ph.D. in Cell & Molecular Pathology from the Medical College of Virginia and completed her undergraduate degree in biology at NC State. In addition to her most recent roles, Presnell has served as the director of cell biology R&D at Becton Dickinson’s corporate research center in RTP, and as the SVP of R&D at Tengion. Her roles have always involved the commercial and clinical translation of basic research and early development in the cell biology space. She serves on the board of the Coulter Foundation at the University of Virginia and is a member of the College of Life Sciences Foundation Board at NC State. In January 2019, Dr. Presnell will begin a new role as President of the Amnion Foundation, a non-profit organization in Winston-Salem.

A few of her relevant publications:

Bioprinted liver provides early insight into the role of Kupffer cells in TGF-β1 and methotrexate-induced fibrogenesis

Integrating Kupffer cells into a 3D bioprinted model of human liver recapitulates fibrotic responses of certain toxicants in a time and context dependent manner.  This work establishes that the presence of Kupffer cells or macrophages are important mediators in fibrotic responses to certain hepatotoxins and both should be incorporated into bioprinted human liver models for toxicology testing.

Bioprinted 3D Primary Liver Tissues Allow Assessment of Organ-Level Response to Clinical Drug Induced Toxicity In Vitro

Abstract: Modeling clinically relevant tissue responses using cell models poses a significant challenge for drug development, in particular for drug induced liver injury (DILI). This is mainly because existing liver models lack longevity and tissue-level complexity which limits their utility in predictive toxicology. In this study, we established and characterized novel bioprinted human liver tissue mimetics comprised of patient-derived hepatocytes and non-parenchymal cells in a defined architecture. Scaffold-free assembly of different cell types in an in vivo-relevant architecture allowed for histologic analysis that revealed distinct intercellular hepatocyte junctions, CD31+ endothelial networks, and desmin positive, smooth muscle actin negative quiescent stellates. Unlike what was seen in 2D hepatocyte cultures, the tissues maintained levels of ATP, Albumin as well as expression and drug-induced enzyme activity of Cytochrome P450s over 4 weeks in culture. To assess the ability of the 3D liver cultures to model tissue-level DILI, dose responses of Trovafloxacin, a drug whose hepatotoxic potential could not be assessed by standard pre-clinical models, were compared to the structurally related non-toxic drug Levofloxacin. Trovafloxacin induced significant, dose-dependent toxicity at clinically relevant doses (≤ 4uM). Interestingly, Trovafloxacin toxicity was observed without lipopolysaccharide stimulation and in the absence of resident macrophages in contrast to earlier reports. Together, these results demonstrate that 3D bioprinted liver tissues can both effectively model DILI and distinguish between highly related compounds with differential profile. Thus, the combination of patient-derived primary cells with bioprinting technology here for the first time demonstrates superior performance in terms of mimicking human drug response in a known target organ at the tissue level.

A great interview with Dr. Presnell and the 3D Models 2017 Symposium is located here:

Please click here for Web based and PDF version of interview

Some highlights of the interview include

  • Exciting advances in field showing we can model complex tissue-level disease-state phenotypes that develop in response to chronic long term injury or exposure
  • Sees the field developing a means to converge both the biology and physiology of tissues, namely modeling the connectivity between tissues such as fluid flow
  • Future work will need to be dedicated to develop comprehensive analytics for 3D tissue analysis. As she states “we are very conditioned to get information in a simple way from biochemical readouts in two dimension, monocellular systems”  however how we address the complexity of various cellular responses in a 3D multicellular environment will be pertinent.
  • Additional challenges include the scalability of such systems and making such system accessible in a larger way
  1. Shrike Zhang, Brigham and Women’s Hospital, Harvard Medical School and Harvard-MIT Division of Health Sciences and Technology

Dr. Zhang currently holds an Assistant Professor position at Harvard Medical School and is an Associate Bioengineer at Brigham and Women’s Hospital. His research interests include organ-on-a-chip, 3D bioprinting, biomaterials, regenerative engineering, biomedical imaging, biosensing, nanomedicine, and developmental biology. His scientific contributions have been recognized by >40 international, national, and regional awards. He has been invited to deliver >70 lectures worldwide, and has served as reviewer for >400 manuscripts for >30 journals. He is serving as Editor-in-Chief for Microphysiological Systems, and Associate Editor for Bio-Design and Manufacturing. He is also on Editorial Board of BioprintingHeliyonBMC Materials, and Essays in Biochemistry, and on Advisory Panel of Nanotechnology.

Some relevant references from Dr. Zhang

Multi-tissue interactions in an integrated three-tissue organ-on-a-chip platform.

Skardal A, Murphy SV, Devarasetty M, Mead I, Kang HW, Seol YJ, Shrike Zhang Y, Shin SR, Zhao L, Aleman J, Hall AR, Shupe TD, Kleensang A, Dokmeci MR, Jin Lee S, Jackson JD, Yoo JJ, Hartung T, Khademhosseini A, Soker S, Bishop CE, Atala A.

Sci Rep. 2017 Aug 18;7(1):8837. doi: 10.1038/s41598-017-08879-x.

 

Reconstruction of Large-scale Defects with a Novel Hybrid Scaffold Made from Poly(L-lactic acid)/Nanohydroxyapatite/Alendronate-loaded Chitosan Microsphere: in vitro and in vivo Studies.

Wu H, Lei P, Liu G, Shrike Zhang Y, Yang J, Zhang L, Xie J, Niu W, Liu H, Ruan J, Hu Y, Zhang C.

Sci Rep. 2017 Mar 23;7(1):359. doi: 10.1038/s41598-017-00506-z.

 

 

A liver-on-a-chip platform with bioprinted hepatic spheroids.

Bhise NS, Manoharan V, Massa S, Tamayol A, Ghaderi M, Miscuglio M, Lang Q, Shrike Zhang Y, Shin SR, Calzone G, Annabi N, Shupe TD, Bishop CE, Atala A, Dokmeci MR, Khademhosseini A.

Biofabrication. 2016 Jan 12;8(1):014101. doi: 10.1088/1758-5090/8/1/014101.

 

Marc Ferrer, National Center for Advancing Translational Sciences, NIH

Marc Ferrer is a team leader in the NCATS Chemical Genomics Center, which was part of the National Human Genome Research Institute when Ferrer began working there in 2010. He has extensive experience in drug discovery, both in the pharmaceutical industry and academic research. Before joining NIH, he was director of assay development and screening at Merck Research Laboratories. For 10 years at Merck, Ferrer led the development of assays for high-throughput screening of small molecules and small interfering RNA (siRNA) to support programs for lead and target identification across all disease areas.

At NCATS, Ferrer leads the implementation of probe development programs, discovery of drug combinations and development of innovative assay paradigms for more effective drug discovery. He advises collaborators on strategies for discovering small molecule therapeutics, including assays for screening and lead identification and optimization. Ferrer has experience implementing high-throughput screens for a broad range of disease areas with a wide array of assay technologies. He has led and managed highly productive teams by setting clear research strategies and goals and by establishing effective collaborations between scientists from diverse disciplines within industry, academia and technology providers.

Ferrer has a Ph.D. in biological chemistry from the University of Minnesota, Twin Cities, and completed postdoctoral training at Harvard University’s Department of Molecular and Cellular Biology. He received a B.Sc. degree in organic chemistry from the University of Barcelona in Spain.

 

Some relevant references for Dr. Ferrer

Fully 3D Bioprinted Skin Equivalent Constructs with Validated Morphology and Barrier Function.

Derr K, Zou J, Luo K, Song MJ, Sittampalam GS, Zhou C, Michael S, Ferrer M, Derr P.

Tissue Eng Part C Methods. 2019 Apr 22. doi: 10.1089/ten.TEC.2018.0318. [Epub ahead of print]

 

Determination of the Elasticity Modulus of 3D-Printed Octet-Truss Structures for Use in Porous Prosthesis Implants.

Bagheri A, Buj-Corral I, Ferrer M, Pastor MM, Roure F.

Materials (Basel). 2018 Nov 29;11(12). pii: E2420. doi: 10.3390/ma11122420.

 

Mutation Profiles in Glioblastoma 3D Oncospheres Modulate Drug Efficacy.

Wilson KM, Mathews-Griner LA, Williamson T, Guha R, Chen L, Shinn P, McKnight C, Michael S, Klumpp-Thomas C, Binder ZA, Ferrer M, Gallia GL, Thomas CJ, Riggins GJ.

SLAS Technol. 2019 Feb;24(1):28-40. doi: 10.1177/2472630318803749. Epub 2018 Oct 5.

 

A high-throughput imaging and nuclear segmentation analysis protocol for cleared 3D culture models.

Boutin ME, Voss TC, Titus SA, Cruz-Gutierrez K, Michael S, Ferrer M.

Sci Rep. 2018 Jul 24;8(1):11135. doi: 10.1038/s41598-018-29169-0.

A High-Throughput Screening Model of the Tumor Microenvironment for Ovarian Cancer Cell Growth.

Lal-Nag M, McGee L, Guha R, Lengyel E, Kenny HA, Ferrer M.

SLAS Discov. 2017 Jun;22(5):494-506. doi: 10.1177/2472555216687082. Epub 2017 Jan 31.

 

Exploring Drug Dosing Regimens In Vitro Using Real-Time 3D Spheroid Tumor Growth Assays.

Lal-Nag M, McGee L, Titus SA, Brimacombe K, Michael S, Sittampalam G, Ferrer M.

SLAS Discov. 2017 Jun;22(5):537-546. doi: 10.1177/2472555217698818. Epub 2017 Mar 15.

 

RNAi High-Throughput Screening of Single- and Multi-Cell-Type Tumor Spheroids: A Comprehensive Analysis in Two and Three Dimensions.

Fu J, Fernandez D, Ferrer M, Titus SA, Buehler E, Lal-Nag MA.

SLAS Discov. 2017 Jun;22(5):525-536. doi: 10.1177/2472555217696796. Epub 2017 Mar 9.

