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Hypothesis Overview

Introduction

This page provides a comprehensive overview of research hypotheses in neurodegenerative disease research, covering major mechanistic theories and emerging concepts that explain the pathogenesis of Alzheimer's Disease (AD), Parkinson's Disease (PD), Amyotrophic Lateral Sclerosis (ALS), and related disorders. Understanding these hypotheses is critical for developing effective therapeutic interventions and biomarkers. [@selkoe2023]

Mechanistic Framework

flowchart TD A["Genetic Risk APOE, LRRK2, SOD1"] --> B["Molecular Triggers Abeta, alpha-syn, TDP-43"] B --> C{"Pathogenic Mechanisms"} C --> D["Protein Aggregation Misfolding and Oligomers"] C --> E["Cellular Dysfunction Mitochondria, Autophagy"] C --> F["Network Failure Synaptic, Circuit"] C --> G["Neuroinflammation Microglia, Astrocytes"] D --> H["Prion-Like Spread Template Propagation"] E --> I["Energy Failure Oxidative Stress"] F --> J["Neural Network Disconnectivity"] G --> K["Cytokine Storm Chronic Inflammation"] H --> L["Brain Region Propagation"] I --> M["Neuronal Death Apoptosis"] J --> N["Cognitive/Motor Decline"] K --> L L --> O["Clinical Manifestation"] M --> O N --> O style A fill:#0a1929,stroke:#333,color:#e0e0e0 style D fill:#3a3000,stroke:#333,color:#e0e0e0 style L fill:#3b1114,stroke:#333,color:#e0e0e0 style O fill:#3b1114,stroke:#333,color:#e0e0e0

Major Mechanistic Hypotheses

Alzheimer's Disease

...

Hypothesis Overview

Introduction

This page provides a comprehensive overview of research hypotheses in neurodegenerative disease research, covering major mechanistic theories and emerging concepts that explain the pathogenesis of Alzheimer's Disease (AD), Parkinson's Disease (PD), Amyotrophic Lateral Sclerosis (ALS), and related disorders. Understanding these hypotheses is critical for developing effective therapeutic interventions and biomarkers. [@selkoe2023]

Mechanistic Framework

Mermaid diagram (expand to render)

Major Mechanistic Hypotheses

Alzheimer's Disease

| Hypothesis | Support Level | Key Evidence | Testability | Therapeutic Potential |
|------------|---------------|---------------|-------------|---------------------|
| [Amyloid cascade](/mechanisms/amyloid-cascade) | Strong | Genetic, biochemical, biomarker | 10/10 | 8/10 |
| [Tau spreading](/mechanisms/tau-pathology) | Strong | Animal models, human imaging | 10/10 | 8/10 |
| [Neuroinflammation](/mechanisms/neuroinflammation) | Moderate-Strong | Genetics, imaging, CSF | 8/10 | 9/10 |
| [Mitochondrial dysfunction](/mechanisms/mitochondrial-dysfunction) | Moderate | Biochemical, genetic | 7/10 | 7/10 |
| [Metabolic failure](/mechanisms/brain-metabolism) | Emerging | Genetics, imaging, PET | 7/10 | 8/10 |
| [Network failure](/mechanisms/network-degeneration) | Strong | fMRI, EEG, connectivity | 9/10 | 7/10 |

Parkinson's Disease

| Hypothesis | Support Level | Key Evidence | Testability | Therapeutic Potential |
|------------|---------------|---------------|-------------|---------------------|
| [Alpha-synuclein aggregation](/proteins/alpha-synuclein) | Strong | Genetic, pathological, biochemical | 10/10 | 9/10 |
| [Mitochondrial dysfunction](/mechanisms/mitochondrial-dysfunction) | Strong | Genetics, biochemical, iPSC | 9/10 | 9/10 |
| [Neuroinflammation](/mechanisms/neuroinflammation) | Moderate-Strong | Imaging, genetics, CSF | 8/10 | 8/10 |
| [Calcium dysregulation](/mechanisms/calcium-dysregulation) | Moderate | Electrophysiology, imaging | 7/10 | 7/10 |
| [Metal dyshomeostasis](/mechanisms/metal-homeostasis) | Limited | Biochemical | 6/10 | 6/10 |
| [Vesicle trafficking](/mechanisms/vesicle-trafficking) | Moderate | Cell biology, genetics | 7/10 | 8/10 |

