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Zammit AR, Klein HU, Yu L, Levey AI, Seyfried NT, Wingo AP, Wingo TS, Schneider JA, Bennett DA, Buchman AS. Proteome-wide Analyses Identified Cortical Proteins Associated With Resilience for Varied Cognitive Abilities. Neurology 2024; 102:e207816. [PMID: 38165375 PMCID: PMC10834136 DOI: 10.1212/wnl.0000000000207816] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 09/26/2023] [Indexed: 01/03/2024] Open
Abstract
BACKGROUND AND OBJECTIVES Prior work suggests that cognitive resilience may contribute to the heterogeneity of cognitive decline. This study examined whether distinct cortical proteins provide resilience for different cognitive abilities. METHODS Participants were from the Religious Orders Study or the Rush Memory and Aging Project who had undergone annual assessments of 5 cognitive abilities and postmortem assessment of 9 Alzheimer disease and related dementia (ADRD) pathologies. Proteome-wide examination of the dorsolateral prefrontal cortex using tandem mass tag and liquid chromatography-mass spectrometry yielded 8,425 high-abundance proteins. We applied linear mixed-effect models to quantify residual cognitive change (cognitive resilience) of 5 cognitive abilities by regressing out cognitive decline related to age, sex, education, and indices of ADRD pathologies. Then we added terms for each of the individual proteins to identify cognitive resilience proteins associated with the different cognitive abilities. RESULTS We included 604 decedents (69% female; mean age at death = 89 years) with proteomic data. A total of 47 cortical proteins that provide cognitive resilience were identified: 22 were associated with specific cognitive abilities, and 25 were common to at least 2 cognitive abilities. NRN1 was the only protein that was associated with more than 2 cognitive abilities (semantic memory: estimate = 0.020, SE = 0.004, p = 2.2 × 10-6; episodic memory: estimate = 0.029, SE = 0.004, p = 5.8 × 10-1; and working memory: estimate = 0.021, SE = 0.004, p = 1.2 × 10-7). Exploratory gene ontology analysis suggested that among top molecular pathways, mitochondrial translation was a molecular mechanism providing resilience in episodic memory, while nuclear-transcribed messenger RNA catabolic processes provided resilience in working memory. DISCUSSION This study identified cortical proteins associated with various cognitive abilities. Differential associations across abilities may reflect distinct underlying biological pathways. These data provide potential high-value targets for further mechanistic and drug discovery studies to develop targeted treatments to prevent loss of cognition.
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Affiliation(s)
- Andrea R Zammit
- From the Rush Alzheimer's Disease Center (A.R.Z., L.Y., J.A.S., D.A.B., A.S.B.), and Departments of Psychiatry and Behavioral Sciences (A.R.Z.), Neurological Sciences (L.Y., J.A.S., D.A.B., A.S.B.), and Pathology (J.A.S.), Rush University Medical Center, Chicago, IL; Department of Neurology (H.-U.K.), Columbia University Medical Center, New York, NY; Departments of Neurology (A.I.L., N.T.S., T.S.W.) Psychiatry (A.P.W.), and Human Genetics (T.S.W.), and the Goizueta Alzheimer's Disease Center (T.S.W.), Emory University School of Medicine, Atlanta, GA; Department of Biochemistry (N.T.S.), Emory University, Atlanta, GA; and Division of Mental Health (A.P.W.), Atlanta VA Medical Center, Decatur, GA
| | - Hans-Ulrich Klein
- From the Rush Alzheimer's Disease Center (A.R.Z., L.Y., J.A.S., D.A.B., A.S.B.), and Departments of Psychiatry and Behavioral Sciences (A.R.Z.), Neurological Sciences (L.Y., J.A.S., D.A.B., A.S.B.), and Pathology (J.A.S.), Rush University Medical Center, Chicago, IL; Department of Neurology (H.-U.K.), Columbia University Medical Center, New York, NY; Departments of Neurology (A.I.L., N.T.S., T.S.W.) Psychiatry (A.P.W.), and Human Genetics (T.S.W.), and the Goizueta Alzheimer's Disease Center (T.S.W.), Emory University School of Medicine, Atlanta, GA; Department of Biochemistry (N.T.S.), Emory University, Atlanta, GA; and Division of Mental Health (A.P.W.), Atlanta VA Medical Center, Decatur, GA