 

Other Articles on 3D Bioprinting on this Open Access Journal include:

Global Technology Conferences on 3D BioPrinting 2015 – 2016

3D Medical BioPrinting Technology Reporting by Irina Robu, PhD – a forthcoming Article in “Medical 3D BioPrinting – The Revolution in Medicine, Technologies for Patient-centered Medicine: From R&D in Biologics to New Medical Devices”

Bio-Inks and 3D BioPrinting

New Scaffold-Free 3D Bioprinting Method Available to Researchers

Gene Editing for Gene Therapies with 3D BioPrinting

 

Read Full Post »


Ninth Annual
New Approaches for Predicting Drug Toxicity
Discovering New Models and Integrating Innovative Strategies
June 15-16, 2016  |  Boston, MA
WorldPreclinicalCongress.com/Drug-Safety-Conference

Final Agenda Now Available

Adverse drug events such as cardiotoxicity, hepatotoxicity and other organ toxicities, keep surfacing in the clinic and idiosyncratic drug toxicity continues to haunt the drug development process. So what are scientists and clinicians doing to make sure that compounds fail early and cheaply? New screening technologies such as, in vitro assays and in vivo models continue to be developed, but are the right tools being used at the right time to predict and detect adverse events? Cambridge Healthtech Institute’s ninth annual conference on Models to Approaches, looks at the scientific and technological progress being made to better predict drug related toxicities at the preclinical stage, and avoid unexpected and costly findings in the clinic. What assays and models are being used, how reliable and predictable is the data, and how is this information impacting decisions before compounds are tested in patients? Hear experiences shared by experts and join the interactive sessions and panel discussions on issues related to drug toxicity.

Register Now!  [Register by March 4th and save up to $400]

Agenda-at-a-Glance


Day 1

DRUG TRANSPORTERS AND THEIR ROLE IN DRUG TOXICITY

Transporter-Mediated Drug Interactions with Endobiotics, Toxins and Nutrients
Adrian Ray, Ph.D., Senior Director, Department of Drug Metabolism, Gilead Sciences, Inc.

Combination of Top-Down and Bottom-Up Strategy to Elucidate Mechanistic Roles of Transporters in Organ Toxicity
Yurong Lai, Ph.D., Senior Principal Scientist, Pharmaceutical Candidate Optimization, Bristol-Myers Squibb

In vitro Human Intestinal Tissue Model to Assess and Predict Drug-Induced-GI Damage
MatTek Corporation
Seyoum Ayehunie, Ph.D., Vice President, Immunological Systems, MatTek Corporation

Assessing Off-Target Drug Activities by Transcription Factor Profiling in FACTORIAL™ AssaysAttagene
Sergei Makarov, Ph.D., CEO, Attagene

UNDERSTANDING TRANSLATIONAL CHALLENGES AND INTERPRETING SAFETY GUIDELINES

The Importance of Reverse Translation for Preclinical Off-Target Mitigation
Laszlo Urban, M.D., Ph.D., Global Head, Preclinical Secondary Pharmacology, Novartis Institutes for BioMedical Research, Inc.

Moving beyond the S6(R1): A Snapshot of Toxicity & Safety Pharmacology Tools to Evaluate Biotherapeutics
Susan M.G. Goody, Ph.D., Senior Principal Scientist, Global Safety Pharmacology, Pfizer, Inc.

Presentation to be AnnouncedMolecular Health

Luncheon Presentation: CiPA: How Comprehensive Does It Have to BeCharles River Discovery
James Kramer, Ph.D., Principal Scientist, Discovery, Charles River

IN VIVO TECHNIQUES FOR MONITORING DRUG TOXICITY

A Disruption of Autonomic Balance: Use of Heart Rate Variability (HRV) in Cardiovascular Safety Pharmacology
Carrie Northcott, Ph.D., Senior Principal Scientist, Global Safety Pharmacology, Pfizer Inc.

Whole-Body Imaging of Drug-Induced Toxicity
Ming Zhao, Ph.D., Associate Professor, Feinberg School of Medicine, Northwestern University

NEW IN VITRO SCREENING APPROACHES FOR SAFETY TESTING

Combination of Screening Assays for Assessing Drug-Induced Liver Injury in Humans
Christoph Funk, Ph.D., Vice Director, Pharmaceutical Sciences, F. Hoffmann-La Roche

In vitro Approach to Classify Drugs According to Their Idiosyncratic, Drug-Induced Liver Injury Liability
Robert A. Roth, Ph.D., DABT, Professor of Pharmacology and Toxicology and Director, Graduate Program in Environmental and Integrative Toxicological Sciences, Michigan State University

Generation of Complex Disease Phenotypes in 3D Bioprinted Human Liver Tissues for the Assessment of Drug-Induced InjuryOrganovo
Leah Norona, Doctoral Candidate Curriculum in Toxicology, University of North Carolina at Chapel Hill

Drug-Induced Vascular Injury (DIVI)- Historical Review of Non-Clinical DIVI and Development of an Early Screening Strategy
Todd Wisialowski, MS, Associate Research Fellow, Global Safety Pharmacology, Pfizer Inc.

Day 2

INTERACTIVE BREAKOUT DISCUSSION GROUPS

TOPIC: Safety Assessments for Biologics
Moderator: Susan M.G. Goody, Ph.D., Senior PrincipalScientist, Global Safety Pharmacology, Pfizer, Inc.

TOPIC: Translation of Preclinical Findings to Clinic
Moderators: Carrie Northcott, Ph.D., Senior Principal Scientist, Global Safety Pharmacology, Pfizer Inc. Ming Zhao, Ph.D., Associate Professor, Feinberg School of Medicine, Northwestern University

TOPIC: Using iPSC for Drug Safety Screening
Moderators: Paul W. Burridge, Ph.D., Assistant Professor, Department of Pharmacology, Center for Pharmacogenomics, Northwestern University Feinberg School ofMedicine Xi Yang, Ph.D., DABT, Principal Investigator, Division of Systems Biology, National Center for Toxicological Research (NCTR), U.S. FDA

TOPIC: Key Issues Related to Drug Transporters in a Pharma R&D Setting
Moderator: Christoph Funk, Ph.D., Vice Director, Pharmaceutical Sciences, F. Hoffmann La-Roche

USE OF iPS CELLS FOR DRUG TOXICITY SCREENING

Utilization of iPSCs in Developing Human-on-a-Chip Systems for Phenotypic Screening Applications
James J. Hickman, Ph.D., Founding Director, NanoScience Technology Center; Professor, Nanoscience Technology, Chemistry, Biomolecular Science, Material Science and Electrical Engineering, University of Central Florida

Human-Induced Pluripotent Stem Cells Recapitulate Breast Cancer Patients’ Predilection to Doxorubicin-Induced Cardiotoxicity
Paul W. Burridge, Ph.D., Assistant Professor, Department of Pharmacology, Center for Pharmacogenomics, Northwestern University Feinberg School of Medicine

Utilization of Induced Pluripotent Stem Cells to Understand Tyrosine Kinase Inhibitors (TKIs)-Induced Hepatotoxicity
Qiang Shi, Ph.D., Principal Investigator, Division of Systems Biology, National Center for Toxicological Research (NCTR), U.S. FDA

UNDERSTANDING MECHANISMS TO BETTER PREDICT DRUG TOXICITY

Predict Tyrosine Kinase Inhibitors (TKIs)-Induced Cardiotoxicity Using Induced Pluripotent Stem Cell-Derived Cardiomyocytes
Xi Yang, Ph.D., DABT, Principal Investigator, Division of Systems Biology, National Center for Toxicological Research (NCTR), U.S. FDA

Prediction of Transporter-Related Drug-Induced Liver Injury (DILI) Using Integrated Approaches
Mingxiang Liao, Ph.D., Senior Scientist I, DMPK, Takeda Pharmaceutical Intl. Company

Bridging Luncheon Presentation: Case Studies in Cardiac and Neuro Safety / Toxicity Assessment Using Human iPSC-Derived Cell SystemsAxioGenesis
Greg Luerman, Ph.D., Head, Applications Development, Axiogenesis Inc.

Plenary Sessions

June 16, 1:45-2:45 pm
PLENARY KEYNOTE PRESENTATIONS:

 

INSIGHTS ON INNOVATIVE APPROACHES TO TRANSFORM DRUG DISCOVERY

This year’s Plenary Keynote Presentations feature two prominent thought-leaders who are playing an important role in innovating drug discovery. They share their experiences and their perspectives on what has changed and what can be changed to improve preclinical research, help translate preclinical findings to the clinic, and to foster effective communication and collaboration. Attendees will have an opportunity to ask questions and gain valuable insights from their learnings.

Keynote Speakers:
Anthony CoyleAnthony J. Coyle Ph.D., Chief Scientific Officer and Senior Vice President, Centers for Therapeutic Innovation, Pfizer Inc.

 

James WilsonJames Wilson, M.D., Ph.D., Professor, Department of Pathology and Laboratory Medicine, Perelman School of Medicine; Director, Orphan Disease Center and Director, Gene Therapy Program, University of Pennsylvania

 

June 16, 2:45-3:30 pm
PLENARY KEYNOTE PANEL:

 

INSIGHTS ON INNOVATIVE TECHNOLOGIES ENABLING PRECLINICAL RESEARCH

This year’s Plenary Keynote Panel features a group of technical experts from life science technology and service companies, who share their perspectives on various trends and tools that will likely change the way in which we traditionally approach preclinical drug discovery and development. Attendees will have an opportunity to ask questions and understand the impact of recent technical advances.

Panelists:
Matthew GevaertMatt Gevaert, Ph.D., CEO and Co-founder, KIYATEC

 

Amit VasanjiAmit Vasanji, Ph.D., CTO & CSO, ImageIQ

 

Biographies:

Dr. Anthony Coyle is the founding CSO of the Centers for Therapeutic Innovation (CTI) and is responsible for CTI’s strategy and scientific direction. Before leading CTI, Dr. Coyle was the Vice President and Global Head of Respiratory, Inflammation, and Autoimmunity Research at MedImmune Biologics, a Division of AstraZeneca. At MedImmune, Dr. Coyle advanced a biologic portfolio from discovery to Phase II in the areas of respiratory and autoimmune diseases, specifically targeting lupus, asthma and COPD. Prior to his work at MedImmune, Dr. Coyle was Director of Research at Millennium Pharmaceuticals, where he led a group responsible for the identification of novel target genes, as well as for late stage lead optimization and delivery of both small-molecule and biologic development candidates. Dr. Coyle has been Associate Professor in the Department of Pathology and Experimental Therapeutics at McMaster University in Ontario since 1992. He has authored more than 200 manuscripts. Dr. Coyle holds a BSc (with honors) and a Ph.D. from Kings College, University of London. Dr. Coyle is a member of the scientific board for the Alliance for Lupus Research, the C4 NCATS consortium and the Boston Children’s Hospital Technology Fund Advisory Board.

