Resolving Proteomic and Structural Alterations of Superoxide Dismutase 1 in Amyotrophic Lateral Sclerosis Through Mass Spectrometry Open Access

Manly, Lester S. (Spring 2026)

Permanent URL: https://etd.library.emory.edu/concern/etds/bz60cz024?locale=en
Published

Abstract

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by progressive motor neuron loss and limited therapeutic options. A major challenge in ALS research is linking molecular alterations across biological scales - from proteome-wide changes to protein-level structural mechanisms - into a unified understanding of disease pathogenesis. This dissertation addresses this challenge through an integrated, multiscale investigation of superoxide dismutase 1 (SOD1)-associated ALS.

First, systems-level quantitative proteomics was applied to spinal cord tissue from hSOD1G37R mice to define proteomic alterations at motor symptom onset. Tandem mass tag (TMT)-based proteomics combined with weighted gene co-expression network analysis (WGCNA) identified coordinated disruptions in synaptic, mitochondrial, immune, and proteostasis pathways. Cross-species network comparisons revealed that synaptic dysfunction is a conserved feature between mouse spinal cord and human ALS cerebrospinal fluid, supporting its translational relevance. Treatment with the ALS therapeutic candidate CuATSM selectively modulated disease-associated pathways, partially restoring neuronal and metabolic functions while reducing neuroinflammatory signaling.

Second, methodological advances in mass spectrometry were developed to enable proteoform-resolved characterization of proteins. These included the implementation of electron capture dissociation for top-down proteomics and its application to chromatographic timescale analyses, expanding the ability to characterize intact protein species.

Finally, native ion mobility–mass spectrometry combined with collision-induced unfolding and electron capture dissociation was used to resolve structural and metalloproteoform heterogeneity of SOD1. These studies demonstrate how metal occupancy and ALS-associated mutations alter SOD1 stability and conformation, providing mechanistic insight into protein misfolding and toxicity.

Together, this work establishes an integrated framework that connects systems-level proteomic networks with proteoform-resolved structural biology to define conserved molecular mechanisms and vulnerabilities in ALS. These findings support a proteoform-centric model of SOD1 toxicity and provide a foundation for therapeutic strategies targeting metallation state and protein stability.

Table of Contents

List of Figures 1

List of Tables 3

List of Supplementals 4

List of Acronyms & Abbreviations 5

Chapter 1 - Introductions 6

Preface 6

Introduction 6

Amyotrophic Lateral Sclerosis 10

Superoxide Dismutase 1 16

Mass Spectrometry 23

The Dissertation 30

Chapter 2 - Proteomics reveals immune, synaptic and metabolic alterations modulated by CuATSM in hSOD1G37R mice 31

Abstract 31

Introduction 33

Materials and Methods 35

Results 42

Discussion & Conclusions 55

Figures & Tables 63

Chapter 3 - Electron Capture Dissociation for Discovery Top-Down Proteomics of Peptides and Small Proteins on Chromatographic Time Scale 79

Abstract 79

Introduction 81

Experimental Section 85

Results & Discussion 89

Conclusions 96

Figures & Tables 97

Supplemental Figures & Tables 107

Chapter 4 - Structural and Stability Characterization of Superoxide Dismutase 1 Metalloproteoforms Using Collision-Induced Unfolding, Ion Mobility, and Electron Capture Dissociation 113

Abstract 113

Introduction 115

Experimental Section 117

Results & Discussion 121

Conclusions 132

Figures & Tables 133

Supplemental Figures & Tables 157

Chapter 5 – Discussions, Future Directions, and Perspectives 162

Overview 162

SOD1 Toxic Intermediate Hypothesis 165

Interpreting SOD1 Models in ALS Pathogenesis and Therapy 166

Connecting Proteome and Proteoform Insights 168

Translational Relevance 170

Future Directions 172

Perspectives 174

Chapter 6 - Conclusions 176

References 178

About this Dissertation

Rights statement
  • Permission granted by the author to include this thesis or dissertation in this repository. All rights reserved by the author. Please contact the author for information regarding the reproduction and use of this thesis or dissertation.
School
Department
Subfield / Discipline
Degree
Submission
Language
  • English
Research Field
Keyword
Committee Chair / Thesis Advisor
Committee Members
Last modified

Primary PDF

Thumbnail Title Date Uploaded Actions
Resolving Proteomic and Structural Alterations of Superoxide Dismutase 1 in Amyotrophic Lateral Sclerosis Through Mass Spectrometry () 2026-05-04 16:55:46 -0400

Supplemental Files

Thumbnail Title Date Uploaded Actions