Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Podsumowanie

Here, we present a protocol to utilize the latest version of the US Environmental Protection Agency Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool. This protocol demonstrates the application of the online tool to rapidly analyze protein conservation and provide customizable and easily interpretable predictions of chemical susceptibility across species.

Streszczenie

The US Environmental Protection Agency Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool is a fast, freely available, online screening application that allows researchers and regulators to extrapolate toxicity information across species. For biological targets in model systems such as human cells, mice, rats, and zebrafish, toxicity data are available for a variety of chemicals. Through the evaluation of protein target conservation, this tool can be used to extrapolate data generated from such model systems to thousands of other species lacking toxicity data, yielding predictions of relative intrinsic chemical susceptibility. The latest releases of the tool (versions 2.0-6.1) have incorporated new features that allow for the rapid synthesis, interpretation, and use of the data for publication plus presentation-quality graphics.

Among these features are customizable data visualizations and a comprehensive summary report designed to summarize SeqAPASS data for ease of interpretation. This paper describes the protocol to guide users through submitting jobs, navigating the various levels of protein sequence comparisons, and interpreting and displaying the resulting data. New features of SeqAPASS v2.0-6.0 are highlighted. Furthermore, two use-cases focused on transthyretin and opioid receptor protein conservation using this tool are described. Finally, SeqAPASS' strengths and limitations are discussed to define the domain of applicability for the tool and highlight different applications for cross-species extrapolation.

Wprowadzenie

Traditionally, the field of toxicology has relied heavily on the use of whole-animal testing to provide the data necessary for chemical safety evaluations. Such methods are typically costly and resource-intensive. However, due to the large number of chemicals currently used and the rapid pace at which new chemicals are being developed, globally there is a recognized need for more efficient methods of chemical screening^1,2. This need and the resulting paradigm shift away from animal testing has led to the development of many new approach methods, including high-throughput screening assays, high-throughput trans....

Protokół

1. Getting started

NOTE: The protocol presented here is focused on tool utility and key features. Detailed descriptions of methods, features, and components can be found on the website in a comprehensive User Guide (Table 1).

Table 1: Evolution of the SeqAPASS tool. A list of features and updates added to the SeqAPASS tool from its initial deployment. Abbreviations: SeqAPASS = Sequence Alignment to Predict Across Species Susceptibility; ECOTOX = ECOTOXicology knowledgebase.

Wyniki

To demonstrate the application of the SeqAPASS tool and highlight new features, two case studies are described representing instances in which protein conservation predicts that there are differences in chemical susceptibility across species (human transthyretin) and that there are no differences (µ opioid receptor [MOR]). The first of these examples addresses protein sequence/structural comparisons to predict the domain of applicability for adverse outcome pathways (AOPs, see Table 2 for definition.......

Dyskusje

There is widespread recognition that it is not feasible to empirically test enough species to capture the genomic, phenotypic, physiological, and behavioral diversity of living organisms that may be exposed to chemicals of toxicological interest. The goal of SeqAPASS is to maximize the use of existing and continuously expanding protein sequence and structural data to aid and inform the extrapolation of chemical toxicity data/knowledge from tested organisms to hundreds or thousands of other species through molecular-level.......

Materiały

Name	Company	Catalog Number	Comments
Spreadsheet program	N/A	N/A	Any program that can be used to view and work with csv files (e.g. Microsoft Excel, OpenOffice Calc, Google Docs) can be used to access data export files.
Basic computing setup and internet access	N/A	N/A	SeqAPASS is a free, online tool that can be easily used via an internet connection. No software downloads are required.