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Nucleus- and cell-specific gene expression in monkey thalamus Karl D. Murray, Prabhakara V. Choudary, and Edward G. Jones* Center for Neuroscience and Department of Psychiatry and Behavioral Sciences, University of California, Davis, CA 95616 Contributed by Edward G. Jones, December 6, 2006 (sent for review November 16, 2006) Nuclei of the mammalian thalamus are aggregations of neurons with unique architectures and input– output connections, yet the molecular determinants of their organizational specificity remain unknown. By comparing expression profiles of thalamus and cerebral cortex in adult rhesus monkeys, we identified transcripts that are unique to dorsal thalamus or to individual nuclei within it. Real-time quantitative PCR and in situ hybridization analyses con- firmed the findings. Expression profiling of individual nuclei mi- crodissected from the dorsal thalamus revealed additional subsets of nucleus-specific genes. Functional annotation using Gene On- tology (GO) vocabulary and Ingenuity Pathways Analysis revealed overrepresentation of GO categories related to development, mor- phogenesis, cell– cell interactions, and extracellular matrix within the thalamus- and nucleus-specific genes, many involved in the Wnt signaling pathway. Examples included the transcription factor TCF7L2, localized exclusively to excitatory neurons; a calmodulin- binding protein PCP4; the bone extracellular matrix molecules SPP1 and SPARC; and other genes involved in axon outgrowth and cell matrix interactions. Other nucleus-specific genes such as CBLN1 are involved in synaptogenesis. The genes identified likely underlie nuclear specification, cell phenotype, and connectivity during de- velopment and their maintenance in the adult thalamus. development excitatory neurons inhibitory neurons thalamocortical Wnt signaling pathway T he mammalian thalamus is made up of groupings of neurons that reflect its evolutionary and developmental history, its function as a sensory relay, and its involvement in forebrain activities that underlie states of consciousness (1–4). The three major subdivisions of thalamus (epithalamus, dorsal thalamus, and ventral thalamus) emerge during embryogenesis from the wall of the diencephalic alar plate (5–7). Aggregation of fate- determined postmitotic neurons leads to the formation of mul- tiple subnuclei within these divisions characterized by different chemo-, cyto-, and myeloarchitectures and differing patterns of connections. The establishment of architecture and connections in all brain regions is modulated by molecular cues that govern cell aggregation, neurotransmitter phenotype, axon guidance, and synaptogenesis (8, 9). The unique architecture, connectivity, and transmitter/receptor characteristics of each thalamic nucleus are unlikely to be estab- lished or maintained in the absence of molecular genetic guidance. Clues to the nature of underlying mechanisms can be found by identifying genes that give a molecular identity to thalamic nuclei. Sets of regulatory genes distinguish the three major thalamic subdivisions in the developing and adult rodent and primate (10, 11), but expression occurs across multiple nuclei, in regional rather than nucleus-specific patterns. Some examples of nucleus-specific expression, however, do occur, e.g., Id-2 in the primate centre me ´dian nucleus (CM; ref. 10). Expression of neurotransmitter- or receptor-related genes in the thalamus also tends to be regional rather than nucleus-specific, but there are exceptions to this rule as well (12, 13). To determine the extent to which subnuclei of the major thalamic divisions are molecularly distinct, we used high-density oligonucleotide arrays to identify thalamus-specific genes in adult monkeys. By comparing expression profiles of thalamus and cerebral cortex, we identified genes not hitherto known to be expressed in thalamus. Further profiling of microdissected nuclei identified more comprehensive sets of genes with nucleus- specific expression. Confirmation of gene expression by RT- PCR, in situ hybridization histochemistry, and/or immunohisto- chemistry revealed remarkable cell- and nucleus-specific patterns of expression. Functionally, the genes are related to development and cell–cell interactions, implying their involve- ment in the establishment and maintenance of thalamic nuclear and cellular specificity. Results Genes specific to thalamus were identified by comparing expres- sion patterns in posterior thalamus (PT) with those in visual cortex (VC) and frontal cortex (FC). The vast majority of genes called ‘‘present’’ were equally distributed between cortex and thalamus. Of 1,978 genes called ‘‘present’’ in PT, VC, and FC, 89 (4.4%) were enriched in PT by 1.2-fold. A more stringent cutoff of 3-fold reduced this number to 31 (1.5%) thalamus- specific genes [supporting information (SI) Table 3]. A significant overrepresentation of thalamus-enriched probe sets was found for Gene Ontology (GO) terms related to development, morphogenesis, and cell signaling. The terms structural molecule activity (six genes, P 0.001), cell differ- entiation (six genes, P 0.001), morphogenesis (13 genes, P 0.01), and extracellular matrix (ECM) (three genes, P 0.01) were all overrepresented. Of the 17 most overrepresented genes (SI Table 4), 12 were associated with cellular growth and development (FGFR2, HSPA2, ILGFBP7, MOG, NDRG1, NHLH2, NTNG1, PCP4, PRDX1, SPARC, SPP1, and WWP1). Four genes associated with cell– cell interactions (NTNG1, RLN, SPARC, and SPP1) were localized to the ECM. Validation of the microarray results by RT-PCR was limited to the 31 genes enriched in PT by 3-fold. Twenty-five (81%) were successfully amplified (Figs. 1 and 2, Table 1). Twenty (65%) displayed elevated expression in PT vs. VC. Transcriptional profiling of samples microdissected from an- terior nuclei of dorsal thalamus, CM, mediodorsal nucleus, pulvinar, and ventral posterior nuclei confirmed and extended the thalamus-specific results. Unsupervised hierarchical cluster- ing broadly parsed thalamic nuclei into groups displaying similar Author contributions: K.D.M., P.V.C., and E.G.J. designed research; K.D.M., P.V.C., and E.G.J. performed research; K.D.M., P.V.C., and E.G.J. analyzed data; and K.D.M., P.V.C., and E.G.J. wrote the paper. The authors declare no conflict of interest. Freely available online through the PNAS open access option. Abbreviations: ECM, extracellular matrix; CM, centre me ´ dian nucleus; FC, frontal cortex; GO, Gene Ontology; PT, posterior thalamus; Pf, parafascicular nucleus; VC, visual cortex; dLGN, dorsal lateral geniculate nucleus. Data deposition: The sequences reported in this paper have been deposited in the GEO database (accession no. GSE6708). *To whom correspondence should be addressed. E-mail: [email protected]. This article contains supporting information online at www.pnas.org/cgi/content/full/ 0610742104/DC1. © 2007 by The National Academy of Sciences of the USA www.pnas.orgcgidoi10.1073pnas.0610742104 PNAS February 6, 2007 vol. 104 no. 6 1989 –1994 NEUROSCIENCE Downloaded by guest on April 30, 2020

