Healthcare analytics, AI solutions for biological big data, providing an AI platform for the biotech, life sciences, medical and pharmaceutical industries, as well as for related technological approaches, i.e., curation and text analysis with machine learning and other activities related to AI applications to these industries.
The role of the patient has evolved dramatically over the past decade. Not only are patients increasingly more involved in their healthcare decision making, they are also passionate advocates who work tirelessly to advance drug development research and development and secure a public policy environment that is patient-centric. Join a discussion with patient advocates as they discuss their journeys to diagnosis and their viewpoints on our healthcare system. They will share their perspectives on what it means to be a patient and how they are advocating in their own unique ways to achieve a common goal: bringing new treatments to patients.
Christopher Anselmo: affected by MS but did not understand why he should be involved in a study at the time or share your story but he saw others who benefited from both of these and now is fervent patient advocate. Each patient is worth their weight in gold as needed for other patient support. The why needs to be asked of oneself before go out to other patients or into new trials. Might not see through to end if don’t have that discussion of why doing this.
Eve Bukowski: she had stomach aches, went to hospital, and diagnosed with constipation, but had stage III colon cancer. She was campaigning for Hillary Clinton but then started to campaign for her life. She wound up having multiple therapies and even many I/O trials. Fighting cancer is a mental challenge. She has been fighting for eleven years but has an amazing strength and will.
Emily Kramer: cystic fibrosis patient. Advocates for research as she has a mutant allele (nonsense mut) that is not targeted by the current new therapy against known mutants of CFTR. So started Emily’s Entourage for this orphan of an orphan disease. Funded $4 million in grants and helped develop a new startup and get early seed funding. Noticed that the infrastructure to get these drugs to market was broken and also is investing to shore up these breaks in drug pipeline infrastructure for orphan diseases. For progressive diseases she would like drug developers to shift the timelines or speed with which they get to take a chance and try that new possibility. As a patient advocacy org, they want to partner every step of the way with biotech/pharma, they understand co’s and stakeholders can only do so much but let’s break out of convention.
Julie: many patient advocacy groups go person to person and make a support network.
SINGLE CELL GENOMICS 2019, September 24-26, 2019, Djurönäset, Stockholm, Sweden
Reporter: Aviva Lev-Ari, PhD, RN
4.1.6 SINGLE CELL GENOMICS 2019 – sometimes the sum of the parts is greater than the whole, September 24-26, 2019, Djurönäset, Stockholm, Sweden http://www.weizmann.ac.il/conferences/SCG2019/single-cell-genomics-2019, Volume 2 (Volume Two: Latest in Genomics Methodologies for Therapeutics: Gene Editing, NGS and BioInformatics, Simulations and the Genome Ontology), Part 4: Single Cell Genomics
Single cell genomics has emerged as a revolutionary technology transforming nearly every field of biomedical research. Through its many applications (single cell genome sequencing, single cell transcriptomics, various single cell epigenetic profiling approaches, and spatially resolved methods), researchers can characterize the genetic and functional properties of individual cells in their native conditions, leading to numerous experimental and clinical opportunities. As technology is leaping forward, many critical questions are arising:
• How can the behavior of groups of thousands or tens of thousands of single cells be analyzed and modeled?
• How can samples of precise single-cell-states be converted to inferred cellular behaviour, in space and time?
• How can multimodal single-cell datasets be integrated?
• What can we learn about cell-cell interactions?
• What are the immediate implications to fields like neuroscience, immunology, cancer research and stem cells?
• What will the longer-term impacts be for clinical research and practice?
The conference will bring together many of the pioneers and leading experts in the field to three days of extensive, interdisciplinary and informal discussion. Our goal is to create a forum where knowledge is shared, hoping to define together the agenda of this new community. The meeting will include presentations from invited leaders and several selected abstracts, a poster session and many opportunities for interaction. We encourage students and postdocs to participate by presenting abstracts.
BioInformatic Resources at the Environmental Protection Agency: Tools and Webinars on Toxicity Prediction, Volume 2 (Volume Two: Latest in Genomics Methodologies for Therapeutics: Gene Editing, NGS and BioInformatics, Simulations and the Genome Ontology), Part 1: Next Generation Sequencing (NGS)
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.”
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.