Amyotrophic Lateral Sclerosis

| Hypothesis | Support Level | Key Evidence | Testability | Therapeutic Potential |
|------------|---------------|---------------|-------------|---------------------|
| [RNA metabolism](/mechanisms/rna-metabolism) | Strong | Genetics, pathology, biochemistry | 8/10 | 7/10 |
| [Protein aggregation](/proteins/misfolded-proteins) | Strong | Pathology, genetics | 9/10 | 8/10 |
| [Mitochondrial dysfunction](/mechanisms/mitochondrial-dysfunction) | Moderate | Biochemical, cell models | 7/10 | 7/10 |
| [Neuroinflammation](/mechanisms/neuroinflammation) | Moderate-Strong | Imaging, genetics, CSF | 8/10 | 8/10 |
| [Cytoskeletal defects](/mechanisms/cytoskeleton-dysfunction) | Moderate | Pathology, genetics | 7/10 | 6/10 |

Evidence Assessment

Alzheimer's Disease Hypotheses

Amyloid Cascade Hypothesis — STRONG

The amyloid cascade hypothesis, first proposed by Hardy and Higgins in 1992, remains the dominant framework for understanding AD pathogenesis. [@Hardy1992] The hypothesis posits that accumulation of amyloid-beta (Aβ) peptides, particularly the Aβ42 isoform, is the primary initiating event that triggers a cascade of downstream pathologies including tau hyperphosphorylation, neuroinflammation, synaptic loss, and neuronal death.

Evidence Breakdown:

Genetic Evidence (Strong): [APP](/genes/app) and [PSEN1](/genes/psen1)/[PSEN2](/genes/psen2) mutations cause early-onset familial AD with 100% penetrance; [APOE](/proteins/apoe) ε4 allele increases risk 3-4x and reduces Aβ clearance
Biochemical Evidence (Strong): Aβ plaques are the defining pathological feature; Aβ oligomers are more toxic than fibrils; CSF Aβ42 decreases before clinical symptoms
Animal Models (Strong): APP/PS1 mice develop plaques and some tau pathology; anti-Aβ antibodies reduce plaques but show modest cognitive benefits (lecanemab, donanemab)
Clinical Trials (Moderate): Aducanumab, lecanemab, and donanemab successfully reduce plaques but clinical benefits are modest, suggesting Aβ alone is insufficient

Confidence Level: Strong — Supported by multiple independent lines of evidence including genetics, biochemistry, imaging, and therapeutic response.

Testability Score: 10/10 — Easily testable via amyloid PET, CSF biomarkers, and anti-amyloid antibodies.

Therapeutic Potential Score: 8/10 — Anti-amyloid therapies have shown efficacy but disease modification requires combination approaches.

Tau Spreading Hypothesis — STRONG

The tau spreading hypothesis, based on Braak staging, proposes that tau pathology spreads along neural circuits in a predictable pattern beginning in the entorhinal cortex and progressing to the hippocampus and neocortex. [@braak2003] This prion-like propagation model explains the pattern of memory impairment followed by cortical deficits in AD.

Evidence Breakdown:

Neuropathology (Strong): Braak stages correlate with clinical severity; tau pathology follows anatomically connected pathways
Imaging (Strong): Tau PET ligands (Flortaucipir) show progressive spreading that correlates with cognitive decline
Biomarkers (Strong): CSF p-tau181 and p-tau217 increase as tau pathology spreads; blood-based p-tau markers show promise
Experimental (Strong): Inoculation of tau aggregates into mouse brain induces spread; exosome-mediated transfer documented

Confidence Level: Strong — Extensive human and experimental evidence supports templated propagation of tau pathology.

Testability Score: 10/10 — Tau PET and fluid biomarkers allow direct visualization and measurement of tau pathology.

Therapeutic Potential Score: 8/10 — Anti-tau therapies in development; timing critical as interventions must occur before widespread spread.