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Page 1: Nucleus- and cell-specific gene expression in monkey thalamus · Nucleus- and cell-specific gene expression in monkey thalamus Karl D. Murray, Prabhakara V. Choudary, and Edward G

Nucleus- and cell-specific gene expressionin monkey thalamusKarl D. Murray, Prabhakara V. Choudary, and Edward G. Jones*

Center for Neuroscience and Department of Psychiatry and Behavioral Sciences, University of California, Davis, CA 95616

Contributed by Edward G. Jones, December 6, 2006 (sent for review November 16, 2006)

Nuclei of the mammalian thalamus are aggregations of neuronswith unique architectures and input–output connections, yet themolecular determinants of their organizational specificity remainunknown. By comparing expression profiles of thalamus andcerebral cortex in adult rhesus monkeys, we identified transcriptsthat are unique to dorsal thalamus or to individual nuclei within it.Real-time quantitative PCR and in situ hybridization analyses con-firmed the findings. Expression profiling of individual nuclei mi-crodissected from the dorsal thalamus revealed additional subsetsof nucleus-specific genes. Functional annotation using Gene On-tology (GO) vocabulary and Ingenuity Pathways Analysis revealedoverrepresentation of GO categories related to development, mor-phogenesis, cell–cell interactions, and extracellular matrix withinthe thalamus- and nucleus-specific genes, many involved in theWnt signaling pathway. Examples included the transcription factorTCF7L2, localized exclusively to excitatory neurons; a calmodulin-binding protein PCP4; the bone extracellular matrix molecules SPP1and SPARC; and other genes involved in axon outgrowth and cellmatrix interactions. Other nucleus-specific genes such as CBLN1 areinvolved in synaptogenesis. The genes identified likely underlienuclear specification, cell phenotype, and connectivity during de-velopment and their maintenance in the adult thalamus.

development � excitatory neurons � inhibitory neurons � thalamocortical �Wnt signaling pathway

The mammalian thalamus is made up of groupings of neuronsthat reflect its evolutionary and developmental history, its

function as a sensory relay, and its involvement in forebrainactivities that underlie states of consciousness (1–4). The threemajor subdivisions of thalamus (epithalamus, dorsal thalamus,and ventral thalamus) emerge during embryogenesis from thewall of the diencephalic alar plate (5–7). Aggregation of fate-determined postmitotic neurons leads to the formation of mul-tiple subnuclei within these divisions characterized by differentchemo-, cyto-, and myeloarchitectures and differing patterns ofconnections.

The establishment of architecture and connections in all brainregions is modulated by molecular cues that govern cell aggregation,neurotransmitter phenotype, axon guidance, and synaptogenesis (8,9). The unique architecture, connectivity, and transmitter/receptorcharacteristics of each thalamic nucleus are unlikely to be estab-lished or maintained in the absence of molecular genetic guidance.Clues to the nature of underlying mechanisms can be found byidentifying genes that give a molecular identity to thalamic nuclei.Sets of regulatory genes distinguish the three major thalamicsubdivisions in the developing and adult rodent and primate (10,11), but expression occurs across multiple nuclei, in regional ratherthan nucleus-specific patterns. Some examples of nucleus-specificexpression, however, do occur, e.g., Id-2 in the primate centremedian nucleus (CM; ref. 10). Expression of neurotransmitter- orreceptor-related genes in the thalamus also tends to be regionalrather than nucleus-specific, but there are exceptions to this rule aswell (12, 13).