| | - Lei Yu
- From the Rush Alzheimer's Disease Center (A.R.Z., L.Y., J.A.S., D.A.B., A.S.B.), and Departments of Psychiatry and Behavioral Sciences (A.R.Z.), Neurological Sciences (L.Y., J.A.S., D.A.B., A.S.B.), and Pathology (J.A.S.), Rush University Medical Center, Chicago, IL; Department of Neurology (H.-U.K.), Columbia University Medical Center, New York, NY; Departments of Neurology (A.I.L., N.T.S., T.S.W.) Psychiatry (A.P.W.), and Human Genetics (T.S.W.), and the Goizueta Alzheimer's Disease Center (T.S.W.), Emory University School of Medicine, Atlanta, GA; Department of Biochemistry (N.T.S.), Emory University, Atlanta, GA; and Division of Mental Health (A.P.W.), Atlanta VA Medical Center, Decatur, GA
| | - Allan I Levey
- From the Rush Alzheimer's Disease Center (A.R.Z., L.Y., J.A.S., D.A.B., A.S.B.), and Departments of Psychiatry and Behavioral Sciences (A.R.Z.), Neurological Sciences (L.Y., J.A.S., D.A.B., A.S.B.), and Pathology (J.A.S.), Rush University Medical Center, Chicago, IL; Department of Neurology (H.-U.K.), Columbia University Medical Center, New York, NY; Departments of Neurology (A.I.L., N.T.S., T.S.W.) Psychiatry (A.P.W.), and Human Genetics (T.S.W.), and the Goizueta Alzheimer's Disease Center (T.S.W.), Emory University School of Medicine, Atlanta, GA; Department of Biochemistry (N.T.S.), Emory University, Atlanta, GA; and Division of Mental Health (A.P.W.), Atlanta VA Medical Center, Decatur, GA
| | - Nicholas T Seyfried
- From the Rush Alzheimer's Disease Center (A.R.Z., L.Y., J.A.S., D.A.B., A.S.B.), and Departments of Psychiatry and Behavioral Sciences (A.R.Z.), Neurological Sciences (L.Y., J.A.S., D.A.B., A.S.B.), and Pathology (J.A.S.), Rush University Medical Center, Chicago, IL; Department of Neurology (H.-U.K.), Columbia University Medical Center, New York, NY; Departments of Neurology (A.I.L., N.T.S., T.S.W.) Psychiatry (A.P.W.), and Human Genetics (T.S.W.), and the Goizueta Alzheimer's Disease Center (T.S.W.), Emory University School of Medicine, Atlanta, GA; Department of Biochemistry (N.T.S.), Emory University, Atlanta, GA; and Division of Mental Health (A.P.W.), Atlanta VA Medical Center, Decatur, GA
| | - Aliza P Wingo
- From the Rush Alzheimer's Disease Center (A.R.Z., L.Y., J.A.S., D.A.B., A.S.B.), and Departments of Psychiatry and Behavioral Sciences (A.R.Z.), Neurological Sciences (L.Y., J.A.S., D.A.B., A.S.B.), and Pathology (J.A.S.), Rush University Medical Center, Chicago, IL; Department of Neurology (H.-U.K.), Columbia University Medical Center, New York, NY; Departments of Neurology (A.I.L., N.T.S., T.S.W.) Psychiatry (A.P.W.), and Human Genetics (T.S.W.), and the Goizueta Alzheimer's Disease Center (T.S.W.), Emory University School of Medicine, Atlanta, GA; Department of Biochemistry (N.T.S.), Emory University, Atlanta, GA; and Division of Mental Health (A.P.W.), Atlanta VA Medical Center, Decatur, GA
| | - Thomas S Wingo
- From the Rush Alzheimer's Disease Center (A.R.Z., L.Y., J.A.S., D.A.B., A.S.B.), and Departments of Psychiatry and Behavioral Sciences (A.R.Z.), Neurological Sciences (L.Y., J.A.S., D.A.B., A.S.B.), and Pathology (J.A.S.), Rush University Medical Center, Chicago, IL; Department of Neurology (H.-U.K.), Columbia University Medical Center, New York, NY; Departments of Neurology (A.I.L., N.T.S., T.S.W.) Psychiatry (A.P.W.), and Human Genetics (T.S.W.), and the Goizueta Alzheimer's Disease Center (T.S.W.), Emory University School of Medicine, Atlanta, GA; Department of Biochemistry (N.T.S.), Emory University, Atlanta, GA; and Division of Mental Health (A.P.W.), Atlanta VA Medical Center, Decatur, GA
| | - Julie A Schneider