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.
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.
Aggregated Computational Toxicology Resource (ACToR) ACToR is an online warehouse of publicly available chemical toxicity data and can be used to find all publicly available data about potential chemical risks to human health and the environment. ACToR aggregates data from over 1000 public sources on over 500,000 environmental chemicals searchable by chemical name, other identifiers and by chemical structure.
Chemical and Product Category Database Contains information on how chemicals are used in consumer products. It includes information mapping over 43,000 chemicals to a set of terms categorizing their usage in consumer products or function.
Ecotoxicology Database (EcoTox) Source for finding single chemical toxicity data for aquatic life, terrestrial plants and wildlife.
Toxicity Reference Database (ToxRefDB) ToxRefDB contains thousands of animal toxicity studies on hundreds of chemicals from 30 years worth of animal toxicity studies.
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
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.
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.
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.
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
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
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
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
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
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
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
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
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
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
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.
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.
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)
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.
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).
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
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)
Katherine Phillips, Research Chemist, Human Exposure and Dose Modeling Branch, Computational Exposure Division, EPA’s National Exposure Research Laboratory (NERHL)
3.3.8 The 3rd STATONC Annual Symposium, April 25-27, 2019, Hilton Hartford, CT, 315 Trumbull St., Hartford, CT 06103, Volume 2 (Volume Two: Latest in Genomics Methodologies for Therapeutics: Gene Editing, NGS and BioInformatics, Simulations and the Genome Ontology), Part 2: CRISPR for Gene Editing and DNA Repair
SYMPOSIUM OBJECTIVES
The three-day symposium aims to bring oncologists and statisticians together to share new research, discuss novel ideas, ask questions and provide solutions for cancer clinical trials. In the era of big data, precision medicine, and genomics and immune-based oncology, it is crucial to provide a platform for interdisciplinary dialogues among clinical and quantitative scientists. The Stat4Onc Annual Symposium serves as a venue for oncologists and statisticians to communicate their views on trial design and conduct, drug development, and translations to patient care. To be discussed includes big data and genomics for oncology clinical trials, novel dose-finding designs, drug combinations, immune oncology clinical trials, and umbrella/basket oncology trials. An important aspect of Stat4Onc is the participation of researchers across academia, industry, and regulatory agency.
Meeting Agenda will be announced coming soon. For Updated Agenda and Program Speakers please CLICK HERE
JP Morgan Healthcare Conference Update: Sage, Mersana, Shutdown Woes and Babies
Published: Jan 10, 2019By Alex Keown
With the J.P. Morgan Healthcare Conference winding down, companies remain busy striking deals and informing investors about pipeline advances. BioSpace snagged some of the interesting news bits to come out of the conference from Wednesday.
SAGE Therapeutics – Following a positive Phase III report that its postpartum depression treatment candidate SAGE-217 hit the mark in its late-stage clinical trial, Sage Therapeutics is eying the potential to have multiple treatment options available for patients. At the start of J.P. Morgan, Sage said that patients treated with SAGE-217 had a statistically significant improvement of 17.8 points in the Hamilton Rating Scale for Depression, compared to 13.6 for placebo. The company plans to seek approval for SAGE-2017, but before that, the FDA is expected to make a decision on Zulresso in March. Zulresso already passed muster from advisory committees in November, and if approved, would be the first drug specifically for postpartum depression. In an interview with the Business Journal, Chief Business Officer Mike Cloonan said the company believes there is room in the market for both medications, particularly since the medications address different patient populations.
Mersana Therapeutics – After a breakup with Takeda Pharmaceutical and the shelving of its lead product, Cambridge, Mass.-based Mersana is making a new path. Even though a partial clinical hold was lifted following the death of a patient the company opted to shelve development of XMT-1522. During a presentation at JPM, CEO Anna Protopapas noted that many other companies are developing therapies that target the HER2 protein, which led to the decision, according to the Boston Business Journal. Protopapas said the HER2 space is highly competitive and now the company will focus on its other asset, XMT-1536, an ADC targeting NaPi2b, an antigen highly expressed in the majority of non-squamous NSCLC and epithelial ovarian cancer. XMT-1536 is currently in Phase 1 clinical trials for NaPi2b-expressing cancers, including ovarian cancer, non-small cell lung cancer and other cancers. Data on XMT-1536 is expected in the first half of 2019.