To determine the extent to which subnuclei of the majorthalamic divisions are molecularly distinct, we used high-densityoligonucleotide arrays to identify thalamus-specific genes in

adult monkeys. By comparing expression profiles of thalamusand cerebral cortex, we identified genes not hitherto known tobe expressed in thalamus. Further profiling of microdissectednuclei identified more comprehensive sets of genes with nucleus-specific expression. Confirmation of gene expression by RT-PCR, in situ hybridization histochemistry, and/or immunohisto-chemistry revealed remarkable cell- and nucleus-specificpatterns of expression. Functionally, the genes are related todevelopment and cell–cell interactions, implying their involve-ment in the establishment and maintenance of thalamic nuclearand cellular specificity.

ResultsGenes specific to thalamus were identified by comparing expres-sion patterns in posterior thalamus (PT) with those in visualcortex (VC) and frontal cortex (FC). The vast majority of genescalled ‘‘present’’ were equally distributed between cortex andthalamus. Of 1,978 genes called ‘‘present’’ in PT, VC, and FC, 89(4.4%) were enriched in PT by �1.2-fold. A more stringentcutoff of �3-fold reduced this number to 31 (1.5%) thalamus-specific genes [supporting information (SI) Table 3].

A significant overrepresentation of thalamus-enriched probesets was found for Gene Ontology (GO) terms related todevelopment, morphogenesis, and cell signaling. The termsstructural molecule activity (six genes, P � 0.001), cell differ-entiation (six genes, P � 0.001), morphogenesis (13 genes, P �0.01), and extracellular matrix (ECM) (three genes, P � 0.01)were all overrepresented. Of the 17 most overrepresented genes(SI Table 4), 12 were associated with cellular growth anddevelopment (FGFR2, HSPA2, ILGFBP7, MOG, NDRG1,NHLH2, NTNG1, PCP4, PRDX1, SPARC, SPP1, and WWP1).Four genes associated with cell–cell interactions (NTNG1, RLN,SPARC, and SPP1) were localized to the ECM.

Validation of the microarray results by RT-PCR was limitedto the 31 genes enriched in PT by �3-fold. Twenty-five (81%)were successfully amplified (Figs. 1 and 2, Table 1). Twenty(65%) displayed elevated expression in PT vs. VC.

Transcriptional profiling of samples microdissected from an-terior nuclei of dorsal thalamus, CM, mediodorsal nucleus,pulvinar, and ventral posterior nuclei confirmed and extendedthe thalamus-specific results. Unsupervised hierarchical cluster-ing broadly parsed thalamic nuclei into groups displaying similar

Author contributions: K.D.M., P.V.C., and E.G.J. designed research; K.D.M., P.V.C., and E.G.J.performed research; K.D.M., P.V.C., and E.G.J. analyzed data; and K.D.M., P.V.C., and E.G.J.wrote the paper.

The authors declare no conflict of interest.

Freely available online through the PNAS open access option.

Abbreviations: ECM, extracellular matrix; CM, centre median nucleus; FC, frontal cortex;GO, Gene Ontology; PT, posterior thalamus; Pf, parafascicular nucleus; VC, visual cortex;dLGN, dorsal lateral geniculate nucleus.

Data deposition: The sequences reported in this paper have been deposited in the GEOdatabase (accession no. GSE6708).

*To whom correspondence should be addressed. E-mail: [email protected].

This article contains supporting information online at www.pnas.org/cgi/content/full/0610742104/DC1.

© 2007 by The National Academy of Sciences of the USA

www.pnas.org�cgi�doi�10.1073�pnas.0610742104 PNAS � February 6, 2007 � vol. 104 � no. 6 � 1989–1994

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gene expression profiles (Fig. 3). When further analyzed by theDrawn Gene function in GeneSpring software (Agilent Tech-nologies, Foster City, CA) (Fig. 3), �550 genes expressed in anucleus-specific manner were identified within the dorsal thal-amus (SI Dataset 1).

Ingenuity Pathways Analysis of the nucleus-enriched genesalso showed significant overrepresentation of functions relatedto development and cell signaling (Fig. 4). Analysis of candidategenes for potential interactions revealed putative protein net-works involving development and cell signaling as top functionalcategories (Table 2). Other top network functions included cellcycle, cancer, and gene expression. Strikingly, members of thecanonical Wnt/�-catenin signaling cascade featured prominentlyin four of the five top networks (Table 2).

The distribution of genes validated by RT-PCR and of certainof those defined by nucleus-specific assay was examined by in situhybridization. Four patterns of expression were observed (Table1): (i) restricted to thalamus, (ii) enriched in thalamus, (iii) equalin thalamus and cortex, and (iv) associated with fiber tracts. Forexample, expression of SPP1, TCF7L2, and CBLN1 was re-stricted to thalamus. Expression of SPARC, PCP4, and SEPT4was enriched in thalamic nuclei. Expression of CALR, FGFR2,and ST18 was equal in cortex and thalamus. Expression of genesassociated with myelin production MAG, MOG, and MOBP wasrestricted to fiber tracts.

