what does the transcriptome know about the connectome€¦ · conclusions of part 1 • connectome...
TRANSCRIPT
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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
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