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Winfree RL, Nolan E, Dumitrescu L, Blennow K, Zetterberg H, Gifford KA, Pechman KR, Seto M, Petyuk VA, Wang Y, Schneider J, Bennett DA, Jefferson AL, Hohman TJ. Variants in the MS4A cluster interact with soluble TREM2 expression on biomarkers of neuropathology. Mol Neurodegener 2024; 19:41. [PMID: 38760857 PMCID: PMC11101336 DOI: 10.1186/s13024-024-00727-7] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 04/11/2024] [Indexed: 05/19/2024] Open
Abstract
Recent evidence suggests that Alzheimer's disease (AD) genetic risk variants (rs1582763 and rs6591561) of the MS4A locus are genome-wide significant regulators of soluble TREM2 levels such that the minor allele of the protective variant (rs1582763) is associated with higher sTREM2 and lower AD risk while the minor allele of (rs6591561) relates to lower sTREM2 and higher AD risk. Our group previously found that higher sTREM2 relates to higher Aβ40, worse blood-brain barrier (BBB) integrity (measured with the CSF/plasma albumin ratio), and higher CSF tau, suggesting strong associations with amyloid abundance and both BBB and neurodegeneration complicate interpretation. We expand on this work by leveraging these common variants as genetic tools to tune the interpretation of high CSF sTREM2, and by exploring the potential modifying role of these variants on the well-established associations between CSF sTREM2 as well as TREM2 transcript levels in the brain with AD neuropathology. Biomarker analyses leveraged data from the Vanderbilt Memory & Aging Project (n = 127, age = 72 ± 6.43) and were replicated in the Alzheimer's Disease Neuroimaging Initiative (n = 399, age = 73 ± 7.39). Autopsy analyses were performed leveraging data from the Religious Orders Study and Rush Memory and Aging Project (n = 577, age = 89 ± 6.46). We found that the protective variant rs1582763 attenuated the association between CSF sTREM2 and Aβ40 (β = -0.44, p-value = 0.017) and replicated this interaction in ADNI (β = -0.27, p = 0.017). We did not observe this same interaction effect between TREM2 mRNA levels and Aβ peptides in brain (Aβ total β = -0.14, p = 0.629; Aβ1-38, β = 0.11, p = 0.200). In contrast to the effects on Aβ, the minor allele of this same variant seemed to enhance the association with blood-brain barrier dysfunction (β = 7.0e-4, p = 0.009), suggesting that elevated sTREM2 may carry a much different interpretation in carriers vs. non-carriers of this allele. When evaluating the risk variant (rs6591561) across datasets, we did not observe a statistically significant interaction against any outcome in VMAP and observed opposing directions of associations in ADNI and ROS/MAP on Aβ levels. Together, our results suggest that the protective effect of rs1582763 may act by decoupling the associations between sTREM2 and amyloid abundance, providing important mechanistic insight into sTREM2 changes and highlighting the need to incorporate genetic context into the analysis of sTREM2 levels, particularly if leveraged as a clinical biomarker of disease in the future.
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Affiliation(s)
- Rebecca L Winfree
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA.
- Pharmacology Department, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Emma Nolan
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Epidemiology Doctoral Program, School of Medicine, Vanderbilt University, Nashville, TN, USA
| | - Logan Dumitrescu
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, 431 41, 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, 431 41, 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
- Hong Kong Center for Neurodegenerative Diseases, Clear Water Bay, Hong Kong, China
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Katherine A Gifford
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kimberly R Pechman
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mabel Seto
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yanling Wang
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Julie Schneider
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
- Department of Pathology, Rush University Medical Center, Chicago, IL, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Angela L Jefferson
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Timothy J Hohman
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Pharmacology Department, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
- Epidemiology Doctoral Program, School of Medicine, Vanderbilt University, Nashville, TN, USA
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Oveisgharan S, Yu L, de Paiva Lopes K, Petyuk VA, Tasaki S, Vialle R, Menon V, Wang Y, De Jager PL, Schneider JA, Bennett DA. G-protein coupled estrogen receptor 1, amyloid-β, and tau tangles in older adults. Commun Biol 2024; 7:569. [PMID: 38750228 PMCID: PMC11096330 DOI: 10.1038/s42003-024-06272-9] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 04/30/2024] [Indexed: 05/18/2024] Open
Abstract
Accumulation of amyloid-β (Aβ) and tau tangles are hallmarks of Alzheimer's disease. Aβ is extracellular while tau tangles are typically intracellular, and it is unknown how these two proteinopathies are connected. Here, we use data of 1206 elders and test that RNA expression levels of GPER1, a transmembrane protein, modify the association of Aβ with tau tangles. GPER1 RNA expression is related to more tau tangles (p = 0.001). Moreover, GPER1 expression modifies the association of immunohistochemistry-derived Aβ load with tau tangles (p = 0.044). Similarly, GPER1 expression modifies the association between Aβ proteoforms and tau tangles: total Aβ protein (p = 0.030) and Aβ38 peptide (p = 0.002). Using single nuclei RNA-seq indicates that GPER1 RNA expression in astrocytes modifies the relation of Aβ load with tau tangles (p = 0.002), but not GPER1 in excitatory neurons or endothelial cells. We conclude that GPER1 may be a link between Aβ and tau tangles driven mainly by astrocytic GPER1 expression.
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Affiliation(s)
- Shahram Oveisgharan
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA.
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA.
| | - Lei Yu
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Katia de Paiva Lopes
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Shinya Tasaki
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Ricardo Vialle
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Vilas Menon
- Department of Neurology and Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Center for Translational and Computational Neuroimmunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Yanling Wang
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Philip L De Jager
- Department of Neurology, Center for Translational and Computational Neuroimmunology, Columbia University Irving Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Julie A Schneider
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
- Department of Pathology, Rush University Medical Center, Chicago, IL, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
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Raj-Kumar PK, Lin X, Liu T, Sturtz LA, Gritsenko MA, Petyuk VA, Sagendorf TJ, Deyarmin B, Liu J, Praveen-Kumar A, Wang G, McDermott JE, Shukla AK, Moore RJ, Monroe ME, Webb-Robertson BJM, Hooke JA, Fantacone-Campbell L, Mostoller B, Kvecher L, Kane J, Melley J, Somiari S, Soon-Shiong P, Smith RD, Mural RJ, Rodland KD, Shriver CD, Kovatich AJ, Hu H. Proteogenomic characterization of difficult-to-treat breast cancer with tumor cells enriched through laser microdissection. Breast Cancer Res 2024; 26:76. [PMID: 38745208 PMCID: PMC11094977 DOI: 10.1186/s13058-024-01835-4] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 05/05/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Breast cancer (BC) is the most commonly diagnosed cancer and the leading cause of cancer death among women globally. Despite advances, there is considerable variation in clinical outcomes for patients with non-luminal A tumors, classified as difficult-to-treat breast cancers (DTBC). This study aims to delineate the proteogenomic landscape of DTBC tumors compared to luminal A (LumA) tumors. METHODS We retrospectively collected a total of 117 untreated primary breast tumor specimens, focusing on DTBC subtypes. Breast tumors were processed by laser microdissection (LMD) to enrich tumor cells. DNA, RNA, and protein were simultaneously extracted from each tumor preparation, followed by whole genome sequencing, paired-end RNA sequencing, global proteomics and phosphoproteomics. Differential feature analysis, pathway analysis and survival analysis were performed to better understand DTBC and investigate biomarkers. RESULTS We observed distinct variations in gene mutations, structural variations, and chromosomal alterations between DTBC and LumA breast tumors. DTBC tumors predominantly had more mutations in TP53, PLXNB3, Zinc finger genes, and fewer mutations in SDC2, CDH1, PIK3CA, SVIL, and PTEN. Notably, Cytoband 1q21, which contains numerous cell proliferation-related genes, was significantly amplified in the DTBC tumors. LMD successfully minimized stromal components and increased RNA-protein concordance, as evidenced by stromal score comparisons and proteomic analysis. Distinct DTBC and LumA-enriched clusters were observed by proteomic and phosphoproteomic clustering analysis, some with survival differences. Phosphoproteomics identified two distinct phosphoproteomic profiles for high relapse-risk and low relapse-risk basal-like tumors, involving several genes known to be associated with breast cancer oncogenesis and progression, including KIAA1522, DCK, FOXO3, MYO9B, ARID1A, EPRS, ZC3HAV1, and RBM14. Lastly, an integrated pathway analysis of multi-omics data highlighted a robust enrichment of proliferation pathways in DTBC tumors. CONCLUSIONS This study provides an integrated proteogenomic characterization of DTBC vs LumA with tumor cells enriched through laser microdissection. We identified many common features of DTBC tumors and the phosphopeptides that could serve as potential biomarkers for high/low relapse-risk basal-like BC and possibly guide treatment selections.
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Affiliation(s)
- Praveen-Kumar Raj-Kumar
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Xiaoying Lin
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Tao Liu
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Lori A Sturtz
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | | | | | | | - Brenda Deyarmin
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
| | - Jianfang Liu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
| | | | - Guisong Wang
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | | | - Anil K Shukla
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ronald J Moore
- Pacific Northwest National Laboratory, Richland, WA, USA
| | | | | | - Jeffrey A Hooke
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Leigh Fantacone-Campbell
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Brad Mostoller
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
| | - Leonid Kvecher
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Jennifer Kane
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
| | - Jennifer Melley
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
| | - Stella Somiari
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
| | | | | | - Richard J Mural
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
| | | | - Craig D Shriver
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
- Department of Surgery, Walter Reed National Military Medical Center, Bethesda, MD, USA.
| | - Albert J Kovatich
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Hai Hu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA.
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
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4
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Amar D, Gay NR, Jean-Beltran PM, Bae D, Dasari S, Dennis C, Evans CR, Gaul DA, Ilkayeva O, Ivanova AA, Kachman MT, Keshishian H, Lanza IR, Lira AC, Muehlbauer MJ, Nair VD, Piehowski PD, Rooney JL, Smith KS, Stowe CL, Zhao B, Clark NM, Jimenez-Morales D, Lindholm ME, Many GM, Sanford JA, Smith GR, Vetr NG, Zhang T, Almagro Armenteros JJ, Avila-Pacheco J, Bararpour N, Ge Y, Hou Z, Marwaha S, Presby DM, Natarajan Raja A, Savage EM, Steep A, Sun Y, Wu S, Zhen J, Bodine SC, Esser KA, Goodyear LJ, Schenk S, Montgomery SB, Fernández FM, Sealfon SC, Snyder MP, Adkins JN, Ashley E, Burant CF, Carr SA, Clish CB, Cutter G, Gerszten RE, Kraus WE, Li JZ, Miller ME, Nair KS, Newgard C, Ortlund EA, Qian WJ, Tracy R, Walsh MJ, Wheeler MT, Dalton KP, Hastie T, Hershman SG, Samdarshi M, Teng C, Tibshirani R, Cornell E, Gagne N, May S, Bouverat B, Leeuwenburgh C, Lu CJ, Pahor M, Hsu FC, Rushing S, Walkup MP, Nicklas B, Rejeski WJ, Williams JP, Xia A, Albertson BG, Barton ER, Booth FW, Caputo T, Cicha M, De Sousa LGO, Farrar R, Hevener AL, Hirshman MF, Jackson BE, Ke BG, Kramer KS, Lessard SJ, Makarewicz NS, Marshall AG, Nigro P, Powers S, Ramachandran K, Rector RS, Richards CZT, Thyfault J, Yan Z, Zang C, Amper MAS, Balci AT, Chavez C, Chikina M, Chiu R, Gritsenko MA, Guevara K, Hansen JR, Hennig KM, Hung CJ, Hutchinson-Bunch C, Jin CA, Liu X, Maner-Smith KM, Mani DR, Marjanovic N, Monroe ME, Moore RJ, Moore SG, Mundorff CC, Nachun D, Nestor MD, Nudelman G, Pearce C, Petyuk VA, Pincas H, Ramos I, Raskind A, Rirak S, Robbins JM, Rubenstein AB, Ruf-Zamojski F, Sagendorf TJ, Seenarine N, Soni T, Uppal K, Vangeti S, Vasoya M, Vornholt A, Yu X, Zaslavsky E, Zebarjadi N, Bamman M, Bergman BC, Bessesen DH, Buford TW, Chambers TL, Coen PM, Cooper D, Haddad F, Gadde K, Goodpaster BH, Harris M, Huffman KM, Jankowski CM, Johannsen NM, Kohrt WM, Lester B, Melanson EL, Moreau KL, Musi N, Newton RL, Radom-Aizik S, Ramaker ME, Rankinen T, Rasmussen BB, Ravussin E, Schauer IE, Schwartz RS, Sparks LM, Thalacker-Mercer A, Trappe S, Trappe TA, Volpi E. Temporal dynamics of the multi-omic response to endurance exercise training. Nature 2024; 629:174-183. [PMID: 38693412 PMCID: PMC11062907 DOI: 10.1038/s41586-023-06877-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/16/2023] [Indexed: 05/03/2024]
Abstract
Regular exercise promotes whole-body health and prevents disease, but the underlying molecular mechanisms are incompletely understood1-3. Here, the Molecular Transducers of Physical Activity Consortium4 profiled the temporal transcriptome, proteome, metabolome, lipidome, phosphoproteome, acetylproteome, ubiquitylproteome, epigenome and immunome in whole blood, plasma and 18 solid tissues in male and female Rattus norvegicus over eight weeks of endurance exercise training. The resulting data compendium encompasses 9,466 assays across 19 tissues, 25 molecular platforms and 4 training time points. Thousands of shared and tissue-specific molecular alterations were identified, with sex differences found in multiple tissues. Temporal multi-omic and multi-tissue analyses revealed expansive biological insights into the adaptive responses to endurance training, including widespread regulation of immune, metabolic, stress response and mitochondrial pathways. Many changes were relevant to human health, including non-alcoholic fatty liver disease, inflammatory bowel disease, cardiovascular health and tissue injury and recovery. The data and analyses presented in this study will serve as valuable resources for understanding and exploring the multi-tissue molecular effects of endurance training and are provided in a public repository ( https://motrpac-data.org/ ).
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Day NJ, Kelly SS, Lui LY, Mansfield TA, Gaffrey MJ, Trejo JB, Sagendorf TJ, Attah IK, Moore RJ, Douglas CM, Newman AB, Kritchevsky SB, Kramer PA, Marcinek DJ, Coen PM, Goodpaster BH, Hepple RT, Cawthon PM, Petyuk VA, Esser KA, Qian WJ, Cummings SR. Signatures of cysteine oxidation on muscle structural and contractile proteins are associated with physical performance and muscle function in older adults: Study of Muscle, Mobility and Aging (SOMMA). Aging Cell 2024:e14094. [PMID: 38332629 DOI: 10.1111/acel.14094] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/05/2024] [Accepted: 01/10/2024] [Indexed: 02/10/2024] Open
Abstract
Oxidative stress is considered a contributor to declining muscle function and mobility during aging; however, the underlying molecular mechanisms remain poorly described. We hypothesized that greater levels of cysteine (Cys) oxidation on muscle proteins are associated with decreased measures of mobility. Herein, we applied a novel redox proteomics approach to measure reversible protein Cys oxidation in vastus lateralis muscle biopsies collected from 56 subjects in the Study of Muscle, Mobility and Aging (SOMMA), a community-based cohort study of individuals aged 70 years and older. We tested whether levels of Cys oxidation on key muscle proteins involved in muscle structure and contraction were associated with muscle function (leg power and strength), walking speed, and fitness (VO2 peak on cardiopulmonary exercise testing) using linear regression models adjusted for age, sex, and body weight. Higher oxidation levels of select nebulin Cys sites were associated with lower VO2 peak, while greater oxidation of myomesin-1, myomesin-2, and nebulin Cys sites was associated with slower walking speed. Higher oxidation of Cys sites in key proteins such as myomesin-2, alpha-actinin-2, and skeletal muscle alpha-actin were associated with lower leg power and strength. We also observed an unexpected correlation (R = 0.48) between a higher oxidation level of eight Cys sites in alpha-actinin-3 and stronger leg power. Despite this observation, the results generally support the hypothesis that Cys oxidation of muscle proteins impairs muscle power and strength, walking speed, and cardiopulmonary fitness with aging.
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Affiliation(s)
- Nicholas J Day
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Shane S Kelly
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Li-Yung Lui
- San Francisco Coordinating Center, California Pacific Medical Center Research Institute, San Francisco, California, USA
| | - Tyler A Mansfield
- San Francisco Coordinating Center, California Pacific Medical Center Research Institute, San Francisco, California, USA
| | - Matthew J Gaffrey
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Jesse B Trejo
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Tyler J Sagendorf
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Isaac K Attah
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Collin M Douglas
- Department of Physiology and Aging, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Anne B Newman
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Stephen B Kritchevsky
- Department of Internal Medicine-Gerontology and Geriatric Medicine, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
| | - Philip A Kramer
- Department of Internal Medicine-Gerontology and Geriatric Medicine, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
| | - David J Marcinek
- Department of Radiology, University of Washington, Seattle, Washington, USA
| | - Paul M Coen
- Translational Research Institute, AdventHealth, Orlando, Florida, USA
| | - Bret H Goodpaster
- Translational Research Institute, AdventHealth, Orlando, Florida, USA
| | - Russell T Hepple
- Department of Physical Therapy, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Peggy M Cawthon
- San Francisco Coordinating Center, California Pacific Medical Center Research Institute, San Francisco, California, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Karyn A Esser
- Department of Physiology and Aging, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Steven R Cummings
- San Francisco Coordinating Center, California Pacific Medical Center Research Institute, San Francisco, California, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
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Schutzer SE, Liu T, Tsai CF, Petyuk VA, Schepmoes AA, Wang YT, Weitz KK, Bergquist J, Smith RD, Natelson BH. Myalgic encephalomyelitis/chronic fatigue syndrome and fibromyalgia are indistinguishable by their cerebrospinal fluid proteomes. Ann Med 2023; 55:2208372. [PMID: 37722890 PMCID: PMC10512920 DOI: 10.1080/07853890.2023.2208372] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 04/24/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) and fibromyalgia have overlapping neurologic symptoms particularly disabling fatigue. This has given rise to the question whether they are distinct central nervous system (CNS) entities or is one an extension of the other. MATERIAL AND METHODS To investigate this, we used unbiased quantitative mass spectrometry-based proteomics to examine the most proximal fluid to the brain, cerebrospinal fluid (CSF). This was to ascertain if the proteome profile of one was the same or different from the other. We examined two separate groups of ME/CFS, one with (n = 15) and one without (n = 15) fibromyalgia. RESULTS We quantified a total of 2083 proteins using immunoaffinity depletion, tandem mass tag isobaric labelling and offline two-dimensional liquid chromatography coupled to tandem mass spectrometry, including 1789 that were quantified in all the CSF samples. ANOVA analysis did not yield any proteins with an adjusted p value <.05. CONCLUSION This supports the notion that ME/CFS and fibromyalgia as currently defined are not distinct entities.Key messageME/CFS and fibromyalgia as currently defined are not distinct entities.Unbiased quantitative mass spectrometry-based proteomics can be used to discover cerebrospinal fluid proteins that are biomarkers for a condition such as we are studying.