- From the Rush Alzheimer's Disease Center (A.R.Z., L.Y., J.A.S., D.A.B., A.S.B.), and Departments of Psychiatry and Behavioral Sciences (A.R.Z.), Neurological Sciences (L.Y., J.A.S., D.A.B., A.S.B.), and Pathology (J.A.S.), Rush University Medical Center, Chicago, IL; Department of Neurology (H.-U.K.), Columbia University Medical Center, New York, NY; Departments of Neurology (A.I.L., N.T.S., T.S.W.) Psychiatry (A.P.W.), and Human Genetics (T.S.W.), and the Goizueta Alzheimer's Disease Center (T.S.W.), Emory University School of Medicine, Atlanta, GA; Department of Biochemistry (N.T.S.), Emory University, Atlanta, GA; and Division of Mental Health (A.P.W.), Atlanta VA Medical Center, Decatur, GA
| | - David A Bennett
- From the Rush Alzheimer's Disease Center (A.R.Z., L.Y., J.A.S., D.A.B., A.S.B.), and Departments of Psychiatry and Behavioral Sciences (A.R.Z.), Neurological Sciences (L.Y., J.A.S., D.A.B., A.S.B.), and Pathology (J.A.S.), Rush University Medical Center, Chicago, IL; Department of Neurology (H.-U.K.), Columbia University Medical Center, New York, NY; Departments of Neurology (A.I.L., N.T.S., T.S.W.) Psychiatry (A.P.W.), and Human Genetics (T.S.W.), and the Goizueta Alzheimer's Disease Center (T.S.W.), Emory University School of Medicine, Atlanta, GA; Department of Biochemistry (N.T.S.), Emory University, Atlanta, GA; and Division of Mental Health (A.P.W.), Atlanta VA Medical Center, Decatur, GA
| | - Aron S Buchman
- From the Rush Alzheimer's Disease Center (A.R.Z., L.Y., J.A.S., D.A.B., A.S.B.), and Departments of Psychiatry and Behavioral Sciences (A.R.Z.), Neurological Sciences (L.Y., J.A.S., D.A.B., A.S.B.), and Pathology (J.A.S.), Rush University Medical Center, Chicago, IL; Department of Neurology (H.-U.K.), Columbia University Medical Center, New York, NY; Departments of Neurology (A.I.L., N.T.S., T.S.W.) Psychiatry (A.P.W.), and Human Genetics (T.S.W.), and the Goizueta Alzheimer's Disease Center (T.S.W.), Emory University School of Medicine, Atlanta, GA; Department of Biochemistry (N.T.S.), Emory University, Atlanta, GA; and Division of Mental Health (A.P.W.), Atlanta VA Medical Center, Decatur, GA
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Zhu T, Li Y, Pang Y, Han Y, Li J, Wang Z, Liu X, Li H, Hua Y, Jiang H, Teng H, Quan J, Liu Y, Geng M, Li M, Hui F, Liu J, Qiu Q, Li Q, Ren Y. Chromosome-level genome assembly of Lethenteron reissneri provides insights into lamprey evolution. Mol Ecol Resour 2020; 21:448-463. [PMID: 33053263 DOI: 10.1111/1755-0998.13279] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 09/29/2020] [Accepted: 10/01/2020] [Indexed: 11/29/2022]
Abstract
The reissner lamprey Lethenteron reissneri, belonging to the class Cyclostomata, serves as a bridge between invertebrates and jawed vertebrates, and is considered the sister group of jawed vertebrates. However, despite this evolutionary significance, the genetic mechanisms underlying the adaptive evolution of the lamprey lineage remain unclear. Here, we assembled a 1.06 Gb chromosome-level draft genome of L. reissneri, with 72 chromosomes (ranging in length from 4.5 Mb to 25.9 Mb) and a scaffold N50 length of 13.23 Mb. Genome quality comparisons revealed that the reissner lamprey genome has higher completeness and contiguity than the previously published sea lamprey and Japanese lamprey genomes. Moreover, reissner lamprey, sea lamprey, and Japanese lamprey species share similar transposable element profiles and Hox gene cluster compositions, suggesting that a burst of transposable element activity and whole genome duplication occurred before their divergence. Additionally, the Lip gene copy numbers, which have been studied for their functions in the host defence system, were found to be expanded uniquely in lamprey lineages, suggesting key roles for these genes in lamprey evolution and adaptation. We also identified two neural-related genes, Nrn1 and Unc13a, with copy number expansions in jawed vertebrates, which may be functionally relevant to the origin of lamprey brains. Hence, this study not only provides the first chromosome-level reference genome for Cyclostomata, but also highlights features of the unique biology and adaptive evolution of the lamprey lineage.
