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Connectomics and genomics data integration

Neuroscience 500 Dec 7 2011

Paul Pavlidis

Department of Psychiatry

and

Centre for High-Throughput Biology

paul@chibi.ubc.ca

Outline

• What is the connectome and how is it studied

• What is the brain transcriptome and questions about it

• Studies comparing the transcriptome and connectome

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The connectome: “wiring diagram” of the brain

Hagmann P, Cammoun L, Gigandet X, Meuli R, Honey CJ, Wedeen VJ, Sporns O (2008) Mapping the structural core of human cerebral cortex. PLoS Biology 6, e159.

http://www.scholarpedia.org/article/Connectome

Connectomics

• What does the connectome explain about the function of the brain?

• How is it influenced by factors such as genetics?

• How does it change over lifespan?

• How does it go wrong in disease?

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Where does the connectome come from?

• During development: Axons finding targets through complex pathfinding and recognition processes

• Expansion and refinement – axons continue to grow, pruning

• Stabilization at adulthood (with plasticity at small scales)

Toga, A.W.; Thompson, P.M.; Sowell, E.R. Trends in Neurosciences Volume 29, Issue 3, March 2006, Pages 148-159

How is the connectome determined?

• Electrophysiological mapping of connections

• Tract tracing

– Golgi staining (short range)

– Wallerian degeneration

– Tracer injections

• Serial electron microscopy

• Fluorescent protein expression

• Diffusion-tensor MRI

• MRI BOLD signal correlation (“functional network”)

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DTI of major white matter tracts

http://dx.doi.org/10.1016/j.neuroimage.2007.12.053

http://www.nature.com/nrn/journal/v9/n6/full/nrn2391.html

http://www.olympusbioscapes.com/gallery/2007/index.html

“Brainbow”

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The mind of a worm

White et al. Phil. Trans. Royal Soc. London. Series B, Biol Scien. Vol.314, Issue 1165 (Nov 12, 1986), 1-340 http://www.wormatlas.org/ver1/MoW_built0.92/toc.html

Reconstructions were done by hand from a total of about 8000 prints

C. elegans complete connectome

http://www.wormatlas.org/ver1/MoW_built0.92/toc.html; http://arxiv.org/abs/0907.2373 Varshney et al.; http://www.wormatlas.org/neuronalwiring.html

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Tract tracing in large brains

http://www.colorado.edu/intphys/Class/IPHY3730/image/figure4-5.jpg

PHA-L = Phaseolus vulgaris-leucoagglutinin (kidney bean lectin) - anterograde tracer Detected by anti-PHAL antibodies

Brain Research (1984) 290:219-238

Genetically-encoded trans-synaptic tracers

http://www.jneurosci.org/content/30/49/16509.long

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2629495/

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Tract tracing results

Neuroscience Letters Volume 380, Issue 3, 3 June 2005, Pages 276-279

JOURNAL OF COMPARATIVE NEUROLOGY 399:189–209 (1998)

For a modern take with fluorescent imaging: http://www.pnas.org/content/early/2010/07/28/1009112107

Building up circuit diagrams

Macaque visual system

• 305 pathways

• 32 brain regions

Daniel J. Felleman, and David C. Van Essen. Distributed Hierarchical Processing in the Primate Cerebral Cortex, Cerebral Cortex 1991; 1:1-47, © Oxford University Press

1991, page 30

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Brain Architecture Management System • Manually curated from tract tracing experiments in rat

• 961 brain regions

• 7,308 neuroanatomical connections

• Far from complete

Bota, M., H.W. Dong, and L.W. Swanson, Neuroinformatics, 2005. 3(1): p. 15-48.

Text mining the connectome literature

The nucleus raphe dorsalis projects to the ventral posterolateral nucleus.

