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Patterson KL, Arul AB, Choi MJ, Oliver NC, Whitaker MD, Bodrick AC, Libby JB, Hansen S, Dumitrescu L, Gifford KA, Jefferson AL, Hohman TJ, Robinson RAS. Establishing Quality Control Procedures for Large-Scale Plasma Proteomics Analyses. J Am Soc Mass Spectrom 2023. [PMID: 37163770 DOI: 10.1021/jasms.3c00050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Proteomics research has been transformed due to high-throughput liquid chromatography (LC-MS/MS) tandem mass spectrometry instruments combined with highly sophisticated automated sample preparation and multiplexing workflows. However, scaling proteomics experiments to large sample cohorts (hundreds to thousands) requires thoughtful quality control (QC) protocols. Robust QC protocols can help with reproducibility, quantitative accuracy, and provide opportunities for more decisive troubleshooting. Our laboratory conducted a plasma proteomics study of a cohort of N = 335 patient samples using tandem mass tag (TMTpro) 16-plex batches. Over the course of a 10-month data acquisition period for this cohort we collected 271 pooled QC LC-MS/MS result files obtained from MS/MS analysis of a patient-derived pooled plasma sample, representative of the entire cohort population. This sample was tagged with TMTzero or TMTpro reagents and used to inform the daily performance of the LC-MS/MS instruments and to allow within and across sample batch normalization. Analytical variability of a number of instrumental and data analysis metrics including protein and peptide identifications, peptide spectral matches (PSMs), number of obtained MS/MS spectra, average peptide abundance, percent of peptides with a Δ m/z between ±0.003 Da, percent of MS/MS spectra obtained at the maximum injection time, and the retention time of selected tracking peptides were evaluated to help inform the design of a robust LC-MS/MS QC workflow for use in future cohort studies. This study also led to general tips for using selected metrics to inform real-time troubleshooting of LC-MS/MS performance issues with daily QC checks.
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Affiliation(s)
- Khiry L Patterson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Albert B Arul
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Min Ji Choi
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Nekesa C Oliver
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Marsalas D Whitaker
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Angel C Bodrick
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Cancer Biology, Neuroscience, and Pharmacology, Meharry Medical College, Nashville, Tennessee 37208, United States
| | - Julia B Libby
- Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Shania Hansen
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, Tennessee 37212, United States
| | - Logan Dumitrescu
- Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Katherine A Gifford
- Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, Tennessee 37212, United States
| | - Angela L Jefferson
- Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Timothy J Hohman
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, Tennessee 37212, United States
- Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
- Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
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Libby JB, Seto M, Khan OA, Liu D, Petyuk V, Oliver NC, Choi MJ, Whitaker M, Patterson KL, Arul AB, Gifford KA, Blennow K, Zetterberg H, Dumitrescu L, Robinson RA, Jefferson AL, Hohman TJ. Whole blood transcript and protein abundance of the vascular endothelial growth factor family relate to cognitive performance. Neurobiol Aging 2023; 124:11-17. [PMID: 36680854 PMCID: PMC9957941 DOI: 10.1016/j.neurobiolaging.2023.01.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/29/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023]
Abstract
The vascular endothelial growth factor (VEGF) family of genes has been implicated in the clinical development of Alzheimer's Disease (AD). A previous study identified associations between gene expression of VEGF family members in the prefrontal cortex and cognitive performance and AD pathology. This study explored if those associations were also observed in the blood. Consistent with previous observations in brain tissue, higher blood gene expression of placental growth factor (PGF) was associated with a faster rate of memory decline (p=0.04). Higher protein abundance of FMS-related receptor tyrosine kinase 4 (FLT4) in blood was associated with biomarker levels indicative of lower amyloid and tau pathology, opposite the direction observed in brain. Also, higher gene expression of VEGFB in blood was associated with better baseline memory (p=0.008). Notably, we observed that higher gene expression of VEGFB in blood was associated with lower expression of VEGFB in the brain (r=-0.19, p=0.02). Together, these results suggest that the VEGFB, FLT4, and PGF alterations in the AD brain may be detectable in the blood compartment.