Expression of TCF7L2, PCP4, CBLN1, and SPP1 was delim-ited by the borders of thalamic nuclei. TCF7L2 expression was

restricted to nuclei of the dorsal thalamus (Fig. 2), except forsome aspects of the ventral thalamus (the deep lamina of thepregeniculate nucleus, the posterior division of the zona incerta,and among scattered cells of the field of Forel), as well as in asmall focus in the medial habenular nucleus of the epithalamus(Fig. 2). PCP4 was expressed throughout dorsal thalamus, withthe notable exception of the CM and parafascicular nucleus (Pf);CBLN1, by contrast, was expressed only in CM and Pf (Fig. 4).PCP4 was also expressed in the striatum (caudate nucleus andputamen) and in layer V of the cerebral cortex. SPP1 and PCP4were expressed only in the parvo- and magnocellular layers of thedorsal lateral geniculate nucleus; TCF7L2 was expressed only inthe parvocellular, s layers, and interlaminar layers (Fig. 2).

Immunocytochemistry for TCF7L2 protein showed enrichmentin the dorsal thalamus (SI Fig. 5). In double-labeling experimentswith markers of excitatory and inhibitory neurons, TCF7L2 immu-nostaining was absent from GABA neurons (SI Fig. 5) in dorsalthalamus, reticular nucleus, zona incerta, or pregeniculate nucleus.TCF7L2 was coexpressed in dorsal thalamic neurons immuno-stained for � type II calcium/calmodulin-dependent protein kinase,a marker for excitatory neurons (14–16) (SI Fig. 5). SPP1 and PCP4immunoreactive cells could be costained for neuronal markers,whereas SPARC immunoreactive cells could not be costained forneuronal, astrocytic, or oligodendrocytic markers, implying theymay be microglial cells (data not shown).

DiscussionThalamic nuclei, classically defined by cyto-, myelo-, and che-moarchitecture and by connectional and physiological charac-teristics, are molecularly distinct. Expression profiling revealeda subset of genes that were enriched or exclusively expressed innuclei of adult thalamus. Most prominent were genes associatedwith development, cell signaling, morphogenesis, the ECM, andthe Wnt signaling pathway. Cell signaling molecules encoded byseveral candidate genes are localized to ECM, suggesting thatmolecules within the extracellular environs are important de-terminants of how thalamic cells aggregate into nuclei.

The results demonstrate that human oligonucleotide arrayscan be successfully used for large-scale transcriptional profilingof other Old World primate brains, as demonstrated by thedelineation of novel thalamic markers, e.g., TCF7L2, PCP4, andCBLN1, whose expression is not only limited to specific thalamicnuclei, but in the case of TCF7L2, restricted to excitatoryneurons. Two members of the bone matricellular family, SPP1(Osteopontin) and SPARC (Osteonectin), with cell type- andnucleus-specific patterns of expression, were also detected.Although from the same protein family, SPP1 and SPARC areexpressed in neurons and nonneuronal cells, respectively, sug-gesting they may contribute to nuclear and cellular identities inunique ways.

The thalamus-specific genes identified, whether highly re-stricted (e.g., SPP1 and CBLN1) or broad (e.g., TCF7L2 andPCP4) in their expression, were invariably delimited by classicalnuclear boundaries, and none redefined thalamic boundaries.Similar adherence of expression patterns to cytoarchitectureoccurs in mouse hippocampus (17, 18) and amygdala (19), oftenproviding less equivocal delineations of borders than cytoarchi-tecture alone (20). Establishment of nuclear identity fromhomogenous masses of cells in the developing thalamus isassociated with determination of cell size, aggregation, packingdensity, and establishment of connections; the GO associationsof the majority of the genes identified implicate them in theseactivities.

Expression of two genes, PCP4 and SPP1, was restricted tocells of dorsal thalamus, but none to ventral thalamus, althoughTCF7L2 marked subpopulations of non-GABA cells in thepregeniculate nucleus, zona incerta, and field of Forel. In ferrets,Kawasaki et al. (21) demonstrated molecular distinctions be-

Fig. 1. RT-PCR measures of regional transcript expression levels confirmmicroarray results. Bar graph indicates relative expression between PT and VCfor transcripts overrepresented in thalamus by �3-fold in microarray analysis.Dotted line indicates a ratio of 1, denoting no change in expression. Error barsindicate standard deviation of the mean. Glyceraldehyde-3-phosphate dehy-drogenase (G3PDH) and �-actin genes were included as internal controls.Asterisks indicate probe sets analyzed by in situ hybridization histochemistry.