Dr. James M. Wilson is a Professor in the Perelman School of Medicine at the University of Pennsylvania where he has led an effort to develop the field of gene therapy. Dr. Wilson began his work in gene therapy during his graduate studies at the University of Michigan over 30 years ago. He then moved to Boston to do a residency in Internal Medicine at the Massachusetts General Hospital and continued his work in gene therapy at MIT. He created the first and largest academic-based program in gene therapy after being recruited to University of Pennsylvania in 1993. He initially focused on the clinical translation of existing gene transfer technologies but soon redirected his efforts to the development of second and third generation gene transfer platforms; the first of which was licensed to a biotechnology company he founded that resulted in the first, and only, commercially approved gene therapy in the western hemisphere. More recently, his laboratory discovered a family of viruses from primates that could be engineered to be very effective gene transfer vehicles. These so called “vectors” have become the technology platform of choice and have set the stage for the recent resurgence of the field of gene therapy. Dr. Wilson has also been active in facilitating the commercial development of these new gene therapy platforms through the establishment of several biotechnology companies. Throughout his career, the focus of Dr. Wilson’s research has been rare inherited diseases, ranging from cystic fibrosis to dyslipidemias to a variety of metabolic disorders. Dr. Wilson has published over 550 papers, reviews, commentaries and editorials in the peer-reviewed literature and is an inventor on over 117 patents.

Dr. Matthew (Matt) Gevaert is the CEO of KIYATEC Inc., a life sciences company in Greenville, SC. KIYATEC specializes in ex vivo 3D cell culture and tissue systems that more accurately replicate in vivo human biology and function, with a focus on methods to accurately predict individual cancer patients’response to drugs by culturing and treating live patient derived primary cells. Dr. Gevaert co-founded the company and has served as CEO since 2007. Possessing a background which combines both business and technology, before his role at KIYATEC Dr. Gevaert led the commercialization of Clemson University’s biomedical and biotechnology intellectual property portfolio for nearly 5 years, working with both entrepreneurial start-ups and large, industry leading corporations. He has previous experience with Merck, 3M and Dow Chemica l, and has been published in Science magazine and the journal of the US National Academy of Engineering. Currently he serves as a board member of SCBIO, the state of South Carolina’s life science industry organization, and a board member of NEXT, which provides entrepreneur services and infrastructure to high-growth ventures in Greenville and Upstate South Carolina. Dr. Gevaert grew up the fifth of six children on a farm in Ontario, Canada and graduated from the University of Waterloo with a bachelor’s degree in Applied Chemistry. He also holds a master’s degree and a doctorate in Bioengineering from Clemson University. He maintains current appointments as adjunct professor in the Clemson University Department of Bioengineering and as a lecturer in the Clemson MBA in Entrepreneurship & Innovation.

Dr. Amit Vasanji has over 17 years of experience with basic and clinical research image acquisition, processing, analysis, visualization and biomedical software engineering. He was the founder of Cleveland Clinic’s Biomedical Imaging and Analysis Center, and served as its Executive Director. During his tenure at the Cleveland Clinic, he authored over 50 publications — many in high impact journals, participated in the writing of numerous federally funded grants, served as a consultant and/or co-investigator on many federal, state, corporate, and institutional grants, presented at national scientific meetings, and won various awards for innovation and service. Dr. Vasanji received a BS in Biomedical Engineering from the University of Miami, and a Ph.D. in biomedical engineering from Case Western Reserve University

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Liver Toxicity halts Clinical Trial of IAP Antagonist for Advanced Solid Tumors

Writer/Curator Stephen J. Williams, Ph.D.

A recent press release on FierceBiotech reported the FDA had put a halt on a phase 1 study for advanced refractory solid tumors and lymphomas of Curis Inc. oral inhibitor of apoptosis (IAP) antagonist CUDC-427.  The FDA placed the trial on partial clinical hold following reports of a death of a patient from severe liver failure.  The single-agent, dose escalation Phase 1 study was designed to determine the maximum tolerated dose and recommended doses for a Phase 2 trial. The press release can be found at:

http://www.fiercebiotech.com/press-releases/curis-reports-third-quarter-2013-financial-results-and-provides-cudc-427-de.

According to the report one patient with breast cancer that had metastasized to liver, lungs, bone, and ovaries developed severe hepatotoxicity as evidenced by elevated serum transaminase activities (AST and ALT) and hyper-billirubinemia.  Serum liver enzyme activities did not attenuate upon discontinuation of CUDC-427.  This was unlike prior experience to the CUDC-427 drug, in which decreased hepatic function was reversed upon drug discontinuation.  The patient died from liver failure one month after discontinuation of CUDC-427.

It was noted that no other patient had experienced such a serious, irreversible liver dysfunction.

Although any incidence of hepatotoxicity can be cause for concern, the incidence of IDIOSYNCRATIC IRREVERSIBLE HEPATOTOXICITY warrants a higher scrutiny.

Four general concepts can explain toxicity profiles and divergences between individuals:

  1. Toxicogenomics: Small differences in the genetic makeup between individuals (such as polymorphisms (SNP) could result in differences in toxicity profile for a drug.  This ais a serious possibility as only one patient presented with such irreversible liver damage
  2. Toxicodynamics:  The toxicologic effect is an extension of the pharmacologic mechanism of action (or  lack thereof: could there have been alternate signaling pathways activated in this patient or noncanonical mechanism)
  3. Toxicokinetic:  The differences in toxicological response due to differences in absorption, distribution, metabolism, excretion etc. (kinetic parameters)
  4. Idiosyncratic: etiology is unknown; usually a minority of adverse effects

 

Since there is not enough information to investigate toxicogenomic or toxicokinetic mechanisms for this compound, the rest of this post will investigate the possible mechanisms of hepatotoxicity due to IAP antagonists and clues from other clinical trials which might shed light on a mechanism of toxicity (toxicodynamic) or idiosyncratic events.

Therefore this post curates the current understanding of drug-induced liver injury (DILI), especially focusing on a type of liver injury referred to as idiosyncratic drug-induced liver injury (IDILI) in the context of:

  1. Targeted and newer chemotherapies such as IAP antagonists
  2. Current concepts of mechanisms of IDILI including:

i)        Inflammatory responses provoked by presence of disease

ii)      Cellular stresses, provoked by disease, uncovering NONCANONICAL toxicity pathways

iii)    Pharmacogenomics risk factors of IDILI

Eventually this post aims to stimulate the discussion: 

  • Given inflammation, genetic risk factors, and cellular stresses (seen in clinical setting) have been implicated in idiosyncratic drug-induced liver injury from targeted therapies, should preclinical hepatotoxicity studies also be conducted in the presence of the metastatic disease?
  • Does inflammation and cellular stress from clinical disease unmask NONCANONICAL pharmacologic and/or toxicological mechanisms of action?

Classification of types of Cellular Liver injury:  A listing of types of cellular injury is given for review

I.     Hepatic damage after Acute Exposure

A. Cytotoxic (Necrotic):  irreversible cell death characterized by loss of cell membrane integrity, intracellular swelling, nuclear shrinkage (pyknosis) and eventual cytoplasmic breakdown of nuclear DNA (either by a process known as karyolysis or karyorhexus) localized inflammation as a result of release of cellular constituents.  Intracellular ATP levels are commonly seen in necrotic death.  Necrosis, unlike apoptosis, does not require a source of ATP.  A nice review by Yoshihide Tsujimoto describing and showing (by microscopy) the  differences between apoptosis and necrosis can be found here.

B. Cholestatic:  hepatobiliary dysfunction with bile stasis and accumulation of bile salts.  Cholestatic injury can result in lipid (particularly cholesterol) accumulation in cannicular membranes resulting in decreased permeability of the membrane, hyperbillirubinemia and is generally thought to result in metabolic defects.

C. Lipid Peroxidation: free radical generation producing peroxide of cellular lipids, generally resulting in a cytotoxic cell death

II.     Hepatic damage after Chronic Exposure

A. Chirrotic: Chronic morphologic alteration of the liver characterized by the presence of septae of collagen distributed throughout the major portion of the liver; Forms fibrous sheaths altering hepatic blood flow, resulting in a necrotic process with scar tissue; Alteration of hepatic metabolic systems.

B. Carcinogenesis

III. Idiosyncratic Drug Induced Liver Injury

The aforementioned mechanisms of hepatotoxicity are commonly referred to as the “intrinsic” (or end target-organ) toxicity mechanisms.  Idiosyncratic drug-induced liver injury (IDILI) is not well understood but can be separated into allergic and nonallergic reactions.  Although the risk of acute liver failure associated with idiosyncratic hepatotoxins is low (about 1 in ten thousand patients) there are more than 1,000 drugs and herbal products associated with this type of toxic reaction. Idiosyncratic drug induced liver failure usually gets a black box warning from the FDA. Idiosyncratic drug-induced liver injury differs from “intrinsic” toxicity in that IDILI:

  • Happens in a minority of patients (susceptible patients)
  • Not reproducible in animal models
  • Not dose-dependent
  • Variable time of onset
  • Variable liver pathology (not distinctive lesions)
  • Not related to drug’s pharmacologic mechanism of action (trovafloxacin IDILI vs. levofloxacin)

A great review in Perspectives in Pharmacology written by Robert Roth and Patricia Ganey at Michigan State University explains these differences between intrinsic and idiosyncratic drug-induced hepatotoxicity[1] (however authors do note that there are many similarities between the two mechanisms).    It is felt that drug sensitivity (allergic) and inflammatory responses (nonallergic) may contribute to the occurrence of IDILI.  For instance lipopolysaccharide (LPS) form bacteria can potentiate acetaminophen toxicity.  In fact animal models of IDILI have been somewhat successful:

  • co-treatment of rats and mice with nontoxic doses of trovafloxacin (casues IDILI in humans) and LPS resulted in marked hepatotoxicity while no hepatotoxicity seen with levofloxacin plus LPS[2]
  • correlates well with incidence of human IDILI (adapted from a review Inflammatory Stress and Idiosyncratic Hepatotoxicity: Hints from Animal Models (in Pharmacology Reviews)[3].  Idiosyncratic injury damage has been reported for diclofenac, halothane, and sulinac.  These drugs also show hepatotoxicity in the LPS model for IDILI.
  • Roth and Ganey suggest the reason why idiosyncratic hepatotoxicity is not seen  in most acute animal toxicity studies is that, in absence of stress/inflammation  IDILI occurrence is masked by lethality but stress/inflammation shifts increases sensitivity to liver injury at a point before lethality is seen

IDILdosestressrossmantheory

Figure.  Idiosyncratic toxic responses of the liver.    In the absence of stress and/or genetic factors, drug exposure may result in an idiosyncratic liver injury (IDILI) at a point (or dose) beyond the therapeutic range and lethal exposure for that drug.  Preclinical studies, usually conducted at sublethal doses, would not detect DILI .  Stress and/or genetic factors sensitize the liver to toxic effects of the drug (synergism) and DILI is detected at exposure levels closer to therapeutic range.  Note IDILI is not necessarily dose-dependent but cellular stress (like ROS or inflammation) may expose NONCANONICAL mechanisms of drug action or toxicity which result in IDILI. Model adapted from Roth and Ganey.