“nucleus raphe dorsalis”

hasConnectionTo:

“ventral posterolateral nucleus”

Preliminary data • Applied to 12,557 abstracts • 28,107 extracted connections

• Estimated to be 60-70% precise • Filters for recency and frequency increase accuracy

Leon French

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The next era

• Three mouse connectome projects http://www.mouseconnectome.org/

http://connectivity.brain-map.org/

http://brainarchitecture.org/mouse

• Big human study: http://www.humanconnectomeproject.org/

Injection in visceral cortex on the right side. PHA-L labeled fibers seen traveling through corpus callosum to contralateral hemisphere and terminating onto CTb labeled neurons which in turn project back to the injection site.

http://www.mouseconnectome.org

Conclusions of Part 1

• Connectome is only partly described, except in worm

• Technology is rapidly advancing and the next few years will see completely new understanding of the connectome

– At the level of brain regions

– At the microcircuitry level

– In relation to functional networks

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The brain transcriptome

• The expression patterns of genes at the level of RNA

• Extensive information is available (though less on splice variants, or on small RNAs)

• About 80-90% of mouse genes are expressed in the adult brain

Allen Brain Atlas

• Colorimetric In Situ Hybridization

• Male 56 day old C57BL/6J mice

• 20,444 genes

• 207 regions

Lein ES, Hawrylycz MJ, Ao N et al. Genome-wide atlas of gene expression in the adult mouse brain, Nature 2007;445:168-176.

Data for human (microrray), developing brain, spinal cord also available

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Expression variability and region specificity

• Genes not expressed uniformly in the nervous system

• Major brain regions only explain part of the patterns

Nature 445, 168-176 (11 January 2007)

Many genes show expression patterns that don’t cluster by major brain division

Brain Regions

Bra

in R

egi

on

s

Leon French, from Allen Atlas data

• Could reflect differences in cell populations among regions

• Alternatively, could reflect interactions among brain regions

• Or otherwise reflect functional variation not captured by regional parcellation

• Or could be “Noise”

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Expression of neuronal development and axon guidance genes in adulthood • In regions of adult neurogenesis as might be expected, but

also in terminally differentiated neurons

• Hypothesized to play roles in plasticity: synapse formation and removal; responses to injury

• Examples: – Semaphorins & receptors

– Doublecortin

– Wnt/β-catenin pathway

Mann et al. Progress in Neurobiology Volume 82, Issue 2, June 2007, Pages 57-79 Nacher et al., Journal of Comparative Neurology (2000) v.424, Issue 4, pages 628–639, O’Connor et al., Neural Dev. 2009 May 23;4:18 Nacher et al., European Journal of Neuroscience Volume 14, Issue 4, pages 629–644, August 2001 Tsim et al., Neuroscience Volume 123, Issue 4, 2004, Pages 951-965 http://www.frontiersin.org/neuroanatomy/10.3389/fnana.2010.00025/full PNAS February 6, 2007 vol. 104 no. 6 1989-1994 (http://www.pnas.org/content/104/6/1989.full)

Plexin A4 in adult mouse brain

Roles of axon guidance genes in maturity

• Experiments in vitro suggest roles in controlling synapse strength or stability

• Experiments in vivo show changes in expression after injury or disease

– Doesn’t explain “baseline” expression.

O’Connor et al., Neural Dev. 2009 May 23;4:18

Overexpression of Sema5B reduces number of synaptic inputs

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Changes in Semaphorin and Neuropilin gene expression in animal models of neuronal

pathologies Disease Gene Expression

Traumatic injury of the CNS: Provoked damage of the CNS, leading to major motor, sensory and cognitive deficits

- Sema3A, Sema3B, Sema3C, Sema3E, Sema3F, Sema6B, Npn1

- mRNA expression in scar tissue

- Sema3A, Sema4F, Npn1, Nrp2 - Up-regulation of mRNA and protein expression in axotomized neurons and in regenerating axons in the brain, retina and spinal cord

- Sema4D - Up-regulation of protein expression in oligodendrocytes at the periphery of the lesion

Traumatic injury of the PNS: Provoked damage of peripheral nerves, leading to motor and sensory deficits

- Sema3A - Down-regulation of mRNA expression in regenerating spinal motor neurons and induction in terminal Schwann cells (TSCs)

- Sema3A, Sema3B, Sema3C, Sema3E, Sema3F, Npn1, Npn2

- Up-regulation of mRNA expression in the distal part of the crushed sciatic nerve

