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Computational Approaches to Transcriptome
Signatures in the Human Brain
Mike Hawrylycz, Ph.D.
February 18, 2016
Agilent Technologies eSeminar
| For Research Use Only. Not for use in diagnostic procedures.
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ALLEN Adult Human Atlas – Online tools
For Research Use Only. Not for use in diagnostic procedures.
| For Research Use Only. Not for use in diagnostic procedures.
An Anatomic Transcriptional Atlas of Glioblastoma
Puchalski, Shah, Miller, et al, submitted
Science
Ivy-Allen Glioblastoma atlas project http://glioblastoma.alleninstitute.org/
Only large data set to profile distinct anatomical structures of GBM using RNA-Seq and ISH, and machine learning annotation providing an invaluable resource.
Cellu
lar
tum
or
Leadin
g e
dge
P
seudopalis
adin
g c
ells
aro
und n
ecro
sis
Mic
rovascula
r
pro
lifera
tion
“Proliferation” and “migratory” classes of stem cell markers correspond to two GBM subtypes: “classical” and “proneural.”
Our GBM atlas allows for computational assessment of anatomical composition of any bulk GBM samples.
CD44 EZH2
This novel finding is a potential simplification from current understanding.
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Allen Human Brain Atlas Platform
Hawrylycz, Lein, et
al, Nature, 2012
Lein, Hawrylycz,
Nature, 2014
For Research Use Only. Not for use in diagnostic procedures.
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Allen Human Brain Atlas Platform
For Research Use Only. Not for use in diagnostic procedures.
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Microarray Data Generation
Agilent 8x60K array, custom-designed by Beckman Coulter Genomics in conjunction
with the Allen Institute, was used to generate microarray data.
The array design included the existing 4x44K Agilent Whole Human Genome probe set
supplemented with an additional 16,000 probes.
At least two different probes were available for 93% of genes with EntrezGeneIDs
(21,245 genes). Probes were located on different exons as much as possible when
multiple probes were available for a gene. Other probes on the microarray were for
transcripts with UCSC IDs (1,852 transcripts) and Agilent IDs (1,268 transcripts).
An additional set of probes were included to overlap with the 1,000- and 60-gene sets
that were characterized by ISH for the 1,000 Gene Survey in Cortex and the Subcortex
Study, respectively, both of which are integrated into the Allen Human Brain Atlas
Total RNA in the amount of 50 ng per sample was sent to Beckman Coulter Genomics
for processing on Agilent 8x60K gene expression arrays.
RNA-Sequencing (RNA-Seq) data were generated for a selected set of 240 samples
(120 from each brain) representing 29 cortical and subcortical regions matched across
two brains (H0351.2001 and H0351.2002), using aliquots of the same total RNA
isolates used to generate microarray data.
For Research Use Only. Not for use in diagnostic procedures.
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Spatial genomic landscape of gene classes
For Research Use Only. Not for use in diagnostic procedures.
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Spatial Topography of the Neocortex Microarray and RNA-seq
Miller et al., BMC Genomics, 2014 For Research Use Only. Not for use in diagnostic procedures.
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Reproducible Differential Gene Expression: Six Brains
• Genes DE between
structures in at least 5 brains
• 96 regions
• Same direction
• FC > 3
• B&H p-value < 0.01
For Research Use Only. Not for use in diagnostic procedures.
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The Genetic Geography of the Brain http://casestudies.brain-map.org/ggb
Tim Dolbeare For Research Use Only. Not for use in diagnostic procedures.
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The Genetic Geography of the Brain: Vignette
Tim Dolbeare
Anil Jegga, CCHMC For Research Use Only. Not for use in diagnostic procedures.
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Protocadherin 8 (PCDH8) Gene Expression in
Six Brains
Consistent expression pattern of an exemplary gene, PCDH8, across 96 brain regions for the six brains
(numbered 1-6). CTX: cortex; HP: hippocampus; AMG: amygdala; STR: striatum; HY: hypothalamus;
TH: thalamus; CB: cerebellum; P: pons; MB: midbrain; WM: white matter. Structures shown are a
subset of those in (A) with cortex reduced to its major lobes (FL: frontal lobe, OL: occipital lobe, TL:
temporal lobe, PL: parietal lobe).
For Research Use Only. Not for use in diagnostic procedures.
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Differential Stability and the Brain
DS as average
Kendall Tau
DS versus mean
expression level and
variability
DS versus average
Pearson based metric
C
For Research Use Only. Not for use in diagnostic procedures.
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Parvalbumin (PVALB), DS = 0.806 The most stable gene in human brain in this dataset.
Consistent expression pattern of an exemplary gene, across 96 brain regions for the six brains (numbered 1-6). CTX: cortex;
HP: hippocampus; AMG: amygdala; STR: striatum; HY: hypothalamus; TH: thalamus; CB: cerebellum; P: pons; MB:
midbrain; WM: white matter. Structures shown are a subset of those in (A) with cortex reduced to its major lobes (FL: frontal
lobe, OL: occipital lobe, TL: temporal lobe, PL: parietal lobe).