What Stress factors contribute to IDILI?

Various stresses including inflammation from bacterial, viral infections ,inflammatory cytokines  and stress from reactive oxygen (ROS) have been suggested as mechanisms for IDILI.

  1. Inflammation/Cytokines (also discussed in other sections of this post):  Inflammation has long been associated with human cases of DILI.    Many cytokines and inflammatory mediators have been implicated including TNFα, IL7, TGFβ, and IFNϒ (viral infection) leading some to conclude that serum measurement of cytokines could be a potential biomarker for DILI[4].  In addition, ROS (see below) is generated from inflammation and also considered a risk factor for DILI[5].
  2. Reactive Oxygen (ROS)/Reactive Metabolites: Oxidative stress, either generated from reactive drug metabolites or from mitochondrial sources, has been shown to be involved in apoptotic and necrotic cell death.  Both alterations in the enzymes involved in the generation of and protection from ROS have been implicated in increased risk to DILI including (as discussed further) alterations in mitochondrial superoxide dismutase 2 (SOD2) and glutathione S-transferases.  Both ROS and inflammatory cytokines can promote JNK signaling, which has been implicated in DILI[6].

Dr. Neil Kaplowitz suggested that we:

“develop a unifying hypothesis that involves underlying genetic or acquired mitochondrial abnormalities as a major determinant of susceptibility for a number of drugs that target mitochondria and cause DILI. The mitochondrial hypothesis, implying gradually accumulating and initially silent mitochondrial injury in heteroplasmic cells which reaches a critical threshold and abruptly triggers liver injury, is consistent with the findings that typically idiosyncratic DILI is delayed (by weeks or months), that increasing age and female gender are risk factors and that these drugs are targeted to the liver and clearly exhibit a mitochondrial hazard in vitro and in vivo. New animal models (e.g., the Sod2(+/-) mouse) provide supporting evidence for this concept. However, genetic analyses of DILI patient samples are needed to ultimately provide the proof-of-concept”[7].

Clin Infect Dis. 2004 Mar 38(Supplement 2) S44-8, Figure 1

Clin Infect Dis. 2004 Mar 38(Supplement 2) S44-8, Figure 3

Figures. Mechanisms of Drug-Induced Liver Injury and Factors related to the occurrence of  DILI (used with permission from Oxford Press; reference [7])

To this end, Dr. Brett Howell and other colleagues at the Hamner-UNC Institute for Drug Safety Sciences (IDSS) developed an in-silico model of DILI ( the DILISym™ model)which is based on  depletion of cellular ATP and reactive metabolite formation as indices of DILI.

Have there been Genetic Risk Factors identified for DILI?

Candidate-gene-associated studies (CGAS) have been able to identify several genetic risk factors for DILI including:

  1. Uridine Diphosphate Glucuronosyltransferase 2B7 (UGT2B7): variant increased susceptibility to diclofenac-induced DILI
  2. Adenosine triphosphate-binding cassette C2 (ABCC2) variant ABCC-24CT increased susceptibility to diclofenac-induced DILI
  3. Glutathione S-transferase (GSTT1): patients with a double GSTT1-GSTM1 null genotype had a significant 2.7 fold increased risk of DILI from nonsteroidal anti-inlammatory agents, troglitazone and tacrine.  GSTs are involved in the detoxification of phase 1 metabolites and also protect against cellular ROS.

Although these CGAS confirmed these genetic risk factors,  Stefan Russman suggests a priori genome-wide association studies (GWAS) might provide a more complete picture of genetic risk factors for DILI as CGAS is limited due to

  1. Candidate genes are selected based on current mechanisms and knowledge of DILI so genetic variants with no known knowledge of or mechanistic information would not be detected
  2. Many CGAS rely on analysis of a limited number of SNP and did not consider intronic regions which may control gene expression

A priori GWAS have the advantage of being hypothesis-free, and although they may produce a high number of false-positives, new studies of genetic risk factors of ximelagatran, flucioxaciliin and diclofenac-induced liver injury are using a hybrid approach which combines the whole genome and unbiased benefits of GWAS with the confirmatory and rational design of CGAS[8-10].

Even though idiosyncratic DILI is rare, the severity, unpredictable onset, and unknown etiology and risk factors have prompted investigators such as Stefan Russmann from University Hospital Zurich and Ignazio Grattagliano from University of Bari to suggest:

Identification of risk factors for rare idiosyncratic hepatotoxicity requires special networks that contribute to data collection and subsequent identification of environmental as well as genetic risk factors for clinical cases of idiosyncratic DILI[11].

Therefore, a DILI network project (DILIN) had been developed to collect samples and detailed genetic and clinical data on IDILI cases from multiple medical centers.  The project aims to identify the upstream and downstream genetic risk factors for IDILI[12].  Please see a SlideShare presentation here of the goals of the DILI network project.

Drs Colin Spraggs and Christine Hunt had reviewed possible genetic risk factors of DILI seen with various tyrosine kinase inhibitors (TKIs) including Lapatinib (Tykerb/Tyverb©, a dual inhibitor of  HER2/EGFR heterodimer) and paopanib (Votrient©; a TKI that targets VEGFR1,2,3 and PDGFRs)[13].

From a compilation of studies:

  • Elevation in serum bilirubin during treatment with lapatinib and pazopanib are associated with UGT1A1 polymorphism related to Gilbert’s syndrome (a clinically benign syndrome)
  • Anecdotal evidence shows that polymorphisms of lapatinib and pazopanib metabolizing enzymes may contribute to differences seen in onset of DILI
  • Pazopanib-induced elevations of ALT correlate with HFE variants, suggesting alterations in iron transport may predispose to DILI
  • Strong correlations between lapatinib-induced DILI and class II HLA locus suggest inflammatory stress response important in DILI

Note that these clinical findings were not evident from the preclinical tox studies. According to the European Medicines Agency assessment report for Tykerb states: “the major findings in repeat dose toxicity studies were attributed to lapatinib pharmacology (epithelial effect in skin and GI system.  The toxic events occurred at exposures close to the human exposure at the recommended dose.  Repeat-dose toxicity studies did not reveal important safety concerns than what would be expected from the mode of action”.

However, it should be noted that in high dose repeat studies in mice and rats, severe lethality was seen with hematologic, gastrointestinal toxicities in combination with altered blood chemistry parameters and yellowing of internal organs.

IAP Antagonists, Mechanism of Action, and Clinical Trials:

A few IAP antagonists which are in early stage development include:

  • Norvatis IAP Inhibitor LCL161: at 2012 San Antonia Breast Cancer Symposium, a phase 1 trial in triple negative breast cancer showed promising results when given in combination with paclitaxel.
  • Ascenta Therapeutics IAP inhibitor AT-406 in phase 1 in collaboration with Debiopharm S.A. showed antitumor efficacy in xenograft models of breast, pancreatic, prostate and lung cancer. The development of this compound is described in a paper by Cai et. al.

National Cancer Institute sponsored trials using antagonists of IAPs include

  • Phase II Study of Birinapant for Advanced Ovarian, Fallopian Tube, and Peritoneal Cancer (NCI-12-C-0191). Principle Investigator: Dr. Christina Annunziata. See the protocol summary. More open trials for this drug are located here.  Closed trials including safety studies can be found here.
  • A Phase 1 non-randomized dose escalation study to determine maximum tolerated dose (MTD) and characterize the safety for the TetraLogic compound TL32711 had just been completed. Results have not been published yet.
  • Closed Clinical trials with the IAP antagonist HGS1029 in advanced solid tumors determined that weekly i.v. administration of HGS1029 reported a safety issue for primary outcome measures

A great review on IAP proteins and their role as regulators of apoptosis and potential targets for cancer therapy [14] can be found as a part of a Special Issue in Experimental Oncology “Apoptosis: Four Decades Later”.  Human IAPs (inhibitors of apoptosis) consist of eight proteins involved in cell death, immunity, inflammation, cell cycle, and migration including:

In general, IAP proteins are directly involved in inhibiting apoptosis by binding and directly inhibiting the effector cysteine protease caspases (caspase 3/7) ultimately responsible for the apoptotic process [15].  IAPs were actually first identified in baculoviral genomes because of their ability to suppress host-cell death responses during viral infection [16]. IAP proteins are often overexpressed in cancers [17].

Apoptosis is separated into two pathways, defined by the initial stress or death signal and the caspases involved:

  1. Extrinsic pathway: initiated by TNFα and death ligand FasLigand;  involves caspase-8; process inhibited by IAP1/2
  2. Intrinsic pathway: initiated by DNA damage, irradiation, chemotherapeutics; mitochondrial pathway involving caspase 9 and cytochrome c release from mitochondria; mitochondria also releases SMAC/DIABLO, which binds and inhibits XIAP (XIAP inhibits the Intrinsic apoptotic pathway.

 intrinsicextrinsicapoptosiswikidot

 

Intrinsic and Extrinsic pathways of apoptosis. Figure photocredit (wikidot.com)

The Curis IAP antagonist (and others) is a SMAC small molecule mimetic. It is interesting to note [18, 19] that IAP antagonists can result in death by

  • Apoptosis: an IAP antagonist in presence of competent TNFα signaling
  • Necrosis: seen with IAP inhibitors in cells with altered TNFα signaling or with presence of caspase inhibitors

IAPs are also involved in the regulation of signaling pathways such as:

NF-ΚB signaling pathway

NF-ΚB is a “rapid-acting” transcription factor which has been found to be overexpressed in various cancers.  Under most circumstances NF-ΚB translocation to the nucleus results in transcription of genes related to cell proliferation and survival.  NF-ΚB signaling is broken down in two pathways

  1. Canonical:  Canonical pathway can be initiated (for example in inflammation) when TNF-α binds its receptors activating  death domains (TRADD)
  2. Noncanonical: since requires new protein synthesis takes longer than canonical signaling.  Can be initiated by other TNF like ligands like CD40

IAP1/2 is a negative regulator of the noncanonical NF-ΚB signaling pathway by promoting proteosomal degradation of the TRAF signaling complex. A wonderfully annotated list of NF-ΚB target genes can be found on the Thomas Gilmore lab site at Boston University at http://www.bu.edu/nf-kb/gene-resources/target-genes/ .

