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AMP-AD Target Discovery and Preclinical Validation Project

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Project Description

The central goal of the Accelerating Medicines Partnership-Alzheimer’s Disease (AMP-AD) Target Discovery and Preclinical Validation Project is to shorten the time between the discovery of potential drug targets and the development of new drugs for Alzheimer’s disease treatment and prevention, by integrating the analyses of large-scale molecular data from human brain samples with network modeling approaches and experimental validation.

The project is a consortium of four multi-institutional, multidisciplinary cooperative agreement grants. The grant awardees are applying cutting-edge systems and network biology approaches to integrate multidimensional human “omic” data (genomic, epigenomic, RNAseq, proteomic) from more than 2,000 human brains at all stages of the disease with clinical and pathological data to:

  • discover novel therapeutic targets for Alzheimer’s disease
  • gain a systems-level understanding of the gene, protein, and metabolic networks within which these novel targets operate
  • evaluate their drugability in multiple model organisms

AMP-AD Knowledge Portal

To achieve this project’s central goal, grant awardees are expected to engage in broad sharing of biological data, analytical methodology, and disease models before publication. Rapid sharing of data and analytical tools is enabled through the AMP-AD Knowledge Portal.

The AMP-AD Knowledge Portal was developed and is maintained by Sage Bionetworks, a nonprofit organization, and is hosted on Synapse, an informatics data platform. This platform is an Institutional Review Board (IRB)-approved environment where data can be stored, accessed, and collaboratively analyzed. The Sage Bionetworks team facilitates data sharing and data integration activities within the AMP-AD Target Discovery Consortium and collaborative analyses between the academic and industry partners.

The AMP-AD Knowledge Portal will host all data generated by the AMP-AD Target Discovery Consortium members. Newly generated data will be deposited into the portal as soon as quality control is completed and made available quarterly to all qualified users.

Access to AMP-AD data is subject to data-use conditions as determined by the informed consent documents for each study guided by the local IRB. No publication embargo will be imposed on the use of data after the data are made available through the AMP-AD Knowledge Portal. However, the data contributors must be acknowledged as specified in the Data Use Terms for each study.

Agora Platform

Supported by the NIA and developed by Sage Bionetworks in collaboration with members of the AMP-AD academic and industry teams, Agora is an interactive, web-based tool designed to allow researchers to explore curated genomic analyses from AMP-AD and associated consortia. Agora includes the first set of 100-plus candidate targets nominated by the AMP-AD teams. These genes and proteins were derived from unbiased computational analyses of genomic, proteomic, and metabolomic data generated from brain and plasma samples collected from multiple longitudinal cohorts and several Alzheimer’s Disease Research Centers’ brain banks. Researchers can use Agora to survey the AMP-AD target nominations and to see how genes of interest are performing on a set of genomic meta-analyses. Watch this video for more information.

Target Discovery Consortium Grants

The grants that constitute the consortium were developed in response to the NIA funding opportunity RFA AG13-013: Interdisciplinary Research for the Identification and Validation of Novel Therapeutic Targets for Alzheimer’s Disease.

Pathway Discovery, Validation and Compound Identification for Alzheimer's Disease (U01AG046152)

Principal Investigators:
Philip L. De Jager (Contact PI), Brigham and Women's Hospital and the Broad Institute, Inc.
David A. Bennett, Rush University

Integrative Biology Approach to Complexity of Alzheimer's Disease (U01AG046170)

Principal Investigators:
Eric Schadt (Contact PI), Icahn School of Medicine at Mount Sinai
Bin Zhang, Icahn School of Medicine at Mount Sinai
Jun Zhu, Icahn School of Medicine at Mount Sinai
Sam Gandy, Icahn School of Medicine at Mount Sinai
Michelle Ehrlich, Icahn School of Medicine at Mount Sinai
Vahram Haroutunian, Icahn School of Medicine at Mount Sinai
Koichi Iljima, Thomas Jefferson University
Scott Noggle, New York Stem Cell Foundation

A System Approach to Targeting Innate Immunity in Alzheimer’s Disease (U01AG046139)

Principal Investigators:
Todd Golde (Contact PI), University of Florida
Nathan Price, Institute for Systems Biology
Nilufer Ertekin-Taner, Mayo Clinic Jacksonville
Steven Younkin, Mayo Clinic Jacksonville

Discovery of Novel Proteomic Targets for Treatment of Alzheimer's Disease (U01AG046161)

Principal Investigators:
Allan Levey, Emory University
David Bennett, Rush University
Tom Montine, University of Washington
Juan Troncoso, The Johns Hopkins University
Dan Geschwind, UCLA
Giovanni Coppola, UCLA
John Trojanowski, University of Pennsylvania

Metabolic Networks and Pathways in Alzheimers Disease (R01AG046171)

 Principal Investigator:
 Rima Kaddurah-Daouk, Duke University School of Medicine

Targeting a Novel Regulator of Brain Aging and Alzheimers Disease (R01AG046174)

Principal Investigators:
Bruce Yankner, Harvard University (contact)
Li Huei Tsai, MIT

Sage Bionetworks facilitates data sharing and data integration activities within the Target Discovery and Preclinical Validation AMP-AD project. The data enablement provided by Sage Bionetworks includes the development and maintenance of the AMP-AD Knowledge Portal and is supported through administrative supplements to the above cooperative agreement grants. Lara Mangravite and Stephen Friend lead the Sage Bionetworks team responsible for the AMP-AD data enablement effort.