Amyotrophic lateral sclerosis: Gradual degeneration of motor neurons

- Sema3A - Up-regulation of mRNA expression in TSCs at the neuromuscular junction of fast fatigable muscle fibres

Ischemic stroke: Decrease in cerebral blood flow, resulting in retrograde neuronal degeneration and neuron death

- Sema3A, Sema3F, Npn1, Npn2 - Modulation of mRNA expression in neurons of the infacted cerebral cortex

- Npn1, Npn2 - Up-regulation of mRNA expression in activated microglia

Epileptic seizure: Abnormal electrophysiologic phenomena in the brain, leading to axonal sprouting and synaptic reorganization

- Sema3C, Sema3F, Npn2 - Decreased mRNA expression in CA1 and CA3 fields of the hippocampus

- Npn2 - Up-regulation of protein expression in the dentate gyrus and entorhinal cortex

Progress in Neurobiology Volume 82, Issue 2, June 2007, Pages 57-79

Conclusions of part II

• Genes are expressed in complex patterns in the brain that are poorly understood

• Genes involved in development continue to be expressed, and probably play functional roles, in the adult

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Does the connectome explain anything about the transcriptome (or vice versa)

• We expect that transmitter systems will show patterns of expression relevant to receptor-ligand relationships

• Dopamine receptors are expressed at significantly higher levels in regions that received connections from the substantia nigra

• Does this type of relationship explain much of the variation in gene expression?

Anders Björklund and Stephen B. Dunnett, Dopamine neuron systems in the brain: an update. Trends in Neurosciences. Volume 30, Issue 5, May 2007, Pages 194-202

C. elegans expression patterns carries information about connectivity

• Using a subset of the worm connectome where the is gene expression data

• 98 neurons, 289 genes

• Genes correlated with connectivity tend to be involved in axon guidance and synapse formation

Kaufman et al. PLoS Comput Biol. 2006 Dec 8;2(12):e167. Also: Baruch et al. PLoS Comput Biol. 2008 Jul 11;4(7):e1000120 Varadan et al. Bioinformatics. 2006 Jul 15;22(14):e497-506.

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Taking this idea into the mammalian brain

Needs: • Data on expression – Allen Atlas • Data on connectome – BAMS • Methods for comparing regions

– Physical distance – Connectedness – Shared connections – Gene expression profiles

• Methods for comparing networks – Mantel test et al.

Past CHiBi retreat presentation

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Themes in the genes found • Significant enrichment for genes involved in

axon guidance, neuronal development

– Heparan sulfate proteoglycans

– Semaphorins 3a, 6a, Neuropilins 1 & 2, Plexins A2 and B2, Ephrins B1 and A7, Slit1

– Stat5a, Uch1

– L1Cam, Cntfr, Cit, Lhx2

French and Pavlidis, PLoS Computational Biology

Enrichment of Autism candidate genes

• Human orthologs in AUTS1 locus (7q)

• Enrichment of genes from a autism research database

– 17 matched genes of 163

Reelin, Cadps2, En2, Dpp6, Btg3

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Seeking large-scale themes in expression patterns

Leon French, Patrick Tan

Anterior Posterior

912 most anti-correlated gene pairs represent only 102 genes

Brain Regions

Ge

nes

Pattern OE

Pattern NE

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Cell-type specific expression

Alternative approach: Principal components

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Correlation with connectedness

Pattern NE • Neuron - enriched

• Anterior expression

• Expressed highly in regions with many connections

• Evolutionarily more recent genes

Pattern OE • Oligodendrocyte - enriched

• Posterior expression

• Expressed highly in regions with few connections

• Evolutionarily more ancient

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Conclusions of Part III

• Using neuroinformatics databases as resources, is now feasible to analyze the mammalian connectome in the context of other information about the brain

• There are statistical relationships between gene expression and connectivity

• May be relevant to understanding plasticity in the adult nervous system or providing insights into development

• Leon French • Patrick Tan • Allen Institute for Brain Research • The Brain Architecture Centre