Cited by 93Advanced Proteomics Techniques and ApplicationsAlzheimer's disease research and treatmentsDementia and Cognitive Impairment Research

Targeted mass spectrometry to quantify brain-derived cerebrospinal fluid biomarkers in Alzheimer’s disease

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Zhou, Maotian, Haque, Rafi U., Dammer, Eric B., Duong, Duc M., Ping, Lingyan, Johnson, Erik C. B., Lah, James J., Levey, Allan I. +1 more·2020·Clinical Proteomics

Abstract

Introduction: Alzheimer’s disease (AD) is the most common cause of dementia, characterized by progressive cognitive decline. Protein biomarkers of AD brain pathology, including β-amyloid and Tau, are reflected in cerebrospinal fluid (CSF), yet the identification of additional biomarkers linked to other brain pathophysiologies remains elusive. We recently reported a multiplex tandem-mass tag (TMT) CSF proteomic analysis of nearly 3000 proteins, following depletion of highly abundant proteins and off-line fractionation, across control and AD cases. Of these, over 500 proteins were significantly increased or decreased in AD, including markers reflecting diverse biological functions in brain. Here, we use a targeted mass spectrometry (MS) approach, termed parallel reaction monitoring (PRM), to quantify select CSF biomarkers without pre-depletion or fractionation to assess the reproducibility of our findings and the specificity of changes for AD versus other causes of cognitive impairment. Method: We nominated 41 proteins (94 peptides) from the TMT CSF discovery dataset, representing a variety of brain cell-types and biological functions, for label-free PRM analysis in a replication cohort of 88 individuals that included 20 normal controls, 37 clinically diagnosed AD cases and 31 cases with non-AD cognitive impairment. To control for technical variables, isotopically labeled synthetic heavy peptide standards were added into each of the 88 CSF tryptic digests. Furthermore, a peptide pool, representing an equivalent amount of peptide from all samples, was analyzed (n = 10) across each batch. Together, this approach enabled us to assess both the intra- and inter-sample differences in peptide signal response and retention time. Results: Despite differences in sample preparation, quantitative MS approaches and patient samples, 25 proteins, including Tau, had a consistent and significant change in AD in both the discovery and replication cohorts. Validated CSF markers with low coefficient of variation included the protein products for neuronal/synaptic (GDA, GAP43, SYN1, BASP1, YWHAB, YWHAZ, UCHL1, STMN1 and MAP1B), glial/inflammation (SMOC1, ITGAM, CHI3L1, SPP1, and CHIT1) and metabolic (PKM, ALDOA and FABP3) related genes. Logistical regression analyses revealed several proteins with high sensitivity and specificity for classifying AD cases from controls and other non-AD dementias. SMOC1, YWHAZ, ALDOA and MAP1B emerged as biomarker candidates that could best discriminate between individuals with AD and non-AD cognitive impairment as well as Tau/β-amyloid ratio. Notably, SMOC1 levels in postmortem brain are highly correlated with AD pathology even in the preclinical stage of disease, indicating that CSF SMOC1 levels reflect underlying brain pathology specific for AD. Conclusion: Collectively these findings highlight the utility of targeted MS approaches to quantify biomarkers associated with AD that could be used for monitoring disease progression, stratifying patients for clinical trials and measuring therapeutic response.

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  • MDK, SMOC1, and NTN1 have been shown to colocalize with Aβ plaque and are promising biomarkers associated with AD pathology.

    “These proteins have been shown to colocalize with Aβ plaque and are promising biomarkers associated with AD pathology.”

    From Unraveling sex differences in Alzheimer's disease and related endophenotypes with brain proteomes (2025) · cites this paper as [52]

    The Results and Discussion identify SMOC1 as a promising CSF biomarker associated with AD pathology. Our copy does not report that SMOC1 colocalizes with Aβ plaques, or establish the stated findings for MDK and NTN1 (searched: colocalization, plaques, MDK, and NTN1). (LLM, conf=0.87)

    Experimental — accuracy not yet measured
  • SMOC1, YWHAZ, ALDOA, and MAP1B emerged as biomarkers that could best discriminate between individuals with AD and non-AD cognitive impairment, correlating well with Aβ and tau levels.

    “SMOC1, YWHAZ, ALDOA, and MAP1B emerged as biomarkers that could best discriminate between individuals with AD and non-AD cognitive impairment, correlating well with Aβ and tau levels [192].”
  • Several proteins, including tau and neurofilaments, were significantly increased in AD CSF and capable of distinguishing AD cases from controls and non-AD dementia.

    “Several proteins, including tau and neurofilaments, were significantly increased in AD CSF and capable of distinguishing AD cases from controls and non-AD dementia.”
  • Zhou and colleagues used PRM to quantify a panel of brain-derived proteins significantly altered in a discovery-driven proteomic analysis of AD CSF.

    “In this study, Zhou and colleagues used PRM to quantify a panel of brain-derived proteins significantly altered in a discovery-driven proteomic analysis of AD CSF.”

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Research works printed but not linked: 1

  1. [10]Johnson ECB Dammer EB Duong DM Ping L Zhou M Yin L Higginbotham LA Guajardo A White B Troncoso JC Thambisetty M Montine TJ Lee EB Trojanowski JQ Beach TG Reiman EM Haroutunian V Wang M Schadt E Zhang B Dickson DW Ertekin-Taner N Golde TE Petyuk VA De Jager PL Bennett DA Wingo TS Rangaraju S Hajjar I Shulman JM Lah JJ Levey AI Seyfried NT Large-scale proteomic analysis of Alzheimer’s disease brain and cerebrospinal fluid reveals early changes in energy metabolism associated with microglia and astrocyte activation Nat Med 2020 26 5 769 780 32284590 PMC7405761

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Authors
Zhou, M., Haque, R. U., Dammer, E. B., Duong, D. M., Ping, L., Johnson, E. C. B., Lah, J. J., Levey, A. I., & Seyfried, N. T.
Affiliations
Emory University (US)
Corresponding author
Seyfried, Nicholas T.
Venue
Clinical Proteomics
Published
2020-05-29
Volume
17
Issue
1
Pages
19-19
ISSN
  • 1542-6416 (ISSN-L)
  • 1559-0275
OpenAlex
W3029074972
Cited by
92
References
53
Citations by year
2026: 5 · 2025: 16 · 2024: 19 · 2023: 21 · 2022: 13 · 2021: 13 · 2020: 4
FWCI
4.87
Type
journal article
Language
en
Open access
Locations
  • Clinical Proteomics (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
National Institute on Aging (R01AG053960, R01AG061800, RF1AG057471, RF1AG057470, R01AG057339, RF1AG062181, U01AG046161, U01AG061357, P50AG025688)
Topics
  • Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
  • Health Sciences › Medicine › Physiology › Alzheimer's disease research and treatments
  • Health Sciences › Medicine › Psychiatry and Mental health › Dementia and Cognitive Impairment Research
Keywords
Alzheimer's disease, cerebrospinal fluid biomarkers, targeted mass spectrometry, parallel reaction monitoring, CSF proteomics, tau protein, SMOC1, 14-3-3ζ, non-AD dementia, diagnostic biomarkers, protein quantification, reproducibility, dementia classification

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