Neuroinflammation Hypothesis — MODERATE-STRONG

The neuroinflammation hypothesis proposes that chronic activation of [microglia](/cell-types/microglia-neuroinflammation) and [astrocytes](/cell-types/astrocytes) drives neurodegeneration through pro-inflammatory cytokines, complement activation, and synaptic pruning. [@neuroinf2021] This hypothesis has gained substantial traction with the identification of genetic risk factors including [TREM2](/proteins/trem2) variants that impair microglial function.

Evidence Breakdown:

Genetics (Strong): TREM2, CD33, CR1 variants affect microglial function and AD risk; MS4A cluster variants influence CSF p-tau levels
Imaging (Strong): TSPO PET shows increased microglial activation in AD; correlates with disease severity
Biochemistry (Strong): Elevated cytokines (IL-1β, IL-6, TNF-α) in AD brain and CSF; complement activation products elevated
Experimental (Strong): Microglial depletion reduces amyloid pathology but increases tau pathology; complex bidirectional interactions

Confidence Level: Moderate-Strong — Strong genetic and imaging evidence but mechanisms remain incompletely characterized.

Testability Score: 8/10 — TSPO PET and cytokine measurements allow assessment of neuroinflammation status.

Therapeutic Potential Score: 9/10 — Microglial modulation represents a highly promising therapeutic strategy with multiple targets.

Parkinson's Disease Hypotheses

Alpha-Synuclein Aggregation — STRONG

The α-synuclein aggregation hypothesis is the central mechanistic framework for PD pathogenesis. [Alpha-synuclein](/proteins/alpha-synuclein) is a presynaptic protein that can misfold into β-sheet-rich aggregates that form Lewy bodies and propagate throughout the nervous system. [@park2014]

Evidence Breakdown:

Genetic Evidence (Strong): SNCA multiplications cause PD; point mutations (A53T, E46K, G50Q) cause familial PD; [GBA](/genes/gba) variants increase risk
Pathological Evidence (Strong): Lewy bodies in >95% of PD cases; contain aggregated α-synuclein; correlate with clinical progression
Experimental (Strong): α-synuclein preformed fibrils induce PD-like pathology in mice; propagation documented
Biomarkers (Strong): CSF α-synuclein seeding assays detect pathology; skin biopsy evidence of peripheral aggregation

Confidence Level: Strong — Multiple independent evidence streams converge on α-synuclein as central to PD pathogenesis.

Testability Score: 10/10 — Seed amplification assays (RT-QuIC, PMCA) detect α-synuclein pathology in CSF and tissue.

Therapeutic Potential Score: 9/10 — Immunotherapies (prasinezumab,运动抗体) in clinical trials; gene therapy approaches in development.

Mitochondrial Dysfunction — STRONG

The mitochondrial hypothesis proposes that defects in mitochondrial function, particularly in complex I of the electron transport chain, are central to PD pathogenesis. This is supported by toxin-induced parkinsonism (MPTP, rotenone) and genetic evidence.

Evidence Breakdown:

Toxin Models (Strong): MPTP, rotenone, and 6-OHDA selectively target dopaminergic neurons; reproduce key PD features
Genetics (Strong): [PARKIN](/genes/parkin), [PINK1](/genes/pink1), [DJ-1](/genes/dj1), [LRRK2](/genes/lrrk2) mutations affect mitophagy and mitochondrial quality control
iPSC Studies (Strong): Patient-derived neurons show mitochondrial dysfunction; complex I deficiency documented
Biochemistry (Strong): Complex I activity reduced in PD substantia nigra; oxidative stress markers elevated

Confidence Level: Strong — Robust evidence from multiple model systems and human tissue.

Testability Score: 9/10 — Multiple readouts including mitochondrial function assays, imaging, and genetic testing available.

Therapeutic Potential Score: 9/10 — Mitochondrial quality control enhancers in development; coenzyme Q10 and mitophagy modulators being tested.

Emerging Hypotheses

Cross-Disease Mechanisms

Mermaid diagram (expand to render)

Protein aggregation spreading: [Prion-like propagation](/hypotheses/proteinopathic-processes-spread-through-brain) — Template-directed misfolding allows pathological proteins to spread through connected neural networks. Documented for Abeta, tau, alpha-synuclein, TDP-43, and SOD1. [@prion2020]

Network degeneration: Connected circuit vulnerability — Neurodegeneration spreads along anatomically and functionally connected networks. Explains predictable patterns of progression in AD, PD, and FTLD.

