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Reddy JS, Heath L, Vander Linden A, Allen M, de Paiva Lopes K, Seifar F, Wang E, Ma Y, Poehlman WL, Quicksall ZS, Runnels A, Wang Y, Duong DM, Yin L, Xu K, Modeste ES, Shantaraman A, Dammer EB, Ping L, Oatman SR, Scanlan J, Ho C, Carrasquillo MM, Atik M, Yepez G, Mitchell AO, Nguyen TT, Chen X, Marquez DX, Reddy H, Xiao H, Seshadri S, Mayeux R, Prokop S, Lee EB, Serrano GE, Beach TG, Teich AF, Haroutunian V, Fox EJ, Gearing M, Wingo A, Wingo T, Lah JJ, Levey AI, Dickson DW, Barnes LL, De Jager P, Zhang B, Bennett D, Seyfried NT, Greenwood AK, Ertekin-Taner N. Bridging the Gap: Multi-Omics Profiling of Brain Tissue in Alzheimer's Disease and Older Controls in Multi-Ethnic Populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.16.589592. [PMID: 38659743 PMCID: PMC11042309 DOI: 10.1101/2024.04.16.589592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
INTRODUCTION Multi-omics studies in Alzheimer's disease (AD) revealed many potential disease pathways and therapeutic targets. Despite their promise of precision medicine, these studies lacked African Americans (AA) and Latin Americans (LA), who are disproportionately affected by AD. METHODS To bridge this gap, Accelerating Medicines Partnership in AD (AMP-AD) expanded brain multi-omics profiling to multi-ethnic donors. RESULTS We generated multi-omics data and curated and harmonized phenotypic data from AA (n=306), LA (n=326), or AA and LA (n=4) brain donors plus Non-Hispanic White (n=252) and other (n=20) ethnic groups, to establish a foundational dataset enriched for AA and LA participants. This study describes the data available to the research community, including transcriptome from three brain regions, whole genome sequence, and proteome measures. DISCUSSION Inclusion of traditionally underrepresented groups in multi-omics studies is essential to discover the full spectrum of precision medicine targets that will be pertinent to all populations affected with AD.
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Affiliation(s)
- Joseph S Reddy
- Mayo Clinic Florida, 4500 San Pablo Rd S, Jacksonville, FL 32224
| | - Laura Heath
- Sage Bionetworks, 2901 3rd Ave #330, Seattle, WA 98121
| | | | - Mariet Allen
- Mayo Clinic Florida, 4500 San Pablo Rd S, Jacksonville, FL 32224
| | - Katia de Paiva Lopes
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W Harrison St, Chicago, IL 60612
| | - Fatemeh Seifar
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Erming Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1428 Madison Ave, New York, NY 10029
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY 10029
| | - Yiyi Ma
- Columbia University Irving Medical Center, 622 W 168th St, New York, NY 10032
| | | | | | - Alexi Runnels
- New York Genome Center, 101 6th Ave, New York, NY 10013
| | - Yanling Wang
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W Harrison St, Chicago, IL 60612
| | - Duc M Duong
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Luming Yin
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Kaiming Xu
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Erica S Modeste
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | | | - Eric B Dammer
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Lingyan Ping
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | | | - Jo Scanlan
- Sage Bionetworks, 2901 3rd Ave #330, Seattle, WA 98121
| | - Charlotte Ho
- Mayo Clinic Florida, 4500 San Pablo Rd S, Jacksonville, FL 32224
| | | | - Merve Atik
- Mayo Clinic Florida, 4500 San Pablo Rd S, Jacksonville, FL 32224
| | - Geovanna Yepez
- Mayo Clinic Florida, 4500 San Pablo Rd S, Jacksonville, FL 32224
| | | | - Thuy T Nguyen
- Mayo Clinic Florida, 4500 San Pablo Rd S, Jacksonville, FL 32224
| | - Xianfeng Chen
- Mayo Clinic Florida, 4500 San Pablo Rd S, Jacksonville, FL 32224
| | - David X Marquez
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W Harrison St, Chicago, IL 60612
- University of Illinois Chicago, 1200 West Harrison St., Chicago, Illinois 60607
| | - Hasini Reddy
- Columbia University Irving Medical Center, 622 W 168th St, New York, NY 10032
| | - Harrison Xiao
- Columbia University Irving Medical Center, 622 W 168th St, New York, NY 10032
| | - Sudha Seshadri
- The Glen Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas, 8300 Floyd Curl Drive, San Antonio TX 78229
| | - Richard Mayeux
- Columbia University Irving Medical Center, 622 W 168th St, New York, NY 10032
