Lineage tracing and differential expression analysis of single nuclei RNA-sequencing data from human neocortex identifies novel genes and pathways involved in progression of Alzheimer’s disease
Anatoly Buchin
Cajal Neuroscience, Human Multi-Omics Team
GWAS provides information about AD risk genes
Bellenguez et al 2022
What happens during the course of disease development?
Goedert et al 2015
A-beta and tau have a stereotypical progression
A-beta
Tau
Extract hidden structure in gene expression data
Correlation with
Braak stage,
Thal phase,
Cognitive decline
Human cortical data
Tissue processing
Analysis of snRNA-seq data of patients with different stages of disease development evaluated by Braak score
1.2 M cells
84 donors
Middle Temporal Gyrus (MTG)
MTG
Pseudotime analysis of gene expression: single nuclei RNA-seq
Haghverdi et al 2016
Pseudotime
gene x
gene y
gene z
Braak stage
Correlation
Start: healthy
End: diseased
Hidden structure
Cetti et al 2019
Transcripts correlated with pseudotime: microglia PVM-1
Upregulated genes
Pseudotime
Trajectory
start
corr 0.51
pval 7.014 E-107
corr -0.39
pval 8.24 E-60
Correlation
(pseudotime, expression)
COLEC12
F13A1
Down-regulated genes
Analysis of microglial subclusters
Microglia subclusters
Braak stage
Microglia-PVM_1
Pseudotime
Braak stage
Trajectory
start
Analysis of microglial subclusters
Microglia subclusters
Braak stage
Microglia-PVM_1
Pseudotime
Trajectory
start
Micro-PVM_1 corr 0.173 pval 0.0
Micro-PVM_1_1 corr 0.217 pval 0.0
Micro-PVM_2 corr 0.169 pval 0.0
Micro-PVM_2_1 corr 0.154 pval 0.009
Micro-PVM_2_2 corr 0.105 pval 0.002
Micro-PVM_2_3 corr 0.15 pval 0.0
Micro-PVM_3 corr 0.227 pval 0.0
Micro-PVM_4 corr 0.566 pval 0.0
Braak stage and pseudotime correlations
Enrichment analysis of microglia
Enrichment terms
Microglia subtypes
Upregulated genes
Replication pathways
Immune pathways
Response to bacterium: PDE4B, AHR, IL10RA, IL15, C3, IL7R, IL15, … (155 genes)
Analysis of astrocyte subclusters
Pseudotime
Braak stage
Astrocyte subclusters
Braak stage
Analysis of astrocyte subclusters
Braak stage and pseudotime correlations
Astro_1 corr 0.11 pval 0.0
Astro_2 corr 0.16 pval 0.0
Astro_3 corr 0.12 pval 0.0
Astro_4 corr 0.55 pval 0.0
Astro_5 corr 0.10 pval 0.0
Astro_6 corr 0.12 pval 0.0
Pseudotime
Astrocyte subclusters
Braak stage
Enrichment analysis of astrocytes
Enrichment terms
Astrocyte subtypes
Downregulated genes
Cholesterol / Translation pathways
Synaptic
pathways
Cellular respiration
pathways
Cholesterol pathway: GPAM, APOE, PGP, ALOX12, ACSS1, ACOT2, CYP4V2, … (46 genes)
Pathways affected by Alzheimer’s disease
Murdock and Tsai 2022
Conclusions
Trajectory
start
Microglia
Astrocytes
Plan for the presentation
-Problem statement: many different genes affect idiopathic Alzheimer’s disease (Bellenguez graph). How could we go from genes to cellular mechanisms?
-Recent work on single cell identified many different genes involved in disease development
-Disease development: Tau staging by Braak and brain regions. Figure from paper
-Novel method of gene expression analysis: general method idea
-Analysis of cortical data: more about MTG dataset
-Analysis of excitatory cells, inhibitory cells, microglia, astrocytes. More about MTG, then ETX, SFG and PFC
-On the analysis of specific pathway: show the specific cell type
-Common pathways across cortical areas and cell types. Microglia, Oligodendrocytes
-
The logic behind pseudotime analysis
Neurons
Pseudotime analysis of gene expression: single nuclei RNA-seq
Cells
Braak score
Enrichment analysis of microglia
Enrichment terms
Microglia subtypes
Downregulated genes
Immune pathways 1
Immune pathways 2
Analysis of excitatory subclusters
Excitatory subclusters
Braak stage
Pseudotime
Braak stage
Analysis of excitatory subclusters
Excitatory subclusters
Braak stage
Pseudotime
L2/3 IT_1 corr 0.143 pval 0.0
L2/3 IT_10 corr 0.296 pval 0.0
L2/3 IT_12 corr 0.323 pval 0.0
L2/3 IT_13 corr 0.28 pval 0.0
L2/3 IT_2 corr 0.146 pval 0.0
L2/3 IT_3 corr 0.274 pval 0.0
L2/3 IT_5 corr 0.175 pval 0.0
L2/3 IT_6 corr 0.189 pval 0.0
L2/3 IT_7 corr 0.27 pval 0.0
L2/3 IT_8 corr 0.264 pval 0.0
Braak stage and pseudotime correlations
Enrichment analysis of excitatory cells
Enrichment terms
Excitatory subtypes
Upregulated genes
Stress / ubiquitin / viral pathways
Mitochondrial / synapse pathways
Neuron projection: NTNG1, PTPRD, GRIN2B, APP, NRG3, ZNF804A, … (151 gene)