Oligomeric toxicity: Soluble aggregates as toxic species — Soluble oligomers of Abeta, tau, and alpha-synuclein are more toxic than fibrillar plaques/tangles. Targeting oligomers may be more effective than removing plaques.

Glial involvement: [Astrocyte](/cell-types/astrocytes) and [microglia](/cell-types/microglia-neuroinflammation) contributions — Glial cells play active roles in disease progression through neuroinflammation, metabolic support, and debris clearance.

Novel Concepts

Epigenetic dysregulation: Aging-related changes in DNA methylation, histone modifications, and non-coding RNAs contribute to neurodegeneration.
Metabolic reprogramming: [Altered energy metabolism](/mechanisms/brain-metabolism) — Warburg-like metabolic shifts in neurons and glia.
Vesicle trafficking: Intracellular transport defects — Dysfunction in endosomal and lysosomal pathways.
Cellular senescence: Inflammatory senescence — Senescent neurons and glia produce SASP factors that drive pathology.

Hypothesis Testing Approaches

Experimental Models

| Hypothesis | Model Systems | Readouts | Key References |
|------------|---------------|----------|----------------|
| Amyloid | [APP](/genes/app)/[PS1](/genes/psen1) mice, iPSC neurons, organoids | Behavior, biochemistry, imaging | [@ Hardy1992] |
| Tau | P301S mice, iPSC-derived neurons, brain organoids | Pathology, behavior, tau PET | [@braak2003] |
| Synuclein | α-syn transgenic mice, iPSC neurons | Pathology, behavior, seeding assays | [@park2014] |
| Neuroinflammation | Mouse models, human iPSC glia | Imaging, cytokine profiling, RNA-seq | [@neuroinf2021] |
| Mitochondrial | C. elegans, drosophila, mouse models, human iPSC | Complex I activity, mitophagy markers | [@mito2023] |

Human Studies

| Hypothesis | Approaches | Biomarkers | Status |
|------------|------------|------------|--------|
| Amyloid | PET, CSF, blood | [Aβ42](/proteins/amyloid-beta), amyloid PET | Validated |
| Tau | PET, CSF, blood | p-tau181, p-tau217, tau PET | Validated |
| Inflammation | PET, CSF, blood | TSPO, cytokines, soluble receptors | Validated |
| Neurodegeneration | MRI, PET, EEG | Connectivity, metabolism, network dynamics | Validated |
| Synuclein | CSF, tissue, skin biopsy | Seed amplification, RT-QuIC | Emerging |

Historical Evolution

AD Hypotheses

1980s: Cholinergic hypothesis — Basal forebrain cholinergic neuron loss causes cognitive deficits (now known to be downstream)

1990s: [Amyloid cascade hypothesis](/mechanisms/amyloid-cascade) — Aβ accumulation initiates disease process (still dominant framework)

2000s: Tau hypothesis — Tau pathology mediates Aβ-induced neurodegeneration (strong supporting evidence)

2010s: Multi-hit hypothesis — Multiple mechanisms act simultaneously (current consensus)

2020s: Network failure hypothesis — Network dysfunction as final common pathway (integrating previous hypotheses)

PD Hypotheses

1950s: Dopamine deficiency — L-DOPA replacement therapy (symptomatic, not disease-modifying)

1990s: Mitochondrial hypothesis — Complex I dysfunction as primary event (strong evidence for subset of cases)

2000s: [Alpha-synuclein aggregation](/proteins/alpha-synuclein) — Lewy body pathology as defining feature (dominant current framework)

2010s: Spreading hypothesis — Prion-like propagation along neural networks (strong evidence)

2020s: Multiple hit model — Genetic susceptibility + environmental triggers + aging converge (current consensus)

Research Priorities

Most Promising Directions

Combination hypotheses: Multiple mechanisms — Targeting Aβ + tau + neuroinflammation simultaneously

Stage-specific models: Early vs. late disease — Different mechanisms dominate at different disease stages

Genetic subtypes: Mutation-specific mechanisms — PARKIN vs. LRRK2 vs. GBA vs. SNCA have different therapeutic implications

Precision medicine: Personalized models — Biomarker-guided selection of appropriate therapies