| | | | - Edward B Lee
- Center for Neurodegenerative Disease Brain Bank at the University of Pennsylvania, 3600 Spruce Street, Philadelphia, PA 19104-2676
| | - Geidy E Serrano
- Banner Sun Health Research Institute, 10515 W Santa Fe Dr, Sun City, AZ 85351
| | - Thomas G Beach
- Banner Sun Health Research Institute, 10515 W Santa Fe Dr, Sun City, AZ 85351
| | - Andrew F Teich
- Columbia University Irving Medical Center, 622 W 168th St, New York, NY 10032
| | - Varham Haroutunian
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1428 Madison Ave, New York, NY 10029
| | - Edward J Fox
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Marla Gearing
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Aliza Wingo
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Thomas Wingo
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - James J Lah
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Allan I Levey
- Emory University School of Medicine, 1440 Clifton Rd, Atlanta, GA 30322
| | - Dennis W Dickson
- Mayo Clinic Florida, 4500 San Pablo Rd S, Jacksonville, FL 32224
| | - Lisa L Barnes
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W Harrison St, Chicago, IL 60612
| | - Philip De Jager
- Columbia University Irving Medical Center, 622 W 168th St, New York, NY 10032
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1428 Madison Ave, New York, NY 10029
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY 10029
| | - David Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W Harrison St, Chicago, IL 60612
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Modeste ES, Ping L, Watson CM, Duong DM, Dammer EB, Johnson ECB, Roberts BR, Lah JJ, Levey AI, Seyfried NT. Quantitative proteomics of cerebrospinal fluid from African Americans and Caucasians reveals shared and divergent changes in Alzheimer's disease. Mol Neurodegener 2023; 18:48. [PMID: 37468915 PMCID: PMC10355042 DOI: 10.1186/s13024-023-00638-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 06/21/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND Despite being twice as likely to get Alzheimer's disease (AD), African Americans have been grossly underrepresented in AD research. While emerging evidence indicates that African Americans with AD have lower cerebrospinal fluid (CSF) levels of Tau compared to Caucasians, other differences in AD CSF biomarkers have not been fully elucidated. Here, we performed unbiased proteomic profiling of CSF from African Americans and Caucasians with and without AD to identify both common and divergent AD CSF biomarkers. METHODS Multiplex tandem mass tag-based mass spectrometry (TMT-MS) quantified 1,840 proteins from 105 control and 98 AD patients of which 100 identified as Caucasian while 103 identified as African American. We used differential protein expression and co-expression approaches to assess how changes in the CSF proteome are related to race and AD. Co-expression network analysis organized the CSF proteome into 14 modules associated with brain cell-types and biological pathways. A targeted mass spectrometry method, selected reaction monitoring (SRM), with heavy labeled internal standards was used to measure a panel of CSF module proteins across a subset of African Americans and Caucasians with or without AD. A receiver operating characteristic (ROC) curve analysis assessed the performance of each protein biomarker in differentiating controls and AD by race. RESULTS Consistent with previous findings, the increase of Tau levels in AD was greater in Caucasians than in African Americans by both immunoassay and TMT-MS measurements. CSF modules which included 14-3-3 proteins (YWHAZ and YWHAG) demonstrated equivalent disease-related elevations in both African Americans and Caucasians with AD, whereas other modules demonstrated more profound disease changes within race. Modules enriched with proteins involved with glycolysis and neuronal/cytoskeletal proteins, including Tau, were more increased in Caucasians than in African Americans with AD. In contrast, a module enriched with synaptic proteins including VGF, SCG2, and NPTX2 was significantly lower in African Americans than Caucasians with AD. Following SRM and ROC analysis, VGF, SCG2, and NPTX2 were significantly better at classifying African Americans than Caucasians with AD. CONCLUSIONS Our findings provide insight into additional protein biomarkers and pathways reflecting underlying brain pathology that are shared or differ by race.