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Affiliation(s)
| | - Tao Liu
- Integrative Omics, Biological Sciences, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Chia-Feng Tsai
- Integrative Omics, Biological Sciences, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Vladislav A. Petyuk
- Integrative Omics, Biological Sciences, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Athena A. Schepmoes
- Integrative Omics, Biological Sciences, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yi-Ting Wang
- Analytical Chemistry and Neurochemistry in Department of Chemistry, Uppsala University, Uppsala, Sweden
| | - Karl K. Weitz
- Integrative Omics, Biological Sciences, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jonas Bergquist
- Analytical Chemistry and Neurochemistry in Department of Chemistry, Uppsala University, Uppsala, Sweden
| | - Richard D. Smith
- Integrative Omics, Biological Sciences, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Benjamin H. Natelson
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Day NJ, Kelly SS, Lui LY, Mansfield TA, Gaffrey MJ, Trejo JB, Sagendorf TJ, Attah K, Moore RJ, Douglas CM, Newman AB, Kritchevsky SB, Kramer PA, Marcinek DJ, Coen PM, Goodpaster BH, Hepple RT, Cawthon PM, Petyuk VA, Esser KA, Qian WJ, Cummings SR. Signatures of Cysteine Oxidation on Muscle Structural and Contractile Proteins Are Associated with Physical Performance and Muscle Function in Older Adults: Study of Muscle, Mobility and Aging (SOMMA). medRxiv 2023:2023.11.07.23298224. [PMID: 37986748 PMCID: PMC10659491 DOI: 10.1101/2023.11.07.23298224] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Oxidative stress is considered a contributor to declining muscle function and mobility during aging; however, the underlying molecular mechanisms remain poorly described. We hypothesized that greater levels of cysteine (Cys) oxidation on muscle proteins are associated with decreased measures of mobility. Herein, we applied a novel redox proteomics approach to measure reversible protein Cys oxidation in vastus lateralis muscle biopsies collected from 56 subjects in the Study of Muscle, Mobility and Aging (SOMMA), a community-based cohort study of individuals aged 70 years and older. We tested whether levels of Cys oxidation on key muscle proteins involved in muscle structure and contraction were associated with muscle function (leg power and strength), walking speed, and fitness (VO2 peak on cardiopulmonary exercise testing) using linear regression models adjusted for age, sex, and body weight. Higher oxidation levels of select nebulin Cys sites were associated with lower VO2 peak, while greater oxidation of myomesin-1, myomesin-2, and nebulin Cys sites was associated with slower walking speed. Higher oxidation of Cys sites in key proteins such as myomesin-2, alpha-actinin-2, and skeletal muscle alpha-actin were associated with lower leg power and strength. We also observed an unexpected correlation (r = 0.48) between a higher oxidation level of 8 Cys sites in alpha-actinin-3 and stronger leg power. Despite this observation, the results generally support the hypothesis that Cys oxidation of muscle proteins impair muscle power and strength, walking speed, and cardiopulmonary fitness with aging.
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Affiliation(s)
- Nicholas J. Day
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Shane S. Kelly
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Li-Yung Lui
- San Francisco Coordinating Center, California Pacific Medical Center Research Institute, San Francisco, California, USA
| | - Tyler A. Mansfield
- San Francisco Coordinating Center, California Pacific Medical Center Research Institute, San Francisco, California, USA
| | - Matthew J. Gaffrey
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Jesse B. Trejo
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Tyler J. Sagendorf
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Kwame Attah
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Ronald J. Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Collin M. Douglas
- Department of Physiology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Anne B. Newman
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Stephen B. Kritchevsky
- Department of Internal Medicine-Gerontology and Geriatric Medicine, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
| | - Philip A. Kramer
- Department of Internal Medicine-Gerontology and Geriatric Medicine, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
| | - David J. Marcinek
- Department of Radiology, University of Washington, Seattle, Washington, USA
| | - Paul M. Coen
- Translational Research Institute, AdventHealth, Orlando, Florida, USA
| | | | - Russell T. Hepple
- Department of Physical Therapy, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Peggy M. Cawthon
- San Francisco Coordinating Center, California Pacific Medical Center Research Institute, San Francisco, California, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, USA
| | - Vladislav A. Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Karyn A. Esser
- Department of Physiology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Steven R. Cummings
- San Francisco Coordinating Center, California Pacific Medical Center Research Institute, San Francisco, California, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, USA
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Fulcher JM, Swensen AC, Chen YC, Verchere CB, Petyuk VA, Qian WJ. Top-Down Proteomics of Mouse Islets With Beta Cell CPE Deletion Reveals Molecular Details in Prohormone Processing. Endocrinology 2023; 164:bqad160. [PMID: 37967211 PMCID: PMC10650973 DOI: 10.1210/endocr/bqad160] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Indexed: 11/17/2023]
Abstract
Altered prohormone processing, such as with proinsulin and pro-islet amyloid polypeptide (proIAPP), has been reported as an important feature of prediabetes and diabetes. Proinsulin processing includes removal of several C-terminal basic amino acids and is performed principally by the exopeptidase carboxypeptidase E (CPE), and mutations in CPE or other prohormone convertase enzymes (PC1/3 and PC2) result in hyperproinsulinemia. A comprehensive characterization of the forms and quantities of improperly processed insulin and other hormone products following Cpe deletion in pancreatic islets has yet to be attempted. In the present study we applied top-down proteomics to globally evaluate the numerous proteoforms of hormone processing intermediates in a β-cell-specific Cpe knockout mouse model. Increases in dibasic residue-containing proinsulin and other novel proteoforms of improperly processed proinsulin were found, and we could classify several processed proteoforms as novel substrates of CPE. Interestingly, some other known substrates of CPE remained unaffected despite its deletion, implying that paralogous processing enzymes such as carboxypeptidase D (CPD) can compensate for CPE loss and maintain near normal levels of hormone processing. In summary, our quantitative results from top-down proteomics of islets provide unique insights into the complexity of hormone processing products and the regulatory mechanisms.
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Affiliation(s)
- James M Fulcher
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Adam C Swensen
- Integrative Omics, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Yi-Chun Chen
- Department of Surgery, BC Children’s Hospital Research Institute and University of British Columbia, Vancouver, British Columbia, V5Z 4H4, Canada
| | - C Bruce Verchere
- Department of Surgery, BC Children’s Hospital Research Institute and University of British Columbia, Vancouver, British Columbia, V5Z 4H4, Canada
- Department of Pathology and Laboratory Medicine, BC Children’s Hospital Research Institute and University of British Columbia, Vancouver, British Columbia, V5Z 4H4, Canada
| | - Vladislav A Petyuk
- Integrative Omics, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Wei-Jun Qian
- Integrative Omics, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
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Gicas KM, Honer WG, Petyuk VA, Wilson RS, Boyle PA, Leurgans SE, Schneider JA, De Jager PL, Bennett DA. Primacy and recency effects in verbal memory are differentially associated with post-mortem frontal cortex p-tau 217 and 202 levels in a mixed sample of community-dwelling older adults. J Clin Exp Neuropsychol 2023; 45:770-785. [PMID: 37440260 PMCID: PMC10787031 DOI: 10.1080/13803395.2023.2232583] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 06/28/2023] [Indexed: 07/14/2023]
Abstract
INTRODUCTION Serial position effects in verbal memory are associated with in vivo fluid biomarkers and neuropathological outcomes in Alzheimer's disease (AD). To extend the biomarker literature, associations between serial position scores and postmortem levels of brain phosphorylated tau (p-tau) were examined, in the context of Braak stage of neurofibrillary tangle progression. METHOD Participants were 1091 community-dwelling adults (Mage = 80.2, 68.9% female) from the Rush University Religious Orders Study and Memory and Aging Project who were non-demented at enrollment and followed for a mean of 9.2 years until death. The CERAD Word List Memory test administered at baseline and within 1 year of death was used to calculate serial position (primacy, recency) and total recall scores. Proteomic analyses quantified p-tau 217 and 202 from dorsolateral prefrontal cortex samples. Linear regressions assessed associations between cognitive scores and p-tau with Braak stage as a moderator. RESULTS Cognitive status proximal to death indicated 34.7% were unimpaired, 26.2% met criteria for MCI, and 39.0% for dementia. Better baseline primacy recall, but not recency recall, was associated with lower p-tau 217 levels across Braak stages. Delayed recall showed a similar pattern as primacy. There was no main effect of immediate recall, but an interaction with Braak stages indicated a negative association with p-tau 217 level only in Braak V-VI. Within 1 year of death, there were no main effects for cognitive scores; however, recency, immediate and delayed recall scores interacted with Braak stage showing better recall was associated with lower p-tau 217 only in Braak V-VI. No associations were observed with p-tau 202. CONCLUSIONS Primacy recall measured in non-demented adults may be sensitive to emergent tau phosphorylation that occurs in the earliest stages of AD. Serial position scores may complement the routinely used delayed recall score and p-tau biomarkers to detect preclinical AD.
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Affiliation(s)
| | - William G Honer
- Department of Psychiatry, University of British Columbia, Vancouver, Canada
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Robert S Wilson
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, United States
- Department of Psychiatry and Behavioral Sciences, Rush University Medical Center, Chicago, IL, United States
| | - Patricia A Boyle
- Department of Psychiatry and Behavioral Sciences, Rush University Medical Center, Chicago, IL, United States
| | - Sue E Leurgans
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, United States
| | - Julie A Schneider
- Department of Pathology, Rush University Medical Center, Chicago, IL, United States
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center
| | - David A Bennett
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, United States
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10
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Dou Y, Katsnelson L, Gritsenko MA, Hu Y, Reva B, Hong R, Wang YT, Kolodziejczak I, Lu RJH, Tsai CF, Bu W, Liu W, Guo X, An E, Arend RC, Bavarva J, Chen L, Chu RK, Czekański A, Davoli T, Demicco EG, DeLair D, Devereaux K, Dhanasekaran SM, Dottino P, Dover B, Fillmore TL, Foxall M, Hermann CE, Hiltke T, Hostetter G, Jędryka M, Jewell SD, Johnson I, Kahn AG, Ku AT, Kumar-Sinha C, Kurzawa P, Lazar AJ, Lazcano R, Lei JT, Li Y, Liao Y, Lih TSM, Lin TT, Martignetti JA, Masand RP, Matkowski R, McKerrow W, Mesri M, Monroe ME, Moon J, Moore RJ, Nestor MD, Newton C, Omelchenko T, Omenn GS, Payne SH, Petyuk VA, Robles AI, Rodriguez H, Ruggles KV, Rykunov D, Savage SR, Schepmoes AA, Shi T, Shi Z, Tan J, Taylor M, Thiagarajan M, Wang JM, Weitz KK, Wen B, Williams CM, Wu Y, Wyczalkowski MA, Yi X, Zhang X, Zhao R, Mutch D, Chinnaiyan AM, Smith RD, Nesvizhskii AI, Wang P, Wiznerowicz M, Ding L, Mani DR, Zhang H, Anderson ML, Rodland KD, Zhang B, Liu T, Fenyö D. Proteogenomic insights suggest druggable pathways in endometrial carcinoma. Cancer Cell 2023; 41:1586-1605.e15. [PMID: 37567170 PMCID: PMC10631452 DOI: 10.1016/j.ccell.2023.07.007] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 03/25/2023] [Accepted: 07/18/2023] [Indexed: 08/13/2023]
Abstract
We characterized a prospective endometrial carcinoma (EC) cohort containing 138 tumors and 20 enriched normal tissues using 10 different omics platforms. Targeted quantitation of two peptides can predict antigen processing and presentation machinery activity, and may inform patient selection for immunotherapy. Association analysis between MYC activity and metformin treatment in both patients and cell lines suggests a potential role for metformin treatment in non-diabetic patients with elevated MYC activity. PIK3R1 in-frame indels are associated with elevated AKT phosphorylation and increased sensitivity to AKT inhibitors. CTNNB1 hotspot mutations are concentrated near phosphorylation sites mediating pS45-induced degradation of β-catenin, which may render Wnt-FZD antagonists ineffective. Deep learning accurately predicts EC subtypes and mutations from histopathology images, which may be useful for rapid diagnosis. Overall, this study identified molecular and imaging markers that can be further investigated to guide patient stratification for more precise treatment of EC.
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Affiliation(s)
- Yongchao Dou
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lizabeth Katsnelson
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Marina A Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Yingwei Hu
- Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Boris Reva
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Runyu Hong
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Yi-Ting Wang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Iga Kolodziejczak
- International Institute for Molecular Oncology, 20-203 Poznań, Poland; Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Rita Jui-Hsien Lu
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Wen Bu
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Wenke Liu
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Xiaofang Guo
- Division of Gynecologic Oncology, University of South Florida Morsani College of Medicine and Tampa General Hospital Cancer Institute, Tampa, FL 33606, USA
| | - Eunkyung An
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Rebecca C Arend
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, University of Alabama at Birmingham, Birmingham, AL 35249, USA
| | - Jasmin Bavarva
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Lijun Chen
- Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Rosalie K Chu
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Andrzej Czekański
- Wroclaw Medical University and Lower Silesian Oncology, Pulmonology and Hematology Center (DCOPIH), Wrocław, Poland
| | - Teresa Davoli
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Elizabeth G Demicco
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital and Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1X5, Canada
| | - Deborah DeLair
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Kelly Devereaux
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Saravana M Dhanasekaran
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter Dottino
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bailee Dover
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, University of Alabama at Birmingham, Birmingham, AL 35249, USA
| | - Thomas L Fillmore
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - McKenzie Foxall
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, University of Alabama at Birmingham, Birmingham, AL 35249, USA
| | - Catherine E Hermann
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | | | - Marcin Jędryka
- Wroclaw Medical University and Lower Silesian Oncology, Pulmonology and Hematology Center (DCOPIH), Wrocław, Poland
| | - Scott D Jewell
- Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Isabelle Johnson
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Andrea G Kahn
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35249, USA
| | - Amy T Ku
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chandan Kumar-Sinha
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Paweł Kurzawa
- Heliodor Swiecicki Clinical Hospital in Poznan ul. Przybyszewskiego 49, 60-355 Poznań, Poland; Poznań University of Medical Sciences, 61-701 Poznań, Poland
| | - Alexander J Lazar
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rossana Lazcano
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jonathan T Lei
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yi Li
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yuxing Liao
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tung-Shing M Lih
- Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Tai-Tu Lin
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - John A Martignetti
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ramya P Masand
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rafał Matkowski
- Wroclaw Medical University and Lower Silesian Oncology, Pulmonology and Hematology Center (DCOPIH), Wrocław, Poland
| | - Wilson McKerrow
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Jamie Moon
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Michael D Nestor
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Chelsea Newton
- Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | | | - Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA; School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Samuel H Payne
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Kelly V Ruggles
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Division of Precision Medicine, Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Dmitry Rykunov
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sara R Savage
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Athena A Schepmoes
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Zhiao Shi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jimin Tan
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Mason Taylor
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Mathangi Thiagarajan
- Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Joshua M Wang
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Karl K Weitz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Bo Wen
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - C M Williams
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Yige Wu
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Matthew A Wyczalkowski
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Xinpei Yi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xu Zhang
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Rui Zhao
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - David Mutch
- Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Arul M Chinnaiyan
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Maciej Wiznerowicz
- International Institute for Molecular Oncology, 60-203 Poznań, Poland; Heliodor Swiecicki Clinical Hospital in Poznan ul. Przybyszewskiego 49, 60-355 Poznań, Poland; Poznań University of Medical Sciences, 61-701 Poznań, Poland
| | - Li Ding
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - D R Mani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Hui Zhang
- Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Matthew L Anderson
- Division of Gynecologic Oncology, University of South Florida Morsani College of Medicine and Tampa General Hospital Cancer Institute, Tampa, FL 33606, USA.
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR 97221, USA.
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
| | - David Fenyö
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA.
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11
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Rhea EM, Leclerc M, Yassine HN, Capuano AW, Tong H, Petyuk VA, Macauley SL, Fioramonti X, Carmichael O, Calon F, Arvanitakis Z. State of the Science on Brain Insulin Resistance and Cognitive Decline Due to Alzheimer's Disease. Aging Dis 2023:AD.2023.0814. [PMID: 37611907 DOI: 10.14336/ad.2023.0814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/14/2023] [Indexed: 08/25/2023] Open
Abstract
Type 2 diabetes mellitus (T2DM) is common and increasing in prevalence worldwide, with devastating public health consequences. While peripheral insulin resistance is a key feature of most forms of T2DM and has been investigated for over a century, research on brain insulin resistance (BIR) has more recently been developed, including in the context of T2DM and non-diabetes states. Recent data support the presence of BIR in the aging brain, even in non-diabetes states, and found that BIR may be a feature in Alzheimer's disease (AD) and contributes to cognitive impairment. Further, therapies used to treat T2DM are now being investigated in the context of AD treatment and prevention, including insulin. In this review, we offer a definition of BIR, and present evidence for BIR in AD; we discuss the expression, function, and activation of the insulin receptor (INSR) in the brain; how BIR could develop; tools to study BIR; how BIR correlates with current AD hallmarks; and regional/cellular involvement of BIR. We close with a discussion on resilience to both BIR and AD, how current tools can be improved to better understand BIR, and future avenues for research. Overall, this review and position paper highlights BIR as a plausible therapeutic target for the prevention of cognitive decline and dementia due to AD.
