Integrated Proteomics to Understand the Role of Neuritin (NRN1) as a mediator of Cognitive Resilience to Alzheimer’s Disease Pubblico

Abstract

The molecular mechanisms and pathways enabling certain individuals to remain cognitively normal despite high levels of Alzheimer’s disease (AD) pathology remain incompletely understood. These cognitively normal people with AD pathology are described as preclinical or asymptomatic AD (AsymAD) and appear to exhibit cognitive resilience to the clinical manifestations of AD dementia. The body of work presented here provides a novel and comprehensive network-based approach from cases clinically and pathologically defined as AsymAD to map resilience-associated pathways and contributes to mechanistic validation of resilience-associated targets. Multiplex tandem mass tag mass spectrometry (TMT-MS) proteomic data was generated on brain tissue from Brodmann area 6 and Brodmann area 37 (n=109 cases, n=218 total samples) and evaluated by consensus weighted gene correlation network analysis. Notably, Neuritin (NRN1), a neurotrophic factor previously linked to cognitive resilience, was identified as a hub protein in a module associated with synaptic biology. To validate the function of NRN1 with regard to the neurobiology of AD, we conducted microscopy and physiology experiments in a cellular model of AD. NRN1 provided dendritic spine resilience against amyloid-β (Aβ) and blocked Aβ-induced neuronal hyperexcitability in cultured neurons. To better understand the molecular mechanisms of resilience to Aβ provided by NRN1, we assessed how exogenous NRN1 alters the proteome of cultured neurons by TMT-MS and integrated the results with the human AD brain network. This revealed over-lapping synapse-related biology that linked NRN1-induced changes in cultured neurons with human pathways associated with cognitive resilience. Collectively, this work highlights the utility of integrating the proteome from human brain and model systems to advance our understanding of resilience-promoting mechanisms and prioritize therapeutic targets that mediate resilience to AD.

Table of Contents

Table of Contents                                                                                                              Page

1.0 Introduction: Alzheimer’s disease and cognitive resilience............................................ 12

1.1 Alzheimer’s disease: an overview…………………………………………………………… 13

1.1.1 Current impacts........................................................................................................... 13

1.1.2 Defining pathology....................................................................................................... 13

1.1.3 Genetic contributions................................................................................................... 13

1.1.4 Neuroinflammation....................................................................................................... 15

1.1.5 Disease origins and progression................................................................................... 15

1.1.6 Additional risk factors and modifiers ............................................................................. 16

1.1.7 Current treatment options ............................................................................................ 17

1.2 Cognitive resilience........................................................................................................... 18

1.2.1 Healthy brain aging...................................................................................................... 19

1.2.2 Cognitive resilience in AD............................................................................................. 19

1.2.3 Resilience vs reserve................................................................................................... 20

1.3 Synaptic resilience............................................................................................................. 20

1.3.1 Dendritic spines........................................................................................................... 20

1.3.2 Spine changes in aging and disease............................................................................. 21

1.4 Resilience candidates and NRN1..................................................................................... 22

1.4.1 Resilience candidates.................................................................................................. 23

1.4.2 Neuritin....................................................................................................................... 23

1.5 Research aims and contributions...................................................................................... 24

1.6 Figures............................................................................................................................... 27

Figure 1.1: Overview of Alzheimer’s disease........................................................................... 26

Figure 1.2: Features of cognitively resilient individuals............................................................. 27

Figure 1.3: Neuritin (NRN1) as a candidate resilience-promoting protein.................................. 28

2.0 Discovery Proteomics to characterize molecular signatures in cognitively resilient cohorts    30

2.1 Introduction........................................................................................................................ 30

2.2 Results............................................................................................................................... 33

2.2.1 Proteomic measurements align with neuropathological scores ....................................... 33

2.2.2 Regional brain co-expression network analysis reveals modules associated with AD pathology and cognition..................................................................................................................... 35

2.2.3 Nomination of resilience-associated modules and NRN1 as a top protein candidate......... 36

2.3 Materials and methods...................................................................................................... 39

