US20110071049A1 - Methods and compositions for translational profiling and molecular phenotyping - Google Patents

Methods and compositions for translational profiling and molecular phenotyping Download PDF

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US20110071049A1
US20110071049A1 US12/918,761 US91876109A US2011071049A1 US 20110071049 A1 US20110071049 A1 US 20110071049A1 US 91876109 A US91876109 A US 91876109A US 2011071049 A1 US2011071049 A1 US 2011071049A1
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cell
gene
expression
cells
bacarray
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Nathaniel Heintz
Paul Greengard
Myriam Heiman
Anne Schaefer
Joseph P. Doyle
Joseph D. Dougherty
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Rockefeller University
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    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/62—DNA sequences coding for fusion proteins
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01K—ANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K67/00—Rearing or breeding animals, not otherwise provided for; New or modified breeds of animals
    • A01K67/027—New or modified breeds of vertebrates
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    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/111—General methods applicable to biologically active non-coding nucleic acids
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    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/5005—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells
    • G01N33/5008—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics
    • G01N33/502—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics for testing non-proliferative effects
    • G01N33/5023—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics for testing non-proliferative effects on expression patterns
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/5005—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells
    • G01N33/5008—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics
    • G01N33/5044—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics involving specific cell types
    • G01N33/5058—Neurological cells
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01K—ANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K2217/00—Genetically modified animals
    • A01K2217/20—Animal model comprising regulated expression system
    • A01K2217/206—Animal model comprising tissue-specific expression system, e.g. tissue specific expression of transgene, of Cre recombinase
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01K—ANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K2227/00—Animals characterised by species
    • A01K2227/10—Mammal
    • A01K2227/105—Murine
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01K—ANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K2267/00—Animals characterised by purpose
    • A01K2267/01—Animal expressing industrially exogenous proteins
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    • C12N2320/00—Applications; Uses
    • C12N2320/10—Applications; Uses in screening processes
    • C12N2320/12—Applications; Uses in screening processes in functional genomics, i.e. for the determination of gene function
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/28—Neurological disorders
    • G01N2800/285—Demyelinating diseases; Multipel sclerosis

Definitions

  • a paradigm in the development of new diagnostics and therapies for human diseases and disorders is the characterization of the gene expression of defined cell types.
  • the cellular complexity of many tissues poses a challenge for those seeking to characterize gene expression at this level.
  • the enormous heterogeneity of a tissue such as the nervous system is a barrier to the identification and analysis of gene transcripts present in individual cell types.
  • Cellular subtypes are highly heterogeneous and often intermixed.
  • the invention described herein provides methods, compositions, and kits useful in elucidating the biological properties of distinct cellular populations.
  • the embodiments described herein comprise a translating ribosome affinity purification (TRAP) methodology, which is a generalizable method useful for the identification of molecular changes in any genetically defined cell type in response to genetic alterations, disease, environmental, pharmacological, other perturbations.
  • TRIP translating ribosome affinity purification
  • the invention described herein provides a method of identifying a co-regulated gene set for a function, comprising determining translational profiles for a plurality of cell types that express a gene associated with that function, comparing the translational profiles to determine what additional genes are similarly regulated, thereby identifying a co-regulated gene set involved in that function specifically.
  • the method is provided to identify a co-regulated gene set involved in myelination, and in a further embodiment the gene associated with myelination is Mbp.
  • the co-regulated gene set comprises at least two genes listed in Table 9.
  • the gene set comprises at least two genes selected from the group consisting of Plp1, Cnp, Mog, Mal and Mobp.
  • the invention described herein provides a method for detecting one or more cell type-enriched genes not detectable by the whole-tissue microarray technique comprising assessing a translational profile for a cell type, comparing the translational profile to the results of a whole-tissue microarray, and determining the presence of one or more genes in the translational profile that are not present in the results of a whole-tissue microarray, thereby detecting one or more cell type-enriched genes that are not detectable by the whole-tissue microarray technique.
  • greater than 20%, 30% or 40% of the genes enriched in that cell type are not detectable by the whole-tissue microarray technique.