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Affiliation(s)
- Elizabeth M Rhea
- Geriatric Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, WA 98108, USA
- Department of Medicine, Division of Gerontology and Geriatric Medicine, University of Washington, Seattle, WA 98195, USA
| | - Manon Leclerc
- Faculty of Pharmacy, Laval University, Quebec, Quebec, Canada
- Neuroscience Axis, CHU de Québec Research Center - Laval University, Quebec, Quebec, Canada
| | - Hussein N Yassine
- Departments of Neurology and Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Ana W Capuano
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL 60612, USA
| | - Han Tong
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL 60612, USA
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Shannon L Macauley
- Department of Physiology, University of Kentucky, Lexington, KY 40508, USA
| | - Xavier Fioramonti
- Univ. Bordeaux, INRAE, Bordeaux INP, NutriNeuro, UMR 1286, F-33000 Bordeaux, France
- International Associated Laboratory OptiNutriBrain, Bordeaux, France and Quebec, Canada
| | - Owen Carmichael
- Pennington Biomedical Research Center, Baton Rouge, LA 70808, USA
| | - Frederic Calon
- Faculty of Pharmacy, Laval University, Quebec, Quebec, Canada
- Neuroscience Axis, CHU de Québec Research Center - Laval University, Quebec, Quebec, Canada
- International Associated Laboratory OptiNutriBrain, Bordeaux, France and Quebec, Canada
| | - Zoe Arvanitakis
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL 60612, USA
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12
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Yu L, Petyuk VA, de Paiva Lopes K, Tasaki S, Menon V, Wang Y, Schneider JA, De Jager PL, Bennett DA. Associations of VGF with Neuropathologies and Cognitive Health in Older Adults. Ann Neurol 2023; 94:232-244. [PMID: 37177846 PMCID: PMC10524948 DOI: 10.1002/ana.26676] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 04/18/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023]
Abstract
OBJECTIVE VGF is proposed as a potential therapeutic target for Alzheimer's (AD) and other neurodegenerative conditions. The cell-type specific and, separately, peptide specific associations of VGF with pathologic and cognitive outcomes remain largely unknown. We leveraged gene expression and protein data from the human neocortex and investigated the VGF associations with common neuropathologies and late-life cognitive decline. METHODS Community-dwelling older adults were followed every year, died, and underwent brain autopsy. Cognitive decline was captured via annual cognitive testing. Common neurodegenerative and cerebrovascular conditions were assessed during neuropathologic evaluations. Bulk brain RNASeq and targeted proteomics analyses were conducted using frozen tissues from dorsolateral prefrontal cortex of 1,020 individuals. Cell-type specific gene expressions were quantified in a subsample (N = 424) following single nuclei RNASeq analysis from the same cortex. RESULTS The bulk brain VGF gene expression was primarily associated with AD and Lewy bodies. The VGF gene association with cognitive decline was in part accounted for by neuropathologies. Similar associations were observed for the VGF protein. Cell-type specific analyses revealed that, while VGF was differentially expressed in most major cell types in the cortex, its association with neuropathologies and cognitive decline was restricted to the neuronal cells. Further, the peptide fragments across the VGF polypeptide resembled each other in relation to neuropathologies and cognitive decline. INTERPRETATION Multiple pathways link VGF to cognitive health in older age, including neurodegeneration. The VGF gene functions primarily in neuronal cells and its protein associations with pathologic and cognitive outcomes do not map to a specific peptide. ANN NEUROL 2023;94:232-244.
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Affiliation(s)
- Lei Yu
- Rush Alzheimer’s Disease Center, Rush University Medical Center; Chicago, IL, USA
- Department of Neurological Sciences, Rush University Medical Center; Chicago, IL, USA
| | | | - Katia de Paiva Lopes
- Rush Alzheimer’s Disease Center, Rush University Medical Center; Chicago, IL, USA
- Department of Neurological Sciences, Rush University Medical Center; Chicago, IL, USA
| | - Shinya Tasaki
- Rush Alzheimer’s Disease Center, Rush University Medical Center; Chicago, IL, USA
- Department of Neurological Sciences, Rush University Medical Center; Chicago, IL, USA
| | - Vilas Menon
- Center for Translational and Computational Neuroimmunology, Department of Neurology & Taub Institute for Research on Alzheimer’s disease and the Aging Brain, Columbia University Irving Medical Center; New York, NY, USA
| | - Yanling Wang
- Rush Alzheimer’s Disease Center, Rush University Medical Center; Chicago, IL, USA
- Department of Neurological Sciences, Rush University Medical Center; Chicago, IL, USA
| | - Julie A. Schneider
- Rush Alzheimer’s Disease Center, Rush University Medical Center; Chicago, IL, USA
- Department of Neurological Sciences, Rush University Medical Center; Chicago, IL, USA
- Department of Pathology, Rush University Medical Center; Chicago, IL, USA
| | - Philip L. De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology & Taub Institute for Research on Alzheimer’s disease and the Aging Brain, Columbia University Irving Medical Center; New York, NY, USA
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center; Chicago, IL, USA
- Department of Neurological Sciences, Rush University Medical Center; Chicago, IL, USA
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13
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Yu L, Boyle PA, Janelidze S, Petyuk VA, Wang T, Bennett DA, Hansson O, Schneider JA. Plasma p-tau181 and p-tau217 in discriminating PART, AD and other key neuropathologies in older adults. Acta Neuropathol 2023; 146:1-11. [PMID: 37031430 PMCID: PMC10261204 DOI: 10.1007/s00401-023-02570-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 02/09/2023] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 04/10/2023]
Abstract
We examined whether plasma p-tau181 and p-tau217 are specific biomarkers of pathologically confirmed Alzheimer's disease (AD). In particular, we investigated the utility of plasma p-tau for differentiating AD from primary age-related tauopathy (PART), as well as AD with mixed pathologies. Data came from 269 older adults who participated in the Religious Orders Study or the Rush Memory and Aging Project. Blood samples were collected during annual clinical evaluations. Participants died and underwent brain autopsy. P-tau181 and p-tau217 were quantified in the plasma samples proximate to death (average interval before death: 1.4 years) using Lilly-developed MSD immunoassays. Uniform neuropathologic evaluations assessed AD, PART, and other common degenerative and cerebrovascular conditions. Plasma p-tau217 was more strongly correlated with brain β-amyloid and paired helical filament tau (PHFtau) tangles than p-tau181. Both p-tau markers were associated with greater odds of AD, but p-tau217 had higher accuracy (area under the ROC curve (AUC): 0.83) than p-tau181 (AUC: 0.76). Plasma p-tau markers were almost exclusively associated with AD pathologic indices with the exception of cerebral amyloid angiopathy. Compared to p-tau181, p-tau217 showed a higher AUC (0.82 versus 0.74) in differentiating AD from PART. For either p-tau, we did not observe a level difference between individuals with AD alone and those with mixed AD pathologies. In summary, plasma p-tau181and p-tau217 were specifically associated with AD pathological changes. Further, our data provide initial evidence that p-tau217 may be able to differentiate between AD and PART in individuals with comparable burdens of tau tangle pathology. These results demonstrate the specificity of p-tau217 for AD, supporting its use to identify patients suitable for anti-AD therapies including β-amyloid immunotherapies.
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Affiliation(s)
- Lei Yu
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W Harrison Street, Suite 1000, Chicago, IL, 60612, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Patricia A Boyle
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W Harrison Street, Suite 1000, Chicago, IL, 60612, USA
- Department of Psychiatry and Behavioral Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Shorena Janelidze
- Clinical Memory Research Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden
| | | | - Tianhao Wang
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W Harrison Street, Suite 1000, Chicago, IL, 60612, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W Harrison Street, Suite 1000, Chicago, IL, 60612, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Oskar Hansson
- Clinical Memory Research Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden.
- Memory Clinic, Skåne University Hospital, SE-205 02, Malmö, Sweden.
| | - Julie A Schneider
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W Harrison Street, Suite 1000, Chicago, IL, 60612, USA.
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA.
- Department of Pathology, Rush University Medical Center, Chicago, IL, USA.
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14
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Seto M, Dumitrescu L, Mahoney ER, Sclafani AM, De Jager PL, Menon V, Koran MEI, Robinson RA, Ruderfer DM, Cox NJ, Seyfried NT, Jefferson AL, Schneider JA, Bennett DA, Petyuk VA, Hohman TJ. Multi-omic characterization of brain changes in the vascular endothelial growth factor family during aging and Alzheimer's disease. Neurobiol Aging 2023; 126:25-33. [PMID: 36905877 PMCID: PMC10106439 DOI: 10.1016/j.neurobiolaging.2023.01.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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: 10/06/2022] [Revised: 01/20/2023] [Accepted: 01/22/2023] [Indexed: 01/27/2023]
Abstract
The vascular endothelial growth factor (VEGF) signaling family has been implicated in neuroprotection and clinical progression in Alzheimer's disease (AD). Previous work in postmortem human dorsolateral prefrontal cortex demonstrated that higher transcript levels of VEGFB, PGF, FLT1, and FLT4 are associated with AD dementia, worse cognitive outcomes, and higher AD neuropathology. To expand prior work, we leveraged bulk RNA sequencing data, single nucleus RNA (snRNA) sequencing, and both tandem mass tag and selected reaction monitoring mass spectrometry proteomic measures from the post-mortem brain. Outcomes included AD diagnosis, cognition, and AD neuropathology. We replicated previously reported VEGFB and FLT1 results, whereby higher expression was associated with worse outcomes, and snRNA results suggest microglia, oligodendrocytes, and endothelia may play a central role in these associations. Additionally, FLT4 and NRP2 expression were associated with better cognitive outcomes. This study provides a comprehensive molecular picture of the VEGF signaling family in cognitive aging and AD and critical insight towards the biomarker and therapeutic potential of VEGF family members in AD.
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Affiliation(s)
- Mabel Seto
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Logan Dumitrescu
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Emily R Mahoney
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Annah M Sclafani
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Philip L De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA; Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - Vilas Menon
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Mary E I Koran
- Department of Radiology, Stanford Hospital, Stanford, CA, USA
| | - Renã A Robinson
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - Douglas M Ruderfer
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nancy J Cox
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nicholas T Seyfried
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Angela L Jefferson
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Julie A Schneider
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Timothy J Hohman
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.
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15
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Martin EA, Fulcher JM, Zhou M, Monroe ME, Petyuk VA. TopPICR: A Companion R Package for Top-Down Proteomics Data Analysis. J Proteome Res 2023; 22:399-409. [PMID: 36631391 DOI: 10.1021/acs.jproteome.2c00570] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Top-down proteomics is the analysis of proteins in their intact form without proteolysis, thus preserving valuable information about post-translational modifications, isoforms, and proteolytic processing. However, it is still a developing field due to limitations in the instrumentation, difficulties with the interpretation of complex mass spectra, and a lack of well-established quantification approaches. TopPIC is one of the popular tools for proteoform identification. We extended its capabilities into label-free proteoform quantification by developing a companion R package (TopPICR). Key steps in the TopPICR pipeline include filtering identifications, inferring a minimal set of protein accessions explaining the observed sequences, aligning retention times, recalibrating measured masses, clustering features across data sets, and finally compiling feature intensities using the match-between-runs approach. The output of the pipeline is an MSnSet object which makes downstream data analysis seamlessly compatible with packages from the Bioconductor project. It also provides the capability for visualizing proteoforms within the context of the parent protein sequence. The functionality of TopPICR is demonstrated on top-down LC-MS/MS data sets of 10 human-in-mouse xenografts of luminal and basal breast tumor samples.
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Affiliation(s)
- Evan A Martin
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington99352, United States
| | - James M Fulcher
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington99352, United States
| | - Mowei Zhou
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington99352, United States
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington99352, United States
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington99352, United States
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16
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Eissman JM, Wells G, Khan OA, Liu D, Petyuk VA, Gifford KA, Dumitrescu L, Jefferson AL, Hohman TJ. Polygenic resilience score may be sensitive to preclinical Alzheimer's disease changes. Pac Symp Biocomput 2023; 28:449-460. [PMID: 36540999 PMCID: PMC9888419] [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] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Late-onset Alzheimer's disease (LOAD) is a polygenic disorder with a long prodromal phase, making early diagnosis challenging. Twin studies estimate LOAD as 60-80% heritable, and while common genetic variants can account for 30% of this heritability, nearly 70% remains "missing". Polygenic risk scores (PRS) leverage combined effects of many loci to predict LOAD risk, but often lack sensitivity to preclinical disease changes, limiting clinical utility. Our group has built and published on a resilience phenotype to model better-than-expected cognition give amyloid pathology burden and hypothesized it may assist in preclinical polygenic risk prediction. Thus, we built a LOAD PRS and a resilience PRS and evaluated both in predicting cognition in a dementia-free cohort (N=254). The LOAD PRS had a significant main effect on baseline memory (β=-0.18, P=1.68E-03). Both the LOAD PRS (β=-0.03, P=1.19E-03) and the resilience PRS (β=0.02, P=0.03) had significant main effects on annual memory decline. The resilience PRS interacted with CSF Aβ on baseline memory (β=-6.04E-04, P=0.02), whereby it predicted baseline memory among Aβ+ individuals (β=0.44, P=0.01) but not among Aβ- individuals (β=0.06, P=0.46). Excluding APOE from PRS resulted in mainly LOAD PRS associations attenuating, but notably the resilience PRS interaction with CSF Aβ and selective prediction among Aβ+ individuals was consistent. Although the resilience PRS is currently somewhat limited in scope from the phenotype's cross-sectional nature, our results suggest that the resilience PRS may be a promising tool in assisting in preclinical disease risk prediction among dementia-free and Aβ+ individuals, though replication and fine-tuning are needed.
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Affiliation(s)
- Jaclyn M. Eissman
- Vanderbilt Memory and Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, TN 37212, USA,Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37212, USA
| | - Greyson Wells
- Vanderbilt Memory and Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, TN 37212, USA
| | - Omair A. Khan
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37212, USA
| | - Dandan Liu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37212, USA
| | - Vladislav A. Petyuk
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest, National Laboratory, Richland, WA 99354, USA
| | - Katherine A. Gifford
- Vanderbilt Memory and Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, TN 37212, USA
| | - Logan Dumitrescu
- Vanderbilt Memory and Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, TN 37212, USA,Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37212, USA
| | - Angela L. Jefferson
- Vanderbilt Memory and Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, TN 37212, USA
| | - Timothy J. Hohman
- Vanderbilt Memory and Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, TN 37212, USA,Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37212, USA,
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17
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Eissman JM, Khan OA, Liu D, Petyuk VA, Gifford KA, Dumitrescu L, Jefferson AL, Hohman TJ. Cognitive resilience polygenic risk score sensitive to preclinical disease changes. Alzheimers Dement 2022. [DOI: 10.1002/alz.067701] [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)
- Jaclyn M. Eissman
- Vanderbilt Memory & Alzheimer’s Center, Vanderbilt University Medical Center Nashville TN USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center 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
| | - 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, Vanderbilt University Medical Center Nashville TN USA
| | - Logan Dumitrescu
- Vanderbilt Memory & Alzheimer’s Center, Vanderbilt University Medical Center Nashville TN USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center 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
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18
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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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19
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Iturria-Medina Y, Adewale Q, Khan AF, Ducharme S, Rosa-Neto P, O’Donnell K, Petyuk VA, Gauthier S, De Jager PL, Breitner J, Bennett DA. Unified epigenomic, transcriptomic, proteomic, and metabolomic taxonomy of Alzheimer's disease progression and heterogeneity. Sci Adv 2022; 8:eabo6764. [PMID: 36399579 PMCID: PMC9674284 DOI: 10.1126/sciadv.abo6764] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Alzheimer's disease (AD) is a heterogeneous disorder with abnormalities in multiple biological domains. In an advanced machine learning analysis of postmortem brain and in vivo blood multi-omics molecular data (N = 1863), we integrated epigenomic, transcriptomic, proteomic, and metabolomic profiles into a multilevel biological AD taxonomy. We obtained a personalized multilevel molecular index of AD dementia progression that predicts severity of neuropathologies, and identified three robust molecular-based subtypes that explain much of the pathologic and clinical heterogeneity of AD. These subtypes present distinct patterns of alteration in DNA methylation, RNA, proteins, and metabolites, identifiable in the brain and subsequently in blood. In addition, the genetic variations that predispose to the various AD subtypes in brain predict distinct spatial patterns of alteration in cell types, suggesting a unique influence of each putative AD variant on neuropathological mechanisms. These observations support that an individually tailored multi-omics molecular taxonomy of AD may represent distinct targets for preventive or treatment interventions.
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Affiliation(s)
- Yasser Iturria-Medina
- Neurology and Neurosurgery Department, Montreal Neurological Institute, Montreal, Canada
- McConnell Brain Imaging Centre, Montreal Neurological Institute, Montreal, Canada
- Ludmer Centre for Neuroinformatics and Mental Health, Montreal, Canada
| | - Quadri Adewale
- Neurology and Neurosurgery Department, Montreal Neurological Institute, Montreal, Canada
- McConnell Brain Imaging Centre, Montreal Neurological Institute, Montreal, Canada
- Ludmer Centre for Neuroinformatics and Mental Health, Montreal, Canada
| | - Ahmed F. Khan
- Neurology and Neurosurgery Department, Montreal Neurological Institute, Montreal, Canada
- McConnell Brain Imaging Centre, Montreal Neurological Institute, Montreal, Canada
- Ludmer Centre for Neuroinformatics and Mental Health, Montreal, Canada
| | - Simon Ducharme
- McConnell Brain Imaging Centre, Montreal Neurological Institute, Montreal, Canada
- Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, Canada
| | - Pedro Rosa-Neto
- McGill University Research Centre for Studies in Aging, Douglas Research Centre, Montreal, Canada
| | - Kieran O’Donnell
- Ludmer Centre for Neuroinformatics and Mental Health, Montreal, Canada
- Yale School of Medicine, New Haven, CT 06519, USA
| | - Vladislav A. Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Serge Gauthier
- McGill University Research Centre for Studies in Aging, Douglas Research Centre, Montreal, Canada
| | - Philip L. De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology and Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - John Breitner
- Centre for Studies on Prevention of Alzheimer’s Disease (StoP-AD), Douglas Research Centre, Montreal, Canada
- Department of Psychiatry, McGill University, Montreal, Canada
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL 60612, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL 60612, USA
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20
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Yu L, Hsieh YC, Pearse RV, Wang Y, Petyuk VA, Schneider JA, Buchman AS, Seyfried NT, De Jager PL, Young-Pearse TL, Bennett DA. Association of AK4 Protein From Stem Cell-Derived Neurons With Cognitive Reserve: An Autopsy Study. Neurology 2022; 99:e2264-e2274. [PMID: 35948448 PMCID: PMC9694839 DOI: 10.1212/wnl.0000000000201120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 07/01/2022] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND AND OBJECTIVES Identifying protein targets that provide cognitive reserve is a strategy to prevent and treat Alzheimer disease and Alzheimer disease related dementias (AD/ADRD). Previous studies using bulk human brain tissue reported 12 proteins associated with cognitive reserve. This study examined whether the same proteins from induced neurons (iNs) are associated with cognitive reserve of their human donors. METHODS Induced pluripotent stem cell (iPSC) lines were generated from cryopreserved peripheral blood mononuclear cells of older adults who were autopsied as part of the Religious Orders Study or Rush Memory and Aging Project. Neurons were induced from iPSCs using a standard neurogenin2 protocol. Tandem mass tag proteomics analyses were conducted on iNs day 21. Cognitive reserve of their human donors was measured as person-specific slopes of cognitive change not accounted for by common neuropathologies. RESULTS The 53 human donors died at a mean age of 91 years, all were non-Latino White, and 36 (67.9%) were female. Eighteen were diagnosed with Alzheimer dementia proximate to death, and 34 had pathologic AD diagnosis at autopsy. Approximately 60% of the donors had above-average cognitive reserve such that their cognition declined slower than an average person with comparable burdens of neuropathologies. Eight of the 12 candidate proteins were quantified in iNs proteomics analyses. Higher adenylate kinase 4 (AK4) expression in iNs was associated with lower cognitive reserve, consistent with the previous report for brain AK4 expression. DISCUSSION By replicating cortical protein associations with cognitive reserve in human iNs, these data provide a valuable molecular readout for studying complex clinical phenotypes such as cognitive reserve in a dish.
