Alzheimer DataLENS: New Portal that Makes Data Available to Neuroscientists

Blue tinged cell data visual with highlights of yellow and pink

27 July 2022 | Sudeshna Das, Harvard Medical School, Cambridge, USA
IOS Press is supporting the Alzheimer DataLENS initiative, which provides omics analysis and visualizations that will be of interest to and tailored specifically for Alzheimer’s disease (AD) researchers. The aim of this open data portal is to advance AD research by making data available to all neuroscientists. The project was established by the Massachusetts Center for Alzheimer Therapeutics Science (MassCATS), and was the focus of my presentation at the recent IOS Press symposium. This blog post explains the background of this important portal and the ongoing development of the DataLENS 2.0 platform.

Tags:

data

open science

research

Alzheimer's

DataLENS

IOS Press 35

27 July 2022

Omics analysis and visualizations tailored specifically for Alzheimer’s disease researchers

by Sudeshna Das, Harvard Medical School, Cambridge, USA

IOS Press is supporting the Alzheimer DataLENS initiative, which provides omics analysis and visualizations that will be of interest to and tailored specifically for Alzheimer’s disease (AD) researchers. The aim of this open data portal is to advance AD research by making data available to all neuroscientists. The project was established by the Massachusetts Center for Alzheimer Therapeutics Science (MassCATS), and was the focus of my presentation at the recent IOS Press symposium. This blog post explains the background of this important portal and the ongoing development of the DataLENS 2.0 platform.

With the advent of new omics technologies in the past few years, there has been a deluge of complex, high-dimensional data on Alzheimer’s disease and related dementias. In particular, single-nucleus technologies have begun to unveil the molecular underpinnings of various brain cell types and states, their response to Alzheimer’s pathology, and the interactions amongst them. To date, several single-nucleus RNA Sequencing (snRNA-Seq) studies on Alzheimer’s disease have been published [1–9]. In addition, several more studies on epigenomics and genetics of Alzheimer’s disease, all at the single-cell level, have been published [10–12]. Additional data that shed light on the spatial relationships of brain cells with Alzheimer’s pathology are also being generated [13]. There is a dizzying heterogeneity in the platforms used, the brain region or the stage of disease studied, and the key results – making it almost impossible for a neuroscientist to summarize the findings across studies for their gene or pathway of interest.

To address this problem, we developed Alzheimer DataLENS, a data analytics portal that aims to advance research in Alzheimer’s disease and related dementias by making omics data easily accessible to all neuroscientists.

Blue tinged cell data visual with Alzheimer DataLENS logo with magnifying glass

Developing tools to progress research

Although multiple tools exist for omics analysis and visualization, none of them are tailored specifically for Alzheimer’s disease researchers. What is unique in this platform is that Alzheimer DataLENS curates public omics data, applies consistent pipelines to process and analyze the data, and provides easy-to-use web interfaces for query and visualization of these analytics. It gathers information from multiple heterogeneous modalities to present an integrated view of molecular mechanisms to a neuroscientist, thus lowering the barriers to data access. Alzheimer DataLENS provides information on hypothesis- and data- driven research, allowing neuroscientists to share, browse, and visualize comprehensive results from bioinformatics analysis of public omics datasets.

Box 1: Prioritizing omics analysis for AD researchers

ABOUT ALZHEIMER DATALENS
Alzheimer DataLENS provides information on hypothesis-driven and data-driven research, allowing neuroscientists to share, browse, and visualize comprehensive results from bioinformatics analyses of public omics datasets. It also serves as a tool to organize and share results from MassCATS investigations.

ABOUT MASSCATS
Alzheimer DataLENS is a project of the Massachusetts Center for Alzheimer Therapeutics Science (MassCATS), which is a public-private partnership to discover new treatments for Alzheimer's disease, organized through the Massachusetts Life Sciences Center. Leading academic researchers from the Massachusetts General Hospital, Broad Institute, Harvard Medical School, and Massachusetts Institute of Technology are working with healthcare and pharmaceutical partners to find new techniques, mechanisms, and drug targets in the fight against Alzheimer's disease.

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Blue tinged cell data visual with Alzheimer DataLENS welcome text

New portal accommodates more complex data

The current version of the Alzheimer DataLENS portal was designed for bulk omics data and couldn’t be readily adapted for the higher volume and more complex single-cell data. Thus, over the past few months, with support from IOS Press, we have developed the next-generation portal of omics data: DataLENS 2.0. To this new version of the site we have added several public snRNA-Seq datasets, and users will be able to compare expression across cell types and brain regions for their gene of interest. Users can also investigate gene expression or cell-type proportion changes with Alzheimer’s disease pathology across various cell types and brain regions. All visualization is interactive and available either at the individual cell level or at the sample level. In Alzheimer DataLENS 2.0, users can resize, zoom, format, and download images for their publication.

In addition to single-nucleus RNA-Seq data, we also ported bulk gene expression studies from five different brain regions as well as an atlas of astrocyte immunohistochemistry studies. DataLENS 2.0 is developed on a new software platform, R Shiny, that is scalable, flexible, and allows ready development of interactive websites. The website is hosted on an Amazon Web Services (AWS) cloud computing platform, and the software and tools will be openly accessible to all bioinformatics researchers and software developers. We aim to make DataLENS 2.0 available to the Alzheimer’s research community by the end of 2022.

There are future plans to apply this software to other areas of research.

References

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About the Author

Sudeshna Das, PhD, is an assistant professor of neurology at Massachusetts General Hospital (MGH) and Harvard Medical School. She directs the Data Core of the Massachusetts Alzheimer’s Disease Research Center and the MGH Biomedical Informatics Core. Her research focuses on applying statistical inference and machine learning to high-dimensional molecular-omics datasets and healthcare big-data to advance brain research in health and disease.

Discover more about this portal by watching the presentation from the IOS Press symposium below.

More about the author

Tags:

data

open science

research

Alzheimer's

DataLENS

IOS Press 35

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