  • the cell type is selected from the group consisting of striatal cell, cerebellar cell, cortical cell, hypothalamic cell, hippocampal cell, brainstem cell, and a spinal cord cell.
  • the invention described herein provides a method of identifying medium spiny neuron-enriched mRNAs, the method comprising expressing a ribosomal protein regulated by a regulatory region specific to a gene expressed in medium spiny neurons in an organism, isolating complexes comprising the ribosomal protein associated with mRNAs, identifying the mRNAs in the complexes, and comparing the mRNAs to those identified from a reference sample.
  • the regulatory region used for expression is specific to a gene expressed in striatonigral neurons or striatopallidal neurons.
  • the medium spiny neuron is associated with a disease or disorder such as but not limited to Parkinson's disease, addiction, attention deficit hyperactivity disorder, or Huntington's disease.
  • the method can be used in guiding the selection of candidate targets for the treatment of the disease or disorder, and for further screening of potential modulators of the candidate targets.
  • the invention described herein provides a method of identifying motor neuron-enriched mRNAs, the method comprising expressing a ribosomal protein regulated by a regulatory region specific to a gene expressed in motor neurons, isolating complexes comprising the ribosomal protein associated with mRNAs, identifying the mRNAs in the complexes, and comparing the mRNAs to those identified from a reference sample.
  • the regulatory region comprises regulatory sequences from a choline acetyltransferase (Chat) locus. This method can be utilized to identify mRNAS from any motor neuron, such as but not limited to brain stem motor neurons, spinal cord motor neurons, upper motor neurons and others.
  • the invention described herein provides a method for assessing the translational profile of a cerebellar cell, comprising expressing a ribosomal protein regulated by a regulatory region specific to a cerebellar gene in the cell, isolating at least one complex comprising the ribosomal protein associated with a mRNA from the cell, and identifying the mRNA from the complex whereby generating a translational profile.
  • the cerebellar cell is associated with a disease or disorder, such as ataxia.
  • kits comprising a recombinant vector engineered to express a nucleic acid sequence encoding a ribosomal protein and a detectable tag operably linked to an endogenous regulatory region, useful for practicing the methods described herein.
  • FIG. 1 illustrates a CNS disease-related BACarray collection.
  • FIG. 2 presents the translating ribosome affinity purification (TRAP) methodology.
  • FIG. 3 illustrates immunoprecipitation of translated mRNAs from transfected cells.
  • FIG. 4 illustrates the in vivo BACarray strategy.
  • FIG. 5 illustrates BAC vector engineering
  • FIG. 6 illustrates BACarray mouse generation.
  • FIG. 7 illustrates examples of drivers used to produce BACarray mice with specific expression in the cerebral cortex.
  • FIG. 8 illustrates examples of drivers used to produce BACarray mice with specific expression in the hypothalamus.
  • FIG. 9 Panels 1-25 illustrates that BAC transgenesis targets eGFP-L10a to specific CNS cell populations. DAB immunohistochemistry with anti-eGFP antibody on each mouse line reveals a unique and specific pattern of expression for the eGFP-L10a transgene. Panels (10 ⁇ ) show the morphology and localization of cell types expressing the transgene, while inset shows location of panel, for cerebellar (1-9), spinal cord (10), striatal/basal forebrain (11-14) brainstem (15), and cortical (16-25) cell types. Dashed lines (panels 16-25) indicate corpus callosum. A key for all cell types is in FIG. 11A .
  • FIG. 10 illustrates that GENSTAT eGFP and BACarray cortical pyramidal cell lines have same laminar distribution.
  • A) Graph (mean+/ ⁇ SE) of the distance of eGFP+ cell somas from the pial surface for the BACarray and GENSAT eGFP lines for each pyramidal cell BAC driver. The depth of the cells was consistent between both lines for each driver.
  • FIG. 11 illustrates a summary of cell types studied and characterization of lines.