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Affiliation(s)
- Lei Yu
- From the Rush Alzheimer's Disease Center (L.Y., Y.W., J.A.S., A.S.B., D.A.B.) and Department of Neurological Sciences (L.Y., Y.W., J.A.S., A.S.B., D.A.B.), Rush University Medical Center, Chicago, IL; Ann Romney Center for Neurologic Diseases (Y.H., R.V.P., T.L.P.), Department of Neurology, Brigham and Women's Hospital, Boston, MA; Harvard Medical School (Y.H., R.V.P., T.L.P.), Boston, MA; Pacific Northwest National Laboratory (V.A.P.), Richland, WA; Department of Pathology (J.A.S.), Rush University Medical Center, Chicago, IL; Department of Biochemistry (N.T.S.), Emory University, Atlanta, GA; and Center for Translational and Computational Neuroimmunology (P.L.D.), Department of Neurology & Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York.
| | - Yi-Chen Hsieh
- From the Rush Alzheimer's Disease Center (L.Y., Y.W., J.A.S., A.S.B., D.A.B.) and Department of Neurological Sciences (L.Y., Y.W., J.A.S., A.S.B., D.A.B.), Rush University Medical Center, Chicago, IL; Ann Romney Center for Neurologic Diseases (Y.H., R.V.P., T.L.P.), Department of Neurology, Brigham and Women's Hospital, Boston, MA; Harvard Medical School (Y.H., R.V.P., T.L.P.), Boston, MA; Pacific Northwest National Laboratory (V.A.P.), Richland, WA; Department of Pathology (J.A.S.), Rush University Medical Center, Chicago, IL; Department of Biochemistry (N.T.S.), Emory University, Atlanta, GA; and Center for Translational and Computational Neuroimmunology (P.L.D.), Department of Neurology & Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York
| | - Richard V Pearse
- From the Rush Alzheimer's Disease Center (L.Y., Y.W., J.A.S., A.S.B., D.A.B.) and Department of Neurological Sciences (L.Y., Y.W., J.A.S., A.S.B., D.A.B.), Rush University Medical Center, Chicago, IL; Ann Romney Center for Neurologic Diseases (Y.H., R.V.P., T.L.P.), Department of Neurology, Brigham and Women's Hospital, Boston, MA; Harvard Medical School (Y.H., R.V.P., T.L.P.), Boston, MA; Pacific Northwest National Laboratory (V.A.P.), Richland, WA; Department of Pathology (J.A.S.), Rush University Medical Center, Chicago, IL; Department of Biochemistry (N.T.S.), Emory University, Atlanta, GA; and Center for Translational and Computational Neuroimmunology (P.L.D.), Department of Neurology & Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York
| | - Yanling Wang
- From the Rush Alzheimer's Disease Center (L.Y., Y.W., J.A.S., A.S.B., D.A.B.) and Department of Neurological Sciences (L.Y., Y.W., J.A.S., A.S.B., D.A.B.), Rush University Medical Center, Chicago, IL; Ann Romney Center for Neurologic Diseases (Y.H., R.V.P., T.L.P.), Department of Neurology, Brigham and Women's Hospital, Boston, MA; Harvard Medical School (Y.H., R.V.P., T.L.P.), Boston, MA; Pacific Northwest National Laboratory (V.A.P.), Richland, WA; Department of Pathology (J.A.S.), Rush University Medical Center, Chicago, IL; Department of Biochemistry (N.T.S.), Emory University, Atlanta, GA; and Center for Translational and Computational Neuroimmunology (P.L.D.), Department of Neurology & Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York
| | - Vladislav A Petyuk
- From the Rush Alzheimer's Disease Center (L.Y., Y.W., J.A.S., A.S.B., D.A.B.) and Department of Neurological Sciences (L.Y., Y.W., J.A.S., A.S.B., D.A.B.), Rush University Medical Center, Chicago, IL; Ann Romney Center for Neurologic Diseases (Y.H., R.V.P., T.L.P.), Department of Neurology, Brigham and Women's Hospital, Boston, MA; Harvard Medical School (Y.H., R.V.P., T.L.P.), Boston, MA; Pacific Northwest National Laboratory (V.A.P.), Richland, WA; Department of Pathology (J.A.S.), Rush University Medical Center, Chicago, IL; Department of Biochemistry (N.T.S.), Emory University, Atlanta, GA; and Center for Translational and Computational Neuroimmunology (P.L.D.), Department of Neurology & Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York
| | - Julie A Schneider
- From the Rush Alzheimer's Disease Center (L.Y., Y.W., J.A.S., A.S.B., D.A.B.) and Department of Neurological Sciences (L.Y., Y.W., J.A.S., A.S.B., D.A.B.), Rush University Medical Center, Chicago, IL; Ann Romney Center for Neurologic Diseases (Y.H., R.V.P., T.L.P.), Department of Neurology, Brigham and Women's Hospital, Boston, MA; Harvard Medical School (Y.H., R.V.P., T.L.P.), Boston, MA; Pacific Northwest National Laboratory (V.A.P.), Richland, WA; Department of Pathology (J.A.S.), Rush University Medical Center, Chicago, IL; Department of Biochemistry (N.T.S.), Emory University, Atlanta, GA; and Center for Translational and Computational Neuroimmunology (P.L.D.), Department of Neurology & Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York
| | - Aron S Buchman
- From the Rush Alzheimer's Disease Center (L.Y., Y.W., J.A.S., A.S.B., D.A.B.) and Department of Neurological Sciences (L.Y., Y.W., J.A.S., A.S.B., D.A.B.), Rush University Medical Center, Chicago, IL; Ann Romney Center for Neurologic Diseases (Y.H., R.V.P., T.L.P.), Department of Neurology, Brigham and Women's Hospital, Boston, MA; Harvard Medical School (Y.H., R.V.P., T.L.P.), Boston, MA; Pacific Northwest National Laboratory (V.A.P.), Richland, WA; Department of Pathology (J.A.S.), Rush University Medical Center, Chicago, IL; Department of Biochemistry (N.T.S.), Emory University, Atlanta, GA; and Center for Translational and Computational Neuroimmunology (P.L.D.), Department of Neurology & Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York
| | - Nicholas T Seyfried
- From the Rush Alzheimer's Disease Center (L.Y., Y.W., J.A.S., A.S.B., D.A.B.) and Department of Neurological Sciences (L.Y., Y.W., J.A.S., A.S.B., D.A.B.), Rush University Medical Center, Chicago, IL; Ann Romney Center for Neurologic Diseases (Y.H., R.V.P., T.L.P.), Department of Neurology, Brigham and Women's Hospital, Boston, MA; Harvard Medical School (Y.H., R.V.P., T.L.P.), Boston, MA; Pacific Northwest National Laboratory (V.A.P.), Richland, WA; Department of Pathology (J.A.S.), Rush University Medical Center, Chicago, IL; Department of Biochemistry (N.T.S.), Emory University, Atlanta, GA; and Center for Translational and Computational Neuroimmunology (P.L.D.), Department of Neurology & Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York
| | - Philip L De Jager
- From the Rush Alzheimer's Disease Center (L.Y., Y.W., J.A.S., A.S.B., D.A.B.) and Department of Neurological Sciences (L.Y., Y.W., J.A.S., A.S.B., D.A.B.), Rush University Medical Center, Chicago, IL; Ann Romney Center for Neurologic Diseases (Y.H., R.V.P., T.L.P.), Department of Neurology, Brigham and Women's Hospital, Boston, MA; Harvard Medical School (Y.H., R.V.P., T.L.P.), Boston, MA; Pacific Northwest National Laboratory (V.A.P.), Richland, WA; Department of Pathology (J.A.S.), Rush University Medical Center, Chicago, IL; Department of Biochemistry (N.T.S.), Emory University, Atlanta, GA; and Center for Translational and Computational Neuroimmunology (P.L.D.), Department of Neurology & Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York
| | - Tracy L Young-Pearse
- From the Rush Alzheimer's Disease Center (L.Y., Y.W., J.A.S., A.S.B., D.A.B.) and Department of Neurological Sciences (L.Y., Y.W., J.A.S., A.S.B., D.A.B.), Rush University Medical Center, Chicago, IL; Ann Romney Center for Neurologic Diseases (Y.H., R.V.P., T.L.P.), Department of Neurology, Brigham and Women's Hospital, Boston, MA; Harvard Medical School (Y.H., R.V.P., T.L.P.), Boston, MA; Pacific Northwest National Laboratory (V.A.P.), Richland, WA; Department of Pathology (J.A.S.), Rush University Medical Center, Chicago, IL; Department of Biochemistry (N.T.S.), Emory University, Atlanta, GA; and Center for Translational and Computational Neuroimmunology (P.L.D.), Department of Neurology & Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York
| | - David A Bennett
- From the Rush Alzheimer's Disease Center (L.Y., Y.W., J.A.S., A.S.B., D.A.B.) and Department of Neurological Sciences (L.Y., Y.W., J.A.S., A.S.B., D.A.B.), Rush University Medical Center, Chicago, IL; Ann Romney Center for Neurologic Diseases (Y.H., R.V.P., T.L.P.), Department of Neurology, Brigham and Women's Hospital, Boston, MA; Harvard Medical School (Y.H., R.V.P., T.L.P.), Boston, MA; Pacific Northwest National Laboratory (V.A.P.), Richland, WA; Department of Pathology (J.A.S.), Rush University Medical Center, Chicago, IL; Department of Biochemistry (N.T.S.), Emory University, Atlanta, GA; and Center for Translational and Computational Neuroimmunology (P.L.D.), Department of Neurology & Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York
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21
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Xu G, Grimes TD, Grayson TB, Chen J, Thielen LA, Tse HM, Li P, Kanke M, Lin TT, Schepmoes AA, Swensen AC, Petyuk VA, Ovalle F, Sethupathy P, Qian WJ, Shalev A. Exploratory study reveals far reaching systemic and cellular effects of verapamil treatment in subjects with type 1 diabetes. Nat Commun 2022; 13:1159. [PMID: 35241690 PMCID: PMC8894430 DOI: 10.1038/s41467-022-28826-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 02/07/2022] [Indexed: 02/06/2023] Open
Abstract
Currently, no oral medications are available for type 1 diabetes (T1D). While our recent randomized placebo-controlled T1D trial revealed that oral verapamil had short-term beneficial effects, their duration and underlying mechanisms remained elusive. Now, our global T1D serum proteomics analysis identified chromogranin A (CHGA), a T1D-autoantigen, as the top protein altered by verapamil and as a potential therapeutic marker and revealed that verapamil normalizes serum CHGA levels and reverses T1D-induced elevations in circulating proinflammatory T-follicular-helper cell markers. RNA-sequencing further confirmed that verapamil regulates the thioredoxin system and promotes an anti-oxidative, anti-apoptotic and immunomodulatory gene expression profile in human islets. Moreover, continuous use of oral verapamil delayed T1D progression, promoted endogenous beta-cell function and lowered insulin requirements and serum CHGA levels for at least 2 years and these benefits were lost upon discontinuation. Thus, the current studies provide crucial mechanistic and clinical insight into the beneficial effects of verapamil in T1D.
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Affiliation(s)
- Guanlan Xu
- Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.,Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Tiffany D Grimes
- Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.,Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Truman B Grayson
- Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.,Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Junqin Chen
- Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.,Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Lance A Thielen
- Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.,Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Hubert M Tse
- Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.,Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Peng Li
- Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.,School of Nursing, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Matt Kanke
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Tai-Tu Lin
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Athena A Schepmoes
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Adam C Swensen
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Fernando Ovalle
- Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.,Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Praveen Sethupathy
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Anath Shalev
- Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, 35294, USA. .,Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
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22
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Sanford J, Wang Y, Hansen JR, Gritsenko MA, Weitz KK, Sagendorf TJ, Tognon CE, Petyuk VA, Qian WJ, Liu T, Druker BJ, Rodland KD, Piehowski PD. Evaluation of Differential Peptide Loading on Tandem Mass Tag-Based Proteomic and Phosphoproteomic Data Quality. J Am Soc Mass Spectrom 2022; 33:17-30. [PMID: 34813325 PMCID: PMC8739833 DOI: 10.1021/jasms.1c00169] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 10/27/2021] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
Global and phosphoproteome profiling has demonstrated great utility for the analysis of clinical specimens. One barrier to the broad clinical application of proteomic profiling is the large amount of biological material required, particularly for phosphoproteomics─currently on the order of 25 mg wet tissue weight. For hematopoietic cancers such as acute myeloid leukemia (AML), the sample requirement is ≥10 million peripheral blood mononuclear cells (PBMCs). Across large study cohorts, this requirement will exceed what is obtainable for many individual patients/time points. For this reason, we were interested in the impact of differential peptide loading across multiplex channels on proteomic data quality. To achieve this, we tested a range of channel loading amounts (approximately the material obtainable from 5E5, 1E6, 2.5E6, 5E6, and 1E7 AML patient cells) to assess proteome coverage, quantification precision, and peptide/phosphopeptide detection in experiments utilizing isobaric tandem mass tag (TMT) labeling. As expected, fewer missing values were observed in TMT channels with higher peptide loading amounts compared to lower loadings. Moreover, channels with a lower loading have greater quantitative variability than channels with higher loadings. A statistical analysis showed that decreased loading amounts result in an increase in the type I error rate. We then examined the impact of differential loading on the detection of known differences between distinct AML cell lines. Similar patterns of increased data missingness and higher quantitative variability were observed as loading was decreased resulting in fewer statistical differences; however, we found good agreement in features identified as differential, demonstrating the value of this approach.
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Affiliation(s)
- James
A. Sanford
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Yang Wang
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Joshua R. Hansen
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Marina A. Gritsenko
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Karl K. Weitz
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Tyler J. Sagendorf
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Cristina E. Tognon
- Knight
Cancer Institute, Oregon Health & Science
University, Portland, Oregon 97239, United States
- Division
of Hematology and Medical Oncology, Oregon
Health & Science University, Portland, Oregon 97239, United States
| | - Vladislav A. Petyuk
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Wei-Jun Qian
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Tao Liu
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Brian J. Druker
- Knight
Cancer Institute, Oregon Health & Science
University, Portland, Oregon 97239, United States
- Division
of Hematology and Medical Oncology, Oregon
Health & Science University, Portland, Oregon 97239, United States
| | - Karin D. Rodland
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
- Knight
Cancer Institute, Oregon Health & Science
University, Portland, Oregon 97239, United States
| | - Paul D. Piehowski
- Environmental
Molecular Sciences Division, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
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23
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Reyes BC, Otero-Muras I, Petyuk VA. A numerical approach for detecting switch-like bistability in mass action chemical reaction networks with conservation laws. BMC Bioinformatics 2022; 23:1. [PMID: 34983366 PMCID: PMC8725470 DOI: 10.1186/s12859-021-04477-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 11/11/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Theoretical analysis of signaling pathways can provide a substantial amount of insight into their function. One particular area of research considers signaling pathways capable of assuming two or more stable states given the same amount of signaling ligand. This phenomenon of bistability can give rise to switch-like behavior, a mechanism that governs cellular decision making. Investigation of whether or not a signaling pathway can confer bistability and switch-like behavior, without knowledge of specific kinetic rate constant values, is a mathematically challenging problem. Recently a technique based on optimization has been introduced, which is capable of finding example parameter values that confer switch-like behavior for a given pathway. Although this approach has made it possible to analyze moderately sized pathways, it is limited to reaction networks that presume a uniterminal structure. It is this limited structure we address by developing a general technique that applies to any mass action reaction network with conservation laws. RESULTS In this paper we developed a generalized method for detecting switch-like bistable behavior in any mass action reaction network with conservation laws. The method involves (1) construction of a constrained optimization problem using the determinant of the Jacobian of the underlying rate equations, (2) minimization of the objective function to search for conditions resulting in a zero eigenvalue, (3) computation of a confidence level that describes if the global minimum has been found and (4) evaluation of optimization values, using either numerical continuation or directly simulating the ODE system, to verify that a bistability region exists. The generalized method has been tested on three motifs known to be capable of bistability. CONCLUSIONS We have developed a variation of an optimization-based method for the discovery of bistability, which is not limited to uniterminal chemical reaction networks. Successful completion of the method provides an S-shaped bifurcation diagram, which indicates that the network acts as a bistable switch for the given optimization parameters.