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tween the dLGN, a component of dorsal thalamus and theperigeniculate nucleus, a part of the reticular nucleus. In theirstudy, PCP4 was more heavily expressed in larger putative Y cells

of the dLGN than in smaller putative X cells. We observed PCP4expression in both magno- and parvocellular laminae of monkeydLGN and in most other dorsal thalamic nuclei. However, PCP4expression was absent from the CM and Pf nuclei that form thecaudal group of intralaminar nuclei. CM, absent in rodents andmany other mammals, is particularly elaborated in primates anddisplays a unique expression profile compared with other tha-lamic nuclei (Fig. 3 and SI Dataset 1). CM and Pf also exclusivelyexpress CBLN1 and the transcription factor Id-2 (10) and arecharacterized by patterns of GABA and glutamate receptorexpression that are very different from those in other dorsalthalamic nuclei (12, 13). CBLN1, a glycoprotein that is struc-turally related to the C1q and tumor necrosis factor families ofproteins, in the cerebellum is associated with synaptogenesis inPurkinje cells (22).

The transcription factor, TCF7L2, was highly expressed andrestricted to excitatory neurons in dorsal thalamus and tonon-GABA neurons in the ventral thalamus. TCF7L2 is specificfor thalamus, unlike other markers of excitatory thalamic neu-rons, such as � type II calcium/calmodulin-dependent proteinkinase, which are expressed in other forebrain regions as well(13, 14). TCF7L2 is a member of the high mobility group box

Fig. 2. Autoradiogramsandimmunocytochemicalpreporationsfrommonkeythalamusandcortex. Imagesfromfilmaudioradiogramsshowabundanceoftranscriptsof TCF7L2 (A, E, I, and M), PCP4 (B, F, and J), SPP1 (C, G, and K), and SPARC (D, H, and L) in thalamus (A–D and I–M) relative to cortex (E–H). Expression of TCF7L2 andSPP1 is restricted to thalamus, whereas PCP4 and SPARC are expressed in other subcortical regions as well. Higher-magnification images of the dorsal lateral geniculatenucleus (dLGN) illustrate the differential expression of TCF7L2, PCP4, and SPP1 in dLGN (I–L). Dashed line indicates separation between magnocellular (1 and 2) andparvocellular (3–6) layers of the dLGN, as marked in adjacent Nissl section (L). In situ hybridization for TCF7L2 mRNA (M) and immunoreactivity for TCF7L2 (N and O)reveal expression in posterior division of the zona incerta (M), the deep lamina of the pregeniculate nucleus (N), and the field of Forel (O). (Scale bars: A–H, 3 mm; M,1 mm; I–L, N, and O, 500 �m.) CN, caudate nucleus; FF, field of Forel; LP, lateral posterior nucleus; MB, midbrain; MD, mediodorsal nucleus; OT, optic tract; P, putamen;Prg, pregeniculate nucleus; R, reticular nucleus; SPf, sub-Pf; VL, ventral lateral nucleus; VMb, basal ventral medial nucleus; VP, ventral posterior nuclei; VPI, ventralposterior inferior nucleus; VPL, ventral posterior lateral nucleus; VPM, ventral posterior medial nucleus; ZI, zona incerta.

Table 1. Candidate genes validated by in situ hybridization

Expression pattern Gene symbol

Restricted to thalamus SPP1TCF7L2

Enriched in thalamus SPARCSEPT4PCP4

Equal in cortex and thalamus CALRFGFR2ST18

Associated with fiber tracts MAGMOBPMOG

Cortex specific or enriched NONENone detected GPR37

C11ORF9

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proteins of the T cell factor/lymphoid enhancer factor subfamilythat mediate Wnt protein signaling through the canonical �-catenin pathway (23–25). Wnts direct the emergence of func-tionally distinct regions along the developing neuraxis and haveconsequently been implicated in the formation of neuronalconnectivity (26–30). The Wnt pathway also influences axonalremodeling through interactions with the cytoskeleton (31, 32),and interfering with Wnt signaling disrupts synapse formation(31, 33). The Wnt/�-catenin signaling cascade featured promi-nently in the top functional networks (Table 2). Hence, Wnt/�-catenin signaling is a candidate for involvement not only in

formation and maintenance of dorsal thalamic connectivity butalso in the plasticity of connections in the adult. This notion issupported by the observation that mice null for the low-densitylipoprotein receptor-related protein 6, a required signalingcoreceptor for the Wnt/�-catenin pathway, exhibit profounddisruptions in the development of dorsal thalamus and epithal-amus (34).

The present observations illustrate that nuclei of the dorsalthalamus are comprised of groups of cells sharing commonmolecular phenotypes. The variety of cellular and molecularmechanisms likely to be required for establishing and maintain-ing the specific architectural, connectional, and functional sig-natures of each thalamic nucleus is reflected in the range offunctions associated with the thalamus-enriched genes.