  • D Detection of eGFPL10a under the control of a Lypd6 BAC in Parvalbumin positive outer stellate and deep stellate (basket) neurons of the molecular layer, but not in Parvalbumin positive Purkinje cell fibers (arrow).
  • FIG. 12 illustrates that higher transgene expression yields better signal to noise.
  • FIG. 13 illustrates protein and mRNA purification from BACarray lines.
  • eGFP L10a signal is only present in the D1 IP lane because the IP samples were more concentrated relative to In and UB.
  • FIG. 14 illustrates electron microscopy of immunoprecipitated ribosome complexes.
  • FIG. 15 illustrates that microarray signal intensity does not increase with transcript length.
  • A-DD To assess whether longer mRNA's were more efficiently immunoprecipitated than shorter transcripts, transcript length (Y-axis, log base 2), was plotted versus GCRMA normalized signal intensity (X-axis, log base 2) for all 30 samples. None of the immunoprecipitated nor the unbound (whole tissue RNA) samples show positive correlations between length and signal.
  • FIG. 16 illustrates that BACarray can consistently purify RNA efficiently from rare and common cell types.
  • FIG. 17 illustrates that BACarray data are reproducible and cell-type specific.
  • FIG. 18 illustrates that BACarrays can identify known markers, and discover new ones for a variety of cell types.
  • FIG. 19 illustrates that BACarray clusters cells by type and provides greater sensitivity than whole tissue arrays.
  • FIG. 20 illustrates cell type diversity is driven by proteins on the cell surface, such as receptors and ion channels.
  • FIG. 21 illustrates that a comparative analysis reveals unique translational profiles for each cell type.
  • FIG. 22 illustrates the transcriptional sketch of a spinal motor neuron.
  • FIG. 23 illustrates expression of eGFP-L10a in the Chat and Purkinje cell BACarray lines.
  • A Immunohistochemistry to eGFP in adult sagittal sections from the Chat BACarray line DW167.
  • B Indirect immunofluorescent characterization of Chat BACarray line DW167 brain stem facial motor nucleus: eGFP staining (left panel); Chat staining (middle panel) and merge (right panel, with 20 um scale bar).
  • C Immunohistochemistry to eGFP in adult sagittal sections from the Pcp2 BACarray line DR166.
  • FIG. 24 illustrates that BACarray profiles recapitulate known cell-specific markers and reveal new ones for four distinct cell types.
  • Scatterplots of D1, D2, Chat, and Pcp2 BACarray data compared to a reference mRNA sample reveal hundreds of genes enriched in each cell type (A-D). Lines on either side of the diagonal mark 2-fold enrichment. Axes are labeled for expression in powers of 10.
  • Venn diagrams of the top 1,000 enriched probesets (Tables 17-20) (with expression value cut-off>100) for each cell type reveal that each cell type has a unique pattern of enriched genes (E-H).
  • FIG. 25 illustrates expression of eGFP L10a in D1 and D2 BACarray lines.
  • FIG. 26 illustrates the polysome profile from D2 BACarray mouse striatal extracts.
  • FIG. 27 illustrates an analysis of striatal MSN IP values relative to message abundance and length. Lengths of transcripts were based on all available mouse curated RefSeq RNA sequences (ftp://ftp.ncbi.nih.gov/genomes/M_musculus/RNA). Where multiple transcript variants for a single gene were available, the longest one was chosen. RefSeq lengths were plotted against D1 (a) or D2 (b) BACarray IP normalized expression values. There was no correlation observed between transcript length and IP values. Striatal expression values for all Affymetrix Genechip probe sets were obtained by total RNA arrays from wild type striatal tissue (data not shown).
  • FIG. 28 illustrates gene expression analysis of BACarray purified mRNA. Normalized expression values from Affymetrix Mouse Genome 430 2.0 arrays are plotted for D1 and D2 BACarray samples. Middle diagonal line represents equal expression, and lines to each side represent 1.5 fold enrichment in either cell population.
  • FIG. 29 illustrates expression analysis of medium spiny neuron (MSN) enriched genes.
  • MSN medium spiny neuron
  • FIG. 29 illustrates expression analysis of medium spiny neuron (MSN) enriched genes.