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Affiliation(s)
- Brandon C Reyes
- Advanced Computing, Math, and Data Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Irene Otero-Muras
- BioProcess Engineering Group, IIM-CSIC (Spanish National Research Council), 36208, Vigo, Spain
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
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24
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Carlyle BC, Kandigian SE, Kreuzer J, Das S, Trombetta BA, Kuo Y, Bennett DA, Schneider JA, Petyuk VA, Kitchen RR, Morris R, Nairn AC, Hyman BT, Haas W, Arnold SE. Synaptic proteins associated with cognitive performance and neuropathology in older humans revealed by multiplexed fractionated proteomics. Neurobiol Aging 2021; 105:99-114. [PMID: 34052751 PMCID: PMC8338777 DOI: 10.1016/j.neurobiolaging.2021.04.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/18/2021] [Accepted: 04/14/2021] [Indexed: 12/16/2022]
Abstract
Alzheimer's disease (AD) is defined by the presence of abundant amyloid-β (Aβ) and tau neuropathology. While this neuropathology is necessary for AD diagnosis, it is not sufficient for causing cognitive impairment. Up to one third of community dwelling older adults harbor intermediate to high levels of AD neuropathology at death yet demonstrate no significant cognitive impairment. Conversely, there are individuals who exhibit dementia with no gross explanatory neuropathology. In prior studies, synapse loss correlated with cognitive impairment. To understand how synaptic composition changes in relation to neuropathology and cognition, multiplexed liquid chromatography mass-spectrometry was used to quantify enriched synaptic proteins from the parietal association cortex of 100 subjects with contrasting levels of AD pathology and cognitive performance. 123 unique proteins were significantly associated with diagnostic category. Functional analysis showed enrichment of serotonin release and oxidative phosphorylation categories in normal (cognitively unimpaired, low neuropathology) and "resilient" (unimpaired despite AD pathology) individuals. In contrast, frail individuals, (low pathology, impaired cognition) showed a metabolic shift towards glycolysis and increased presence of proteasome subunits.
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Affiliation(s)
- Becky C Carlyle
- Massachusetts General Hospital Department of Neurology, Charlestown, MA, USA; Harvard Medical School, Boston, MA, USA.
| | - Savannah E Kandigian
- Massachusetts General Hospital Department of Neurology, Charlestown, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Johannes Kreuzer
- Harvard Medical School, Boston, MA, USA; Massachusetts General Hospital Cancer Center, Charlestown, MA, USA
| | - Sudeshna Das
- Massachusetts General Hospital Department of Neurology, Charlestown, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Bianca A Trombetta
- Massachusetts General Hospital Department of Neurology, Charlestown, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Yikai Kuo
- Massachusetts General Hospital Department of Neurology, Charlestown, MA, USA; Harvard Medical School, Boston, MA, USA; Massachusetts General Hospital, Cardiology Division, Charlestown, MA, USA
| | | | | | | | - Robert R Kitchen
- Harvard Medical School, Boston, MA, USA; Massachusetts General Hospital, Cardiology Division, Charlestown, MA, USA
| | - Robert Morris
- Harvard Medical School, Boston, MA, USA; Massachusetts General Hospital Cancer Center, Charlestown, MA, USA
| | | | - Bradley T Hyman
- Massachusetts General Hospital Department of Neurology, Charlestown, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Wilhelm Haas
- Harvard Medical School, Boston, MA, USA; Massachusetts General Hospital Cancer Center, Charlestown, MA, USA
| | - Steven E Arnold
- Massachusetts General Hospital Department of Neurology, Charlestown, MA, USA; Harvard Medical School, Boston, MA, USA
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25
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Petyuk VA, Yu L, Olson HM, Yu F, Clair G, Qian WJ, Shulman JM, Bennett DA. Proteomic Profiling of the Substantia Nigra to Identify Determinants of Lewy Body Pathology and Dopaminergic Neuronal Loss. J Proteome Res 2021; 20:2266-2282. [PMID: 33900085 PMCID: PMC9190253 DOI: 10.1021/acs.jproteome.0c00747] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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] [Indexed: 11/29/2022]
Abstract
Proteinaceous aggregates containing α-synuclein protein called Lewy bodies in the substantia nigra is a hallmark of Parkinson's disease. The molecular mechanisms of Lewy body formation and associated neuronal loss remain largely unknown. To gain insights into proteins and pathways associated with Lewy body pathology, we performed quantitative profiling of the proteome. We analyzed substantia nigra tissue from 51 subjects arranged into three groups: cases with Lewy body pathology, Lewy body-negative controls with matching neuronal loss, and controls with no neuronal loss. Using a label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS) approach, we characterized the proteome both in terms of protein abundances and peptide modifications. Statistical testing for differential abundance of the most abundant 2963 proteins, followed by pathway enrichment and Bayesian learning of the causal network structure, was performed to identify likely drivers of Lewy body formation and dopaminergic neuronal loss. The identified pathways include (1) Arp2/3 complex-mediated actin nucleation; (2) synaptic function; (3) poly(A) RNA binding; (4) basement membrane and endothelium; and (5) hydrogen peroxide metabolic process. According to the data, the endothelial/basement membrane pathway is tightly connected with both pathologies and likely to be one of the drivers of neuronal loss. The poly(A) RNA-binding proteins, including the ones relevant to other neurodegenerative disorders (e.g., TDP-43 and FUS), have a strong inverse correlation with Lewy bodies and may reflect an alternative mechanism of nigral neurodegeneration.
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Affiliation(s)
- Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MSIN: K8-98, Richland, Washington 99352, United States
| | - Lei Yu
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois 60612, United States
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois 60612, United States
| | - Heather M Olson
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Geremy Clair
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MSIN: K8-98, Richland, Washington 99352, United States
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MSIN: K8-98, Richland, Washington 99352, United States
| | - Joshua M Shulman
- Departments of Neurology, Molecular & Human Genetics, and Neuroscience, Baylor College of Medicine, Houston, Texas 77030, United States
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030, United States
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois 60612, United States
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois 60612, United States
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26
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Abstract
Proteomic investigations of Alzheimer's and Parkinson's disease have provided valuable insights into neurodegenerative disorders. Thus far, these investigations have largely been restricted to bottom-up approaches, hindering the degree to which one can characterize a protein's "intact" state. Top-down proteomics (TDP) overcomes this limitation; however, it is typically limited to observing only the most abundant proteoforms and of a relatively small size. Therefore, fractionation techniques are commonly used to reduce sample complexity. Here, we investigate gas-phase fractionation through high-field asymmetric waveform ion mobility spectrometry (FAIMS) within TDP. Utilizing a high complexity sample derived from Alzheimer's disease (AD) brain tissue, we describe how the addition of FAIMS to TDP can robustly improve the depth of proteome coverage. For example, implementation of FAIMS with external compensation voltage (CV) stepping at -50, -40, and -30 CV could more than double the mean number of non-redundant proteoforms, genes, and proteome sequence coverage compared to without FAIMS. We also found that FAIMS can influence the transmission of proteoforms and their charge envelopes based on their size. Importantly, FAIMS enabled the identification of intact amyloid beta (Aβ) proteoforms, including the aggregation-prone Aβ1-42 variant which is strongly linked to AD. Raw data and associated files have been deposited to the ProteomeXchange Consortium via the MassIVE data repository with data set identifier PXD023607.
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Affiliation(s)
- James M Fulcher
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Aman Makaju
- Life Sciences Mass Spectrometry Unit, Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois 60612, United States
| | - Philip L De Jager
- Department of Neurology, Center for Translational & Computational Neuroimmunology, Columbia University Medical Center, New York, New York 10032, United States
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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27
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Wang LB, Karpova A, Gritsenko MA, Kyle JE, Cao S, Li Y, Rykunov D, Colaprico A, Rothstein JH, Hong R, Stathias V, Cornwell M, Petralia F, Wu Y, Reva B, Krug K, Pugliese P, Kawaler E, Olsen LK, Liang WW, Song X, Dou Y, Wendl MC, Caravan W, Liu W, Cui Zhou D, Ji J, Tsai CF, Petyuk VA, Moon J, Ma W, Chu RK, Weitz KK, Moore RJ, Monroe ME, Zhao R, Yang X, Yoo S, Krek A, Demopoulos A, Zhu H, Wyczalkowski MA, McMichael JF, Henderson BL, Lindgren CM, Boekweg H, Lu S, Baral J, Yao L, Stratton KG, Bramer LM, Zink E, Couvillion SP, Bloodsworth KJ, Satpathy S, Sieh W, Boca SM, Schürer S, Chen F, Wiznerowicz M, Ketchum KA, Boja ES, Kinsinger CR, Robles AI, Hiltke T, Thiagarajan M, Nesvizhskii AI, Zhang B, Mani DR, Ceccarelli M, Chen XS, Cottingham SL, Li QK, Kim AH, Fenyö D, Ruggles KV, Rodriguez H, Mesri M, Payne SH, Resnick AC, Wang P, Smith RD, Iavarone A, Chheda MG, Barnholtz-Sloan JS, Rodland KD, Liu T, Ding L. Proteogenomic and metabolomic characterization of human glioblastoma. Cancer Cell 2021; 39:509-528.e20. [PMID: 33577785 PMCID: PMC8044053 DOI: 10.1016/j.ccell.2021.01.006] [Citation(s) in RCA: 275] [Impact Index Per Article: 91.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 06/02/2020] [Accepted: 01/11/2021] [Indexed: 02/07/2023]
Abstract
Glioblastoma (GBM) is the most aggressive nervous system cancer. Understanding its molecular pathogenesis is crucial to improving diagnosis and treatment. Integrated analysis of genomic, proteomic, post-translational modification and metabolomic data on 99 treatment-naive GBMs provides insights to GBM biology. We identify key phosphorylation events (e.g., phosphorylated PTPN11 and PLCG1) as potential switches mediating oncogenic pathway activation, as well as potential targets for EGFR-, TP53-, and RB1-altered tumors. Immune subtypes with distinct immune cell types are discovered using bulk omics methodologies, validated by snRNA-seq, and correlated with specific expression and histone acetylation patterns. Histone H2B acetylation in classical-like and immune-low GBM is driven largely by BRDs, CREBBP, and EP300. Integrated metabolomic and proteomic data identify specific lipid distributions across subtypes and distinct global metabolic changes in IDH-mutated tumors. This work highlights biological relationships that could contribute to stratification of GBM patients for more effective treatment.
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Affiliation(s)
- Liang-Bo Wang
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Alla Karpova
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Marina A Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Jennifer E Kyle
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Song Cao
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Yize Li
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Dmitry Rykunov
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Antonio Colaprico
- Sylvester Comprehensive Cancer Center, University of Miami, FL 33136, USA; Division of Biostatistics, Department of Public Health Science, University of Miami, FL 33136, USA
| | - Joseph H Rothstein
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Runyu Hong
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Vasileios Stathias
- Sylvester Comprehensive Cancer Center, University of Miami, FL 33136, USA; Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA; BD2K-LINCS Data Coordination and Integration Center, Miami, FL 33136, USA
| | - MacIntosh Cornwell
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yige Wu
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Boris Reva
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Karsten Krug
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Pietro Pugliese
- Department of Science and Technology, University of Sannio, 82100, Benevento, Italy
| | - Emily Kawaler
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Lindsey K Olsen
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Wen-Wei Liang
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Xiaoyu Song
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yongchao Dou
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael C Wendl
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Mathematics, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Wagma Caravan
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Wenke Liu
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Daniel Cui Zhou
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Jiayi Ji
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Jamie Moon
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Weiping Ma
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rosalie K Chu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Karl K Weitz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Rui Zhao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Xiaolu Yang
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; Poznań University of Medical Sciences, 61-701 Poznań, Poland
| | - Seungyeul Yoo
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alexis Demopoulos
- Department of Neurology, Northwell Health System, Lake Success, NY 11042 USA
| | - Houxiang Zhu
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Matthew A Wyczalkowski
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Joshua F McMichael
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | | | - Caleb M Lindgren
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Hannah Boekweg
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Shuangjia Lu
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Jessika Baral
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Lijun Yao
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Kelly G Stratton
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Lisa M Bramer
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Erika Zink
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Sneha P Couvillion
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Kent J Bloodsworth
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Shankha Satpathy
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Weiva Sieh
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Simina M Boca
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Stephan Schürer
- Sylvester Comprehensive Cancer Center, University of Miami, FL 33136, USA; Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA; BD2K-LINCS Data Coordination and Integration Center, Miami, FL 33136, USA; Institute for Data Science & Computing, University of Miami, FL 33136, USA
| | - Feng Chen
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, MO 63130, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Maciej Wiznerowicz
- International Institute for Molecular Oncology, 60-203 Poznań, Poland; Poznań University of Medical Sciences, 61-701 Poznań, Poland
| | | | - Emily S Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Christopher R Kinsinger
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | | | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - D R Mani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Michele Ceccarelli
- Department of Electrical Engineering and Information Technology, University of Naples "Federico II", 80128, Naples, Italy; BIOGEM, 83031 Ariano Irpino, Italy
| | - Xi S Chen
- Sylvester Comprehensive Cancer Center, University of Miami, FL 33136, USA; Division of Biostatistics, Department of Public Health Science, University of Miami, FL 33136, USA
| | - Sandra L Cottingham
- Department of Pathology, Spectrum Health and Helen DeVos Children's Hospital, Grand Rapids, MI 49503, USA
| | - Qing Kay Li
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Albert H Kim
- Department of Neurological Surgery, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - David Fenyö
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Kelly V Ruggles
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Samuel H Payne
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Adam C Resnick
- Center for Data Driven Discovery in Biomedicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Antonio Iavarone
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY 10032, USA; Department of Neurology, Columbia University Medical Center, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Milan G Chheda
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Neurology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Jill S Barnholtz-Sloan
- Case Comprehensive Cancer Center and Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Research and Education, University Hospitals Health System, Cleveland, OH 44106, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR 97221, USA.
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
| | - Li Ding
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63130, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63130, USA.
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28
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Petralia F, Tignor N, Reva B, Koptyra M, Chowdhury S, Rykunov D, Krek A, Ma W, Zhu Y, Ji J, Calinawan A, Whiteaker JR, Colaprico A, Stathias V, Omelchenko T, Song X, Raman P, Guo Y, Brown MA, Ivey RG, Szpyt J, Guha Thakurta S, Gritsenko MA, Weitz KK, Lopez G, Kalayci S, Gümüş ZH, Yoo S, da Veiga Leprevost F, Chang HY, Krug K, Katsnelson L, Wang Y, Kennedy JJ, Voytovich UJ, Zhao L, Gaonkar KS, Ennis BM, Zhang B, Baubet V, Tauhid L, Lilly JV, Mason JL, Farrow B, Young N, Leary S, Moon J, Petyuk VA, Nazarian J, Adappa ND, Palmer JN, Lober RM, Rivero-Hinojosa S, Wang LB, Wang JM, Broberg M, Chu RK, Moore RJ, Monroe ME, Zhao R, Smith RD, Zhu J, Robles AI, Mesri M, Boja E, Hiltke T, Rodriguez H, Zhang B, Schadt EE, Mani DR, Ding L, Iavarone A, Wiznerowicz M, Schürer S, Chen XS, Heath AP, Rokita JL, Nesvizhskii AI, Fenyö D, Rodland KD, Liu T, Gygi SP, Paulovich AG, Resnick AC, Storm PB, Rood BR, Wang P. Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer. Cell 2020; 183:1962-1985.e31. [PMID: 33242424 PMCID: PMC8143193 DOI: 10.1016/j.cell.2020.10.044] [Citation(s) in RCA: 152] [Impact Index Per Article: 38.0] [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: 12/18/2019] [Revised: 06/19/2020] [Accepted: 10/26/2020] [Indexed: 02/06/2023]
Abstract
We report a comprehensive proteogenomics analysis, including whole-genome sequencing, RNA sequencing, and proteomics and phosphoproteomics profiling, of 218 tumors across 7 histological types of childhood brain cancer: low-grade glioma (n = 93), ependymoma (32), high-grade glioma (25), medulloblastoma (22), ganglioglioma (18), craniopharyngioma (16), and atypical teratoid rhabdoid tumor (12). Proteomics data identify common biological themes that span histological boundaries, suggesting that treatments used for one histological type may be applied effectively to other tumors sharing similar proteomics features. Immune landscape characterization reveals diverse tumor microenvironments across and within diagnoses. Proteomics data further reveal functional effects of somatic mutations and copy number variations (CNVs) not evident in transcriptomics data. Kinase-substrate association and co-expression network analysis identify important biological mechanisms of tumorigenesis. This is the first large-scale proteogenomics analysis across traditional histological boundaries to uncover foundational pediatric brain tumor biology and inform rational treatment selection.
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Affiliation(s)
- Francesca Petralia
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nicole Tignor
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Boris Reva
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mateusz Koptyra
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Shrabanti Chowdhury
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dmitry Rykunov
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Weiping Ma
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yuankun Zhu
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jiayi Ji
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anna Calinawan
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Antonio Colaprico
- Department of Public Health Science, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Vasileios Stathias
- Department of Pharmacology, Institute for Data Science and Computing, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33146, USA
| | - Tatiana Omelchenko
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Xiaoyu Song
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Pichai Raman
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yiran Guo
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Miguel A Brown
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Richard G Ivey
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - John Szpyt
- Thermo Fisher Scientific Center for Multiplexed Proteomics, Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Sanjukta Guha Thakurta
- Thermo Fisher Scientific Center for Multiplexed Proteomics, Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Marina A Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Karl K Weitz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Gonzalo Lopez
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Selim Kalayci
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zeynep H Gümüş
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Seungyeul Yoo
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Hui-Yin Chang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Karsten Krug
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02412, USA
| | - Lizabeth Katsnelson
- Institute for Systems Genetics; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Ying Wang
- Institute for Systems Genetics; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Jacob J Kennedy
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - Lei Zhao
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Krutika S Gaonkar
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Brian M Ennis
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Bo Zhang
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Valerie Baubet
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Lamiya Tauhid
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jena V Lilly
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jennifer L Mason
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Bailey Farrow
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nathan Young
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sarah Leary
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Cancer and Blood Disorders Center, Seattle Children's Hospital, Seattle, WA 98105, USA; Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Jamie Moon
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Javad Nazarian
- Children's National Research Institute, George Washington University School of Medicine, Washington, DC 20010, USA; Department of Oncology, Children's Research Center, University Children's Hospital Zürich, Zürich 8032, Switzerland
| | - Nithin D Adappa
- Department of Otorhinolaryngology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James N Palmer
- Department of Otorhinolaryngology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robert M Lober
- Department of Neurosurgery, Dayton Children's Hospital, Dayton, OH 45404, USA
| | - Samuel Rivero-Hinojosa
- Children's National Research Institute, George Washington University School of Medicine, Washington, DC 20010, USA
| | - Liang-Bo Wang
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Joshua M Wang
- Institute for Systems Genetics; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Matilda Broberg
- Institute for Systems Genetics; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Rosalie K Chu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Rui Zhao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Jun Zhu
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Emily Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - D R Mani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02412, USA
| | - Li Ding
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Antonio Iavarone
- Institute for Cancer Genetics, Department of Neurology, Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Maciej Wiznerowicz
- Poznan University of Medical Sciences, 61-701 Poznań, Poland; International Institute for Molecular Oncology, 61-203 Poznań, Poland
| | - Stephan Schürer
- Department of Pharmacology, Institute for Data Science and Computing, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33146, USA
| | - Xi S Chen
- Department of Public Health Science, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Allison P Heath
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jo Lynne Rokita
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - David Fenyö
- Institute for Systems Genetics; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR 97221, USA
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Steven P Gygi
- Thermo Fisher Scientific Center for Multiplexed Proteomics, Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Adam C Resnick
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
| | - Phillip B Storm
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
| | - Brian R Rood
- Children's National Research Institute, George Washington University School of Medicine, Washington, DC 20010, USA.
| | - Pei Wang
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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29
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Moore AM, Mahoney ER, Dumitrescu L, De Jager PL, Koran MEI, Petyuk VA, Robinson RA, Ruderfer DM, Cox NJ, Schneider JA, Bennett DA, Jefferson AL, Hohman TJ. Single nucleus and bulk homogenate RNA‐sequencing comparison of vascular endothelial growth factor family associations with Alzheimer's disease. Alzheimers Dement 2020. [DOI: 10.1002/alz.046170] [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: 11/06/2022]
Affiliation(s)
| | | | | | | | | | - Vladislav A. Petyuk
- Biological Sciences Division and Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory Richland, WA, USA Richland WA USA
| | | | | | - Nancy J. Cox
- Vanderbilt University Medical Center Nashville TN USA
| | - Julie A. Schneider
- Rush Alzheimer’s Disease Center Rush University Medical Center Chicago IL USA
| | - David A. Bennett
- Rush Alzheimer’s Disease Center Rush University Medical Center Chicago IL USA
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30
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Abstract
The majority of methods for detecting differentially abundant proteins between samples in label-free LC-MS bottom-up proteomics experiments rely on statistically testing inferred protein abundances derived from peptide ionization intensities or averaging peptide level statistics. Here, we statistically test peptide ionization intensities directly and combine the resulting dependent P-values using the Empirical Brown's Method (EBM), avoiding error introduced through the estimation of protein abundances or summarizing test statistics. We show that on a spike-in proteomics dataset, a peptide level approach using EBM outperforms differential abundance detection using a protein level approach and several analysis workflows, including MSstats. Additionally, we demonstrate the effectiveness of this approach by detecting enriched proteins from an activity-based protein profiling dataset.