Materials and MethodsAnimals. Brains from eight adult male rhesus monkeys (Macacamulatta) were used. All procedures were carried out by using

Fig. 3. GeneSpring analysis of five thalamic nuclei. Nuclei of the dorsalthalamus display unique gene expression profiles. (A) Genes with significantexpression (P � 0.05) in at least one of the five regions examined werehierarchically clustered by similarity in expression profile. The resulting heatmap of the dendrogram tree reveals groups of genes with high (red) expres-sion levels in one thalamic nucleus and moderate (black) or low (green) levelsin the other four nuclei. (B) Genes with thalamic nucleus-specific expressionprofiles were identified by using the Drawn Gene function in the GeneSpringanalysis program. For each region examined, sets of genes whose expressionprofiles significantly correlated (R2 � 0.95) to a template pattern (red) wereidentified.

Fig. 4. Microarray results confirmed by in situ hybridization histochemistry (A)and functional analysis of thalamus-enriched genes (B). In situ hybridization andfunctional annotation validate thalamic nucleus-specific gene expression. (A)Images from film autoradiograms show differential expression of CBLN1 (Upper)and PCP4 (Lower) in monkey dorsal thalamus, corroborating the microarrayresults (Right). (B) The Ingenuity Pathways Analysis program enabled biological/functional annotations of candidate genes identified by the Drawn Gene Func-tion in GeneSpring analysis. The top five functions are compared across allregions. Abbreviations are as in Fig. 2.

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protocols approved by the Institutional Animal Care and UseCommittee.

Microarray Probe Generation. Brains were processed according toprotocols developed for postmortem human brain tissue (35).Pieces were excised or micropunched from frozen coronal slicesto give samples from PT, VC, or FC or from different nuclearregions of the thalamus. Total RNA was extracted by TRIzolreagent (Invitrogen, Carlsbad, CA) followed by cleanup by usingan RNeasy Lipid Mini Extraction Kit (Qiagen, Valencia, CA).RNA quality was monitored by agarose gel electrophoresis,spectrophotometry, and an Agilent Bioanalyzer (Agilent, FosterCity, CA). Total RNA was processed for Affymetrix GeneChipanalysis according to the manufacturer’s protocol (Affymetrix,Santa Clara, CA), using human HuU95Av2 or U133A Gene-Chips, as described (36, 37). Criteria used to assess quality of chiphybridization were percent ‘‘present’’ calls, scaling factor, back-ground noise, and mean average difference value.

Microarray Data Analysis. To identify genes enriched in thalamus,mean average difference values for PT were compared withthose for VC and independently for FC. Only genes called‘‘present’’ in all three samples and with the same direction offold-change in both comparisons (PT-VC and PT-FC) wereincluded. A list of genes in rank order of fold difference wasgenerated (SI Table 3). To identify genes displaying regionalexpression in dorsal thalamic nuclei, Affymetrix Cel files werepreprocessed for robust multiarray analysis (RMA) in Gene-Spring GX (Ver. 7.3.1) software (Agilent Technologies) fol-lowed by per-gene and per-chip median polishing. Hierarchicalclustering and GeneSpring Drawn Gene analyses were per-formed on genes filtered by confidence (P � 0.05) and normal-ized expression value (�1.2). Gene profiles highly correlatedwith a drawn template (R2 � 0.95) were included in furtheranalyses.

Gene sets defined by transcriptional profiling on samplesmicropunched from thalamic nuclei were divided into groupsdisplaying similar gene expression profiles by unsupervisedhierarchical clustering and by the Drawn Gene function inGeneSpring.

Genes that were expressed in a region- or nucleus-specificmanner were analyzed for association with biological functionsand/or diseases using Onto-Express (http://vortex.cs.wayne.edu/ontoexpress) (38–40) and Ingenuity Pathways Analysis (Inge-nuity Systems, Redwood City, CA). Fischer’s exact test was usedto determine P values. To interrogate potential functional in-teractions among candidate genes, each gene identifier wasmapped to its corresponding gene object, and these ‘‘FocusGenes’’ were overlaid onto a global molecular network devel-oped from information in the Ingenuity Pathways Knowledge

Base. Networks of the ‘‘Focus Genes,’’ based on their connec-tivity, were then algorithmically generated.

Real-Time RT-PCR. Total RNA was isolated from VC or PT, anda cDNA template was prepared from 1 �g by using oligo(dT)18primer and Moloney murine leukemia virus reverse transcrip-tase (Clontech, Palo Alto, CA). PCRs were performed by using4% of the cDNA product as starting material and measured inreal time as a function of SYBR green I incorporation using theBio-Rad iCycler (BioRad, Hercules, CA) (41). After PCR, a firstderivative melting-curve analysis was performed to confirm thespecificity of the PCR. PCR products were electrophoresed,purified, and sequenced to verify amplicon identity. The relativefold difference in mRNA between samples was calculated bycomparing the threshold cycle (Ct) at which product initiallyappeared above background according to: 2�(�Ct), where �Ct isthe difference between PT and VC values.

In Situ Hybridization. Two monkeys were anesthetized with ket-amine and sodium pentobarbital and perfused with 4% para-formaldehyde in 0.1 M phosphate buffer (pH 7.2). Brains wereremoved, blocked, postfixed for 4 h at 4°C, cryoprotected, andfrozen in dry ice. Microtome-cut sections were placed in fixativeat 4°C for at least 7 days.