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Affiliation(s)
- Erica S. Modeste
- School of Medicine, Department of Biochemistry, Emory University, Atlanta, GA USA
| | - Lingyan Ping
- School of Medicine, Department of Biochemistry, Emory University, Atlanta, GA USA
| | - Caroline M. Watson
- School of Medicine, Department of Neurology, Emory University, Atlanta, GA USA
| | - Duc M. Duong
- School of Medicine, Department of Biochemistry, Emory University, Atlanta, GA USA
| | - Eric B. Dammer
- School of Medicine, Department of Biochemistry, Emory University, Atlanta, GA USA
| | - Erik C. B. Johnson
- School of Medicine, Department of Neurology, Emory University, Atlanta, GA USA
| | - Blaine R. Roberts
- School of Medicine, Department of Biochemistry, Emory University, Atlanta, GA USA
| | - James J. Lah
- School of Medicine, Department of Neurology, Emory University, Atlanta, GA USA
| | - Allan I. Levey
- School of Medicine, Department of Neurology, Emory University, Atlanta, GA USA
| | - Nicholas T. Seyfried
- School of Medicine, Department of Biochemistry, Emory University, Atlanta, GA USA
- School of Medicine, Department of Neurology, Emory University, Atlanta, GA USA
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Dammer EB, Seyfried NT, Johnson ECB. Batch Correction and Harmonization of -Omics Datasets with a Tunable Median Polish of Ratio. FRONTIERS IN SYSTEMS BIOLOGY 2023; 3:1092341. [PMID: 37122388 PMCID: PMC10137904 DOI: 10.3389/fsysb.2023.1092341] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Large scale -omics datasets can provide new insights into normal and disease-related biology when analyzed through a systems biology framework. However, technical artefacts present in most -omics datasets due to variations in sample preparation, batching, platform settings, personnel, and other experimental procedures prevent useful analyses of such data without prior adjustment for these technical factors. Here, we demonstrate a tunable median polish of ratio (TAMPOR) approach for batch effect correction and agglomeration of multiple, multi-batch, site-specific cohorts into a single analyte abundance data matrix that is suitable for systems biology analyses. We illustrate the utility and versatility of TAMPOR through four distinct use cases where the method has been applied to different proteomic datasets, some of which contain a specific defect that must be addressed prior to analysis. We compare quality control metrics and sources of variance before and after application of TAMPOR to show that TAMPOR is effective at removing batch effects and other unwanted sources of variance in -omics data. We also show how TAMPOR can be used to harmonize -omics datasets even when the data are acquired using different analytical approaches. TAMPOR is a powerful and flexible approach for cleaning and harmonization of -omics data prior to downstream systems biology analysis.
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Affiliation(s)
- Eric B Dammer
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Nicholas T Seyfried
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Erik C B Johnson
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
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Macron C, Núñez Galindo A, Cominetti O, Dayon L. A Versatile Workflow for Cerebrospinal Fluid Proteomic Analysis with Mass Spectrometry: A Matter of Choice between Deep Coverage and Sample Throughput. Methods Mol Biol 2020; 2044:129-154. [PMID: 31432411 DOI: 10.1007/978-1-4939-9706-0_9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Human cerebrospinal fluid (CSF) is a sample of choice in the study of brain disorders. This biological fluid circulates in the brain and the spinal cord and contains tissue-specific proteins, indicative of health and disease conditions. Despite its potential as a valid source of biological markers, CSF remains largely understudied as compared to blood, in particular due to its more invasive way of sampling.Challenges remain when performing proteomic analysis in clinical research studies. State-of-the-art mass spectrometry (MS) enables deep characterization of the human proteome. But some technical limitations are cardinal to be addressed, such as the capacity to routinely analyze large cohorts of samples. Importantly, a trade-off still needs to be made between the proteome coverage depth and the number of measured samples. In this context, we developed a scalable automated proteomic pipeline for the analysis of CSF. Because of its versatility, this workflow can be adapted to accommodate proteome coverage and/or sample throughput. It allows us to prepare and quantitatively analyze hundreds to thousands of CSF samples; it can also allow identification of more than 3000 proteins in a CSF sample when coupled with isoelectric focusing fractionation.In this chapter, we describe an end-to-end pipeline for the proteomic analysis of CSF. The main steps of the sample preparation comprise spiking of a standard, protein digestion, isobaric labeling, and purification; these are performed in a 96-well plate format enabling automation. Depending on the targeted depth of the CSF proteome, optional analytical steps can be included, such as the removal of abundant proteins and sample pre-fractionation. Liquid chromatography tandem MS as well as data processing and analysis complete the pipeline.
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Affiliation(s)
- Charlotte Macron
- Proteomics, Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
| | - Antonio Núñez Galindo
- Proteomics, Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
| | - Ornella Cominetti
- Proteomics, Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland
| | - Loïc Dayon
- Proteomics, Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland.