Novavax – During a JPM presentation, Stan Erck, CEO of Novavax, pointed to the company’s RSV vaccine, which is in late-stage development. The vaccine is being developed for the mother, in order to protect an infant. The mother transfers the antibodies to the infant, which will provide the baby with protection from RSV in its first six months. Erck called the program historic. He said the Phase III program is in its fourth year and the company has vaccinated 4,636 women. He said they are tracking the women and the babies. Researchers call the mothers every week through the first six months of the baby’s life to acquire data. Erck said the company anticipates announcing trial data this quarter. If approved, Erck said the market for the vaccine could be a significant revenue driver.
“You have 3.9 million birth cohorts and we expect 80 percent to 90 percent of those mothers to be vaccinated as a pediatric vaccine and in the U.S. the market rate is somewhere between $750 million and a $1 billion and then double that for worldwide market. So it’s a large market and we will be first to market in this,” Erck said, according to a transcript of the presentation.
Denali Therapeutics – Denali forged a collaboration with Germany-based SIRION Biotech to develop gene therapies for central nervous disorders. The two companies plan to develop adeno-associated virus (AAV) vectors to enable therapeutics to cross the blood-brain barrier for clinical applications in neurodegenerative diseases including Parkinson’s, Alzheimer’s disease, ALS and certain other diseases of the CNS.
AstraZeneca – Pharma giant AstraZeneca reported that in 2019 net prices on average across the portfolio will decrease versus 2018. With a backdrop of intense public and government scrutiny over pricing, Market Access head Rick Suarez said the company is increasing its pricing transparency. Additionally, he said the company is looking at new ways to price drugs, such as value-based reimbursement agreements with payers, Pink Sheet reported.
Amarin Corporation – As the company eyes a potential label expansion approval for its cardiovascular disease treatment Vascepa, Amarin Corporation has been proactively hiring hundreds of sales reps. In the fourth quarter, the company hired 265 new sales reps, giving the company a sales team of more than 400, CEO John Thero said. Thero noted that is a label expansion is granted by the FDA, “revenues will increase at least 50 percent over what we did in the prior year, which would give us revenues of approximate $350 million in 2019.”
Government Woes – As the partial government shutdown in the United States continues into its third week, biotech leaders at JPM raised concern as the FDA’s carryover funds are dwindling. With no new funding coming in, reviews of New Drug Applications won’t be able to continue past February, Pink Sheet said. While reviews are currently ongoing, no New Drug Applications are being accepted by the FDA at this time. With the halt of NDA applications, that has also caused some companies to delay plans for an initial public offering. It’s hard to raise potential investor excitement without the regulatory support of a potential drug approval. During a panel discussion, Jonathan Leff, a partner at Deerfield Management, noted that the ongoing government shutdown is a reminder of how “overwhelmingly dependent the whole industry of biotech and drug development is on government,” Pink Sheet said.
Other posts on the JP Morgan 2019 Healthcare Conference on this Open Access Journal include:
Live 2:30-4:30 PM Mediterranean Diet and Lifestyle: A Symposium on Diet and Human Health: October 19, 2018
Reporter: Stephen J. Williams, Ph.D.
2:30 Mediterranean Diet, Intangible Heritage and Sustainable Tourism?
Prof. Fabio Parasecoli, PhD.
Nutrition and Food Department, New York University
We focus on more of the cultural aspects and the relevance of this diet to tourism in Italy where there is a high rate of unemployment. The diet is interesting from a touristic standpoint as the diet have the perspective of the different ingredients inherent in Italy. The mediterranean diet food pyramid totally different than US. How do we explain to consumers these medical concepts; for example in China, Germany they are using different ways to explain the benefits of this diet.
