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Identification of longitudinally dynamic biomarkers in Alzheimer's disease cerebrospinal fluid by targeted proteomics.

Wildsmith KR, Schauer SP, Smith AM, Arnott D, Zhu Y, Haznedar J, Kaur S, Mathews WR, Honigberg LA - Mol Neurodegener (2014)

Bottom Line: Four of 28 quantifiable CSF proteins were significantly different between aged, cognitively-normal controls and AD subjects including chitinase-3-like protein 1, reproducing published results.Four CSF markers demonstrated significant longitudinal change in AD: Amyloid precursor protein, Neuronal pentraxin receptor, NrCAM and Chromogranin A.Using a targeted proteomics approach, we confirmed previous findings for a subset of markers, defined longitudinal performance of our panel of markers, and established a flexible proteomics method for robust multiplexed analyses.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Phamacodynamic Biomarkers within Development Sciences, Genentech, Inc, (a member of the Roche Group), 1 DNA Way, South San Francisco, CA 94080, USA. wildsmith.kristin@gene.com.

ABSTRACT

Background: Alzheimer's disease (AD) is the leading cause of dementia affecting greater than 26 million people worldwide. Although cerebrospinal fluid (CSF) levels of Aβ42, tau, and p-tau181 are well established as diagnostic biomarkers of AD, there is a need for additional CSF biomarkers of neuronal function that continue to change during disease progression and could be used as pharmacodynamic measures in clinical trials. Multiple proteomic discovery experiments have reported a range of CSF biomarkers that differ between AD and control subjects. These potential biomarkers represent multiple aspects of the disease pathology. The performance of these markers has not been compared with each other, and their performance has not been evaluated longitudinally.

Results: We developed a targeted-proteomic, multiple reaction monitoring (MRM) assay for the absolute quantitation of 39 peptides corresponding to 30 proteins. We evaluated the candidate biomarkers in longitudinal CSF samples collected from aged, cognitively-normal control (n = 10), MCI (n = 5), and AD (n = 45) individuals (age > 60 years). We evaluated each biomarker for diagnostic sensitivity, longitudinal consistency, and compared with CSF Aβ42, tau, and p-tau181. Four of 28 quantifiable CSF proteins were significantly different between aged, cognitively-normal controls and AD subjects including chitinase-3-like protein 1, reproducing published results. Four CSF markers demonstrated significant longitudinal change in AD: Amyloid precursor protein, Neuronal pentraxin receptor, NrCAM and Chromogranin A. Robust correlations were observed within some subgroups of proteins including the potential disease progression markers.

Conclusion: Using a targeted proteomics approach, we confirmed previous findings for a subset of markers, defined longitudinal performance of our panel of markers, and established a flexible proteomics method for robust multiplexed analyses.

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Related in: MedlinePlus

Difference in Chitinase-3-like protein 1 (CH3L1 aka YKL-40) is comparable with the change observed for Aβ42, tau and p-tau181 in AD vs. aged cognitively-normal controls (age > 60y) (linear regression, **p = 0.001-0.01, ***p < 0.001). Control, green-circle, MCI blue-square, AD red-triangle. A. CH3L1, B. Aβ42, C. total tau, D. p-tau181.
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Figure 1: Difference in Chitinase-3-like protein 1 (CH3L1 aka YKL-40) is comparable with the change observed for Aβ42, tau and p-tau181 in AD vs. aged cognitively-normal controls (age > 60y) (linear regression, **p = 0.001-0.01, ***p < 0.001). Control, green-circle, MCI blue-square, AD red-triangle. A. CH3L1, B. Aβ42, C. total tau, D. p-tau181.

Mentions: Thirty-nine peptides (Additional file 1: Table S1) were quantitated in baseline CSF tryptic-digests from 10 aged (>60 y), cognitively-normal control, 5 MCI, and 45 AD subjects. The CSF sample demographics are summarized in Table 2. Mini-mental state exam (MMSE) cognitive scores were significantly different between control and MCI and control and AD subjects (t-test, p < 0.001), and were consistent with the clinical diagnosis provided by the vendor (Table 2). Similarly, the trends observed for the classic CSF biomarkers Aβ42, total tau, p-tau181 were consistent with diagnosis (Figure 1A-C). There was a significant difference between the mean age of the groups (control vs. AD p < 0.005, control vs. MCI p < 0.05), so it was important to include as a covariate in our analyses. Four peptides were significantly different between control and AD subjects (linear regression of log values adjusted for age and sex, p < 0.05, corrected by the Benjamini & Hochberg method) (Table 3, Additional file 3: Figure S2). Only Chitinase-3-like protein 1 (CH3L1 aka YKL-40) was at or above the significance level of the common diagnostic biomarkers Aβ42, total tau, p-tau181 and the MMSE cognitive scores. CH3L1 increased in AD by 1.6-fold (Figure 1D), which is similar to the degree of change observed for Aβ42 and tau in these samples (Figure 1A-C). TTHY appears to change in MCI vs. control and 2 biomarkers, PTDGS and APOE_301 reached significance in AD vs. MCI (Table 3, Additional file 3: Figure S2), but due to the low subject number (MCI, n = 5), analysis of a greater number of subjects should be pursued to assess diagnostic potential.