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Li Q, Schissler AG, Gardeux V, Berghout J, Achour I, Kenost C, Li H, Zhang HH, Lussier YA. kMEn: Analyzing noisy and bidirectional transcriptional pathway responses in single subjects. J Biomed Inform 2017; 66:32-41. [PMID: 28007582 PMCID: PMC5316373 DOI: 10.1016/j.jbi.2016.12.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 10/28/2016] [Accepted: 12/16/2016] [Indexed: 10/20/2022]
Abstract
MOTIVATION Understanding dynamic, patient-level transcriptomic response to therapy is an important step forward for precision medicine. However, conventional transcriptome analysis aims to discover cohort-level change, lacking the capacity to unveil patient-specific response to therapy. To address this gap, we previously developed two N-of-1-pathways methods, Wilcoxon and Mahalanobis distance, to detect unidirectionally responsive transcripts within a pathway using a pair of samples from a single subject. Yet, these methods cannot recognize bidirectionally (up and down) responsive pathways. Further, our previous approaches have not been assessed in presence of background noise and are not designed to identify differentially expressed mRNAs between two samples of a patient taken in different contexts (e.g. cancer vs non cancer), which we termed responsive transcripts (RTs). METHODS We propose a new N-of-1-pathways method, k-Means Enrichment (kMEn), that detects bidirectionally responsive pathways, despite background noise, using a pair of transcriptomes from a single patient. kMEn identifies transcripts responsive to the stimulus through k-means clustering and then tests for an over-representation of the responsive genes within each pathway. The pathways identified by kMEn are mechanistically interpretable pathways significantly responding to a stimulus. RESULTS In ∼9000 simulations varying six parameters, superior performance of kMEn over previous single-subject methods is evident by: (i) improved precision-recall at various levels of bidirectional response and (ii) lower rates of false positives (1-specificity) when more than 10% of genes in the genome are differentially expressed (background noise). In a clinical proof-of-concept, personal treatment-specific pathways identified by kMEn correlate with therapeutic response (p-value<0.01). CONCLUSION Through improved single-subject transcriptome dynamics of bidirectionally-regulated signals, kMEn provides a novel approach to identify mechanism-level biomarkers.
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Affiliation(s)
- Qike Li
- Center for Biomedical Informatics and Biostatistics, The University of Arizona, Tucson, AZ 85721, USA; Bio5 Institute, The University of Arizona, Tucson, AZ 85721, USA; Department of Medicine, The University of Arizona, Tucson, AZ 85721, USA; Graduate Interdisciplinary Program in Statistics, The University of Arizona, Tucson, AZ 85721, USA
| | - A Grant Schissler
- Center for Biomedical Informatics and Biostatistics, The University of Arizona, Tucson, AZ 85721, USA; Bio5 Institute, The University of Arizona, Tucson, AZ 85721, USA; Department of Medicine, The University of Arizona, Tucson, AZ 85721, USA; Graduate Interdisciplinary Program in Statistics, The University of Arizona, Tucson, AZ 85721, USA
| | - Vincent Gardeux
- Center for Biomedical Informatics and Biostatistics, The University of Arizona, Tucson, AZ 85721, USA; Bio5 Institute, The University of Arizona, Tucson, AZ 85721, USA; Department of Medicine, The University of Arizona, Tucson, AZ 85721, USA
| | - Joanne Berghout
- Center for Biomedical Informatics and Biostatistics, The University of Arizona, Tucson, AZ 85721, USA; Bio5 Institute, The University of Arizona, Tucson, AZ 85721, USA; Department of Medicine, The University of Arizona, Tucson, AZ 85721, USA
| | - Ikbel Achour
- Center for Biomedical Informatics and Biostatistics, The University of Arizona, Tucson, AZ 85721, USA; Bio5 Institute, The University of Arizona, Tucson, AZ 85721, USA; Department of Medicine, The University of Arizona, Tucson, AZ 85721, USA
| | - Colleen Kenost
- Center for Biomedical Informatics and Biostatistics, The University of Arizona, Tucson, AZ 85721, USA; Bio5 Institute, The University of Arizona, Tucson, AZ 85721, USA; Department of Medicine, The University of Arizona, Tucson, AZ 85721, USA
| | - Haiquan Li
- Center for Biomedical Informatics and Biostatistics, The University of Arizona, Tucson, AZ 85721, USA; Bio5 Institute, The University of Arizona, Tucson, AZ 85721, USA; Department of Medicine, The University of Arizona, Tucson, AZ 85721, USA.
| | - Hao Helen Zhang
- Graduate Interdisciplinary Program in Statistics, The University of Arizona, Tucson, AZ 85721, USA; Department of Mathematics, The University of Arizona, Tucson, AZ 85721, USA.
| | - Yves A Lussier
- Center for Biomedical Informatics and Biostatistics, The University of Arizona, Tucson, AZ 85721, USA; Bio5 Institute, The University of Arizona, Tucson, AZ 85721, USA; Department of Medicine, The University of Arizona, Tucson, AZ 85721, USA; Graduate Interdisciplinary Program in Statistics, The University of Arizona, Tucson, AZ 85721, USA; University of Arizona Cancer Center, The University of Arizona, Tucson, AZ 85721, USA; Institute for Genomics and Systems Biology, The University of Chicago, IL 60637, USA.
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