A Cultural Formation
a way of life, for tourism there is the way of life people want to adopt (easiest way to do this is go to the Mediterranean and learn the lifestyle)
so for example Olive Garden for marketing purposes sent a few chefs for half a day training so the image of learning to cook in the mediterranean diet style can be very powerful communicative tool
2003 UNESCO Convention for Safeguarding the Culturing Heritage: protecting landscapes but then decided to protect other intangible heritage like oral, language, oral traditions like transmitting recipes, social and festive events (how do we cook how do we grow tomatoes, wheat etc)
UNESCO: promoted France Gastronomic, Mediterranean Diet, and traditional Mexican Cuisine (Mayan)
defined Greece, Italy, Morroco then included Cyprus Crotia and Portugal in the Mediterranean diet
has it been used for promotion: no UNESCO did not use this since does not safeguard the culture
(gastrodiplomacy); like Korea and kimchie; included in the list of cultural cuisine but can create tourist bubbles as you tourism places like hotels don’t always use; for reasons of economy or safety or accessibility , local food
Centrality of Territorio: food consumed from tourist should come from the area
Sustainable Tourism: a form of tourism where have the intention to get to know the place;
have to think in three ways
environmental
social
cultural
how do we make a circular economy so no waste; for example certain companies using food waste to make other products
Tourism clusters made of many groups; he is working on a way to jump start these networks in Nigeria;
Sustainable Food Supply Chain Tourism can be used as way to engage people and promote the diet
Question: are there regions where people are not adopting the diet because of taste, preferences
Yes there is always a problem with accessibility, affordability, trade issues and regional acceptance. For instance in Australia a big push back against the Mediterranean diet. Medical professionals need to work with communication experts and media experts in developing ways to communicate the benefits since “no one wants to be preached at” and “as economies get richer people want to be more modern and try new things”
In Nigeria we are working with many different industries like transportation, engineers, the IT industry and chefs to build a scalable model
3.00Italy as a Case Study: Increasing Students’ Level of Awareness of the Historical, Cultural, Political and Culinary Significance of Food
Prof. Lisa Sasson
Nutrition and Food Department, New York University
Started a program at NYU to understand food from a nutritionist and historical point of view as a cultural heritage in Italy, but when students came back students mentioned it changed their food shopping habits
they described diet as wine, pasta, and olive oil
Artisional Production: understanding the taste and flavor; she wanted them to learn about the food culture and educate their tastes
Food Memories: how we pass on recipes and food aromas, food tastes. The students were experienced food in a unique way for the first time, experiencing what cheese, quality oil other foods when fresh tastes like. Artisional foods may be expensive but need only a little of it because the tastes and flavors are so potent due to the phytochemicals
Within six months students:
increased consumption of weekly wine consumption with meals
increased consuming satisfying meals
increased time consuming meals
In the womb the fetus is actually acquiring sense of taste (amniotic fluid changes with mother diet; can detect flavor chemicals)
Student Perceptions after a study Abroad Program
eating foods local and seasonal
replacing butter with quality olive oil
using herbs
very little sugar
unsweetened beverages
limiting red meats
fish a couple of times a week
dairy in moderation
no processed foods
Eating and Dining for Americans is a Challenge: The students ate well and satisfying meals but ate alot but did not gain weight
3:30 Italian Migration and Global Diaspora
Dr. Vincenzo Milione, PhD
Director of Demographics Studies, Calandra Institute, City University of New York
for a PDF of this presentation please click here: sbarro handout.
Dr. Millione used the U.S. Census Bureau Data to estimate the growth of the Italian diaspora descendants in host countries in the Americas and to determine the mixed global ancestry of Italian descendants.
Italian emigration to the US happened in two waves
Wave 1: early 1900 peaking between 1901 and 1911 (turn of century)
Wave 2: 1951-1971 (post WWII)
This pattern was similar between North and South America although South American had first Italian immigration; in 1860 we got rid of slavery so many jobs not filled new orleans
Developing a mathematical model of Italian diaspora: the model is centered on the host country population dynamics but descendants are separated into first generation and multi generation
Model dependent on:
birth and death rates
first generation population growth
multi generational population growth
emigration from host country over time
He was able to calculate an indices he termed Year of Italianization Change (YIC): the year the growth of the multi generation supercedes the first generation immigrant population
Country
Year of Italianlization Change (YIC)
Brazil
1911
Uruguay
1915
Argentina
1918
USA
1936
Venezuela
1963
Canada
1968
Australia
1988
note: as a result there is an increasing loss of language and traditional customs with host country cultural adaptation among the native born descendants
In addition, over the last 20 years Italian-American population growth demonstrates that Italian-American self-identity in the United States has increased. The census data identified two ancestries of the respondent. In mixed ancestry Italian-American respondents to the extent they identify Italian first demonstrating the strong Italian-American identity.