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Affiliation(s)
- Ting Zhu
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Yongxin Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Yue Pang
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Yinglun Han
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Jun Li
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Zhongkai Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Xin Liu
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Haorong Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Yishan Hua
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Hui Jiang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Hongming Teng
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Jian Quan
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Yu Liu
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Ming Geng
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Meiao Li
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Fan Hui
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Jinzhao Liu
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Qiang Qiu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Qingwei Li
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Yandong Ren
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
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Yu L, Tasaki S, Schneider JA, Arfanakis K, Duong DM, Wingo AP, Wingo TS, Kearns N, Thatcher GRJ, Seyfried NT, Levey AI, De Jager PL, Bennett DA. Cortical Proteins Associated With Cognitive Resilience in Community-Dwelling Older Persons. JAMA Psychiatry 2020; 77:1172-1180. [PMID: 32609320 PMCID: PMC7330835 DOI: 10.1001/jamapsychiatry.2020.1807] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 04/22/2020] [Indexed: 12/15/2022]
Abstract
Importance Identifying genes and proteins for cognitive resilience (ie, targets that may be associated with slowing or preventing cognitive decline regardless of the presence, number, or combination of common neuropathologic conditions) provides a complementary approach to developing novel therapeutics for the treatment and prevention of Alzheimer disease and related dementias. Objective To identify proteins associated with cognitive resilience via a proteome-wide association study of the human dorsolateral prefrontal cortex. Design, Setting, and Participants This study used data from 391 community-dwelling older persons who participated in the Religious Orders Study and the Rush Memory and Aging Project. The Religious Orders Study began enrollment January 1, 1994, and the Rush Memory and Aging Project began enrollment September 1, 1997, and data were collected and analyzed through October 23, 2019. Exposures Participants had undergone annual detailed clinical examinations, postmortem evaluations, and tandem mass tag proteomics analyses. Main Outcomes and Measures The outcome of cognitive resilience was defined as a longitudinal change in cognition over time after controlling for common age-related neuropathologic indices, including Alzheimer disease, Lewy bodies, transactive response DNA-binding protein 43, hippocampal sclerosis, infarcts, and vessel diseases. More than 8000 high abundance proteins were quantified from frozen dorsolateral prefrontal cortex tissue using tandem mass tag and liquid chromatography-mass spectrometry. Results There were 391 participants (273 women); their mean (SD) age was 79.7 (6.7) years at baseline and 89.2 (6.5) years at death. Eight cortical proteins were identified in association with cognitive resilience: a higher level of NRN1 (estimate, 0.140; SE, 0.024; P = 7.35 × 10-9), ACTN4 (estimate, 0.321; SE, 0.065; P = 9.94 × 10-7), EPHX4 (estimate, 0.198; SE, 0.042; P = 2.13 × 10-6), RPH3A (estimate, 0.148; SE, 0.031; P = 2.58 × 10-6), SGTB (estimate, 0.211; SE, 0.045; P = 3.28 × 10-6), CPLX1 (estimate, 0.136; SE, 0.029; P = 4.06 × 10-6), and SH3GL1 (estimate, 0.179; SE, 0.039; P = 4.21 × 10-6) and a lower level of UBA1 (estimate, -0.366; SE, 0.076; P = 1.43 × 10-6) were associated with greater resilience. Conclusions and Relevance These protein signals may represent novel targets for the maintenance of cognition in old age.
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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
| | - 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
| | - Konstantinos Arfanakis
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois
- Department of Diagnostic Radiology and Nuclear Medicine, Rush University Medical Center, Chicago, Illinois
- Department of Biomedical Engineering, Illinois Institute of Technology, Chicago
| | - Duc M. Duong
- Department of Biochemistry, Emory University, Atlanta, Georgia
| | - Aliza P. Wingo
- Division of Mental Health, Atlanta Veterans Affairs Medical Center, Decatur, Georgia
- Department of Psychiatry, Emory University School of Medicine, Atlanta, Georgia
| | - Thomas S. Wingo
- Department of Neurology, Emory University, Atlanta, Georgia
- Department of Human Genetics, Emory University, Atlanta, Georgia
| | - Nicola Kearns
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois
| | - Gregory R. J. Thatcher
- Department of Pharmaceutical Sciences, University of Illinois College of Pharmacy, Chicago
| | | | - Allan I. Levey
- Department of Neurology, Emory University, Atlanta, Georgia
| | - 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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