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Affiliation(s)
- Bryan J Killinger
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
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31
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Johnson EC, Dammer EB, Duong D, 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, Jager PL, Bennett DA, Wingo TS, Rangaraju S, Hajjar I, Shulman JM, Lah JJ, Levey AI, Seyfried NT. A consensus proteomic analysis of Alzheimer’s disease brain and cerebrospinal fluid reveals early changes in energy metabolism associated with microglia and astrocyte activation. Alzheimers Dement 2020. [DOI: 10.1002/alz.039504] [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: 11/11/2022]
Affiliation(s)
| | | | - Duc Duong
- Emory University School of Medicine Atlanta GA USA
| | - Lingyan Ping
- Emory University School of Medicine Atlanta GA USA
| | - Maotian Zhou
- Emory University School of Medicine Atlanta GA USA
| | - Luming Yin
- Emory University School of Medicine Atlanta GA USA
| | | | | | | | | | | | | | - Eddie B. Lee
- Center for Neurodegenerative Disease Research University of Pennsylvania Philadelphia PA USA
| | - John Q. Trojanowski
- Center for Neurodegenerative Disease Research University of Pennsylvania Philadelphia PA USA
| | | | | | | | - Minghui Wang
- Icahn School of Medicine at Mount Sinai New York NY USA
| | - Eric Schadt
- Icahn School of Medicine at Mount Sinai New York NY USA
| | - Bin Zhang
- Icahn Institute for Data Science and Genomic Technology New York NY USA
| | | | | | | | - Vladislav A. Petyuk
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory Richland WA USA
| | | | - David A. Bennett
- Rush Alzheimer's Disease Center Rush University Medical Center Chicago IL USA
| | | | | | - Ihab Hajjar
- Emory University School of Medicine Atlanta GA USA
| | | | - James J. Lah
- Emory University School of Medicine Atlanta GA USA
| | - Allan I. Levey
- Emory Goizueta Alzheimer's Disease Research Center Atlanta GA USA
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32
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Li S, Weinstein G, Zare H, Teumer A, Völker U, Friedrich N, Knol MJ, Satizabal CL, Petyuk VA, Adams HHH, Launer LJ, Bennett DA, De Jager PL, Grabe HJ, Ikram MA, Gudnason V, Yang Q, Seshadri S. The genetics of circulating BDNF: towards understanding the role of BDNF in brain structure and function in middle and old ages. Brain Commun 2020; 2:fcaa176. [PMID: 33345186 PMCID: PMC7734441 DOI: 10.1093/braincomms/fcaa176] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 01/04/2023] Open
Abstract
Brain-derived neurotrophic factor (BDNF) plays an important role in brain development and function. Substantial amounts of BDNF are present in peripheral blood, and may serve as biomarkers for Alzheimer’s disease incidence as well as targets for intervention to reduce Alzheimer’s disease risk. With the exception of the genetic polymorphism in the BDNF gene, Val66Met, which has been extensively studied with regard to neurodegenerative diseases, the genetic variation that influences circulating BDNF levels is unknown. We aimed to explore the genetic determinants of circulating BDNF levels in order to clarify its mechanistic involvement in brain structure and function and Alzheimer’s disease pathophysiology in middle-aged and old adults. Thus, we conducted a meta-analysis of genome-wide association study of circulating BDNF in 11 785 middle- and old-aged individuals of European ancestry from the Age, Gene/Environment Susceptibility-Reykjavik Study (AGES), the Framingham Heart Study (FHS), the Rotterdam Study and the Study of Health in Pomerania (SHIP-Trend). Furthermore, we performed functional annotation analysis and related the genetic polymorphism influencing circulating BDNF to common Alzheimer’s disease pathologies from brain autopsies. Mendelian randomization was conducted to examine the possible causal role of circulating BDNF levels with various phenotypes including cognitive function, stroke, diabetes, cardiovascular disease, physical activity and diet patterns. Gene interaction networks analysis was also performed. The estimated heritability of BDNF levels was 30% (standard error = 0.0246, P-value = 4 × 10−48). We identified seven novel independent loci mapped near the BDNF gene and in BRD3, CSRNP1, KDELC2, RUNX1 (two single-nucleotide polymorphisms) and BDNF-AS. The expression of BDNF was associated with neurofibrillary tangles in brain tissues from the Religious Orders Study and Rush Memory and Aging Project (ROSMAP). Seven additional genes (ACAT1, ATM, NPAT, WDR48, TTC21A, SCN114 and COX7B) were identified through expression and protein quantitative trait loci analyses. Mendelian randomization analyses indicated a potential causal role of BDNF in cardioembolism. Lastly, Ingenuity Pathway Analysis placed circulating BDNF levels in four major networks. Our study provides novel insights into genes and molecular pathways associated with circulating BDNF levels and highlights the possible involvement of plaque instability as an underlying mechanism linking BDNF with brain neurodegeneration. These findings provide a foundation for a better understanding of BDNF regulation and function in the context of brain aging and neurodegenerative pathophysiology.
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Affiliation(s)
- Shuo Li
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - Galit Weinstein
- School of Public Health, University of Haifa, Haifa 3498838, Israel
| | - Habil Zare
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, TX, USA.,Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, University of Texas Health Sciences Center, San Antonio, 78229 TX, USA
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, Germany.,DZHK (German Center for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
| | - Uwe Völker
- DZHK (German Center for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany.,Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Germany
| | - Nele Friedrich
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Germany
| | - Maria J Knol
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, 3000 CA, The Netherlands
| | - Claudia L Satizabal
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, University of Texas Health Sciences Center, San Antonio, 78229 TX, USA.,Department of Population Health Sciences, University of Texas Health Science Center, San Antonio, TX 78229, USA.,The Framingham Study, Framingham, MA 01702, USA.,Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA
| | | | - Hieab H H Adams
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, 3000 CA, The Netherlands.,Department of Radiology and Nuclear Medicine, Erasmus MC University Medical Center, Rotterdam 3015 CN, The Netherlands
| | - Lenore J Launer
- Department of Health and Human Services, Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - David A Bennett
- Department of Neurology, Rush University Medical Center, Chicago, IL 60612, USA.,Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL 60612, USA
| | - Philip L De Jager
- Department of Neurology, Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY 10032, USA.,Program in Population and Medical Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Hans J Grabe
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Germany.,German Center for Neurodegererative Diseases (DZNE), Rostock/Greifswald, Germany
| | - M Arfan Ikram
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, 3000 CA, The Netherlands
| | - Vilmundur Gudnason
- Faculty of Medicine, School of Health Sciences, University of Iceland, 101 Reykjavik, Iceland.,Icelandic Heart Association, 201 Kopavogur, Iceland
| | - Qiong Yang
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - Sudha Seshadri
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, University of Texas Health Sciences Center, San Antonio, 78229 TX, USA.,The Framingham Study, Framingham, MA 01702, USA.,Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA
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33
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McDermott JE, Arshad OA, Petyuk VA, Fu Y, Gritsenko MA, Clauss TR, Moore RJ, Schepmoes AA, Zhao R, Monroe ME, Schnaubelt M, Tsai CF, Payne SH, Huang C, Wang LB, Foltz S, Wyczalkowski M, Wu Y, Song E, Brewer MA, Thiagarajan M, Kinsinger CR, Robles AI, Boja ES, Rodriguez H, Chan DW, Zhang B, Zhang Z, Ding L, Smith RD, Liu T, Rodland KD. Correction: Proteogenomic Characterization of Ovarian HGSC Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability. Cell Rep Med 2020; 1. [PMID: 32954372 PMCID: PMC7500561 DOI: 10.1016/j.xcrm.2020.100075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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34
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Piehowski PD, Wang Y, Sanford JA, Hansen JR, Gritsenko MA, Petyuk VA, Weitz KK, Tognon C, Qian WJ, Liu T, Druker BJ, Rodland KD. Abstract 5125: Evaluation of differential peptide loading on TMT-based proteomic on phosphoproteomic data quality in an AML model. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-5125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Mass Spectrometry based proteomics profiling has become a powerful tool for broad quantification of proteins and their post-translational modifications for cancer research. Due to extensive efforts in the field to benchmark and standardize complex workflows, particularly those of the Clinical Proteomics Tumor Analysis Consortium (CPTAC), proteomics is now moving into clinical research. Reliable and reproducible quantification of > 10,000 proteins and >30,000 phosphosites is now routinely attainable from mammalian tissue samples. Integration of deep-scale proteomics analysis of human tumors with genomic data has been shown to improve specificity for identifying pathway alterations caused by tumor associated mutations. Furthermore, phosphoproteome measurements provide information on pathway activation not discernible from genetic measurements and thus provides unique insights for potential therapeutic targets.
A substantial challenge in the field of clinical proteomics is obtaining the sufficiently large clinical specimens necessary for deep coverage of the proteome. This challenge is particularly acute in the case of phosphoproteomics, which requires 100-fold more material than global profiling due to the low stoichiometry of the modification. The current gold standard approach for clinical proteomics employs a tandem mass tags (TMT) isobaric labeling approach to achieve deep quantitative proteomic and phosphoproteomic measurements. In this approach, 10 or 11 patient samples are labeled with unique isobaric labels, mixed in equal proportion, and fractionated prior to liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis. This creates a second challenge since very often due to external variables, differing quantities of protein are obtainable for patients within the same study. In these cases, the analysts need to decide whether to exclude sample-limited patients, reduce the protein loading per patient for the study, or to include that individual patient at reduced protein loading.
In this study, we set out to interrogate the impact of differential channel loading on global and phosphoproteomics results using an established clinical workflow. First, we determined protein yields from patient samples of decreasing cell count. We then used these results to design a 2 TMT plex experiment to explore a range of peptide loadings that we expect to encounter in executing a clinical proteomics experiment. The results were examined for protein/phosphosite coverage and various aspects of quantitative reproducibility. Our results provide a thorough examination of the impacts of differential channel loading and provide researchers with a resource to make informed decisions concerning their study design.
Citation Format: Paul D. Piehowski, Yang Wang, James A. Sanford, Joshua R. Hansen, Marina A. Gritsenko, Vladislav A. Petyuk, Karl K. Weitz, Cristina Tognon, Wei-Jun Qian, Tao Liu, Brian J. Druker, Karin D. Rodland. Evaluation of differential peptide loading on TMT-based proteomic on phosphoproteomic data quality in an AML model [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5125.
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Affiliation(s)
| | - Yang Wang
- 1Pacific Northwest National Laboratory, Richland, WA
| | | | | | | | | | - Karl K. Weitz
- 1Pacific Northwest National Laboratory, Richland, WA
| | | | - Wei-Jun Qian
- 1Pacific Northwest National Laboratory, Richland, WA
| | - Tao Liu
- 1Pacific Northwest National Laboratory, Richland, WA
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35
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Yang HS, White CC, Klein HU, Yu L, Gaiteri C, Ma Y, Felsky D, Mostafavi S, Petyuk VA, Sperling RA, Ertekin-Taner N, Schneider JA, Bennett DA, De Jager PL. Genetics of Gene Expression in the Aging Human Brain Reveal TDP-43 Proteinopathy Pathophysiology. Neuron 2020; 107:496-508.e6. [PMID: 32526197 PMCID: PMC7416464 DOI: 10.1016/j.neuron.2020.05.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [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: 11/01/2019] [Revised: 03/20/2020] [Accepted: 05/07/2020] [Indexed: 12/14/2022]
Abstract
Here, we perform a genome-wide screen for variants that regulate the expression of gene co-expression modules in the aging human brain; we discover and replicate such variants in the TMEM106B and RBFOX1 loci. The TMEM106B haplotype is known to influence the accumulation of TAR DNA-binding protein 43 kDa (TDP-43) proteinopathy, and the haplotype's large-scale transcriptomic effects include the dysregulation of lysosomal genes and alterations in synaptic gene splicing that are also seen in the pathophysiology of TDP-43 proteinopathy. Further, a variant near GRN, another TDP-43 proteinopathy susceptibility gene, shows concordant effects with the TMEM106B haplotype. Leveraging neuropathology data from the same participants, we also show that TMEM106B and APOE-amyloid-β effects converge to alter myelination and lysosomal gene expression, which then contributes to TDP-43 accumulation. These results advance our mechanistic understanding of the TMEM106B TDP-43 risk haplotype and uncover a transcriptional program that mediates the converging effects of APOE-amyloid-β and TMEM106B on TDP-43 aggregation in older adults.
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Affiliation(s)
- Hyun-Sik Yang
- Center for Alzheimer Research and Treatment, Department of Neurology, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Charles C White
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA; Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Hans-Ulrich Klein
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA; Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Lei Yu
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL 60612, USA; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL 60612, USA
| | - Christopher Gaiteri
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL 60612, USA; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL 60612, USA
| | - Yiyi Ma
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA; Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Daniel Felsky
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA; Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Sara Mostafavi
- Department of Statistics, Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada; Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada
| | | | - Reisa A Sperling
- Center for Alzheimer Research and Treatment, Department of Neurology, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Nilüfer Ertekin-Taner
- Department of Neurology, Mayo Clinic, Jacksonville, FL 32224, USA; Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Julie A Schneider
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL 60612, USA; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL 60612, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL 60612, USA; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL 60612, USA
| | - Philip L De Jager
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA; Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, USA.
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36
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Taga M, Petyuk VA, White C, Marsh G, Ma Y, Klein HU, Connor SM, Kroshilina A, Yung CJ, Khairallah A, Olah M, Schneider J, Karhohs K, Carpenter AE, Ransohoff R, Bennett DA, Crotti A, Bradshaw EM, De Jager PL. BIN1 protein isoforms are differentially expressed in astrocytes, neurons, and microglia: neuronal and astrocyte BIN1 are implicated in tau pathology. Mol Neurodegener 2020; 15:44. [PMID: 32727516 PMCID: PMC7389646 DOI: 10.1186/s13024-020-00387-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 06/08/2020] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Identified as an Alzheimer's disease (AD) susceptibility gene by genome wide-association studies, BIN1 has 10 isoforms that are expressed in the Central Nervous System (CNS). The distribution of these isoforms in different cell types, as well as their role in AD pathology still remains unclear. METHODS Utilizing antibodies targeting specific BIN1 epitopes in human post-mortem tissue and analyzing mRNA expression data from purified microglia, we identified three isoforms expressed in neurons and astrocytes (isoforms 1, 2 and 3) and four isoforms expressed in microglia (isoforms 6, 9, 10 and 12). The abundance of selected peptides, which correspond to groups of BIN1 protein isoforms, was measured in dorsolateral prefrontal cortex, and their relation to neuropathological features of AD was assessed. RESULTS Peptides contained in exon 7 of BIN1's N-BAR domain were found to be significantly associated with AD-related traits and, particularly, tau tangles. Decreased expression of BIN1 isoforms containing exon 7 is associated with greater accumulation of tangles and subsequent cognitive decline, with astrocytic rather than neuronal BIN1 being the more likely culprit. These effects are independent of the BIN1 AD risk variant. CONCLUSIONS Exploring the molecular mechanisms of specific BIN1 isoforms expressed by astrocytes may open new avenues for modulating the accumulation of Tau pathology in AD.
