Name: Author Spotlight: Advancing Alzheimer's Research &#8211; Exploring Early Detection and Multi-Omics Approaches
Uploaded: 2023-12-15T14:00:00
Description: Watch this Scientific Journal Video about DeepOmicsAE: Representing Signaling Modules in Alzheimer's Disease with Deep Learning Analysis of Proteomics, Metabolomics, and Clinical Data at JoVE.com

This work was supported by NIH grant CA201402 and the Cornell Center for Vertebrate Genomics (CVG) Distinguished Scholar Award. The results published here are in whole or in part based on data obtained from the AD Knowledge Portal (https://adknowledgeportal.org). Study data were provided through the Accelerating Medicine Partnership for AD (U01AG046161 and U01AG061357) based on samples provided by the Rush Alzheimer&#8217;s Disease Center, Rush University Medical Center, Chicago. Data collection was supported through funding by NIA grants P30AG10161, R01AG15819, R01AG17917, R01AG30146, R01AG36836, U01AG32984, U01AG46152, the Illinois Department of Public Health, and the Translational Genomics Research Institute. The metabolomics dataset was generated at Metabolon and preprocessed by the ADMC.

NOTE: The data used here were ROSMAP data downloaded from the AD Knowledge portal. Informed consent is not needed to download and reuse the data. The protocol presented herein utilizes deep learning to analyze multi-omics data and identify signaling modules that distinguish specific patient or sample groups based, for example, on their diagnosis. The protocol also delivers a small set of extracted features that summarize the original large-scale data and can be used for further analysis such as training a predictive mode...

Analyzing Signaling Modules in Alzheimer's Disease with Deep Learning

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The structure of the dataset is critical to the success of the protocol and should be carefully checked. The data should be formatted as indicated in protocol section 1. The correct assignment of column positions is also critical to the success of the method. Proteomics and metabolomics data are preprocessed differently and feature selection is conducted separately due to the different nature of the data. Therefore, it is critical to assign column positions correctly in protocol steps 1.5, 2.3, and 3.3.
<p class="jov...

