Viktor Petukhov
PhD student at the University of Copenhagen
Identification of epilepsy-associated neuronal subtypes and gene expression underlying epileptogenesis
Pfisterer U**, Petukhov V**, Demharter S**, Meichsner S**, Thompson JJ, Batiuk M, Martinez AA, Vasistha NA, Thakur A, Mikkelsen J, Adorjan I, Pinborg LH, Pers TH, Engelhardt J, Kharchenko PV*, Khodosevich K*
scRNA-seq to study Temporal Lobe Epilepsy
- Temporal Cortex
- 9 control vs 10 epilepsy samples
- 117k nuclei
Plan
- Pre-processing and filtration
- Alignment and annotation
- Identification of changes
- Functional annotation
- Validation
Sample filtration
Cell type annotation
Transcriptional change between conditions
- What cell types are the most affected?
- How exactly are they affected?
The main questions:
Identification of changes
Gene expression analysis
Compositional analysis
%of nuclei
Identification of changes
Proportions of cell types
%of nuclei
Differential expression
Number of DE genes depends on num. of cells
- What cell types are the most affected?
- How exactly they are affected?
The main questions:
Differential expression
There are up to 1000 significant DE genes per type and 2795 unique DE genes in total
- What cell types are the most affected?
- How exactly they are affected?
The main questions:
Differential expression
There are up to 1000 significant DE genes per type and 2795 unique DE genes in total
- What cell types are the most affected?
- How exactly they are affected?
The main questions:
There are up to 300 significant GO terms per type and 796 unique terms in total
Differential expression
Enrichment of epilepsy-related genes
Enrichment of GWAS genes
Gene expression similarity
Gene expression similarity
Gene expression similarity
Gene expression similarity
Z = \frac{\overline{d}_{control} - d_{between}}{\overline{d}_{control}}
Gene expression similarity
Number of GO pathways
Total ranking
Metrics
- Expression similarity
- Adj. number of GO pathways
- Adj. number of DE genes
- Number of cells per type
- GWAS enrichment
- Epilepsy gene enrichment
Affection levels
0: not affected
1: affected
2: highly affected
3: the most affected type
Weights
1.0
0.66
0.66
0.66
0.66
0.33
Total ranking
Expression similarity score
Statistics: similarity statistics
Affected: Upper quartile < 0
Highly affected: below median over all types
Total ranking
Number of DE genes and pathways
Statistics: residuals of regression
Affected: residuals > 0
Highly affected: >75% of positive residuals
Total ranking
Number of cells
Statistics: permutation test p-value
Affected: p-value < 0.2
Highly affected: p-value < 0.05
Total ranking
GWAS and epilepsy enrichment
Statistics: enrichment statistics h
Affected: h > 1
Highly affected: Lower CI of h > 1
Total ranking
Differentially expressed genes
Log2(Fold Change)
Log2(Fold Change)
GO Pathways
Overview
Cluster pathways with similar genes across all subtypes:
446 BP pathways => 186 clusters
Each cluster has the name of the most significant of its pathways
GO Pathways
Biological process clusters
GO Pathways
Coordinated change
GO Pathways
Biological processes
GO Pathways
Biological processes
GO Pathways
Biological processes
developmental processes, neural circuit re-organization and neurotransmission
ion transport and glutamate signaling
protein transport to axons/dendrites
cell adhesion, ion transport and synaptic plasticity
regulation of neuronal morphogenesis
GO Pathways
Pink cluster
developmental processes, neural circuit re-organization and neurotransmission
GO Pathways
Pink cluster
- Dot is a pathway within a cell type
- Adjacent pathways have the same genes over-represented
GO Pathways
Signaling pathways underlying seizure activity
GO Pathways
Signaling pathways underlying seizure activity
smFISH validation
Control
Epilepsy
smFISH validation
smFISH validation
Summary
Shared pathways
Genes underlying seizure activity
Prioritization of the affected subtypes
Thank you!
Konstantin Khodosevich lab
Peter
Kharchenko
Ulrich Pfisterer
Samuel Demharter
Johanna Meichsner
Jonatan J. Thompson
Mykhailo Batiuk
Andrea Asenjo Martinez
Navneet A. Vasistha
Ashish Thakur
Jens Mikkelsen
Istvan Adorjan
Lars H. Pinborg
Tune H. Pers
Jakob von Engelhardt
Peter V. Kharchenko
Konstantin Khodosevich
Co-authors
viktor.s.petuhov@ya.ru
Epilepsy Neuroseminar Sep 2020
By Viktor Petukhov