NF-ΚB has been considered a possible target for chemotherapeutic development however Drs. Veronique Baud and Michael Karin have pondered the utility of IAP antagonists as a good target in their review: Is NF-ΚB a good target for cancer therapy?: Hopes and pitfalls [20].  The authors discuss issues such that IAP antagonism induced both the classical and noncanonical NF-ΚB pathway thru NIK stabilization, resulting in stabilization of NF-ΚB signaling and thereby undoing any chemotherapeutic effect which would be desired.

AKT signaling

IAPs have been shown to interact with other proteins including a report that SIAP regulates AKT activity and caspase-3-dependent cleavage during cisplatin-induced apoptosis in human ovarian cancer cells and could be another mechanism involved in cisplatin resistance[21].   In addition there have been reports that IAPs can regulate JNK and MAPK signaling.

Therefore, IAPs are involved in CANONICAL and NONCANONICAL pathways.

IAPs can Regulate Pro-Inflammatory Cytokines

A recent 2013 JBC paper [22]showed that IAPs and their antagonists can regulate spontaneous and TNF-induced proinflammatory cytokine and chemokine production and release

  • IAP required for production of multiple TNF-induced proinflammatory mediators
  • IAP antagonism decreased TNF-mediated production of chemokines and cytokines
  • But increased spontaneous release of chemokines

In addition Rume Damgaard and Mads Gynd-Hansen have suggested that IAP antagonists may be useful in treating inflammatory diseases like Crohn’s disease as IAPs regulate innate and acquired immune responses[23].

Toxicity profiles of IAP antagonists

NOTE: In a paper in Toxicological Science from 2012[24], Rebecca Ida Erickson form Genentech reported on the toxicity profile of the IAP antagonist GDC-0152 from a study performed in dogs and rats. A dose-dependent toxicity profile from i.v. administration was consistent with TNFα-mediated toxicity with

  • Elevated plasma cytokines and an inflammatory leukogram
  • Increased serum transaminases
  • Inflammatory infiltrate and apoptosis/necrosis in multiple tissues

In a related note, a similar type of fatal idiosyncratic hepatotoxicity was reported in a 62 year-old man treated with the Raf kinase inhibitor sorafenib for renal cell carcinoma[25]: Fatal case of sorafenib-associated idiosyncratic hepatotoxicity in the adjuvant treatment of a patient with renal cell carcinoma; Case Report  in BMC Cancer.

At week four after initiation of sorafenib treatment, the patient noticed increasing fatigue, malaise, gastrointestinal discomfort and abdominal rash.  Although treatment was discontinued, jaundice developed and blood test revealed an acute hepatitis with

  • Elevated serum ALT
  • Elevated serum alkaline phosphatase
  • Increased prothrombin time
  • Increased LDH

…elevated levels seen in the case with the aforementioned IAP antagonist.  Autopsy revealed

  • Lobular hepatitis
  • Mononuclear cell infiltrate
  • Hepatocyte necrosis

These findings are in line with a drug-induced inflammation and IDILI. In addition to hepatotoxicity, renal insufficiency developed in this patient. The authors had suggested the death was probably due to “an idiosyncratic allergic reaction to sorafenib manifesting as hepatotoxicity with associated renal impairment”.  The authors also noted that genome wide association studies of idiosyncratic drug-induced liver injury support involvement of major histocompatibility complex (MHC) polymorphisms[26].  MHC involvement has also been associated with lapatanib and pazopanib hepatotoxicity [27, 28].

Curis has been involved in another novel oncology therapeutic, a first in class.

Last year Roche and Genentech had won approval for a Hedgehog pathway inhibitor vismodegib for treatment of advanced basal cell carcinoma (reported at FierceBiotech©). Vismodegib was initially developed in collaboration with Curis, Inc.  The hedgehog signaling pathway, which controls the function of Gli factors (involved in stem cell differentiation), is overactive in advanced basal cell carcinoma as well as other cancer types.

As an additional reference, the FDA National Center for Toxicological Research has developed THE LIVER TOXICITY KNOWLEDGE BASE (LTKB).

“The LTKB is a project designed to study drug-induced liver injury (DILI). Liver toxicity is the most common cause for the discontinuation of clinical trials on a drug, as well as the most common reason for an approved drug’s withdrawal from the marketplace. Because of this, DILI has been identified by the FDA’s Critical Path Initiatives as a key area of focus in a concerted effort to broaden the agency’s knowledge for better evaluation tools and safety biomarkers.”

A nice SlideShow of Toxicity of Targeted Therapies can be found here: http://www.slideshare.net/RashaHaggag/toxicities-of-targeted-therapies

Also please note that ALL GENES in this article are linked to their GENECARD 

REFERENCES

1.            Roth RA, Ganey PE: Intrinsic versus idiosyncratic drug-induced hepatotoxicity–two villains or one? The Journal of pharmacology and experimental therapeutics 2010, 332(3):692-697.

2.            Waring JF, Liguori MJ, Luyendyk JP, Maddox JF, Ganey PE, Stachlewitz RF, North C, Blomme EA, Roth RA: Microarray analysis of lipopolysaccharide potentiation of trovafloxacin-induced liver injury in rats suggests a role for proinflammatory chemokines and neutrophils. The Journal of pharmacology and experimental therapeutics 2006, 316(3):1080-1087.

3.            Deng X, Luyendyk JP, Ganey PE, Roth RA: Inflammatory stress and idiosyncratic hepatotoxicity: hints from animal models. Pharmacological reviews 2009, 61(3):262-282.

4.            Laverty HG, Antoine DJ, Benson C, Chaponda M, Williams D, Kevin Park B: The potential of cytokines as safety biomarkers for drug-induced liver injury. European journal of clinical pharmacology 2010, 66(10):961-976.

5.            Schwabe RF, Brenner DA: Mechanisms of Liver Injury. I. TNF-alpha-induced liver injury: role of IKK, JNK, and ROS pathways. American journal of physiology Gastrointestinal and liver physiology 2006, 290(4):G583-589.

6.            Seki E, Brenner DA, Karin M: A liver full of JNK: signaling in regulation of cell function and disease pathogenesis, and clinical approaches. Gastroenterology 2012, 143(2):307-320.

7.            Kaplowitz N: Drug-induced liver injury. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2004, 38 Suppl 2:S44-48.

8.            Kindmark A, Jawaid A, Harbron CG, Barratt BJ, Bengtsson OF, Andersson TB, Carlsson S, Cederbrant KE, Gibson NJ, Armstrong M et al: Genome-wide pharmacogenetic investigation of a hepatic adverse event without clinical signs of immunopathology suggests an underlying immune pathogenesis. The pharmacogenomics journal 2008, 8(3):186-195.

9.            Aithal GP, Ramsay L, Daly AK, Sonchit N, Leathart JB, Alexander G, Kenna JG, Caldwell J, Day CP: Hepatic adducts, circulating antibodies, and cytokine polymorphisms in patients with diclofenac hepatotoxicity. Hepatology 2004, 39(5):1430-1440.

10.          Daly AK, Aithal GP, Leathart JB, Swainsbury RA, Dang TS, Day CP: Genetic susceptibility to diclofenac-induced hepatotoxicity: contribution of UGT2B7, CYP2C8, and ABCC2 genotypes. Gastroenterology 2007, 132(1):272-281.

11.          Russmann S, Kullak-Ublick GA, Grattagliano I: Current concepts of mechanisms in drug-induced hepatotoxicity. Current medicinal chemistry 2009, 16(23):3041-3053.

12.          Fontana RJ, Watkins PB, Bonkovsky HL, Chalasani N, Davern T, Serrano J, Rochon J: Drug-Induced Liver Injury Network (DILIN) prospective study: rationale, design and conduct. Drug safety : an international journal of medical toxicology and drug experience 2009, 32(1):55-68.

13.          Spraggs CF, Xu CF, Hunt CM: Genetic characterization to improve interpretation and clinical management of hepatotoxicity caused by tyrosine kinase inhibitors. Pharmacogenomics 2013, 14(5):541-554.

14.          de Almagro MC, Vucic D: The inhibitor of apoptosis (IAP) proteins are critical regulators of signaling pathways and targets for anti-cancer therapy. Experimental oncology 2012, 34(3):200-211.

15.          Deveraux QL, Takahashi R, Salvesen GS, Reed JC: X-linked IAP is a direct inhibitor of cell-death proteases. Nature 1997, 388(6639):300-304.

16.          Crook NE, Clem RJ, Miller LK: An apoptosis-inhibiting baculovirus gene with a zinc finger-like motif. Journal of virology 1993, 67(4):2168-2174.

17.          Tamm I, Kornblau SM, Segall H, Krajewski S, Welsh K, Kitada S, Scudiero DA, Tudor G, Qui YH, Monks A et al: Expression and prognostic significance of IAP-family genes in human cancers and myeloid leukemias. Clinical cancer research : an official journal of the American Association for Cancer Research 2000, 6(5):1796-1803.

18.          Laukens B, Jennewein C, Schenk B, Vanlangenakker N, Schier A, Cristofanon S, Zobel K, Deshayes K, Vucic D, Jeremias I et al: Smac mimetic bypasses apoptosis resistance in FADD- or caspase-8-deficient cells by priming for tumor necrosis factor alpha-induced necroptosis. Neoplasia 2011, 13(10):971-979.

19.          He S, Wang L, Miao L, Wang T, Du F, Zhao L, Wang X: Receptor interacting protein kinase-3 determines cellular necrotic response to TNF-alpha. Cell 2009, 137(6):1100-1111.

20.          Baud V, Karin M: Is NF-kappaB a good target for cancer therapy? Hopes and pitfalls. Nature reviews Drug discovery 2009, 8(1):33-40.