An increasingly large proportion of the population is aging and the burden of age-related diseases, such as neurodegeneration, is expected to sharply increase in the coming decades1. Alzheimer&#39;s disease is the most common type of neurodegenerative disease2. Progress in finding a treatment has been slow given our poor understanding of the fundamental&#160;molecular mechanisms driving the onset and progress of the disease. The majority of information on Alzheimer&#39;s disease is gained postmortem from the examination of brain tissue, which has made distinguishing causes and consequences a difficult task3. The Religious Orders Study/Memory and Aging Project (ROSMAP) is an ambitious effort to gain a broader understanding of neurodegeneration, which involves the study of thousands of individuals who have committed to undergo medical and psychological examinations yearly and to contribute their brains for research after their demise4. The study focuses on the transition from the normal functioning of the brain to Alzheimer&#39;s disease2. Within the project, postmortem brain samples&#160;were analyzed with a plethora of omics approaches, including genomics, epigenomics, transcriptomics, proteomics5, and metabolomics.
Omics technologies that offer functional readouts of cellular states (i.e., proteomics and metabolomics)6,7 are key to interpreting disease8,9,10,11,12, due to the direct relationship between protein and metabolite abundance and cellular activities. Proteins are the primary executors of cellular processes, while metabolites are the substrates and products for biochemical reactions. Multi-omics data analysis offers the possibility to understand the complex relationships between proteomics and metabolomics data instead of appreciating them in isolation. Multi-omics is a discipline that studies multiple layers of high-dimensional biological data, including molecular data (genome sequence and mutations, transcriptome, proteome, metabolome), clinical imaging data, and clinical features. Particularly, multi-omics data analysis aims to integrate such layers of biological data, understand their reciprocal regulation and interaction dynamics, and deliver a holistic understanding of disease onset and progression. However, methods to integrate multi-omics data remain in the early stages of development13.
Autoencoders, a type of unsupervised neural network14, are a powerful tool for multi-omics data integration. Unlike supervised neural networks, autoencoders do not map samples to specific target values (such as healthy or diseased), nor are they used to predict outcomes. One of their primary applications&#160;lies in dimensionality reduction. However, autoencoders offer several advantages over simpler dimensionality reduction methods such as principal component analysis (PCA), t-distributed stochastic neighbor embedding (tSNE), or uniform manifold approximation and projection (UMAP). Unlike PCA, autoencoders can capture non-linear relationships within the data. Unlike tSNE and UMAP, they can detect hierarchical and multi-modal relationships within the data since they rely on multiple layers of computational units each containing non linear activation functions. Therefore, they represent attractive models to capture the complexity of multi-omics data. Finally, while the primary application of PCA, tSNE, and UMAP is that of clustering the data, autoencoders compress the input data into extracted features that are well-suited for downstream predictive tasks15,16.
Briefly, neural networks comprise several layers, each containing multiple computational units or &#34;neurons.&#34; The first and last layers are referred to as the input and output layers, respectively. Autoencoders are neural networks with an hourglass structure, consisting of an input layer, followed by one to three hidden layers and a small &#34;latent&#34; layer typically containing between two and six neurons. This structure&#39;s first half is known as the encoder and is combined with a decoder mirroring the encoder. The decoder ends with an output layer containing the same number of neurons as the input layer. Autoencoders take the input through the bottleneck and reconstruct it in the output layer, with the goal of generating an output that mirrors the original information as closely as possible. This is achieved by mathematically minimizing a parameter termed &#34;reconstruction loss.&#34; The input consists of a set of features, which in the application showcased herein will be protein and metabolite abundances, and clinical characteristics (i.e., sex, education, and age at death). The latent layer contains a compressed and information-rich representation of the input, which can be used for subsequent applications such as predictive models17,18.
This protocol presents a workflow, DeepOmicsAE, which involves: 1) preprocessing of proteomics, metabolomics, and clinical data (i.e., normalization, scaling, outlier removal) to obtain data with a consistent scale for machine learning analysis; 2) selecting appropriate autoencoder input features, since feature overload may obscure relevant disease patterns; 3) optimizing and training the autoencoder, including determining the optimal number of proteins and metabolites to select, and of neurons for the latent layer; 4) extracting features from the latent layer; and 5) utilizing the extracted features for biological interpretation by identifying molecular signaling modules and their relationship with clinical features.
This protocol aims to be simple and applicable by&#160;biologists with limited computational experience who have a basic understanding of programming with Python. The protocol focuses on analyzing multi-omics data, including proteomics, metabolomics, and clinical features, but its use can be extended to other types of molecular expression data, including transcriptomics. One important novel application introduced by this protocol is mapping the importance scores of original features onto individual neurons in the latent layer. As a result, each neuron in the latent layer represents a signaling module, detailing the interactions between specific molecular alterations and the patients&#39; clinical characteristics. Biological interpretation of the molecular signaling modules is obtained by using MetaboAnalyst, a publicly available tool that integrates gene/protein and metabolite data to derive enriched metabolic and cell signaling pathways17.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Computer</td>
			<td>Apple</td>
			<td>Mac Studio</td>
			<td>Apple M1 Ultra with 20-core CPU, 48-core GPU, 32-core Neural Engine; 64 GB unified memory</td>
		</tr>
		<tr>
			<td>Conda v23.3.1</td>
			<td>Anaconda, Inc.</td>
			<td>N/A</td>
			<td>package management system and environment manager</td>
		</tr>
		<tr>
			<td>conda environment 
			DeepOmicsAE</td>
			<td>N/A</td>
			<td>DeepOmicsAE_env.yml</td>
			<td>contains packages necessary to run the worflow</td>
		</tr>
		<tr>
			<td>github repository DeepOmicsAE</td>
			<td>Microsoft</td>
			<td>https://github.com/elepan84/DeepOmicsAE/</td>
			<td>provides scripts, Jupyter notebooks, and the conda environment file</td>
		</tr>
		<tr>
			<td>Jupyter notebook v6.5.4</td>
			<td>Project Jupyter</td>
			<td>N/A</td>
			<td>a platform for interactive data science and scientific computing</td>
		</tr>
		<tr>
			<td>DT01-metabolomics data</td>
			<td>N/A</td>
			<td>ROSMAP_Metabolon_HD4_Brain 
			514_assay_data.csv</td>
			<td>This data was used to generate the Results reported in the article. Specifically, DT01-DT04 were merged by matching them based on the individualID. The column final consensus diagnosis (cogdx) was filtered to keep only patients classified as healthy or AD. Climnical features were filtered to keep the following: age at death, sex and education. Finally, age reported as 90+ was set to 91, then the age column was transformed to float64. 
			The data is available at https://adknowledgeportal.synapse.org</td>
		</tr>
		<tr>
			<td>DT02-TMT proteomics data</td>
			<td>N/A</td>
			<td>C2.median_polish_corrected_log2 
			(abundanceRatioCenteredOn 
			MedianOfBatchMediansPer 
			Protein)-8817x400.csv</td>
			<td></td>
		</tr>
		<tr>
			<td>DT03-clinical data</td>
			<td>N/A</td>
			<td>ROSMAP_clinical.csv</td>
			<td></td>
		</tr>
		<tr>
			<td>DT04-biospecimen metadata</td>
			<td>N/A</td>
			<td>ROSMAP_biospecimen_metadata 
			.csv</td>
			<td></td>
		</tr>
		<tr>
			<td>Python 3.11.3&#160;</td>
			<td>Python Software Foundation</td>
			<td>N/A</td>
			<td>programming language</td>
		</tr>
	</tbody>
</table>