  • MSN medium spiny neuron
  • FIG. 29 illustrates expression analysis in sagittal sections of genes which were amongst the top 100 (a) or 1,000 1,100 (b) genes identified in the study as MSN enriched, with the rank order of each gene noted below the gene name. Non redundant gene ranking was calculated using the highest ranked probeset corresponding to each gene with redundant probesets eliminated.
  • Left panel in situ hybridization images taken from the Allen Brain Atlas (Allen Brain Atlas [Internet]. Seattle (WA): Allen Institute for Brain Science. ⁇ 2006. Available from: http://www.brain map.org.) (3); right panel, in situ hybridization images taken from the Brain Gene Expression Map (BGEM) database (http://www.stjudebgem.org/) (4).
  • BGEM Brain Gene Expression Map
  • BGEM images all correspond to adult brain except for the following, for which the oldest available data were postnatal day 7 (P7): Drd2, Ppp1r1b, Dlx6, Gdnf, Bcl11b, Foxg1, Limd2, Fem1b, Dynll1, Atbf1, Foxo3a, Dnalc4, Mtmr7, Dnmt3a.
  • FIG. 30 illustrates that functional Gpr6 receptors are found in BAC D2 striatopallidal neurons but not BAC D1 striatonigral medium spiny neurons.
  • S1P sphingosine 1 phosphate
  • FIG. 31 illustrates that cocaine treatment increases the frequency of small amplitude GABAergic mIPSCs in BAC D1 striatonigral neurons.
  • FIG. 32 illustrates that cocaine treatment decreases the number of GABAA channels per synapse in BAC D1 striatonigral neurons.
  • FIG. 33 illustrates that cocaine treatment does not alter GABAergic mIPSCs kinetics or GABAA receptor number per synapse or unitary receptor conductance in BAC D2 striatopallidal neurons. Box plot summaries showing mean mIPSCs kinetics and non stationary noise analysis measures of individual striatopallidal neurons taken from saline treated control and 15 day treated cocaine BAC D2.
  • FIG. 34 illustrates BACarray molecular phenotyping of cerebellar cell types in ATM KO mice.
  • FIG. 35 illustrates the characterization of Pcp2 and Sept4 BACarray transgenic mouse lines.
  • A Expression of the eGFP L10a fusion in Purkinje cells in the cerebellum of the Pcp2 BACarray line. Immunohistochemical stain of Pcp2 BACarray brain section using anti eGFP antiserum (top panel). Double immuno fluorescence analysis (bottom panels) of calbindin (Calb1) and eGFP L10a expression in Pcp2 BACarray mice showing co labeling of Purkinje cells (merge).
  • B Expression of the eGFP L10a fusion in Bergmann glia in the cerebellum of the Sept4 BACarray line.
  • FIG. 36 illustrates a scatter Plot analysis of BACarray data for Septin4 and Pcp2 lines.
  • Immunoprecipitated (IP) mRNA from Septin4 (A, C) and Pcp2 (B, D) BAC transgenic lines was directly compared in scatter plot analysis to mRNA samples from total cerebellum. The analysis clearly demonstrates that thousands of genes are enriched in the immunoprecipitated samples relative to total cerebellum.
  • Scatter plots (C) and (D) show the same experiments with known positive control genes for Bergmann glial cells and Purkinje neurons. Bergmann glial positive controls are clearly enriched in the Septin4 IP samples (C) whereas Purkinje cell positive control genes are enriched in Pcp2 IP samples (D).
  • FIG. 37 illustrates cell type specific differential regulation of gene expression in Atm ⁇ / ⁇ cerebellum.
  • A-C Atm ⁇ / ⁇ IP data were compared to Atm+/+IP data in scatter plot analyses for the Septin4 (A), the Pcp2 (B) and the total cerebellum (C) experiments.
  • Scatter plots display the distribution of regulated genes in each experiment. Colors refer to the Venn Diagram analysis (D).
  • FIG. 38 illustrates ventral tegmental area and substantia nigra area specific markers, as revealed by BACarrays.