2.4 Discussion......................................................................................................................... 47

2.5  Figures.............................................................................................................................. 50

Figure 2.1: Proteomic measurements of amyloid and tau align with region-specific neuropathological burden…………………………………………………………………. 50

Figure 2.2: Case classification traits distribution…………………………………………………….. 52

Figure 2.3: Percent coverage and TMT batch correction across BA6 and BA37………………... 54

Figure 2.4: Amyloid beta peptide measurements……………………………………………………. 56

Figure 2.5: Consensus correlation network of a multi-region human brain proteome…………… 58

Figure 2.6: Consensus modules are highly preserved in BA6 and BA37…………………………. 60

Figure 2.7: Consensus network preservation………………………………………………………… 62

Figure 2.8: Integrated proteomics of human brain reveals NRN1 as a top resilience candidate. 64

Figure 2.9: Percent variance in protein expression explained by global cognition………………. 66

3.0 Neuritin (NRN1): candidate resilience-promoting protein................................................ 69

3.1 Introduction........................................................................................................................ 70

3.2 Results............................................................................................................................... 71

3.2.1 NRN1 prevents Aβ42-induced dendritic spine degeneration...................................... 71

3.2.2 NRN1 protects against Aβ42-induced neuronal hyperexcitability………………...…….. 72

3.2.3 NRN1 treatment alters the proteome in cultured neurons……………………………….. 73

3.2.4 NRN1 engages protein targets linked to cognitive resilience in human brain…………. 74

3.3 Materials and methods……………………………………………………………………..… 76

3.4 Discussion……………………………………………………………………………………… 85

3.5 Figures………………………………………………………………………………………..... 88

Figure 3.1: Aβ42-induced dendritic spine degeneration is blocked by NRN1……………….. 88

Figure 3.2: Analysis of dendritic spine length and head diameter among thin, stubby, mushroom spines and filopodia …………………………………………………………………... 90

Figure 3.3: Aggregation of Aβ in the presence or absence of NRN1…………………………. 92

Figure 3.4: NRN1 protects against Aβ42-induced neuronal hyperexcitability……………...… 94

Figure 3.5: Total number of active neurons per microelectrode array………………………… 96

Figure 3.6: NRN1 treatment induces changes in the neuronal proteome related to broad synaptic functions…………………………………………………………………………………… 98

Figure 3.7: NRN1 engages proteins within modules linked to cognitive resilience in human brain..……………………………………………………………………………………………….. 100

4.0 Discussion and future directions……………………………………………….…………… 102

4.1 Summary and contributions………………………………………………………………… 103

4.2 Future directions……………………………………………………………………………... 104

4.2.1 Additional consensus network modules…………………..…………………………...… 104

4.2.2 Possible neuroimmune functions of NRN1………………………………………………. 105

4.2.3 Extensions of the current framework………………………………………………...…… 106

4.2.4 NRN1 biology……………………………………………………………………………….. 107

4.2.5 Model systems for studying cognitive resilience………………………………………... 108

4.3 Additional considerations…………………………………………………………………… 109

4.3.1 Asymptomatic vs preclinical………………………………………………………………...109

4.3.2 NRN1 as a potential biomarker……………………………………………………………..110

4.3.3 An integrative, non-linear workflow……………………………………………………….. 111

4.4 Figures………………………………………………………………………………………... 112

Figure 4.1: schematic representation of dissertation overview………………………………. 112

5.0 References……………………………………………...…………………..…………………… 113

 

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School	Laney Graduate School
Department	Biological and Biomedical Sciences
Subfield / Discipline	Neuroscience
Degree	Ph.D.
Submission	Dissertation
Language	English
Research Field	Biology, Bioinformatics Biology, Molecular Nanoscience
Parola chiave	Bioinformatics Alzheimer's disease Cognitive Resilience Proteomics
Committee Chair / Thesis Advisor	Nicholas Seyfried , Emory University
Committee Members	Matt Rowan, Emory University Gary Bassell, Emory University Shannon Gourley, Emory University Jeremy Herskowitz, University of Alabama Birmingham

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