CKS2 (CDC28 Protein Kinase Regulatory
Subunit) DS = 0.245
Differential Stability and the Brain
For Research Use Only. Not for use in diagnostic procedures.
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High DS Genes and the Brain Top 5th Percentile, n=864 genes
For Research Use Only. Not for use in diagnostic procedures.
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Consistent patterning of Potassium channels
• Most stable gene
class, p<3.19e-12
• Span a broad
distribution of
anatomic patterns
and structural
markers.
• Can we classify or
describe these
patterns?
For Research Use Only. Not for use in diagnostic procedures.
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Consensus Co-expression Patterns in Adult Brain
For Research Use Only. Not for use in diagnostic procedures.
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Anatomic Architecture of 29 Modules
For Research Use Only. Not for use in diagnostic procedures.
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Potassium Channels span Module types
For Research Use Only. Not for use in diagnostic procedures.
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Consensus Co-expression Patterns in Adult Brain
For Research Use Only. Not for use in diagnostic procedures.
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Modules span expression patterns of the brain
Maximum module correlation and DS
ρ>0.4 , 85.6% (14,856/17,349)
5 brains predicts module in 6th brain
For Research Use Only. Not for use in diagnostic procedures.
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Consensus Co-expression Patterns in Adult Brain
Genetic markers for eight
cortical cell types in postnatal
mouse were identified based
on differential expression of
RNA-seq derived
transcriptomes
Zhang Y, Chen K, Sloan S a, et al.
An RNA-Sequencing Transcriptome
and Splicing Database of Glia,
Neurons, and Vascular Cells of the
Cerebral Cortex. J Neurosci.
2014;34(36):11929–47.
For Research Use Only. Not for use in diagnostic procedures.
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Canonical Genetic Signatures of the Adult Human Brain:
(M1-M16)
For Research Use Only. Not for use in diagnostic procedures.
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Module Annotation: Anatomy, ontology, drug, disease
For Research Use Only. Not for use in diagnostic procedures.
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Canonical Genetic Signatures of the Adult Human Brain:
(M1-M16)
For Research Use Only. Not for use in diagnostic procedures.
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Module Annotation: Anatomy, ontology, drug, disease
For Research Use Only. Not for use in diagnostic procedures.
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Module interaction: ontology, pathways, drug
targets, cancer gene sets
For Research Use Only. Not for use in diagnostic procedures.
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Unique anatomical patterning of 48 high DS genes.
GNB4
PRSS23
TES
265 high DS genes uncorrelated with major patterns
For Research Use Only. Not for use in diagnostic procedures.
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Module preservation from
human to mouse.
(A) Mouse-human module preservation index measuring
average within-module gene correlation in an anatomy-
independent fashion, showing highest preservation of the
most neuronal modules (M1, M2, M4).
(B) Conservation of anatomical patterning, defined as the
proportion of mouse genes correlated at > 0.4 to the
corresponding human module eigengene (green bars). A
subset of genes in each module are both poorly correlated to
the human eigengene (gray bars), but instead very highly
correlated to a different human module eigengene (> 0.8).
(C-H) Correspondence of module eigengene anatomical
patterning between human and mouse. Histogram
representation of ME pattern in human (blue) and mouse
(red), with overlap in green, demonstrating highly conserved
patterns for M4, M10, M12 and M19.
For Research Use Only. Not for use in diagnostic procedures.
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Human Connectome Project
www.humanconnectome.org
Van Essen et al., 2013; Smith et al., 2013 For Research Use Only. Not for use in diagnostic procedures.
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Cortex DS and Functional Connectivity
Vilas Menon For Research Use Only. Not for use in diagnostic procedures.
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Taxonomies of Neocortical Cell Types
Anatomical/Morphology Transcriptomic
Data-driven taxonomy of neocortical neuron types
Large-scale quantitative phenotyping of single neurons in adult neocortex
Physiological
For Research Use Only. Not for use in diagnostic procedures.
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Cell Types and Hierarchical Organization
For Research Use Only. Not for use in diagnostic procedures.
Glia
GABA
Glutamatergic
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Genetics of Cell Type based on Cre Lines
For Research Use Only. Not for use in diagnostic procedures.
Tasic, Menon et al.,
Nat. Neuroscience,
2016
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We wish to thank the Allen Institute founders, Paul
G. Allen and Jody Allen, for their vision,
encouragement, and support.
Acknowledgments External Collaborators
• Anil G. Jegga, Bruce J. Aronow,
Kenneth A. Berman, Cincinnati
Children’s Hospital Medical Center
• Matthew F. Glasser, Donna L.
Dierker, David C. Van Essen,
Washington University
• Pascal Grange, Xi’an Jiaotong-
Liverpool University
• Albert-László Barabási, Jörge
Menche, Northeastern University,
Central European University
• Jay Schulkin, Georgetown
University
• David R. Haynor, Lance Stewart,
University of Washington
For Research Use Only. Not for use in diagnostic procedures.