Therapeutic Target Priorities

| Target | Disease | Approach | Status | Priority |
|--------|---------|----------|--------|----------|
| Aβ plaques/tetramers | AD | Antibodies, small molecules | Phase 3-4 | High |
| Tau oligomers/fibrils | AD | Antibodies, inhibitors | Phase 1-2 | High |
| α-synuclein | PD | Antibodies, seeding inhibitors | Phase 1-3 | High |
| TREM2 | AD/PD | Agonists, modulators | Preclinical-Phase 1 | High |
| Mitochondrial quality | PD/AD | Mitophagy enhancers, antioxidants | Phase 2-3 | Medium |
| Neuroinflammation | AD/PD/ALS | Microglial modulators | Phase 1-2 | High |

Cross-Disease Mechanisms

Shared Pathways

Several pathogenic mechanisms are common across multiple neurodegenerative diseases:

| Pathway | AD | PD | ALS | FTLD |
|---------|----|----|-----|------|
| Protein aggregation | Aβ, tau | α-syn | TDP-43, SOD1 | TDP-43, tau |
| Mitochondrial dysfunction | ✓ | ✓++ | ✓ | ✓ |
| Neuroinflammation | ✓++ | ✓++ | ✓++ | ✓+ |
| RNA metabolism | ✓ | ✓ | ✓++ | ✓++ |
| Network failure | ✓++ | ✓+ | ✓+ | ✓+ |

Network-Based Degeneration

The network degeneration hypothesis proposes that pathological proteins spread along functionally connected neural networks, explaining the characteristic patterns of progression in each disease:

AD: Default mode network — Memory systems first, then cortical areas
PD: Motor and limbic networks — Substantia nigra to basal ganglia to cortex
ALS: Motor network — Cortical motor neurons to spinal cord
FTLD: Frontotemporal networks — Frontal and temporal cortical areas

[Hypotheses Index](/hypotheses) — Browse all hypothesis pages
[Hypothesis Rankings](/hypotheses/rankings) — Ranked list by research activity and evidence strength
[Hypotheses Dashboard](/hypotheses/dashboard) — Data visualizations and metrics
[Mechanisms](/mechanisms) — Detailed mechanism pages for each pathway

Disease-Specific Hypotheses

Alzheimer's Disease

[Amyloid plaque and neurofibrillary tangle deposition](/hypotheses/amyloid-plaque-neurofibrillary-tangle-depositi) — Dual pathology requirement for AD models
[Alzheimer's disease pathology originates in the hippocampus](/hypotheses/alzheimer's-disease-pathology-originates-hi) — Origin and spread pattern
[Tau pathology severity/Braak staging](/hypotheses/hyp_436169) — Clinical correlation with pathological staging
[Neuritic amyloid plaques pathologic synergy](/hypotheses/hyp_37312) — Amyloid-tau interaction

Parkinson's Disease

[Prion-like protein propagation](/hypotheses/proteinopathic-processes-spread-through-brain) — Template-directed misfolding
[Gut-immune-brain axis](/hypotheses/gut-immune-brain-axis-parkinsons) — Alpha-synuclein origin in gut
[Exercise-BDNF-mitochondrial resilience](/hypotheses/exercise-bdnf-mitochondrial-resilience-parkinsons) — Protective mechanisms

Cross-Disease Mechanisms

[Metabolic syndrome axis](/hypotheses/metabolic-syndrome-parkinsons-axis) — Systemic metabolic dysfunction
[NLRP3 inflammasome](/hypotheses/nlrp3-inflammasome-parkinsons) — Innate immune activation

External Links

[PubMed](https://pubmed.ncbi.nlm.nih.gov/) — Biomedical literature database
[KEGG Pathways](https://www.genome.jp/kegg/pathway.html) — Pathway databases
[Allen Brain Atlas](https://brain-map.org/) — Brain gene expression data
[Alzheimer's Disease Neuroimaging Initiative](https://adni.loni.usc.edu/) — ADNI research data
[Michael J. Fox Foundation](https://www.michaeljfox.org/) — Parkinson's disease research

References

[Selkoe DJ. Alzheimer's disease. Neuron. 2023](https://pubmed.ncbi.nlm.nih.gov/36893394/)