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Affiliation(s)
- Mariko Taga
- Center for Translational & Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, 630 West 168th st, PH19-311, New York, NY 10032 USA
- Cell Circuits Program, Broad Institute, Cambridge, MA USA
| | | | - Charles White
- Cell Circuits Program, Broad Institute, Cambridge, MA USA
| | | | - Yiyi Ma
- Center for Translational & Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, 630 West 168th st, PH19-311, New York, NY 10032 USA
| | - Hans-Ulrich Klein
- Center for Translational & Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, 630 West 168th st, PH19-311, New York, NY 10032 USA
- Cell Circuits Program, Broad Institute, Cambridge, MA USA
| | - Sarah M. Connor
- Center for Translational & Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, 630 West 168th st, PH19-311, New York, NY 10032 USA
- Cell Circuits Program, Broad Institute, Cambridge, MA USA
| | - Alexandra Kroshilina
- Center for Translational & Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, 630 West 168th st, PH19-311, New York, NY 10032 USA
| | - Christina J. Yung
- Center for Translational & Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, 630 West 168th st, PH19-311, New York, NY 10032 USA
| | - Anthony Khairallah
- Center for Translational & Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, 630 West 168th st, PH19-311, New York, NY 10032 USA
| | - Marta Olah
- Center for Translational & Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, 630 West 168th st, PH19-311, New York, NY 10032 USA
- Cell Circuits Program, Broad Institute, Cambridge, MA USA
| | - Julie Schneider
- Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL USA
| | - Kyle Karhohs
- Imaging Platform, Broad Institute, Cambridge, MA USA
| | | | - Richard Ransohoff
- Third Rock Ventures, 29 Newbury Street, Suite 301, Boston, MA 02116 USA
- Department of Cell Biology, Harvard Medical School, Boston, MA USA
| | - David A. Bennett
- Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL USA
| | | | - Elizabeth M. Bradshaw
- Center for Translational & Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, 630 West 168th st, PH19-311, New York, NY 10032 USA
- Cell Circuits Program, Broad Institute, Cambridge, MA USA
| | - Philip L. De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, 630 West 168th st, PH19-311, New York, NY 10032 USA
- Cell Circuits Program, Broad Institute, Cambridge, MA USA
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Yu L, Petyuk VA, Tasaki S, Boyle PA, Gaiteri C, Schneider JA, De Jager PL, Bennett DA. Association of Cortical β-Amyloid Protein in the Absence of Insoluble Deposits With Alzheimer Disease. JAMA Neurol 2020; 76:818-826. [PMID: 31009033 DOI: 10.1001/jamaneurol.2019.0834] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Importance β-Amyloid deposits are a pathologic hallmark of Alzheimer disease (AD). However, the extent to which cortical β-amyloid protein in the absence of insoluble deposits is associated with classic features of AD appear to be unknown. Objective To examine the associations of cortical β-amyloid protein in the absence of insoluble deposits with cognitive decline, neurofibrillary tangles, other age-associated neuropathologic conditions, and APOE. Design, Setting, and Participants This analysis combines data from 2 community-based clinicopathologic cohort studies of aging. The Religious Orders Study started in 1994, and the Rush Memory and Aging Project started in 1997. Both studies are ongoing. Participants without known dementia were enrolled and agreed to annual clinical evaluations and brain donation after death. Primary analyses focused on individuals without β-amyloid deposits. Data analyses occurred in mid-September 2018. Main Outcomes and Measures β-Amyloid protein abundance was measured by targeted proteomics using selected reaction monitoring. β-Amyloid deposits were detected using immunohistochemistry. Other neuropathologic indices were quantified via uniform structured evaluation. Linear mixed models were used to examine the association of β-amyloid protein with cognitive decline. Regression models examined the protein associations with neuropathologic outcomes and the APOE genotype. Results By mid-September 2018, 3575 older persons were enrolled, and 1559 had died and undergone brain autopsy. Proteomic data were collected in 1208 individuals, and 5 with missing cognitive scores were excluded. Of the remaining 1203, primary analyses focused on 148 individuals (12.3%) without β-amyloid deposits. In this group, the mean (SD) age at death was 87.0 (7.0) years, and 84 individuals (56.8%) were women. In the absence of β-amyloid deposits, we did not observe an association of β-amyloid protein with decline in episodic memory, but the protein was associated with faster rates of decline in processing speed (mean [SE] change, -0.014 [0.005]; P = .008) and visuospatial abilities (mean [SE] change, -0.013 [0.005]; P = .006). We did not observe protein association with paired helical filament tau tangle density. The protein was associated with amyloid angiopathy (odds ratio, 1.38 [95% CI, 1.15-1.67]; P < .001) but no other brain pathology. The associations with cognitive decline were unchanged after controlling for amyloid angiopathy. Neither APOE ε4 nor a polygenic Alzheimer risk score was associated with β-amyloid protein. Conclusions and Relevance Cortical β-amyloid protein was associated with faster cognitive decline in the absence of β-amyloid deposits, which supports the role of cortical soluble β-amyloid as a neurotoxic agent in aging. The lack of protein association with paired helical filament tau tangles, episodic memory decline, or strong genetic drivers of deposited β-amyloid suggests an underlying neuropathologic change that may differ from that of AD.
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Affiliation(s)
- Lei Yu
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois.,Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois
| | | | - Shinya Tasaki
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois.,Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois
| | - Patricia A Boyle
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois.,Department of Behavioral Sciences, Rush University Medical Center, Chicago, Illinois
| | - Chris Gaiteri
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois.,Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois
| | - Julie A Schneider
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois.,Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois.,Department of Pathology, Rush University Medical Center, Chicago, Illinois
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, New York.,Cell Circuits Program, Broad Institute, Cambridge, Massachusetts
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois.,Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois
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38
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Lee JY, Shi T, Petyuk VA, Schepmoes AA, Fillmore TL, Wang YT, Cardoni W, Coppit G, Srivastava S, Goodman JF, Shriver CD, Liu T, Rodland KD. Detection of Head and Neck Cancer Based on Longitudinal Changes in Serum Protein Abundance. Cancer Epidemiol Biomarkers Prev 2020; 29:1665-1672. [PMID: 32532828 DOI: 10.1158/1055-9965.epi-20-0192] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 04/16/2020] [Accepted: 06/02/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Approximately 85% of the U.S. military active duty population is male and less than 50 years of age, with elevated levels of known risk factors for oropharyngeal squamous cell carcinoma (OPSCC), including smoking, excessive use of alcohol, and greater numbers of sexual partners, and elevated prevalence of human papilloma virus (HPV). Given the recent rise in incidence of OPSCC related to the HPV, the Department of Defense Serum Repository provides an unparalleled resource for longitudinal studies of OPSCC in the military for the identification of early detection biomarkers. METHODS We identified 175 patients diagnosed with OPSCC with 175 matched healthy controls and retrieved a total of 978 serum samples drawn at the time of diagnosis, 2 and 4 years prior to diagnosis, and 2 years after diagnosis. Following immunoaffinity depletion, serum samples were analyzed by targeted proteomics assays for multiplexed quantification of a panel of 146 candidate protein biomarkers from the curated literature. RESULTS Using a Random Forest machine learning approach, we derived a 13-protein signature that distinguishes cases versus controls based on longitudinal changes in serum protein concentration. The abundances of each of the 13 proteins remain constant over time in control subjects. The AUC for the derived Random Forest classifier was 0.90. CONCLUSIONS This 13-protein classifier is highly promising for detection of OPSCC prior to overt symptoms. IMPACT Use of longitudinal samples has significant potential to identify biomarkers for detection and risk stratification.
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Affiliation(s)
- Ju Yeon Lee
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington.,Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, Republic of Korea
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Athena A Schepmoes
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Thomas L Fillmore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Yi-Ting Wang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Wayne Cardoni
- Frederick Regional Health System, Frederick, Maryland
| | - George Coppit
- Frederick Regional Health System, Frederick, Maryland
| | - Shiv Srivastava
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, Maryland.,John P. Murtha Cancer Center, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Joseph F Goodman
- Division of Otolaryngology, George Washington University, Washington, DC
| | - Craig D Shriver
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, Maryland.,John P. Murtha Cancer Center, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington.
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington. .,Department of Cell Developmental and Cancer Biology, Oregon Health and Science University, Portland, Oregon
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Sanford JA, Nogiec CD, Lindholm ME, Adkins JN, Amar D, Dasari S, Drugan JK, Fernández FM, Radom-Aizik S, Schenk S, Snyder MP, Tracy RP, Vanderboom P, Trappe S, Walsh MJ, Adkins JN, Amar D, Dasari S, Drugan JK, Evans CR, Fernandez FM, Li Y, Lindholm ME, Nogiec CD, Radom-Aizik S, Sanford JA, Schenk S, Snyder MP, Tomlinson L, Tracy RP, Trappe S, Vanderboom P, Walsh MJ, Lee Alekel D, Bekirov I, Boyce AT, Boyington J, Fleg JL, Joseph LJ, Laughlin MR, Maruvada P, Morris SA, McGowan JA, Nierras C, Pai V, Peterson C, Ramos E, Roary MC, Williams JP, Xia A, Cornell E, Rooney J, Miller ME, Ambrosius WT, Rushing S, Stowe CL, Jack Rejeski W, Nicklas BJ, Pahor M, Lu CJ, Trappe T, Chambers T, Raue U, Lester B, Bergman BC, Bessesen DH, Jankowski CM, Kohrt WM, Melanson EL, Moreau KL, Schauer IE, Schwartz RS, Kraus WE, Slentz CA, Huffman KM, Johnson JL, Willis LH, Kelly L, Houmard JA, Dubis G, Broskey N, Goodpaster BH, Sparks LM, Coen PM, Cooper DM, Haddad F, Rankinen T, Ravussin E, Johannsen N, Harris M, Jakicic JM, Newman AB, Forman DD, Kershaw E, Rogers RJ, Nindl BC, Page LC, Stefanovic-Racic M, Barr SL, Rasmussen BB, Moro T, Paddon-Jones D, Volpi E, Spratt H, Musi N, Espinoza S, Patel D, Serra M, Gelfond J, Burns A, Bamman MM, Buford TW, Cutter GR, Bodine SC, Esser K, Farrar RP, Goodyear LJ, Hirshman MF, Albertson BG, Qian WJ, Piehowski P, Gritsenko MA, Monore ME, Petyuk VA, McDermott JE, Hansen JN, Hutchison C, Moore S, Gaul DA, Clish CB, Avila-Pacheco J, Dennis C, Kellis M, Carr S, Jean-Beltran PM, Keshishian H, Mani D, Clauser K, Krug K, Mundorff C, Pearce C, Ivanova AA, Ortlund EA, Maner-Smith K, Uppal K, Zhang T, Sealfon SC, Zaslavsky E, Nair V, Li S, Jain N, Ge Y, Sun Y, Nudelman G, Ruf-zamojski F, Smith G, Pincas N, Rubenstein A, Anne Amper M, Seenarine N, Lappalainen T, Lanza IR, Sreekumaran Nair K, Klaus K, Montgomery SB, Smith KS, Gay NR, Zhao B, Hung CJ, Zebarjadi N, Balliu B, Fresard L, Burant CF, Li JZ, Kachman M, Soni T, Raskind AB, Gerszten R, Robbins J, Ilkayeva O, Muehlbauer MJ, Newgard CB, Ashley EA, Wheeler MT, Jimenez-Morales D, Raja A, Dalton KP, Zhen J, Suk Kim Y, Christle JW, Marwaha S, Chin ET, Hershman SG, Hastie T, Tibshirani R, Rivas MA. Molecular Transducers of Physical Activity Consortium (MoTrPAC): Mapping the Dynamic Responses to Exercise. Cell 2020; 181:1464-1474. [DOI: 10.1016/j.cell.2020.06.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/19/2020] [Accepted: 06/01/2020] [Indexed: 12/31/2022]
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Reyes BC, Otero-Muras I, Shuen MT, Tartakovsky AM, Petyuk VA. CRNT4SBML: a Python package for the detection of bistability in biochemical reaction networks. Bioinformatics 2020; 36:3922-3924. [PMID: 32289149 DOI: 10.1093/bioinformatics/btaa241] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 04/01/2020] [Accepted: 04/08/2020] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Signaling pathways capable of switching between two states are ubiquitous within living organisms. They provide the cells with the means to produce reversible or irreversible decisions. Switch-like behavior of biological systems is realized through biochemical reaction networks capable of having two or more distinct steady states, which are dependent on initial conditions. Investigation of whether a certain signaling pathway can confer bistability involves a substantial amount of hypothesis testing. The cost of direct experimental testing can be prohibitive. Therefore, constraining the hypothesis space is highly beneficial. One such methodology is based on chemical reaction network theory (CRNT), which uses computational techniques to rule out pathways that are not capable of bistability regardless of kinetic constant values and molecule concentrations. Although useful, these methods are complicated from both pure and computational mathematics perspectives. Thus, their adoption is very limited amongst biologists. RESULTS We brought CRNT approaches closer to experimental biologists by automating all the necessary steps in CRNT4SMBL. The input is based on systems biology markup language (SBML) format, which is the community standard for biological pathway communication. The tool parses SBML and derives C-graph representations of the biological pathway with mass action kinetics. Next steps involve an efficient search for potential saddle-node bifurcation points using an optimization technique. This type of bifurcation is important as it has the potential of acting as a switching point between two steady states. Finally, if any bifurcation points are present, continuation analysis with respect to a user-defined parameter extends the steady state branches and generates a bifurcation diagram. Presence of an S-shaped bifurcation diagram indicates that the pathway acts as a bistable switch for the given optimization parameters. AVAILABILITY AND IMPLEMENTATION CRNT4SBML is available via the Python Package Index. The documentation can be found at https://crnt4sbml.readthedocs.io. CRNT4SBML is licensed under the Apache Software License 2.0.
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Affiliation(s)
- Brandon C Reyes
- Advanced Computing, Mathematics, and Data Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Irene Otero-Muras
- BioProcess Engineering Group, IIM-CSIC (Spanish National Research Council), Vigo, Spain
| | - Michael T Shuen
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Alexandre M Tartakovsky
- Advanced Computing, Mathematics, and Data Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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41
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Zhang T, Gaffrey MJ, Monroe ME, Thomas DG, Weitz KK, Piehowski PD, Petyuk VA, Moore RJ, Thrall BD, Qian WJ. Block Design with Common Reference Samples Enables Robust Large-Scale Label-Free Quantitative Proteome Profiling. J Proteome Res 2020; 19:2863-2872. [PMID: 32407631 DOI: 10.1021/acs.jproteome.0c00310] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Label-free quantitative proteomics has become an increasingly popular tool for profiling global protein abundances. However, one major limitation is the potential performance drift of the LC-MS platform over time, which, in turn, limits its utility for analyzing large-scale sample sets. To address this, we introduce an experimental and data analysis scheme based on a block design with common references within each block for enabling large-scale label-free quantification. In this scheme, a large number of samples (e.g., >100 samples) are analyzed in smaller and more manageable blocks, minimizing instrument drift and variability within individual blocks. Each designated block also contains common reference samples (e.g., controls) for normalization across all blocks. We demonstrated the robustness of this approach by profiling the proteome response of human macrophage THP-1 cells to 11 engineered nanomaterials at two different doses. A total of 116 samples were analyzed in six blocks, yielding an average coverage of 4500 proteins per sample. Following a common reference-based correction, 2537 proteins were quantified with high reproducibility without any imputation of missing values from 116 data sets. The data revealed the consistent quantification of proteins across all six blocks, as illustrated by the highly consistent abundances of house-keeping proteins in all samples and the high levels of correlation among samples from different blocks. The data also demonstrated that label-free quantification is robust and accurate enough to quantify even very subtle abundance changes as well as large fold-changes. Our streamlined workflow is easy to implement and can be readily adapted to other large cohort studies for reproducible label-free proteome quantification.
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Affiliation(s)
- Tong Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Matthew J Gaffrey
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Dennis G Thomas
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Karl K Weitz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Paul D Piehowski
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Brian D Thrall
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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42
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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; 26:769-780. [PMID: 32284590 PMCID: PMC7405761 DOI: 10.1038/s41591-020-0815-6] [Citation(s) in RCA: 464] [Impact Index Per Article: 116.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 02/27/2020] [Indexed: 12/12/2022]
Abstract
Our understanding of Alzheimer's disease (AD) pathophysiology remains incomplete. Here we used quantitative mass spectrometry and coexpression network analysis to conduct the largest proteomic study thus far on AD. A protein network module linked to sugar metabolism emerged as one of the modules most significantly associated with AD pathology and cognitive impairment. This module was enriched in AD genetic risk factors and in microglia and astrocyte protein markers associated with an anti-inflammatory state, suggesting that the biological functions it represents serve a protective role in AD. Proteins from this module were elevated in cerebrospinal fluid in early stages of the disease. In this study of >2,000 brains and nearly 400 cerebrospinal fluid samples by quantitative proteomics, we identify proteins and biological processes in AD brains that may serve as therapeutic targets and fluid biomarkers for the disease.
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Affiliation(s)
- 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.
| | - 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
| | - Duc M Duong
- 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
| | - Lingyan Ping
- 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
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Maotian Zhou
- 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
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Luming Yin
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | | | | | | | | | - Madhav Thambisetty
- Clinical and Translational Neuroscience Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Thomas J Montine
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Edward B Lee
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - John Q Trojanowski
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Thomas G Beach
- Department of Pathology, Banner Sun Health Research Institute, Sun City, AZ, USA
| | - Eric M Reiman
- Banner Alzheimer's Institute, Arizona State University and University of Arizona, Phoenix, AZ, USA
| | - Vahram Haroutunian
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- JJ Peters VA Medical Center MIRECC, Bronx, NY, USA
| | - Minghui Wang
- Department of Genetics and Genomic Sciences, Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric Schadt
- Department of Genetics and Genomic Sciences, Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Department of Neurology, Mayo Clinic, Jacksonville, FL, USA
| | - Todd E Golde
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Philip L De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Taub Institute, Columbia University Irving Medical Center, New York Presbyterian Hospital, New York, NY, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Thomas S Wingo
- 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
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Srikant Rangaraju
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Ihab Hajjar
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Joshua M Shulman
- Departments of Neurology, Neuroscience and Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurologic Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - James J Lah
- 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
| | - Allan I Levey
- 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.
| | - Nicholas T Seyfried
- 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.
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA.