The foreign born Italian Americans mirror the immigration pattern of Italian immigration from Italy until 1980 where more Italian Americans self identify as foreign born in other countries and not in Italy
Summary
over 5 million Italians have emigrated from Italy from 1980 to present
most went to North and South America but many went to other global countries
the Italian immigration to the different countries in the Americas varies over the period of mass emigration when the growth of multi generational Italian descendants is greater then first generation Italians (Year of Italianization Change) goes from 1911 in Brazil to 1988 in Australia
Immigrants to the USA was not just from Italy but from almost all nations globally over all geographical continents
Italina immigrants descendants greatly grew after 1930 with appreciable increase with other ethnicities such that 61% of Italian Americans are mixed ancestry in 2014: to date mixed ancestry represents 98% of Italian Americans
younger italian americans more likely to have mixed ancestry with Central and South America, Asian and African ethnicities
over time during immigration eating habits has changed but more research is needed if and how the italian recipes and diet has changed as well
4:15Conclusions
Prof. Antonio Giordano, MD, PhD.
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Live 12:00 – 1:00 P.M Mediterranean Diet and Lifestyle: A Symposium on Diet and Human Health : October 19, 2018
Reporter: Stephen J. Williams, Ph.D.
12.00 The Italian Mediterranean Diet as a Model of Identity of a People with a Universal Good to Safeguard Health?
Prof. Antonino De Lorenzo, MD, PhD.
Director of the School of Specialization in Clinical Nutrition, University of Rome “Tor Vergata”
It is important to determine how our bodies interacts with the environment, such as absorption of nutrients.
Studies shown here show decrease in life expectancy of a high sugar diet, but the quality of the diet, not just the type of diet is important, especially the role of natural probiotics and phenolic compounds found in the Mediterranean diet.
The WHO report in 2005 discusses the unsustainability of nutrition deficiencies and suggest a proactive personalized and preventative/predictive approach of diet and health.
Most of the noncommunicable diseases like CV (46%) cancer 21% and 11% respiratory and 4% diabetes could be prevented and or cured with proper dietary approaches
Italy vs. the US diseases: in Italy most disease due to environmental contamination while US diet plays a major role
The issue we are facing in less than 10% of the Italian population (fruit, fibers, oils) are not getting the proper foods, diet and contributing to as we suggest 46% of the disease
The Food Paradox: 1.5 billion are obese; we notice we are eating less products of quality and most quality produce is going to waste;
growing BMI and junk food: our studies are correlating the junk food (pre-prepared) and global BMI
modern diet and impact of human health (junk food high in additives, salt) has impact on microflora
Western Diet and Addiction: We show a link (using brain scans) showing correlation of junk food, sugar cravings, and other addictive behaviors by affecting the dopamine signaling in the substantia nigra
developed a junk food calculator and a Mediterranean diet calculator
the intersection of culture, food is embedded in the Mediterranean diet; this is supported by dietary studies of two distinct rural Italian populations (one of these in the US) show decrease in diet
Impact of diet: have model in Germany how this diet can increase health and life expectancy
from 1950 to present day 2.7 unit increase in the diet index can increase life expectancy by 26%
so there is an inverse relationship with our index and breast cancer
Environment and metal contamination and glyphosate: contribution to disease and impact of maintaining the healthy diet
huge problem with use of pesticides and increase in celiac disease
Cancer as a disease of the environment. Weinberg’s hallmarks of Cancer reveal how environment and epigenetics can impact any of these hallmarks.
