Economy > $80 billion/year. Neuropsychiatric conditions are the leading cause of disability in young people worldwide. 70% 70% of youth in thejuvenile justice system are living with at least one mental healthcondition. Traumatic brain injury is the leading cause of long-term disability in children andadults younger than 35years. 1 in 4 experience mentalillness in a givenyear. More veterans die of suicide than in combat at rate of 20 suicides perday. 3
FRONTIER 65+ YEARS: WAITING FOR A BREAKTHROUGH Molecular targets of all current psychotherapeutic drugs are the same as their 1950’s prototypes. 1957 Sputnik I 1952 Discovery of Antipsychotic Chlorpromazine (DRD2 blockade) 2018 Antipsychotics for treatment of schizophrenia all work via DRD2 blockade ? 4
Human postmortem brains 1000+ Cell lines from individuals Genomics + Transcriptomics + Proteomics 8 Mechanisms of Illness Clinical Genetics BrainSeq: A Human Brain Genomics Consortium THE SCIENTIFIC FRONTIER
Human postmortem brains 1000+ Cell lines from individuals Genomics + Transcriptomics + Proteomics 8 Mechanisms of Illness Clinical Genetics BrainSeq: A Human Brain Genomics Consortium DLPFC 495 samples BrainSeq Phase I polyA+ Jaffe et al., bioRxiv, 2017 THE SCIENTIFIC FRONTIER
processing methods 2.Apply strict expression cutoffs 3.Use replication when possible 4.Adjust for RNA quality degradation confounding • Using the qSVA method 5.Avoid potential batch effects • Drop problematic samples 6.Take into account correlation at the individual level
Unaffected Controls Patients with Schizophrenia RNA Sequencing Genotyping + + + Gene Exons Expressed Regions Transcripts Junctions Age CC CA AA SZ CONT DLPFC HIPPO + region differences For public data, check recount2
on raw reads (FastQC) 2. Failed QC? Then trim reads (Trimmomatic) 3. Align reads to the genome (HISAT2) 4. Count features (featureCounts + others) 5. Calculate coverage (bam2wig) 6. Quantify transcripts (Salmon) 7. Create count tables (R): RangedSummarizedExperiment objects 8. Genotype samples (samtools + vcftools) L. Collado-Torres & Emily E. Burke Nextflow version in preparation with Winter Genomics
or fetal ages • Using only adult samples or only prenatal samples • Test for differences between DLFPC and HIPPO • Development • Linear age splines with breakpoints at developmental stages • Test for interaction between age and brain region at these splines • Case-control • By brain region • Test for differences between non-psychiatric controls and individuals with schizophrenia • For the first two models, we account for the fact that an individual can have two correlated samples: one for each brain region limma::duplicateCorrelation()
1,612 DE genes with Bonferroni < 0.01 that replicate in BrainSpan • For prenatal samples: 32 DE genes L. Collado-Torres 23 6 2 0 3 0 3 gene exon jxn DE features grouped by gene id (prenatal) 328 422 778 23 839 647 388 gene exon jxn DE features grouped by gene id (adult)
processes L. Collado-Torres G−protein coupled serotonin receptor signaling pathway serotonin receptor signaling pathway pallium development cGMP−mediated signaling small GTPase mediated signal transduction regulation of small GTPase mediated signal transduction positive regulation of GTPase activity behavior regulation of GTPase activity axon development axonogenesis regulation of membrane potential regulation of hormone levels positive regulation of neuron projection development positive regulation of cell development regulation of cell morphogenesis positive regulation of neuron differentiation regulation of neuron projection development positive regulation of neurogenesis positive regulation of nervous system development cell morphogenesis involved in neuron differentiation G:E:J (714) E:J (583) G:E (260) GeneRatio 0.02 0.04 0.06 0.08 0.01 0.02 0.03 0.04 0.05 p.adjust ontology: BP G: gene, E: exon, J: exon-exon junction
contain differentially expressed exons and splice junctions that replicated in BrainSpan (Bonferroni < 1%) L. Collado-Torres 2354 2260 1762 243 5982 8501 1558 gene exon jxn DE features grouped by gene id
model E / = 1 0 + 1 1 45 DEqual plots demonstrate effectiveness of statistical correction HIPPO 333 samples r = 0.412 Slide adapted from Amy Peterson Log2 FC Dx Log2 FC Degradation
(FDR <1%) corresponding to 1,484 genes • Includes 5 PCG2 schizophrenia risk loci • We will soon update our eQTL browser at http://eqtl.brainseq.org/ Emily E. Burke 19394 10734 6493 2622 3937 4398 34259 gene exon jxn eQTLs grouped by SNP id 488 246 319 18 99 63 251 gene exon jxn eQTLs grouped by gene id
false positives • Quantified expression at different feature levels • Widespread development differences between HIPPO and DLPFC in postnatal life • Adapted the qSVA framework for 2 brain regions and set the ground work for N > 2 • Results suggest regional specificity for case-control effects with enrichment towards genes with decreased expression in schizophrenia • Potential need to have regionally targeted therapies for schizophrenia because schizophrenia risk seems region-specific In progress: pre-print
E. Burke • Amy Peterson (JHU MPH class 2018) o amy-peterson.github.io • Joo Heon Shin • Stephen A. Semick • Anandita Rajpurohit • Courtney Williams • Ran Tao • Amy Deep-Soboslay • Thomas M. Hyde • Joel E. Kleinman • Daniel R. Weinberger+ • Andrew E. Jaffe+ o andrew.jaffe@libd.org o @andrewjaffe 35 • BrainSeq Consortium • LIBD @lieberinstitute More from our team at #BOG18: • Poster 48 by Emily E. Burke, Wed 2pm • Poster 251 by Stephen A. Semick, Fri 2pm Funding We are hiring! Multiple positions open