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McDermott JE, Arshad OA, Petyuk VA, Fu Y, Gritsenko MA, Clauss TR, Moore RJ, Schepmoes AA, Zhao R, Monroe ME, Schnaubelt M, Tsai CF, Payne SH, Huang C, Wang LB, Foltz S, Wyczalkowski M, Wu Y, Song E, Brewer MA, Thiagarajan M, Kinsinger CR, Robles AI, Boja ES, Rodriguez H, Chan DW, Zhang B, Zhang Z, Ding L, Smith RD, Liu T, Rodland KD. Proteogenomic Characterization of Ovarian HGSC Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability. Cell Rep Med 2020; 1. [PMID: 32529193 PMCID: PMC7289043 DOI: 10.1016/j.xcrm.2020.100004] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In the absence of a dominant driving mutation other than uniformly present TP53 mutations, deeper understanding of the biology driving ovarian high-grade serous cancer (HGSC) requires analysis at a functional level, including post-translational modifications. Comprehensive proteogenomic and phosphoproteomic characterization of 83 prospectively collected ovarian HGSC and appropriate normal precursor tissue samples (fallopian tube) under strict control of ischemia time reveals pathways that significantly differentiate between HGSC and relevant normal tissues in the context of homologous repair deficiency (HRD) status. In addition to confirming key features of HGSC from previous studies, including a potential survival-associated signature and histone acetylation as a marker of HRD, deep phosphoproteomics provides insights regarding the potential role of proliferation-induced replication stress in promoting the characteristic chromosomal instability of HGSC and suggests potential therapeutic targets for use in precision medicine trials. Comparison of ovarian cancer and normal precursors identifies key signaling pathways Mitotic and cyclin-dependent kinases emerge as potential therapeutic targets Previously identified hallmarks of homologous repair status and survival are confirmed Replication stress appears to drive increased chromosomal instability
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Affiliation(s)
- Jason E McDermott
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA.,Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR 97201, USA.,These authors contributed equally
| | - Osama A Arshad
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA.,These authors contributed equally
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Yi Fu
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD 21205, USA
| | - Marina A Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Therese R Clauss
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Athena A Schepmoes
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Rui Zhao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Michael Schnaubelt
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD 21205, USA
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Samuel H Payne
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Chen Huang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Liang-Bo Wang
- The McDonnell Genome Institute, Washington University in St. Louis, St Louis, MO 63108, USA
| | - Steven Foltz
- The McDonnell Genome Institute, Washington University in St. Louis, St Louis, MO 63108, USA
| | - Matthew Wyczalkowski
- The McDonnell Genome Institute, Washington University in St. Louis, St Louis, MO 63108, USA
| | - Yige Wu
- The McDonnell Genome Institute, Washington University in St. Louis, St Louis, MO 63108, USA
| | - Ehwang Song
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Molly A Brewer
- Department of Obstetrics and Gynecology, University of Connecticut, Farmington, CT 06030, USA
| | - Mathangi Thiagarajan
- Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Christopher R Kinsinger
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Emily S Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Daniel W Chan
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD 21205, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhen Zhang
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD 21205, USA
| | - Li Ding
- The McDonnell Genome Institute, Washington University in St. Louis, St Louis, MO 63108, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA.,Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR 97201, USA.,Lead Contact
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Moore AM, Mahoney E, Dumitrescu L, De Jager PL, Koran MEI, Petyuk VA, Robinson RA, Ruderfer DM, Cox NJ, Schneider JA, Bennett DA, Jefferson AL, Hohman TJ. APOE ε4-specific associations of VEGF gene family expression with cognitive aging and Alzheimer's disease. Neurobiol Aging 2020; 87:18-25. [PMID: 31791659 PMCID: PMC7064375 DOI: 10.1016/j.neurobiolaging.2019.10.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [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: 05/24/2019] [Revised: 09/11/2019] [Accepted: 10/29/2019] [Indexed: 12/25/2022]
Abstract
Literature suggests vascular endothelial growth factor A (VEGFA) is protective among those at highest risk for Alzheimer's disease (AD). Apolipoprotein E (APOE) ε4 allele carriers represent a highly susceptible population for cognitive decline, and VEGF may confer distinct protection among APOE-ε4 carriers. We evaluated interactions between cortical expression of 10 VEGF gene family members and APOE-ε4 genotype to clarify which VEGF genes modify the association between APOE-ε4 and cognitive decline. Data were obtained from the Religious Orders Study and Rush Memory and Aging Project (N = 531). Linear regression assessed interactions on global cognition. VEGF genes NRP1 and VEGFA interacted with APOE-ε4 on cognitive performance (p.fdr < 0.05). Higher NRP1 expression correlated with worse outcomes among ε4 carriers but better outcomes among ε4 noncarriers, suggesting NRP1 modifies the risk for poor cognitive scores based on APOE-ε4 status. NRP1 regulates angiogenesis, and literature suggests vessels in APOE-ε4 brains are more prone to leaking, perhaps placing young vessels at risk for ischemia. Results suggest that future therapeutics targeting brain angiogenesis should also consider ε4 allele status.
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Affiliation(s)
- Annah M Moore
- Vanderbilt Memory and 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 Medical Center, Nashville, TN, USA
| | - Emily Mahoney
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Logan Dumitrescu
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Philip L De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA; Cell Circuits Program, Broad Institute, Cambridge MA, USA
| | | | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Renã As Robinson
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - Douglas M Ruderfer
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nancy J Cox
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Julie A Schneider
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Angela L Jefferson
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Timothy J Hohman
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.
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Dou Y, Kawaler EA, Cui Zhou D, Gritsenko MA, Huang C, Blumenberg L, Karpova A, Petyuk VA, Savage SR, Satpathy S, Liu W, Wu Y, Tsai CF, Wen B, Li Z, Cao S, Moon J, Shi Z, Cornwell M, Wyczalkowski MA, Chu RK, Vasaikar S, Zhou H, Gao Q, Moore RJ, Li K, Sethuraman S, Monroe ME, Zhao R, Heiman D, Krug K, Clauser K, Kothadia R, Maruvka Y, Pico AR, Oliphant AE, Hoskins EL, Pugh SL, Beecroft SJI, Adams DW, Jarman JC, Kong A, Chang HY, Reva B, Liao Y, Rykunov D, Colaprico A, Chen XS, Czekański A, Jędryka M, Matkowski R, Wiznerowicz M, Hiltke T, Boja E, Kinsinger CR, Mesri M, Robles AI, Rodriguez H, Mutch D, Fuh K, Ellis MJ, DeLair D, Thiagarajan M, Mani DR, Getz G, Noble M, Nesvizhskii AI, Wang P, Anderson ML, Levine DA, Smith RD, Payne SH, Ruggles KV, Rodland KD, Ding L, Zhang B, Liu T, Fenyö D. Proteogenomic Characterization of Endometrial Carcinoma. Cell 2020; 180:729-748.e26. [PMID: 32059776 PMCID: PMC7233456 DOI: 10.1016/j.cell.2020.01.026] [Citation(s) in RCA: 247] [Impact Index Per Article: 61.8] [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: 05/29/2019] [Revised: 11/11/2019] [Accepted: 01/16/2020] [Indexed: 02/07/2023]
Abstract
We undertook a comprehensive proteogenomic characterization of 95 prospectively collected endometrial carcinomas, comprising 83 endometrioid and 12 serous tumors. This analysis revealed possible new consequences of perturbations to the p53 and Wnt/β-catenin pathways, identified a potential role for circRNAs in the epithelial-mesenchymal transition, and provided new information about proteomic markers of clinical and genomic tumor subgroups, including relationships to known druggable pathways. An extensive genome-wide acetylation survey yielded insights into regulatory mechanisms linking Wnt signaling and histone acetylation. We also characterized aspects of the tumor immune landscape, including immunogenic alterations, neoantigens, common cancer/testis antigens, and the immune microenvironment, all of which can inform immunotherapy decisions. Collectively, our multi-omic analyses provide a valuable resource for researchers and clinicians, identify new molecular associations of potential mechanistic significance in the development of endometrial cancers, and suggest novel approaches for identifying potential therapeutic targets.
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Affiliation(s)
- Yongchao Dou
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Emily A Kawaler
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Daniel Cui Zhou
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Marina A Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Chen Huang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lili Blumenberg
- Department of Medicine, NYU School of Medicine, New York, NY 10016, USA
| | - Alla Karpova
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Sara R Savage
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shankha Satpathy
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Wenke Liu
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Yige Wu
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Bo Wen
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhi Li
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Song Cao
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Jamie Moon
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Zhiao Shi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - MacIntosh Cornwell
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Matthew A Wyczalkowski
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Rosalie K Chu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Suhas Vasaikar
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hua Zhou
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Qingsong Gao
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Kai Li
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sunantha Sethuraman
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Rui Zhao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - David Heiman
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Karsten Krug
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Karl Clauser
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ramani Kothadia
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yosef Maruvka
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexander R Pico
- Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Amanda E Oliphant
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Emily L Hoskins
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Samuel L Pugh
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Sean J I Beecroft
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - David W Adams
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Jonathan C Jarman
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Andy Kong
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hui-Yin Chang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Boris Reva
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yuxing Liao
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dmitry Rykunov
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Antonio Colaprico
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Division of Biostatistics, Department of Public Health Science, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Xi Steven Chen
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Division of Biostatistics, Department of Public Health Science, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Andrzej Czekański
- Department of Oncology, Wroclaw Medical University, 50-367 Wrocław, Poland; Wroclaw Comprehensive Cancer Center, 53-413 Wrocław, Poland
| | - Marcin Jędryka
- Department of Oncology, Wroclaw Medical University, 50-367 Wrocław, Poland; Wroclaw Comprehensive Cancer Center, 53-413 Wrocław, Poland
| | - Rafał Matkowski
- Department of Oncology, Wroclaw Medical University, 50-367 Wrocław, Poland; Wroclaw Comprehensive Cancer Center, 53-413 Wrocław, Poland
| | - Maciej Wiznerowicz
- Poznan University of Medical Sciences, 61-701 Poznań, Poland; University Hospital of Lord's Transfiguration, 60-569 Poznań, Poland; International Institute for Molecular Oncology, 60-203 Poznań, Poland
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Emily Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Christopher R Kinsinger
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - David Mutch
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Katherine Fuh
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Matthew J Ellis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Deborah DeLair
- Department of Pathology, NYU Langone Health, New York, NY 10016, USA
| | - Mathangi Thiagarajan
- Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - D R Mani
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Gad Getz
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael Noble
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Matthew L Anderson
- College of Medicine Obstetrics & Gynecology, University of South Florida Health, Tampa, FL 33620, USA
| | - Douglas A Levine
- Gynecologic Oncology, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Samuel H Payne
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Kelly V Ruggles
- Department of Medicine, NYU School of Medicine, New York, NY 10016, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR 97221, USA.
| | - Li Ding
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA.
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
| | - David Fenyö
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA.
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Zhang T, Gaffrey MJ, Thomas DG, Weber TJ, Hess BM, Weitz KK, Piehowski PD, Petyuk VA, Moore RJ, Qian WJ, Thrall BD. A proteome-wide assessment of the oxidative stress paradigm for metal and metal-oxide nanomaterials in human macrophages. NanoImpact 2020; 17:100194. [PMID: 32133426 PMCID: PMC7055704 DOI: 10.1016/j.impact.2019.100194] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Responsible implementation of engineered nanomaterials (ENMs) into commercial applications is an important societal issue, driving demand for new approaches for rapid and comprehensive evaluation of their bioactivity and safety. An essential part of any research focused on identifying potential hazards of ENMs is the appropriate selection of biological endpoints to evaluate. Herein, we use a tiered strategy employing both targeted biological assays and untargeted quantitative proteomics to elucidate the biological responses of human THP-1 derived macrophages across a library of metal/metal oxide ENMs, raised as priority ENMs for investigation by NIEHS's Nanomaterial Health Implications Research (NHIR) program. Our results show that quantitative cellular proteome profiles readily distinguish ENM types based on their cytotoxic potential according to induction of biological processes and pathways involved in the cellular antioxidant response, TCA cycle, oxidative stress, endoplasmic reticulum stress, and immune responses as major processes impacted. Interestingly, bioinformatics analysis of differentially expressed proteins also revealed new biological processes that were influenced by all ENMs independent of their cytotoxic potential. These included biological processes that were previously implicated as mechanisms cells employ as adaptive responses to low levels of oxidative stress, including cell adhesion, protein translation and protein targeting. Unsupervised clustering revealed the most striking proteome changes that differentiated ENM classes highlight a small subset of proteins involved in the oxidative stress response (HMOX1), protein chaperone functions (HS71B, DNJB1), and autophagy (SQSTM), providing a potential new panel of markers of ENM-induced cellular stress. To our knowledge, the results represent the most comprehensive profiling of the biological responses to a library of ENMs conducted using quantitative mass spectrometry-based proteomics. The results provide a basis to identify the patterns of a diverse set of cellular pathways and biological processes impacted by ENM exposure in an important immune cell type, laying the foundation for multivariate, pathway-level structure activity assessments of ENMs in the future.
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Affiliation(s)
- Tong Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA 99352
| | - Matthew J Gaffrey
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA 99352
| | - Dennis G Thomas
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA 99352
| | - Thomas J Weber
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA 99352
| | - Becky M Hess
- Signatures Sciences and Technology Division, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Karl K Weitz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA 99352
| | - Paul D Piehowski
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA 99352
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA 99352
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA 99352
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA 99352
| | - Brian D Thrall
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA 99352
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47
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Tasaki S, Gaiteri C, Petyuk VA, Blizinsky KD, De Jager PL, Buchman AS, Bennett DA. Genetic risk for Alzheimer's dementia predicts motor deficits through multi-omic systems in older adults. Transl Psychiatry 2019; 9:241. [PMID: 31582723 PMCID: PMC6776503 DOI: 10.1038/s41398-019-0577-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/24/2019] [Indexed: 12/13/2022] Open
Abstract
Alzheimer's disease manifests with both cognitive and motor deficits. However, the degree to which genetic risk of Alzheimer's dementia contributes to late-life motor impairment, and the specific molecular systems underlying these associations, are uncertain. Here, we adopted an integrative multi-omic approach to assess genetic influence on motor impairment in older adults and identified key molecular pathways that may mediate this risk. We built a polygenic risk score for clinical diagnosis of Alzheimer's dementia (AD-PRS) and examined its relationship to several motor phenotypes in 1885 older individuals from two longitudinal aging cohorts. We found that AD-PRS was associated with a previously validated composite motor scores and their components. The major genetic risk factor for sporadic Alzheimer's dementia, the APOE/TOMM40 locus, was not a major driver of these associations. To identify specific molecular features that potentially medicate the genetic risk into motor dysfunction, we examined brain multi-omics, including transcriptome, DNA methylation, histone acetylation (H3K9AC), and targeted proteomics, as well as diverse neuropathologies. We found that a small number of factors account for the majority of the influence of AD-PRS on motor function, which comprises paired helical filament tau-tangle density, H3K9AC in specific chromosomal regions encoding genes involved in neuromuscular process. These multi-omic factors have the potential to elucidate key molecular mechanisms developing motor impairment in the context of Alzheimer's dementia.
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Affiliation(s)
- Shinya Tasaki
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA.
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA.
| | - Chris Gaiteri
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Katherine D Blizinsky
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, USA
- Cell Circuits Program, Broad Institute, Cambridge, MA, USA
| | - Aron S Buchman
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
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Buchman AS, Yu L, Petyuk VA, Gaiteri C, Tasaki S, Blizinsky KD, Schneider JA, De Jager PL, Bennett DA. Cognition may link cortical IGFBP5 levels with motor function in older adults. PLoS One 2019; 14:e0220968. [PMID: 31404102 PMCID: PMC6690580 DOI: 10.1371/journal.pone.0220968] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/26/2019] [Indexed: 12/21/2022] Open
Abstract
Alzheimer's disease and related disorders (ADRD) may manifest cognitive and non-cognitive phenotypes including motor impairment, suggesting a shared underlying biology. We tested the hypothesis that five cortical proteins identified from a gene network that drives AD and cognitive phenotypes are also related to motor function in the same individuals. We examined 1208 brains of older adults with motor and cognitive assessments prior to death. Cortical proteins were quantified with SRM proteomics and we collected indices of AD and other related pathologies. A higher level of IGFBP5 was associated with poorer motor function proximate to death but AK4, HSPB2, ITPK1 and PLXNB1 were unrelated to motor function. The association of IGFBP5 with motor function was unrelated to the presence of indices of brain pathologies. In contrast, the addition of a term for cognition attenuated the association of IGFBP5 with motor function by about 90% and they were no longer related. These data lend support for the idea that unidentified cortical proteins like IGFBP5, which may not manifest a known pathologic footprint, may contribute to motor and cognitive function in older adults.
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Affiliation(s)
- Aron S. Buchman
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, United States of America
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Lei Yu
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, United States of America
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Vladislav A. Petyuk
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Chris Gaiteri
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, United States of America
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Shinya Tasaki
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, United States of America
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Katherine D. Blizinsky
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, United States of America
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Julie A. Schneider
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, United States of America
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, United States of America
- Department of Pathology (Neuropathology), Rush University Medical Center, Chicago, Illinois, United States of America
| | - Philip L. De Jager
- Department of Neurology, Center for Translational & Computational Neuroimmunology, Columbia University Medical Center, New York, New York, United States of America
- Cell Circuits Program, Broad Institute, Cambridge, Massachusetts, United States of America
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, United States of America
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, United States of America
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Abstract
The reproducibility of bioinformatics analyses can be elevated to equal status with biological discovery. To achieve this, reproducibility must become part of the process, not an afterthought.
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Affiliation(s)
| | - Laurent Gatto
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
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Arshad OA, Danna V, Petyuk VA, Piehowski PD, Liu T, Rodland KD, McDermott JE. An Integrative Analysis of Tumor Proteomic and Phosphoproteomic Profiles to Examine the Relationships Between Kinase Activity and Phosphorylation. Mol Cell Proteomics 2019; 18:S26-S36. [PMID: 31227600 PMCID: PMC6692771 DOI: 10.1074/mcp.ra119.001540] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [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: 05/02/2019] [Revised: 06/18/2019] [Indexed: 12/18/2022] Open
Abstract
Phosphorylation of proteins is a key way cells regulate function, both at the individual protein level and at the level of signaling pathways. Kinases are responsible for phosphorylation of substrates, generally on serine, threonine, or tyrosine residues. Though particular sequence patterns can be identified that dictate whether a residue will be phosphorylated by a specific kinase, these patterns are not highly predictive of phosphorylation. The availability of large scale proteomic and phosphoproteomic data sets generated using mass-spectrometry-based approaches provides an opportunity to study the important relationship between kinase activity, substrate specificity, and phosphorylation. In this study, we analyze relationships between protein abundance and phosphopeptide abundance across more than 150 tumor samples and show that phosphorylation at specific phosphosites is not well correlated with overall kinase abundance. However, individual kinases show a clear and statistically significant difference in correlation among known phosphosite targets for that kinase and randomly selected phosphosites. We further investigate relationships between phosphorylation of known activating or inhibitory sites on kinases and phosphorylation of their target phosphosites. Combined with motif-based analysis, this approach can predict novel kinase targets and show which subsets of a kinase's target repertoire are specifically active in one condition versus another.
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Affiliation(s)
- Osama A Arshad
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Vincent Danna
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Paul D Piehowski
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352; School of Medicine, Oregon Health & Sciences University, Portland, OR 97239
| | - Jason E McDermott
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352; School of Medicine, Oregon Health & Sciences University, Portland, OR 97239.
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