Epigenetic effects
gene gatekeepers (Rb and P53)
DNA repair and damage stabilization
Heavy Metals and Dioxins:( alterations of the immune system as well as epigenetic regulations)
Asbestos and Mesothelioma: they have demonstrated that p53 can be involved in development of mesothelioma as reactivating p53 may be a suitable strategy for therapy
Diet, Tomato and Cancer
looked at tomato extract on p53 function in gastric cancer: tomato extract had a growth reduction effect and altered cell cycle regulation and results in apoptosis
RBL2 levels are increased in extract amount dependent manner so data shows effect of certain tomato extracts of the southern italian tomato ( )
Antonio Giordano: we tested whole extracts of almost 30 different varieties of tomato. The tomato variety with highest activity was near Ravela however black tomatoes have shown high antitumor activity. We have done a followup studies showing that these varieties, if grow elsewhere lose their antitumor activity after two or three generations of breeding, even though there genetics are similar. We are also studying the effects of different styles of cooking of these tomatoes and if it reduces antitumor effect
Live 11:00 AM- 12:00 Mediterranean Diet and Lifestyle: A Symposium on Diet and Human Health : Opening Remarks October 19, 2018
Reporter: Stephen J. Williams, Ph.D.
11:00Welcome
Prof. Antonio Giordano, MD, PhD.
Director and President of the Sbarro Health Research Organization, College of Science and Technology, Temple University
Welcome to this symposium on Italian lifestyle and health. This is similar to a symposium we had organized in New York. A year ago Bloomberg came out with a study on higher longevity of the italian population and this study was concluded that this increased longevity was due to the italian lifestyle and diet especially in the southern part of Italy, a region which is older than Rome (actually founded by Greeks and Estonians). However this symposium will delve into the components of this healthy Italian lifestyle which contributes to this longevity effect. Some of this work was done in collaboration with Temple University and sponsored by the Italian Consulate General in Philadelphia ( which sponsors programs in this area called Ciao Philadelphia).
Greetings: Fucsia Nissoli Fitzgerald, Deputy elected in the Foreign Circumscription – North and Central America Division
Speaking for the Consulate General is Francesca Cardurani-Meloni. I would like to talk briefly about the Italian cuisine and its evolution, from the influence of the North and South Italy, economic factors, and influence by other cultures. Italian cooking is about simplicity, cooking with what is in season and freshest. The meal is not about the food but about comfort around the table, and comparible to a cullinary heaven, about sharing with family and friends, and bringing the freshest ingredients to the table.
Consul General, Honorable Pier Attinio Forlano, General Consul of Italy in Philadelphia
11:30The Impact of Environment and Life Style in Human Disease
Prof. Antonio Giordano MD, PhD.
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Announcement 11AM- 5PM: Live Conference Coverage from Mediterranean Diet and Lifestyle: A Symposium on Diet and Human Health @S.H.R.O. and Temple University October 19, 2018
Reporter: Stephen J. Williams, Ph.D.
The Sbarro Health Research Organization, in collaboration with the Consulate General of Italy in Philadelphia will sponsor a symposium on the Mediterranean Diet and Human Health on October 19, 2018 at Temple University in Philadelphia, PA. This symposium will discuss recent finding concerning the health benefits derived from a Mediterranean-style diet discussed by the leaders in this field of research.
Mediterranean Diet
The description of the Mediterranean Diet stems from the nutritionist Ancel Keys, who in 1945, in the wake of the US Fifth Army, landed in Southern Italy, where he observed one of the highest concentrations of centenarians in the world. He also noticed that cardiovascular diseases, widespread in the USA, were less frequent there. In particular, among the Southern Italians, the prevalence of “wellness” diseases such as hypertension and diabetes mellitus, was particularly associated with fat consumption, suggesting that the main factor responsible for the observations was the type of diet traditionally consumed among people facing the Mediterranean Sea, which is low in animal fat, as opposed to the Anglo-Saxon diet. The link between serum cholesterol and coronary heart disease mortality was subsequently demonstrated by the Seven Countries Study. Later, the concept of Mediterranean Diet was extended to a diet rich in fruits, vegetables, legumes, whole grains, fish and olive oil as the main source of lipid, shared among people living in Spain, Greece, Southern Italy and other countries facing the Mediterranean basin …
Prof. Antonino De Lorenzo, MD, PhD.
The Symposium will be held at:
Biolife Science Building, Room 234
Temple University, 1900 North 12th street
Philadelphia, PA 19122
For further information, please contact:
Ms. Marinela Dedaj – Sbarro Institute, Office #: 215-204-9521
11:00Welcome
Prof. Antonio Giordano, MD, PhD.