Riboprobes were generated from PCR fragments cloned intopCR4-TOPO vector (Invitrogen). Probes were labeled by in vitrotranscription by using [�-33P]UTP or [�-35S]UTP. Sections wereincubated in hybridization solution containing anti-sense cRNAprobes, at 60°C, and washed in: 4� saline sodium citrate (SSC)at 60°C, twice, 30 min (1� SSC � 0.15 M NaCl/0.015 M sodiumcitrate, pH 7.0); ribonuclease A (0.02 mg/ml in 0.01 M Tris�HClbuffer, pH 8.0/1 mM EDTA/2.9% NaCl) at 45°C, 1 h; and 2�SSC, room temperature, twice, 30 min. Sections were thenexposed to radiographic film at 4°C and counterstained withthionin. Sense-strand RNA probes were used as controls.

Immunocytochemistry. Sections were placed directly in 0.1 Mphosphate buffer, pH 7.4, at 4°C. Standard immunocytochemicaltechniques were used for immunolabeling and visualization with3,3� diaminobenzidine 4 HCl. For double-immunofluorescentlabeling, sections were exposed to a mixture of primary anti-bodies, followed by a mixture of fluorescent-labeled secondaryantibodies (Alexa-488, -568, or -647; Molecular Probes, Eugene,OR), and counterstained with Hoechst 33342 (MolecularProbes).

The following monoclonal or polyclonal antibodies were used:calbindin, parvalbumin, GABA (Sigma, St. Louis, MO), � typeII calcium/calmodulin-dependent protein kinase, glial fibrillaryacidic protein-(GFAP), myelin basic protein, myelin/oligoden-drocyte-specific protein, chondroitin sulfate proteoglycan (NG2;

Table 2. Top gene networks identified in Ingenuity Pathways analysis

Region ScoreFocusgenes

Wnt/�-catenincanonical

pathway genes Top biological functions

Ven DT 24 18 0 Cell-to-cell signaling and interaction, cellular assembly and organization,cellular function and maintenance

CM 23 15 3 Skeletal and muscular system development and function, cancer, cell cycleMed DT 33 21 2 Embryonic development, cellular assembly and organization, cellular

developmentPulv 18 10 3 Cell cycle, carbohydrate metabolism, small molecule biochemistryAn DT 33 16 3 Gene expression, cancer, cellular growth and proliferation

Genes displaying region-specific expression were mapped to corresponding objects in the Ingenuity Pathways Knowledge Base. Ascore based on the number of mapped ‘‘focus’’ genes and network size is used for ranking purposes. The canonical Wnt/�-cateninsignaling pathway was well represented among the top networks. An DT, anterior dorsal thalamus; CM, centre médian nucleus; MedDT, medial dorsal thalamus; Pulv, pulvinar; Ven DT, ventral dorsal thalamus.

Murray et al. PNAS � February 6, 2007 � vol. 104 � no. 6 � 1993

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Page 6: Nucleus- and cell-specific gene expression in monkey thalamus · Nucleus- and cell-specific gene expression in monkey thalamus Karl D. Murray, Prabhakara V. Choudary, and Edward G

Chemicon, Temecula, CA), prospero-related homeobox 1(Prox1; Covance, Berkeley, CA), Tcf7l2 (Upstate Biotechnol-ogy, Lake Placid, NY, and Zymed, San Francisco, CA), SPP1(Osteopontin; Developmental Studies Hybridoma Bank, IowaCity, IA), and SPARC (Osteonectin; US Biologicals, Swamp-scott, MA).

Thalamic nuclei were identified by cytoarchitectural featuresobserved in Nissl-stained sections (ref. 7; www.brainmaps.org).Autoradiographic images were captured by using a Nikon D1Xcamera (Nikon, Melville, NY). Brightfield photomicrographswere obtained by using a Nikon Eclipse 1000 microscopeequipped with a Quantix CCD camera (Photometrics, Tuscon,AZ). Fluorescent images were obtained with a Zeiss

(Oberkochen, Germany) LSM 510 META laser-scanning con-focal microscope. Z-stacked images were collected, collapsed,saved as TIFF files, imported into Adobe Photoshop, and labeledin Adobe Illustrator (Adobe Systems, San Jose, CA).

We thank Xiao-Hong Fan, Phong Nguyen, and Malalai Yusufzai fortechnical assistance. This work was supported by the National Institutesof Health (Grants NS21377 and NS39094) and the W. M. Keck Programin Neuroscience Imaging. K.D.M. is the recipient of a young investigatoraward from the National Alliance for Research in Schizophrenia andDepression and the Sunshine from Darkness Gala. The monoclonalantibody MPIIIB101 was developed by Michael Solursh and AhndersFranzen under the auspices of the National Institute of Child Health andHuman Development.