21.          Asselin E, Mills GB, Tsang BK: XIAP regulates Akt activity and caspase-3-dependent cleavage during cisplatin-induced apoptosis in human ovarian epithelial cancer cells. Cancer research 2001, 61(5):1862-1868.

22.          Kearney CJ, Sheridan C, Cullen SP, Tynan GA, Logue SE, Afonina IS, Vucic D, Lavelle EC, Martin SJ: Inhibitor of apoptosis proteins (IAPs) and their antagonists regulate spontaneous and tumor necrosis factor (TNF)-induced proinflammatory cytokine and chemokine production. The Journal of biological chemistry 2013, 288(7):4878-4890.

23.          Damgaard RB, Gyrd-Hansen M: Inhibitor of apoptosis (IAP) proteins in regulation of inflammation and innate immunity. Discovery medicine 2011, 11(58):221-231.

24.          Erickson RI, Tarrant J, Cain G, Lewin-Koh SC, Dybdal N, Wong H, Blackwood E, West K, Steigerwalt R, Mamounas M et al: Toxicity profile of small-molecule IAP antagonist GDC-0152 is linked to TNF-alpha pharmacology. Toxicological sciences : an official journal of the Society of Toxicology 2013, 131(1):247-258.

25.          Fairfax BP, Pratap S, Roberts IS, Collier J, Kaplan R, Meade AM, Ritchie AW, Eisen T, Macaulay VM, Protheroe A: Fatal case of sorafenib-associated idiosyncratic hepatotoxicity in the adjuvant treatment of a patient with renal cell carcinoma. BMC cancer 2012, 12:590.

26.          Daly AK: Drug-induced liver injury: past, present and future. Pharmacogenomics 2010, 11(5):607-611.

27.          Spraggs CF, Budde LR, Briley LP, Bing N, Cox CJ, King KS, Whittaker JC, Mooser VE, Preston AJ, Stein SH et al: HLA-DQA1*02:01 is a major risk factor for lapatinib-induced hepatotoxicity in women with advanced breast cancer. Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2011, 29(6):667-673.

28.          Xu CF, Reck BH, Goodman VL, Xue Z, Huang L, Barnes MR, Koshy B, Spraggs CF, Mooser VE, Cardon LR et al: Association of the hemochromatosis gene with pazopanib-induced transaminase elevation in renal cell carcinoma. Journal of hepatology 2011, 54(6):1237-1243.

Other articles on the site about Toxicology and Pharmacology of New Classes of Cancer Chemotherapy include:

FDA Guidelines For Developmental and Reproductive Toxicology (DART) Studies for Small Molecules

Gamma Linolenic Acid (GLA) as a Therapeutic tool in the Management of Glioblastoma

DNA Methultransferases – Implications to Epigenetic Regulation and Cancer Therapy Targeting: James Shen, PhD

Molecular Profiling in Cancer Immunotherapy: Debraj GuhaThakurta, PhD

AT13148 – A Novel Oral Multi-AGC Kinase Inhibitor Has Potent Antitumor Activity

Targeting Mitochondrial-bound Hexokinase for Cancer Therapy

Breast Cancer, drug resistance, and biopharmaceutical targets

Ubiquitin-Proteosome pathway, Autophagy, the Mitochondrion, Proteolysis and Cell Apoptosis: Part III

Ubiquinin-Proteosome pathway, autophagy, the mitochondrion, proteolysis and cell apoptosis

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Heroes in Medical Research: Dr. Carmine Paul Bianchi Pharmacologist, Leader, and Mentor

Writer/Curator: Stephen J. Williams, Ph.D.

Past articles in this Heroes in Medical Research series had focused on those seemingly small discoveries, sometimes gained serendipitously and through careful observation and experimentation, which led to some of our most important breakthroughs of our time.  I have tried to make the posts more about the people and less about the discoveries

However, though seminal discoveries are so important to the future of science (and should be celebrated), equally if not MORE IMPORTANT is the MENTORING of future scientists and the PROMOTION of fields of study.  One person who exemplified these values was Dr. Carmine Paul Bianchi, who had recently just passed away this August, and will be sorely missed in the field of pharmacology and toxicology.

For those who were not familiar with Dr. Bianchi I have curated some pertinent information about his work as a scientist, professor and Chairman in pharmacology, and leader and spokesperson for the field of pharmacology.  He was one of the founders of the Mid-Atlantic Pharmacology Society and was an advocate and influential in the careers of many pharmacologists and toxicologists.

Comments from fellow colleagues are very welcome (in comment section at end of post)

The following is separated in 3 sections:

  • An obituary from the Philadelphia Inquirer
  •  A section of the history of the Pharmacology Department at Thomas Jefferson University where Dr. Bianchi was Chairman
  • A few important textbooks and scientific articles he had authored

 

Carmine Paul Bianchi, 86, pharmacology professor

Paul Bianchi

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Carmine Paul Bianchi

By Bonnie L. Cook, Inquirer Staff Writer

Posted: August 20, 2013

Carmine Paul Bianchi, 86, of Boothwyn, a professor of pharmacology in Philadelphia for many years, died Tuesday, Aug. 13, of a digestive ailment at Taylor Hospice House in Ridley Park.

Born in Newark, N.J., and raised in Maplewood, Dr. Bianchi served as an Army surgical technician in Tilton General Hospital at Fort Dix from 1945 to 1947.

He earned a bachelor’s degree in chemistry from Columbia University in 1950, a master’s in physiology and biochemistry from Rutgers University in 1953, and a doctorate in physiology and physical chemistry in 1956 from Rutgers.

In the 1950s, he did research at Rutgers and was a public health fellow and visiting scientist at the National Institutes of Health in Maryland.

From 1961 to 1976, he held a number of jobs in the department of pharmacology in the University of Pennsylvania School of Medicine. That culminated in his being named professor of pharmacology.

Dr. Bianchi left in 1976 for Jefferson Medical College of Thomas Jefferson University, where he became pharmacology professor and chairman of the pharmacology department from 1976 to 1987. In 1987, he stepped down from the chairmanship but remained professor of pharmacology. He retired in 1997 as professor emeritus.

Dr. Bianchi was a member of many professional groups, including the New York Academy of Sciences and the American Association for the Advancement of Science.

He was a leader and author in pharmacology, helping edit an industry journal and making himself available for consultation to medical examiners and experts in toxicology.

He wrote or contributed to three books and 200 scientific papers and lectured widely. He enjoyed mentoring medical and graduate students.

His family called Dr. Bianchi “a true renaissance man” who was as comfortable discussing English, history, and politics as he was the sciences.

 

 

 

The following was taken from a history of  Department of Pharmacology  at Thomas Jefferson University  and can be viewed at: http://jdc.jefferson.edu/cgi/viewcontent.cgi?article=1008&context=wagner2

 

 

Carmine Paul Bianchi, Ph.D;

Third Chairman (1976-1986)

The new Chairman of the Department, effective

July 1, 1976, was Carmine Paul Bianchi, Ph.D.

(Figure 8-3) from the University of Pennsylvania

School of Medicine, where he had been Professor

of Pharmacology since [969 and a member of the

faculty of that Department since 1961.

Dr. Bianchi was born on April 9, [927, in

Newark, New Jersey. After receiving his diploma

at Columbia High School in 1945, he spent two

years in the Army Medical Corps as Technical Sgt.

Fourth Grade. He then attended Columbia

University, where he majored in chemistry and

obtained the B.A. degree in 1950. Like Dr.

Gruber, the first Chairman of the Pharmacology

Department at Jefferson, Bianchi earned his Ph.D.

in physiology. He pursued his graduate studies at

Rutgers University, supplementing his physiology

major with a biochemistry minor for the M.S.

degree in [953 and with a physical chemistry minor

for the Ph.D. degree in 1956. Dr. Bianchi then

spent several years at the National Institutes of

Health-two years as a Public Health Fellow and

one as a Visiting Scientist. Following that he was

Assistant Member of the Institute for Muscle

Disease in New York for one year. In 1961 Dr.

Bianchi became classified professionally as a

pharmacologist by becoming an Associate in the

Department of Pharmacology at the University of

Pennsylvania School of Medicine. There he

advanced to Professorship in 1969 and remained

until he came to Jefferson. The evolution of Dr.

Bianchi’s career from physiology to pharmacology

was the logical result of his investigations of the

effect of various drugs on the metabolism and

distribution of some of the important elements of

the body, notably calcium. His major field of

interest became classified and remained in

electrolyte pharmacology.

Throughout his career Dr. Bianchi has been

very active in the affairs of outside professional

organizations. He is a member of the American

Society for Pharmacology and Experimental

Therapeutics, the American Physiological Society,

the American Chemical Society, and the

International Society of Toxicology, to name

only a few. He served as President of both the

Philadelphia Physiological Society and the John

Morgan Society in the same year (1973-1974), and

of the Philadelphia Chapter of the Society for

Neuroscience (1979-1980). He gave much time

and valuable services as Field Editor for the

Journal of Pharmacology and Experimental

Therapeutics ([970-1979) and as a member of the

Pharmacology Section of the National Board of

Medical Examiners (1981-1985).

After Dr. Bianchi became Chairman no

immediate changes in the general structure and

activities of the Department took place. He

enlarged the Department and filled vacancies

occasioned by the retirement of some faculty

members. The didactic schedules and subject

matter offered to the medical and graduate

students underwent only minor annual changes.

Research activities were augmented by the

addition of Dr. Bianchi’s specialty in electrolyte

pharmacology and the appointments of new staff

members for investigations in that and related

flelds. Through the following decade there was a

marked change in the faculty structure of the

Department. The [975 Jefferson catalogue, for

example, listed 15 faculty appointments in

Pharmacology, of which eight were on a primary

full-time basis with offices and laboratories in the

Department. In 1985 there were 36 faculty

appointments of which eight were on a primary

full-time basis. The large increase in the total

number of faculty resulted from adjunct

appointments from outside organizations and from

secondary appointments of faculty members of the

Clinical Departments at Jefferson. This expansion

reflected a broadening of interests and interactions

on both the scientific and clinical fronts in clinical

pharmacology and clinical toxicology.