[Kalia LV, Lang AE. Parkinson's disease. Lancet. 2023](https://pubmed.ncbi.nlm.nih.gov/37573568/)

[Taylor JP, et al. ALS. Nat Rev Neurol. 2022](https://pubmed.ncbi.nlm.nih.gov/35543106/)

[Hardy JA, Higgins GA. Alzheimer's disease: the amyloid cascade hypothesis. Science. 1992](https://pubmed.ncbi.nlm.nih.gov/1560134/)

[Braak H, et al. Staging of Alzheimer-related cortical destruction. Eur Neurol. 2003](https://pubmed.ncbi.nlm.nih.gov/14606760/)

[Parkkinen L, et al. From alpha-synuclein to Parkinson's disease. Brain. 2014](https://pubmed.ncbi.nlm.nih.gov/25062693/)

[Gutierrez J, et al. Neurovascular unit dysfunction in neurodegenerative diseases. Nat Rev Neurosci. 2020](https://pubmed.ncbi.nlm.nih.gov/33077945/)

[Palop JJ, Mucke L. Network abnormalities and interneuron dysfunction in Alzheimer disease. Nat Rev Neurosci. 2019](https://pubmed.ncbi.nlm.nih.gov/31848461/)

[Heneka MT, et al. Neuroinflammation in Alzheimer's disease. Lancet Neurol. 2021](https://pubmed.ncbi.nlm.nih.gov/34016254/)

[Cómez-Gutierrez P, et al. Metabolic dysfunction in Alzheimer's disease. Trends Neurosci. 2022](https://pubmed.ncbi.nlm.nih.gov/35723874/)

[Sun N, et al. Mitochondrial dysfunction in neurodegenerative disease. Nat Rev Neurosci. 2023](https://pubmed.ncbi.nlm.nih.gov/37138114/)

[Chia JYY, et al. Protein aggregation in neurodegeneration. Nat Rev Neurol. 2021](https://pubmed.ncbi.nlm.nih/34580474/)

[Jucker M, et al. Prion-like mechanisms in neurodegenerative diseases. Nat Rev Neurosci. 2020](https://pubmed.ncbi.nlm.nih/32080227/)

Topics

[Hypotheses Overview](/hypotheses/overview) — This page
[Hypotheses Rankings](/hypotheses/rankings) — Ranked list by research activity
[Hypotheses Dashboard](/hypotheses/dashboard) — Data visualizations and metrics

Summary Statistics

Total Hypothesis Pages: 23+ hypothesis pages in this section
Primary Disease Coverage: Alzheimer's Disease, Parkinson's Disease, ALS, FTLD
Hypothesis Categories: Mechanistic, Therapeutic, Diagnostic, Epidemiological
Last Updated: This section is actively maintained and updated with new evidence

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📊 Evidence Profile Foundational

Evidence Balance

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Certainty

100%

Debates

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Incoming

77

Outgoing

116

0 supporting 0 contradicting 0 neutral

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overview

Hypothesis Overview

Introduction

Mechanistic Framework

Major Mechanistic Hypotheses

Alzheimer's Disease

Hypothesis Overview

Introduction

Mechanistic Framework

Major Mechanistic Hypotheses

Alzheimer's Disease

Parkinson's Disease

Amyotrophic Lateral Sclerosis

Evidence Assessment

Alzheimer's Disease Hypotheses

Amyloid Cascade Hypothesis — STRONG

Tau Spreading Hypothesis — STRONG

Neuroinflammation Hypothesis — MODERATE-STRONG

Parkinson's Disease Hypotheses

Alpha-Synuclein Aggregation — STRONG

Mitochondrial Dysfunction — STRONG

Emerging Hypotheses

Cross-Disease Mechanisms

Novel Concepts

Hypothesis Testing Approaches

Experimental Models

Human Studies

Historical Evolution

AD Hypotheses

PD Hypotheses

Research Priorities

Most Promising Directions

Therapeutic Target Priorities

Cross-Disease Mechanisms

Shared Pathways

Network-Based Degeneration

Related Pages

Disease-Specific Hypotheses

Alzheimer's Disease

Parkinson's Disease

Cross-Disease Mechanisms

See Also

External Links

References

Topics

Summary Statistics

💬 Discussion