deepomicsae: representing signaling modules in alzheimer's disease with deep learning analysis of proteomics, metabolomics, and clinical data

Large omics datasets are becoming increasingly available for research into human health. This paper presents DeepOmicsAE, a workflow optimized for the analysis of multi-omics datasets, including&#160;proteomics, metabolomics, and clinical data. This workflow employs a type of neural network called autoencoder, to extract a concise set of features from the high-dimensional multi-omics input data. Furthermore, the workflow provides a method to optimize the key parameters needed to implement the autoencoder. To showcase this workflow, clinical data were analyzed from a cohort of 142 individuals who were either healthy or diagnosed with Alzheimer&#39;s disease, along with the proteome and metabolome of their postmortem brain samples. The features extracted from the latent layer of the autoencoder retain the biological information that separates healthy and diseased patients. In addition, the individual extracted features represent distinct molecular signaling modules, each of which interacts uniquely with the individuals&#39; clinical features,&#160;providing for a mean to integrate&#160;the proteomics, metabolomics, and clinical data.

Author Spotlight: Advancing Alzheimer's Research &#8211; Exploring Early Detection and Multi-Omics Approaches

DeepOmicsAE: Representing Signaling Modules in Alzheimer's Disease with Deep Learning Analysis of Proteomics, Metabolomics, and Clinical Data

Alzheimer's disease is thought to initiate decades before symptoms emerge. Recent studies suggest that phenotypic traits such as obesity and hypertension, but also the level of education and social engagement can act as risk factors. Our goal is to become able to decipher their contributions and their relation to molecular drivers of disease to learn how to intervene early and in a personalized manner.Multi-omic data analysis can be used for integrating various layers of biological data such as proteomics, transcriptomics, metabolomics, and phenotypic traits to comprehensively understand a disease state. Autoencoder models use deep learning to reduce the dimensionality of multi-omics datasets, effectively summarizing the crucial information, However, it is challenging to interpret how important are individual features in the original data with respect to the summarized output. In Deep-omics AE, we built in an algorithm that derives the importance of individual multi-omics features relative to the learn reduced dimensionality representation.With this approach, we can identify molecularly similar modules and their association with patient's phenotypic traits. Deep-omics AE helps putting in relation patient's phenotypic traits with the molecular makeup of disease. For example, you can use it to ask, what are the molecular pathways that are most implicated in Alzheimer's disease in older patients, and what are those that are most implicated in younger patients?What are those implicated in developing the disease in less educated patients versus more educated patients?

To showcase the protocol, we analyzed&#160;a dataset comprising the proteome, metabolome, and clinical information derived from postmortem brains of 142 individuals who were either healthy or diagnosed with Alzheimer&#39;s disease.
After performing the protocol section 1 to preprocess the data, the dataset included 6,497 proteins, 443 metabolites, and three clinical features (sex, age at death, and education). The target feature is clinical consensus diagnosis of cognitive status at ti...

Watch this Scientific Journal Video about DeepOmicsAE: Representing Signaling Modules in Alzheimer's Disease with Deep Learning Analysis of Proteomics, Metabolomics, and Clinical Data at JoVE.com

DeepOmicsAE is a workflow centered on the application of a deep learning method (i.e., an autoencoder) to reduce the dimensionality of multi-omics data, providing a foundation for predictive models and signaling modules representing multiple layers of omics data.

Large omics datasets are becoming increasingly available for research into human health. This paper presents DeepOmicsAE, a workflow optimized for the ...