Identification of longitudinally dynamic biomarkers in Alzheimer's disease cerebrospinal fluid by targeted proteomics.

Wildsmith KR, Schauer SP, Smith AM, Arnott D, Zhu Y, Haznedar J, Kaur S, Mathews WR, Honigberg LA - Mol Neurodegener (2014)

Difference in Chitinase-3-like protein 1 (CH3L1 aka YKL-40) is comparable with the change observed for Aβ42, tau and p-tau181 in AD vs. aged cognitively-normal controls (age > 60y) (linear regression, **p = 0.001-0.01, ***p < 0.001). Control, green-circle, MCI blue-square, AD red-triangle. A. CH3L1, B. Aβ42, C. total tau, D. p-tau181.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4061120&req=5

Figure 1: Difference in Chitinase-3-like protein 1 (CH3L1 aka YKL-40) is comparable with the change observed for Aβ42, tau and p-tau181 in AD vs. aged cognitively-normal controls (age > 60y) (linear regression, **p = 0.001-0.01, ***p < 0.001). Control, green-circle, MCI blue-square, AD red-triangle. A. CH3L1, B. Aβ42, C. total tau, D. p-tau181.
Mentions: Thirty-nine peptides (Additional file 1: Table S1) were quantitated in baseline CSF tryptic-digests from 10 aged (>60 y), cognitively-normal control, 5 MCI, and 45 AD subjects. The CSF sample demographics are summarized in Table 2. Mini-mental state exam (MMSE) cognitive scores were significantly different between control and MCI and control and AD subjects (t-test, p < 0.001), and were consistent with the clinical diagnosis provided by the vendor (Table 2). Similarly, the trends observed for the classic CSF biomarkers Aβ42, total tau, p-tau181 were consistent with diagnosis (Figure 1A-C). There was a significant difference between the mean age of the groups (control vs. AD p < 0.005, control vs. MCI p < 0.05), so it was important to include as a covariate in our analyses. Four peptides were significantly different between control and AD subjects (linear regression of log values adjusted for age and sex, p < 0.05, corrected by the Benjamini & Hochberg method) (Table 3, Additional file 3: Figure S2). Only Chitinase-3-like protein 1 (CH3L1 aka YKL-40) was at or above the significance level of the common diagnostic biomarkers Aβ42, total tau, p-tau181 and the MMSE cognitive scores. CH3L1 increased in AD by 1.6-fold (Figure 1D), which is similar to the degree of change observed for Aβ42 and tau in these samples (Figure 1A-C). TTHY appears to change in MCI vs. control and 2 biomarkers, PTDGS and APOE_301 reached significance in AD vs. MCI (Table 3, Additional file 3: Figure S2), but due to the low subject number (MCI, n = 5), analysis of a greater number of subjects should be pursued to assess diagnostic potential.

Bottom Line: Four of 28 quantifiable CSF proteins were significantly different between aged, cognitively-normal controls and AD subjects including chitinase-3-like protein 1, reproducing published results.Four CSF markers demonstrated significant longitudinal change in AD: Amyloid precursor protein, Neuronal pentraxin receptor, NrCAM and Chromogranin A.Using a targeted proteomics approach, we confirmed previous findings for a subset of markers, defined longitudinal performance of our panel of markers, and established a flexible proteomics method for robust multiplexed analyses.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Phamacodynamic Biomarkers within Development Sciences, Genentech, Inc, (a member of the Roche Group), 1 DNA Way, South San Francisco, CA 94080, USA. wildsmith.kristin@gene.com.

ABSTRACT

Background: Alzheimer's disease (AD) is the leading cause of dementia affecting greater than 26 million people worldwide. Although cerebrospinal fluid (CSF) levels of Aβ42, tau, and p-tau181 are well established as diagnostic biomarkers of AD, there is a need for additional CSF biomarkers of neuronal function that continue to change during disease progression and could be used as pharmacodynamic measures in clinical trials. Multiple proteomic discovery experiments have reported a range of CSF biomarkers that differ between AD and control subjects. These potential biomarkers represent multiple aspects of the disease pathology. The performance of these markers has not been compared with each other, and their performance has not been evaluated longitudinally.

Results: We developed a targeted-proteomic, multiple reaction monitoring (MRM) assay for the absolute quantitation of 39 peptides corresponding to 30 proteins. We evaluated the candidate biomarkers in longitudinal CSF samples collected from aged, cognitively-normal control (n = 10), MCI (n = 5), and AD (n = 45) individuals (age > 60 years). We evaluated each biomarker for diagnostic sensitivity, longitudinal consistency, and compared with CSF Aβ42, tau, and p-tau181. Four of 28 quantifiable CSF proteins were significantly different between aged, cognitively-normal controls and AD subjects including chitinase-3-like protein 1, reproducing published results. Four CSF markers demonstrated significant longitudinal change in AD: Amyloid precursor protein, Neuronal pentraxin receptor, NrCAM and Chromogranin A. Robust correlations were observed within some subgroups of proteins including the potential disease progression markers.

Conclusion: Using a targeted proteomics approach, we confirmed previous findings for a subset of markers, defined longitudinal performance of our panel of markers, and established a flexible proteomics method for robust multiplexed analyses.

Show MeSH
Related in: MedlinePlus