A notable addition to the faculty of the

Department in 1978 was Dr. Hyman Menduke

as Professor of Pharmacology

(Biostatistics). After receiving his Ph.D. in

Economic Statistics at the University of

Pennsylvania, Menduke came to Jefferson in 1953

as Assistant Professor of Biostatistics with no

official Departmental affiliation until 1963, when

he was appointed Professor of Preventive

Medicine (Biostatistics). When Dr. Menduke first

came to Jefferson he gave a ten-hour course in

biostatistics to the second-year medical students in

time provided during their pharmacology course.

Through the years his offerings expanded to a

12-hour course for freshman medical students and

introductory and advanced courses for graduate

students. An early and valuable contribution was a

series of individual conferences with graduate

students on the statistical planning of their

research problems and the later analysis of their

data.

 

The interests and activities of the Department in

research in toxicology have been emphasized.

Toxicology continued as an important part of the

research program after Dr. Bianchi became

Chairman in 1976, although under his direction

the major emphasis in research became redirected

toward the general areas of cell pharmacology and

neuropharmacology.

In accord with its continuing research and

teaching activities in toxicology, the Department

starting in 1977 organized a series of annual

workshops on Industrial Toxicology sponsored by

the College of Graduate Studies. These were

four-day symposia on important toxicologic

problems in industry and the general environment,

presented by toxicologically involved Jefferson

faculty and by invited experts from other

universities, industry, and government.

In 1979 the Department was awarded a training

grant in Industrial and Environmental Toxicology

by the National Institute of Environmental Health

Sciences. The purpose of this award was to

provide postdoctoral training in toxicology for

individuals who had previously received their

Ph.D. degrees in other sciences. Ten M.S. degrees

were subsequently awarded in this program

through the years from 1981 to 1986.

On December 14, 1978, a full day’s workshop

with outside invited experts was held to discuss

the formation of a Toxicology Center and the

establishment of a Chair in Toxicology-Pathology

to broaden the base of research and training in

toxicology at Jefferson. It was envisioned that the

Center would be an administrative Division within

the Department of Pharmacology, with research

participation from other basic science departments

and the Department of Medicine. Although funds

accumulated in support of a Toxicology Center,

disagreements developed relating to the

administrative base of the Center.

 

A few articles from Dr. Bianchi showing the diversity of his research interests including calcium mobilization, neurotoxicology, and cellular metabolism and physiology.

Muscle fatigue and the role of transverse tubules.

Bianchi CP, Narayan S.

Science. 1982 Jan 15;215(4530):295-6. No abstract available.

 

Effect of adenosine on oxygen uptake and electrolyte content of frog sartorius muscle.

Prosdocimi M, Bianchi CP.

J Pharmacol Exp Ther. 1981 Jul;218(1):92-6.

 

The effect of diazepam on tension and electrolyte distribution in frog muscle.

Degroof RC, Bianchi CP, Narayan S.

Eur J Pharmacol. 1980 Aug 29;66(2-3):193-9.

 

Steady state maintenance of electrolytes in the spinal cord of the frog.

Bianchi CP, Erulkar SD.

J Neurochem. 1979 Jun;32(6):1671-7. No abstract available.

An in-vitro model of anesthetic hypertonic hyperpyrexia, halothane–caffeine-induced muscle contractures: prevention of contracture by procainamide.

Strobel GE, Bianchi CP.

Anesthesiology. 1971 Nov;35(5):465-73. No abstract available.

 

The effects of psychoactive agents on calcium uptake by preparations of rat brain mitochondria.

Tjioe S, Haugaard N, Bianchi CP.

J Neurochem. 1971 Nov;18(11):2171-8. No abstract available.

 

The effect of veratridine on sodium-sensitive radiocalcium uptake in frog sartorius muscle.

Johnson P, Bianchi CP.

Eur J Pharmacol. 1971 Sep;16(1):90-9. No abstract available.

 

The function of ATP in Ca2+ uptake by rat brain mitochondria.

Tjioe S, Bianchi CP, Haugaard N.

Biochim Biophys Acta. 1970 Sep 1;216(2):270-3. No abstract availabl

 

The effects of pH gradients on the uptake and distribution of C14-procaine and lidocaine in intact and desheathed sciatic nerve trunks.

Strobel GE, Bianchi CP.

J Pharmacol Exp Ther. 1970 Mar;172(1):18-32. No abstract available

 

 

More articles by CP Bianchi  can be found at: http://www.ncbi.nlm.nih.gov/pubmed/?term=Bianchi%20CP[auth]

The following is one of the seminal books Dr. Bianchi authored:

 

Role of Calcium Channels of the Sarcolemma and the Sarcoplasmic Reticulum in Skeletal Muscle Functions

http://link.springer.com/article/10.1007%2F978-1-4615-3362-7_17/lookinside/000.png

AND

Advances in General and Cellular Pharmacology (1976)

Toshio Narahashi; Carmine Paul Bianchi

The author of the Advances in General and Cellular Pharmacology is Toshio Narahashi; Carmine Paul Bianchi – very good writer. You can download this e-book absolutely for free. This ebook’s ISBN number is 9781461582007. if you were searching for for free download of kindle books, google books, free pdf books, pdf ebooks, e-books, pdf files or pdf ebooks just stay here for a while, download what you wanted for free and enjoy!

Advances in General and Cellular Pharmacology – Toshio Narahashi; Carmine Paul Bianchi – PDF Free Download Ebook also for Kindle

 

Other articles in this series published on this site include:

Heroes in Medical Research: Dr. Robert Ting, Ph.D. and Retrovirus in AIDS and Cancer

Heroes in Medical Research: Barnett Rosenberg and the Discovery of Cisplatin

Volume Two: Interviews with Scientific Leaders

 

 

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The SCID Pig:  How Pigs are becoming a Great Alternate Model for Cancer Research[1]

Author/Writer: Stephen J. Williams, Ph.D.©

The need for alternate models of human cancer

Many worldwide regulatory bodies are in agreement that proper choice of animal model is necessary for adequate extrapolation of toxicity and efficacy data from animal to human, considering the varied classes of therapeutics now being developed for oncology.  The inability of screens, reliant on human xenografts grown in immunocompromised mice to evaluate host-immune and species-dependent effects, has made development of alternative animal-models a priority.   This is evident in the fact that ninety percent of new anticancer drugs which showed anti-tumor efficacy in mouse preclinical models failed in human clinical studies. A recently developed “humanized” mouse model may assist in testing the metabolism of cancer drugs but still relies on older “immunosuppression” mouse models (http://stehlin.org/mouse-model-development/). This inadequacy of older, accepted models is clearly evident when evaluating safety and efficacy of adenoviral based gene therapies such as oncolytic conditionally-replicative adenovirus (CRAd).  Although new-generation CRAds present with a relative safe profile[2, 3], adenoviral particles, especially the Ad5 based virus used for most CRAds, have the tendency to replicate in non-tumor tissue, such as liver and lung, resulting in tissue-specific toxicities[4-7].  The manifestation of these toxicities is only evident in species permissive for viral replication, such as the pig. Indeed, one of the first clinical trials with older adenovirus gene therapy, resulting in severe hepatic toxicity and fatality, may have been prevented if more appropriate preclinical screens were conducted.  Thereafter, strict regulatory guidelines for adenoviral-based clinical trials have been issued, with particular emphasis on vector dosage, safety and toxicity[8]. Indeed, at Schering-Plough, a toxicology program was initiated to evaluate SCH 58500, and adenoviral gene therapy directed against p53, which involved use of non-immunogenic rats compared with testing in Yorkshire pigs made immunoreactive to the vector[9, 10].  In fact, data from the pig study revealed a faster clearance of virus as well as toxicities not seen in non-immunogenic, non-permissive hosts such as rat and mouse.

Therefore, development of a porcine model of cancer would permit both testing of both the efficacy and safety of these therapies in the same animal.

Development of large animal models of cancer

To date, large animal tumor models have been used for studying spontaneously formed tumors in dogs and cats [11](Vail, 2000, Cancer Invest), the most common being canine [12] and feline non-Hodgkin’s lymphoma [13]. The advantages of these companion models are the outbred nature of the animals, comparable size and kinetics to human tumors [14-18], and high incidence rates. Allografts of the outbred-canine transplanted venereal tumor have been used to test the ability to detect tumors using X-ray computed tomography and MRI with the ultimate goal of imaging-guided intervention. Researchers have recently utilized the spontaneously arising canine and feline soft tissue sarcomas to study effects of hyperthermia on chemotherapy pharmocokinetics, development of hypoxic cell markers, and cancer imaging techniques [15, 19-26]

Although it appears that, for a select number of tumor types, spontaneously arising tumors in large outbred animals can be useful to model the human disease, it is disappointing these spontaneous arising tumors are limited to discrete tumor types. However, due to recent advances in sequencing of several domestic animal genomes and the development of new cloning strategies, it is now very feasible to utilize other animal models more relevant to human disease, notably the miniature pig.

gottingen minipigThe Gottingen mini-pig

Large animals in medical research: Advantages of the minipig

Due to recent advances in sequencing of several domestic animal genomes [27, 28] and the development of new organism cloning technologies [29-31], it is now very feasible to utilize other species to model human disease, notably the pig. The development of porcine models of human disease has gained much interest lately. Advantages include the resemblance in anatomy, physiology, and genetic makeup with the human, as well as new methods to manipulate the pig genome [32, 33]. To date, porcine models of human metabolic syndrome [34] and diabetes [35], aortic aneurism [36], infectious disease resistance [32, 37], seizure [38], neurologic syndromes [33], and pancreatitis [39] have been developed. Recently, a genetically-engineered porcine model of cystic fibrosis was produced in collaboration with investigators at University of Iowa and Exemplar Genetics [40-42]. Additionally, Cho et al. successfully transplanted spontaneously transformed leukemic and lymphatic tumor cells in a major histocompatibility complex (MHC)-defined inbred miniature swine model [43], suggesting feasibility of an ex vivo strategy to develop a porcine tumor model. Porcine models have, also, been used to develop, test and refine surgical [44, 45] and laparoscopic techniques [46, 47], radio- and cryoablation protocols of tissues [48-52] and robotic surgery using the da Vinci Surgical SystemÒ [53, 54].  In addition, because of the size of porcine organs and their resemblance to the human (in genetics) the minipig is very useful and abundant of a source to isolate specific cell types for in vitro studies.  Below is a figure showing the comparable size of human and porcine ovaries to the mouse and  ability to purify  porcine ovarian epithelial cells and their similarity to human and mouse ovarian epithelial cells.

newslidemousehumanpigovarysizejpeg

Figure 1.  The human and pig ovary have similar size and can yield a greater number of isolated cells than one can get from a mouse ovary.

posehosemosepicforpostjpg

Figure 2.  Isolation and morphology of ovarian epithelial cells from three sources:

A) Devonshire/Yorkshire pig

B) normal human ovary

c) SV129/BL6  mouse

note cobblestone epithelial morphology from all three sources©

To date, there has been no allograft or xenograft model of cancer in pigs. The consensus amongst many surgeons suggests development of a minipig tumor model would be an invaluable tool for developing surgical skills. 

