Postmortem Brain Transcriptomes in Dup15q and Idiopathic Autism

Postmortem brain transcriptomes in Dup15q and idiopathic autism T Grant Belgard, DPhil Dan Geschwind’s Lab UCLA Neuropsychiatric Institute Many genetic causes of autism, none particularly dominant

Is there molecular convergence? (for understanding & translation) Sequence RNA from frontal & temporal cortex • 8 Dup15q, 37 idiopathic cases, and 30 controls from two brain banks (University of Maryland & Autism Tissue Program) • Dissected grey matter from frontal cortex (ba9) and temporal cortex (ba 41/42/22) • RNA-seq using rRNA-depleted RNA to an average depth of 50M read pairs (50 nt from each end) • Removed non-expressed genes, normalized, removed outliers, etc. • Penalized cubic splines regression to remove effects of RIN and differential white matter contribution • Linear mixed-effects model with age and sex as covariates Expression diﬀerences across the 15q region

Some changes are unique to Dup15q Others are shared with idiopathic autism Some genes have lower expression in Dup15q/idiopathic ASD 15q region expression: breakpoints 1-2

Dup15q + autism idiopathic autism control Diﬀerentially expressed in 15q vs idiopathic + control 15q region expression: breakpoints 2-3

Dup15q + autism idiopathic autism control 15q region expression: breakpoints 3-5

Dup15q + autism idiopathic autism control

Differentially expressed in 15q vs idiopathic + control, but significantly more so in 15q Global expression differences: most changes outside the 15q region

Characteristic gene expression signature in idiopathic autism This signature is even stronger in Dup15q Uncorrelated with seizures Activated glial genes up; synaptic genes down Idiopathic autism gene expression signature replicates

requiring p<0.005 in at least one comparison rho = 0.65; N=382 t=16.7 p tiny Also replicates across platforms

Chi-squared 279; p incalculably tiny 3.6 fold enrichment (Chi-squared)

new brains 252 215 2744 with RNA- Voineagu seq et al. brains on arrays

Both circles FDR 5% and fold change > 1.3 Dup15q shares this same gene expression signature

2158 genes overlap

All at FDR 5% These gene sets are inversely correlated in individual samples

Neelroop Parikshak Signature is stronger in Dup15q than in idiopathic autism

We get the slope for each sample like this… 4

2 Control Idiopathic

slope 1 15q Dup

-1

-2 Gene expression changes are unrelated to seizures • Correlation, t test & F test not close to significant • Presumably not seizure medications • No apparent relationship with age or cause of death

(Morgan et al. 2012 Brain Res) Keenmann et al. Neuron 2013 One possible model for autism pathogenesis?*

Synaptic Excitatory/ Seizures Genetic dysfunction: inhibitory variation activity- imbalance dependent protein Impaired synthesis or systems-level breakdown, Altered brain connectivity Environmental cell adhesion or physiology insult growth trajectory

Microglial “Autism” inﬂammation & synaptic pruning? Fewer or less *speculation! active synapses

Causal Consistent with gene expression in Dup15q Could one intervene retrospectively in Dup15q?*

Restore Correct the Seizures Genetic excitatory/ variation synaptic dysfunction inhibitory X balance Impaired Altered systems-level brain connectivity growth or physiology trajectory X Boost synapse Reduce microglial activity or “Autism” activation and promote new pruning? synapse *speculation! formation Conclusions and future directions • Idiopathic autism and especially Dup15q are characterized by two highly anticorrelated sets of genes in frontal and temporal cortex o Immune/microglial genes up o Synaptic genes down

• This signature is uncorrelated to seizures

• Need to determine exactly what these changes reflect and if there might be a pharmacological pressure point therein Acknowledgements • Dan Geschwind • The families of the • Neelroop Parikshak deceased • Irina Voineagu • Autism Tissue Program • Vivek Swarup • University of Maryland Brain Bank • Jing Ou • Joe DeYoung • Claire Orosco • Jason Stein • Yuan Tian Questions, comments, suggestions?

[email protected]