1. Jones EG (1998) Adv Neurol 77:49–71.2. Llinas R, Ribary U, Contreras D, Pedroarena C (1998) Philos Trans R Soc

London B 353:1841–1849.3. Llinas R, Ribary U (2001) Ann NY Acad Sci 929:166–175.4. Llinas RR, Pare, D (1991) Neuroscience 44:521–535.5. Puelles L, Rubenstein JL (1993) Trends Neurosci 16:472–479.6. Puelles L, Rubenstein JL (2003) Trends Neurosci 26:469–476.7. Jones EG (2006) The Thalamus (Cambridge Univ Press, Cambridge, UK),

2nd Ed.8. Jan YN, Jan LY (2003) Neuron 40:229–242.9. Tessier-Lavigne M (2002) Harvey Lect 98:103–143.

10. Jones EG, Rubenstein JL (2004) J Comp Neurol 477:55–80.11. Nakagawa Y, O’Leary DD (2001) J Neurosci 21:2711–2725.12. Huntsman MM, Leggio MG, Jones EG (1996) J Neurosci 16:3571–3589.13. Jones EG, Tighilet B, Tran BV, Huntsman MM (1998) J Comp Neurol

397:371–393.14. Benson DL, Isackson PJ, Hendry SH, Jones EG (1991) J Neurosci 11:1540–

1564.15. Benson DL, Isackson PJ, Gall CM, Jones EG (1992) Neuroscience 46:825–849.16. Liu XB, Jones EG (1996) Proc Natl Acad Sci USA 93:7332–7336.17. Lein ES, Zhao X, Gage FH (2004) J Neurosci 24:3879–3889.18. Zhao X, Lein ES, He A, Smith SC, Aston C, Gage FH (2001) J Comp Neurol

441:187–196.19. Zirlinger M, Kreiman G, Anderson DJ (2001) Proc Natl Acad Sci USA

98:5270–5275.20. Lein ES, Callaway EM, Albright TD, Gage FH (2005) J Comp Neurol 485:1–10.21. Kawasaki H, Crowley JC, Livesey FJ, Katz LC (2004) J Neurosci 24:9962–9970.22. Hirai H, Pang Z, Bao D, Miyazaki T, Li L, Miura E, Parris J, Rong, Y Watanabe

M, Yuzaki M, Morgan JL (2005) Nat Neurosci 8:1534–1541.23. Cho EA, Dressler GR (1998) Mech Dev 77:9–18.

24. Korinek V, Barker N, Willert K, Molenaar M, Roose J, Wagenaar G, MarkmanM, Lamers W, Destree O, Clevers H (1998) Mol Cell Biol 18:1248–1256.

25. Lee YJ, Swencki B, Shoichet S, Shivdasani RA (1999) J Biol Chem 274:1566–1572.

26. Charron F, Tessier-Lavigne M (2005) Development (Cambridge, UK) 132:2251–2262.

27. Christiansen JH, Coles EG, Wilkinson DG (2000) Curr Opin Cell Biol12:719–724.

28. Patapoutian A, Reichardt LF (2000) Curr Opin Neurobiol 10:392–399.29. Ciani L, Salinas PC (2005) Nat Rev Neurosci 6:351–362.30. Pleasure SJ (2001) Trends Neurosci 24:69–71.31. Hall AC, Lucas FR, Salinas PC (2000) Cell 100:525–535.32. Krylova O, Messenger MJ, Salinas PC (2000) J Cell Biol 151:83–94.33. Luo ZG, Wang Q, Zhou JZ, Wang J, Luo Z, Liu M, He X, Wynshaw-Boris A,

Xiong WC, Lu B, et al. (2002) Neuron 35:489–505.34. Zhou CJ, Pinson KI, Pleasure SJ (2004) J Neurosci 24:7632–7639.35. Jones EG, Hendry SHC, Liu XB, Hodgins S, Potkin SG, Tourtellotte WW

(1992) J Neurosci Methods 44:133–144.36. Bunney WE, Bunney BG, Vawter MP, Tomita H, Li J, Evans SJ, Choudary PV,

Myers RM, Jones EG, Watson SJ, et al. (2003) Am J Psychiatry 160:657–666.37. Choudary PV, Molnar M, Evans SJ, Tomita H, Li JZ, Vawter MP, Myers RM,

Bunney WE, Jr, Akil H, Watson SJ, et al. (2005) Proc Natl Acad Sci USA102:15653–15658.

38. Anderle P, Duval M, Draghici S, Kuklin A, Littlejohn TG, Medrano JF,Vilanova D, Roberts MA (2003) BioTechniques Suppl:36–44.

39. Draghici S, Khatri P, Bhavsar P, Shah A, Krawetz SA, Tainsky MA (2003)Nucleic Acids Res 31:3775–3781.

40. Khatri P, Draghici S, Ostermeier GC, Krawetz SA (2002) Genomics 79:266–270.

41. Murray KD, Isackson PJ, Jones EG (2003) Neuroscience 122:407–420.

1994 � www.pnas.org�cgi�doi�10.1073�pnas.0610742104 Murray et al.

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Apr

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