A recent advancement in porcine tumor modeling was made by collaboration between researchers from the laboratories of Dr. Stefan Bossmann and Deryl Troyer at Kansas State and Iowa State, respectively[1].  The joint collaboration resulted in the development of the first severe combined immunodeficient pig line (SCID pig) which was shown to be able to accept human tumor xenografts.  The line of immunodeficient pig was discovered when Yorkshire pigs were bred for increased feed efficiency and a line of pigs exhibited SCID-like symptoms including:

  • Decreased levels of circulating lymphocytes
  • Atrophied thymus and lymph nodes

The SCID phenotype in mice have been ascribed to defects in a DNA-dependent protein kinase gene which prevents variable-diversity-joining [V(D)J] gene region recombination[55].  There have been multiple genetic defects found in humans resulting in SCID, including defects in adenylate kinase2, Janus kinase 3, the IL2 receptor, and the IL-7 receptor[56]. The SCID phenotype in this pig line has a simple autosomal recessive inheritance pattern which, as described below in an interview with the authors, allows for the propagation of this porcine line.

An important feature of SCID models is the ability of these animals to act as a recipient of human tumorigenic cell lines.  In fact, growth of cell lines in SCID mice is a common test for tumorigenicity.  Therefore, to test if these pigs could act as recipients for human cancer cell lines, the authors inoculated the SCID Yorkshire pigs with 4 million A3755M human melanoma cells or PANC1 human pancreatic carcinoma cells subcutaneously in the left and right ears respectively of three pigs.  Some features of the results include:

  • All injection sites showed evidence (either histologic or palpable) of tumor growth
  • Tumors showed characteristic histologic features of malignant neoplasm including
  1. Bizarre and atypical mitotic figures
  2. Anisocytosis (different cell sizes and shapes; feature of malignancy)
  3. Anisokaryosis (different size and shape of nucleus)
  • tumors stained with anti-human mitochondrial antibody (a marker of epithelial cancer cells) showed strong cytoplasmic staining of neoplastic cells
  • interestingly no necrotic regions in the tumor

 

scidpigfig1Figure 3. Visual evidence of human tumor cells growing in SCID pig ear (day 20). B) Same picture as A) but circle outlines growth.  From reference 1. Basel et al., used with permission from Mary Liebert.

It is interesting to note that these tumors only grew roughly 10 x 5.5 mm, which is genrally large enough to do preclinical studies but may be too expensive to be of use for xenograft studies.  However it would be very feasible to conduct allograft studies in these SCID pigs.

Dr. Jack Dekkers, C.F. Curtiss Distinguished Professor and Section Leader of Animal Breeding and Genetics at Iowa State University, was kind to answer a few questions about the SCID pig model.

Question: You had mentioned this line was identified after breeding Yorkshire pigs for increased feed efficiency.  Have you identified or hypothesize which altered pathway or molecular defect which results in a SCID phenotype?  Is this SCID phenotype a result of a metabolic syndrome these pigs could have?

Dr. Dekkers: We indeed identified the SCID phenotype in a line of pigs that we had selected for increased feed efficiency. However, I don’t think this phenotype has anything to do with the selection we practiced; it was either already present in the founders of the line or it was a random mutation that occurred in the line, independent of the selection for feed efficiency. We have narrowed the mutation that causes the SCID in our pigs down to a chromosomal region and have a very strong candidate gene in that region that we are currently pursuing.

Question: In your opinion, is it possible to produce a highly inbred immunocompromised strain of pig such as a Gottingen minipig?

Dr. Dekkers: We are working on breeding the SCID mutation into mini pigs. But in the meantime, we have used bone marrow transfer to create a male that is homozygous SCID (it’s an autosomal recessive) and reproducing. This allows us to produce litters that are 50% SCID and 50% normal (carriers) by mating him to carrier females.

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Other articles on this site pertaining to Alternate Animal Models and Cancer and Disease include:

Guidelines for the welfare and use of animals in cancer research

Demythologizing sharks, cancer, and shark fins

Predicting Drug Toxicity for Acute Cardiac Events

FDA Guidelines For Developmental and Reproductive Toxicology (DART) Studies for Small Molecules

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FDA Guidelines For Developmental and Reproductive Toxicology (DART) Studies for Small Molecules. Author-Writer: Stephen J. Williams, Ph.D.

This posting is a follow-up on the Report on the Fall Mid-Atlantic Society of Toxicology Meeting “Reproductive Toxicology of Biologics: Challenges and Considerations post and gives a brief synopsis of the current state of FDA regulatory guidelines with respect to DART studies on small molecule (non-biological based) therapeutics.    The following is adapted from the book Principles and Methods of Toxicology by Dr. A Wallace Hayes (1) and is an excellent reference on reproductive toxicology and testing methods.

Chemical insult occurs to the human reproductive system at a multitude of stages in development and the life cycle, leading to the extensive testing which must be performed to diligently the reproductive and development toxicity of a chemical/drug.  Abnormalities and toxic manifestations in the offspring may result from insult to the adult reproductive (either female or male) and neuroendocrine systems, as well as damage to the embryo resulting in embryolethality, fetus at any period during organogenesis, juvenile development or, in the case of certain antibody therapies, immune system development.  The latter, toxic insult to the developing immune system could possibly be manifested as either an immune defect in the newborn or, later in life, as tolerance to said therapy.  It is estimated that exposure to the pregnant woman, of either environmental contaminants or drug, is significant.  It is estimated that a mother may be taking an average of 8-9 different drug preparations, mostly over the counter preparations such as antacids, vitamin preparations, cathartics etc. with the maximal drug intake occurring between 24 and 36 weeks of gestation.

Toxic insult to the developing embryo is dependent on

  • Fetal development stage during drug/chemical exposure
  • Maternal/placental xenobiotic metabolism
  • Pharmacokinetic parameters affecting bioavailability and fetal/maternal drug binding

The following table shows the dependency of developmental stage to teratogenicity: adapted from J. Manson, H. Zenick, and R.D. Costlow from Principles and Methods of Toxicology.

Developmental Stage Major Susceptibility
Preimplantation Embryolethality
Organogenesis Births defects; embryolethality
Fetal Growth retardation, fetal death, functional deficits
Neonatal Growth retardation, nervous system alterations, immune and endocrine systems

It is not generally accepted that there is a dose dependency of teratogenesis however most teratogens have specific mechanisms of action and teratogenic effects occur at much lower doses than result in maternal toxicity.   However, the developmental toxicity may be manifested later in life, including as reproductive toxicity affecting adult fertility and familial generations.

FDA Guidelines for DART Studies on Non-Biologics (Small Molecule Therapeutics)

The basic design for DART studies incorporate the aforementioned principles of tetralogy:

  • developmental stage of fetal exposure
  • parental effects on reproduction and development
  • toxicity may be manifested over multiple generations including fertility rates

Therefore two designs are generally used for DART studies

  1. exposure across several generations
  2. exposure during one generation

FDA requires one control group and two treatment groups, and evaluation of at least two species.  However, most studies will use two rodent and one nonrodent species.

Multigenerational Design

Multigenerational DART studies are conducted for compounds likely to concentrate in the body following long-term exposure.  Examples of types of compounds include pesticides and food additives.

Figure 1.  General Design of a Multigenerational DART study.  Weanlings (30-30 days of age) from the parental generation are treated for a period up to 60 days. At 100-120 days of parental generation, animals are mated.  Fx = filialx .

Three Segment, Single Generation Tests

The single generation design is more suitable for DART studies on drugs, as most therapeutic would be taken over short periods (during pregnancy) and have relatively short half-lives in the body.  FDA guidelines separate these studies in three phases:

I.            Phase I: evaluation of fertility and general reproductive performance

II.            Phase II: assessment of teratogenicity and embryotoxicity

III.            Phase III: peri- and postnatal evaluations.

All figures are adapted from Principles and Methods of Toxicology.(1)

FDA guidelines Guidance for Industry Reproductive and Developmental Toxicities —Integrating Study Results to Assess Concerns can be found at: http://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Guidances/ucm079240.pdf

FDA Guideline for reproductive toxicity testing for small molecule therapeutics can be found at:

http://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Guidances/ucm074950.pdf

1.            Hayes, A. W. (1986) Principles and Methods of Toxicology, Raven Press, New York

Other research papers on Pharmaceutical Intelligence and Reproductive Biology, Bio Insrumentation, Endocrinology Genetics were published on this Scientific Web site as follows

Non-small Cell Lung Cancer drugs – where does the Future lie?

Reboot evidence-based medicine and reconsider the randomized, placebo-controlled clinical trial

Every sperm is sacred: Sequencing DNA from individual cells vs “humans as a whole.”

Leptin and Puberty

Gene Trap Mutagenesis in Reproductive Research

Genes involved in Male Fertility and Sperm-egg Binding

Hope for Male Contraception: A small molecule that inhibits a protein important for chromatin organization can cause reversible sterility in male mice

Pregnancy with a Leptin-Receptor Mutation

The contribution of comparative genomic hybridization in reproductive medicine

Sperm collide and crawl the walls in chaotic journey to the ovum

Impact of evolutionary selection on functional regions: The imprint of evolutionary selection on ENCODE regulatory elements is manifested between species and within human populations

Biosimilars: CMC Issues and Regulatory Requirements

Biosimilars: Intellectual Property Creation and Protection by Pioneer and by Biosimilar Manufacturers

Assisted Reproductive Technology Cycles and Cumulative Birth Rates

Innovations in Bio instrumentation in Reproductive Clinical and Male Fertility Labs in the US

Increased risks of obesity and cancer, Decreased risk of type 2 diabetes: The role of Tumor-suppressor phosphatase and tensin homologue (PTEN)

Guidelines for the welfare and use of animals in cancer research

Every sperm is sacred: Sequencing DNA from individual cells vs “humans as a whole.”

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