Director and President of the Sbarro Health Research Organization, College of Science and Technology, Temple University
Greetings
Fucsia Nissoli Fitzgerald
Deputy elected in the Foreign Circumscription – North and Central America Division
Consul General, Honorable Pier Attinio Forlano
General Consul of Italy in Philadelphia
11:30The Impact of Environment and Life Style in Human Disease
Prof. Antonio Giordano MD, PhD.
12.00 The Italian Mediterranean Diet as a Model of Identity of a People with a Universal Good to Safeguard Health?
Prof. Antonino De Lorenzo, MD, PhD.
Director of the School of Specialization in Clinical Nutrition, University of Rome “Tor Vergata”
Professor of Molecular Biology at Temple University in Philadelphia, PA where he is also Director of the Sbarro Institute for Cancer Research and Molecular Medicine. He is also Professor of Pathology at the University of Siena, Italy. He has published over 500 articles, received over 40 awards for his contributions to cancer research and is the holder of 17 patents.
Full Professor of Human Nutrition and Director of the Specialization School in Food Science at the University of Rome “Tor Vergata”. He is the Coordinator of the Specialization Schools in Food Science at the National University Council and Coordinator of the PhD. School of “Applied Medical-Surgical Sciences” Director of UOSD “Service of Clinical Nutrition, Parenteral Therapy and Anorexia”. He also serves as President of “Istituto Nazionale per la Dieta Mediterranea e la Nutrigenomica”.
Iris Maria Forte is an oncology researcher of INT G. Pascale Foundation of Naples, Italy. She majored in Medical Biotechnology at the “Federico II” University of Naples, earned a PhD. in “Oncology and Genetics” at the University of Siena in 2012 and a Master of II level in “Environment and Cancer” in 2014. Iris Maria Forte has worked with Antonio Giordano’s group since 2008 and her research interests include both molecular and translational cancer research. She published 21 articles mostly focused in understanding the molecular basis of human cancer. She worked on different kinds of human solid tumors but her research principally focused on pleural mesothelioma and on cell cycle deregulation in cancer.
Professor in the Department of Nutrition and Food Studies. He has a Doctorate in Agricultural Sciences (Dr.sc.agr.) from Hohenheim University, Stuttgart (Germany), MA in Political Sciences from the Istituto Universitario Orientale, Naples (Italy), BA/MA in Modern Foreign Languages and Literature from the Università La Sapienza, Rome (Italy). His research explores the intersections among food, media, and politics. His most recent projects focus on Food Design and the synergies between Food Studies and design.
Prof. Lisa Sasson, MS
Dietetic Internship Director and a Clinical Associate Professor in the department. She has interests in dietetic education, weight and behavior management, and problem-based learning. She also is a private practice nutritionist with a focus on weight management. She serves as co-director of the Food, Nutrition and Culture program in Florence Italy, the New York State Dietetic Association and the Greater New York Dietetic Association (past president and treasurer).
Director of Demographic Studies for The John D. Calandra Italian American Institute, Queens College, City University of New York. He has conducted social science research on Italian Americans. His research has included the educational and occupational achievements; Italian language studies at the elementary and secondary levels, high school non-completion rates; negative media portrayals of ethnic populations including migration studies and global diaspora.
Agricultural entrepreneur, Manager of the Italian Consortium for Biogas (CIB) and delegate for the Bioeconomy National Department of Confagricoltura. He developed A.R.T.E based on a model of agricultural circular economy, beginning and ending in the ground. He constructed the first biogas plant in the territory creating a new way to make agriculture, investing in research and development, experimentation and most of all, in people. In a few short years, he succeeded to close the production chain producing goods characterized by their high quality and usage of renewable energy.
Vice-President for Institutional and International Relations of the Istituto Nazionale per la Dieta Mediterranea e la Nutrigenomica (I.N.D.I.M.). Has managed relations with the academic institutions to increase awareness and develops projects for the diffusion of the Mediterranean Diet. She served as Director of Finance for the National Institute of Nutrition, for the Ministry of Agriculture and Forestry.
About the Sbarro Health Research Organization
The Sbarro Health Research Organization (SHRO) is non-profit charity committed to funding excellence in basic genetic research to cure and diagnose cancer, cardiovascular diseases, diabetes and other chronic illnesses and to foster the training of young doctors in a spirit of professionalism and humanism. To learn more about the SHRO please visit www.shro.org
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