Team lcolladotor Journal Club: APOE genotype determines cell-type-specific pathological landscape of Alzheimer’s disease

Team lcolladotor Journal Club: APOE genotype determines cell-type-specific pathological landscape of Alzheimer’s disease
Li et al., Neuron, 2025
doi: https://doi.org/10.1016/j.neuron.2025.02.017

Presented by: Louise Huuki-Myers, March 28, 2025
Recording of our journal club meeting: youtube.com/watch?v=Hi5Eg1rBRnc

Single cell RNA-seq analaysis temporal cortex, investigating transcriptonal differnces between AD and control donors, stratified by APOE genotype. HIhglighted diffrences in synatptic pathways in neurons, mylenation in Oligo, and immune response in Microglia.

▶️ youtu.be/L4J9jFS-Pic

Transcript

1. APOE genotype determines cell-type-specific pathological landscape of Alzheimer’s disease Li et al., Neuron, 2025 https://doi.org/10.1016/j.neuron.2025.02.017 Presented by: Louise Huuki-Myers Team Lcolladotorres Journal Club May 28, 2025
2. Experimental Design • Human Temporal Cortex • Balanced APOE genotypes across AD case vs. control ◦ 29 AD/27 control • Single nucleus RNA-seq ◦ 343k nuclei ◦ 7 major cell types (Excit, Inhib, Oligo, OPC, Astro, Micro, Vascu) Fig 1
3. Single nucleus data set • AD samples had lower counts and detected features, similar mitochondrial rate & n nuclei • Proportion differences ◦ Higher proportion of Oligo in AD vs. control ◦ Microglia: APOE4 > APOE3 ◦ OPC: AD < Control for APOE4 Fig S2. F
4. Cell Type DGE • AD vs. Control within each genotype ◦ Model included RIN and sequencing saturation • Very different results between genotypes (Fig1D) • Gene Set Enrichment ◦ -log10(p val) vs. normalized enrichment score (NES) ◦ APOE2: excit, inhib, OPC, Astro ◦ APOE3: Excit, OPC, Astro ◦ APOE4: Microglia ▪ Immune response
5. Excitatory Neurons • APOE4 ◦ ↓ synaptic vesicle cycle, vesicle mediated transport ◦ ↓ SH3GL2, PCLO, and GRIA1 • APOE2 ◦ ↑ cognition, learning & memory, synaptic transmission ◦ ↑ STXBP1 and SLC17A7 • APOE3 ◦ No pathways, but down reg of synapse genes ◦ ↓ SV2B, BSN, and SYT12
6. Excitatory Neurons - subcluster • 14 sub-populations ◦ Cortical layers ◦ Similar compositions between AD vs. control • Consistent enrichment of gene sets across subclusters
7. Synaptic Protein Loss • Observed synaptic transcriptomic changes, does this result in differential protein loss? ◦ vGlut1 & PSD-95 ◦ Immunohistostaining & co-immunofluorescence had similar results • Suggests APOE modifies synaptic changes in AD ◦ Preserved in APOE2, reduced with AD in APOE4, unchanged proteins in APOE4 (but transcriptionally down regulated) Preserved ✅ Reduced in AD Reduced in both control & AD vGlut1
8. Oligo myelination changes • Myelin loss is a symptom of AD • Transcriptomic data showed upregulation of myelination pathways in APOE2 Fig 1G
9. • APOE2: most DEGs ◦ ↑ myelination genes, axon ensheathment, MBP • APOE3 ◦ ↓ myelination genes, axon ensheathment, MBP • APOE4 ◦ ↑ CNP • Similar changes across Oligo subclusters ◦ APOE2: Oligo 3, 4, 5 ◦ APOE4: Oligo 1 & 4 Oligo myelination changes
10. MBP changes • Lower expression of MBP and MOBP in Oligo nuc • IHC of MBP ◦ APOE2: maintained ◦ APOE3: reduced MBP in AD ▪ E3E3 AD lowest MBP in GM than E2 or E4 heterozygotes ◦ APOE4: Increased MBP in AD 🤔 ▪ lower MBP levels overall ▪ Supported by other studies
11. Degraded MBP • Myelin damage in AD leads to increased levels of dMBP ◦ APOE4: Increased MBP in AD 🤔 - is this preserved MBP or dMBP? • In AD: ◦ APOE2: minimal dMBP ◦ APOE4: high dMBP • MBP conclusions ◦ E2: preserved myelin content ◦ E3/E3: MBP loss in AD ◦ E4 carriers: myelin damage in AD (accumulate dMBP)
12. APOE4 inflammation in Microglia • APOE4: enrichment of inflammatory responses in microglia • Subcluster to 8 microglia + macrophage ◦ No differences in proportions between AD & Control ◦ Inflammatory & surveillant microglia enriched for inflammation response ◦ Homeostatic microglia had distinct changes ◦ Annotations could be helpful • DEGs ◦ APOE3: most DE signal ◦ APOE4: most genes not DE ▪ Diminished response to Aβ ?
13. APOE4 Microglia Response to Aβ • “APOE4 carriers had reduced number and activation of microglia proximal to Ab plaques compared with APOE3 homozygotes” • Similar responsiveness from E2 & E3 microglia • “APOE4 might mediate heightened microglia-mediated pro-inflammatory responses to AD pathology beyond Ab deposition”
14. Other Cell Types • Inhib: ◦ similar transcriptomic changes as Excit neurons ◦ most DEGs in E2 • OPC: ◦ changes in immune response pathways ◦ differences in subclusters • Astro: ◦ E3/E3 ↑ cytokine production • Vascular: ◦ Immune response (E2)
15. Discussion • Weaknesses ◦ Low sample sizes - better power would help in minor cell populations ◦ Discrepancies between transcript & protein changes • Main findings ◦ Synaptic dysfunction: E2 protective, E4 damaging (Neurons) ◦ Myelin damage ▪ E2 protective vs. E3 ▪ E4 AD increased MBP, but increased degraded MBP ◦ Microglia ▪ E4 upregulation of proinflammatory pathways ▪ E4 microglia response to Aβ is lower ▪ Differences between Microglia in this study and animal models (could be human specific) ◦ Many complex changes across cell types in AD modulated by APOE
16. Thoughts • Nice validation experiments • Used MAST for differential expression • Found most signal at broad cell type ◦ Subcluster differences in Microglia and Oligo ◦ Could leverage information on microglia annotations • Control compared to AD (by APOE) vs. comparing APOE genotypes - what can we expect? ◦ Cell type composition changes (?) ◦ Synapse pathways ◦ Lower MBP in E4 ◦ Inflammatory pathways in Microglia ◦ Could leverage DE results