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Affiliation(s)
- Julia B Libby
- Vanderbilt Memory & Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mabel Seto
- Vanderbilt Memory & Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Pharmacology, Vanderbilt University, Nashville, TN, USA
| | - Omair A Khan
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dandan Liu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Vlad Petyuk
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Nekesa C Oliver
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - Min Ji Choi
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | | | | | - Albert B Arul
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - Katherine A Gifford
- Vanderbilt Memory & Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Mölndal, Sweden; Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Mölndal, Sweden; Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden; Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK; UK Dementia Research Institute at UCL, London, UK
| | - Logan Dumitrescu
- Vanderbilt Memory & Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Renã As Robinson
- Vanderbilt Memory & Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - Angela L Jefferson
- Vanderbilt Memory & Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Timothy J Hohman
- Vanderbilt Memory & Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA.
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Nho K, Risacher SL, Apostolova L, Bice PJ, Brosch J, Deardorff R, Faber K, Farlow MR, Foroud T, Gao S, Rosewood T, Kim JP, Nudelman K, Yu M, Aisen P, Sperling R, Hooli B, Shcherbinin S, Svaldi D, Jack CR, Jagust WJ, Landau S, Vasanthakumar A, Waring JF, Doré V, Laws SM, Masters CL, Porter T, Rowe CC, Villemagne VL, Dumitrescu L, Hohman TJ, Libby JB, Mormino E, Buckley RF, Johnson K, Yang HS, Petersen RC, Ramanan VK, Vemuri P, Cohen AD, Fan KH, Kamboh MI, Lopez OL, Bennett DA, Ali M, Benzinger T, Cruchaga C, Hobbs D, De Jager PL, Fujita M, Jadhav V, Lamb BT, Tsai AP, Castanho I, Mill J, Weiner MW, Saykin AJ. Novel CYP1B1-RMDN2 Alzheimer's disease locus identified by genome-wide association analysis of cerebral tau deposition on PET. medRxiv 2023:2023.02.27.23286048. [PMID: 36993271 PMCID: PMC10055458 DOI: 10.1101/2023.02.27.23286048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Determining the genetic architecture of Alzheimer's disease (AD) pathologies can enhance mechanistic understanding and inform precision medicine strategies. Here, we performed a genome-wide association study of cortical tau quantified by positron emission tomography in 3,136 participants from 12 independent studies. The CYP1B1-RMDN2 locus was associated with tau deposition. The most significant signal was at rs2113389, which explained 4.3% of the variation in cortical tau, while APOE4 rs429358 accounted for 3.6%. rs2113389 was associated with higher tau and faster cognitive decline. Additive effects, but no interactions, were observed between rs2113389 and diagnosis, APOE4 , and Aβ positivity. CYP1B1 expression was upregulated in AD. rs2113389 was associated with higher CYP1B1 expression and methylation levels. Mouse model studies provided additional functional evidence for a relationship between CYP1B1 and tau deposition but not Aβ. These results may provide insight into the genetic basis of cerebral tau and novel pathways for therapeutic development in AD.
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Libby JB, Seto M, Khan OA, Liu D, Petyuk VA, Gifford KA, Dumitrescu L, Jefferson AL, Hohman TJ. Whole Blood Expression of the Vascular Endothelial Growth Factor Family Relates to Cognitive Performance. Alzheimers Dement 2022. [DOI: 10.1002/alz.066076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Julia B. Libby
- Vanderbilt Memory & Alzheimer's Center, Vanderbilt University Medical Center Nashville TN USA
| | | | - Omair A. Khan
- Vanderbilt Memory & Alzheimer’s Center, Vanderbilt University Medical Center Nashville TN USA
| | - Dandan Liu
- Vanderbilt Memory & Alzheimer’s Center, Vanderbilt University Medical Center Nashville TN USA
| | - Vladislav A Petyuk
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA Richland WA USA
| | - Katherine A. Gifford
- Vanderbilt Memory & Alzheimer’s Center, Department of Neurology, Vanderbilt University Medical Center Nashville TN USA
| | - Logan Dumitrescu
- Vanderbilt Memory and Alzheimer’s Center, Vanderbilt University Medical Center Nashville TN USA
| | - Angela L. Jefferson
- Vanderbilt Memory & Alzheimer’s Center, Department of Neurology, Vanderbilt University Medical Center Nashville TN USA
| | - Timothy J. Hohman
- Vanderbilt Memory & Alzheimer’s Center, Department of Neurology, Vanderbilt University Medical Center Nashville TN USA
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