  • FIG. 39 illustrates dopaminergic cell loss in the rodent substantia nigra with the use of 6-OHDA.
  • FIG. 40 illustrates a therapeutic opportunity for Parkinson's disease, by developing new strategies for stimulation of Sub-Thalamic Nucleus, by using antagonists of Gpr6.
  • the present disclosure provides for methods and compositions useful in translational profiling and molecular phenotyping of heterogeneous tissues and cell types.
  • the methods can be used to define previously undefined cell types, identify molecular targets for diseases and disorders, and provide a way in which to identify co-regulated gene sets for particular biological and/or medically relevant functions.
  • Translational profiling is the profiling, identification, or isolation of translated mRNAs. In some embodiments such profiling is a measure of the nascent proteome. In other embodiments, this profiling allows for the identification of mRNAs being actively translated, or otherwise associated with the cellular translational machinery.
  • Molecular phenotyping is the molecular and/or gene expression description of organs, tissues, and cell types.
  • the present disclosure provides for methods and compositions to practice translating ribosome affinity purification (TRAP) profiling methodology.
  • these profiling methods are be utilized to further distinguish morphologically, anatomically, developmentally, or otherwise indistinguishable, cells into cellular subtypes, further defining cell populations and sub-populations.
  • these otherwise indistinguishable cells are intermixed.
  • these cells are spatially separated.
  • these cells are cells of the central or peripheral nervous system, for example neurons or glia, only distinguishable by their translational profiles and molecular phenotypes. In other cases these are cells outside the nervous system.
  • these profiling methods are be utilized to identify translated mRNAs in single cell types with a sensitivity that is may not be achievable by techniques such as whole-tissue microarray.
  • these profiling methods are used to identify co-regulated gene sets for particular biological functions in cells that are spatially separated or intermixed, morphologically distinct or indistinct, in different developmental stages, associated with different tissues or regions of a tissue, or from different individuals with the same disease, disorder or state.
  • the methods provided herein allow for isolation of mRNAs associated with ribosomes or polysomes (clusters of ribosomes) from specific cell types, allowing for cell translational profiling and molecular phenotyping of the cell types and subtypes. In some cases, the cells are genetically targeted.
  • the methods described herein in allow for identifying translated mRNAs in any cell subtype of interest.
  • the methodology involves expression of a tagged functional ribosomal protein, which enables tagging of polysomes for purification of mRNA, in specific cell populations.
  • the purification of polysomes is by affinity or immunoaffinity purification.
  • the cell subtypes are genetically targeted.
  • the tagged ribosomes are expressed in transgenic animals.
  • the translating ribosome affinity purification methodology for translational profiling and molecular phenotyping involves expression of a tagged ribosomal protein, which enables tagging of polysomes for affinity-based, sometimes immunoaffinity-based, purification of mRNA, in specific cell populations. In some cases this is achieved with the use of animals or transgenic animals, allowing translation profiling and molecular phenotyping from whole animals. Methods provided herein allow for defining the distinguishing molecular characteristics of closely related or critical cell types. Methods also demonstrate that methods described herein can be employed to analyze physiological adaptations of specific cell types in vitro, in vivo, ex vivo, or in situ.
  • Embodiments of this invention provide methods for isolating cell type- or cell subtype-specific polysomal, mRNA.
  • the methods include using molecularly tagged ribosomal proteins resulting in functional tagged ribosomes or ribosomal complexes, able to support translation, assemble into polysomal complexes.
  • Ribosomes can be molecularly tagged and expressed in one or more cell types or cell subtypes of interest.
  • Molecularly tagged ribosomal proteins for the purposes of this disclosure will interchangeably be referred to as a ‘fusion proteins’ or ‘tagged proteins’ or ‘molecularly tagged fusion proteins’ or ‘molecularly tagged ribosomal proteins’.
  • these fusion proteins contain all or a portion of a ribosomal proteins.
  • ribosome tagging causes no disruption of native function or distribution of the tagged protein, thus resulting in a functional ribosome, functional ribosomal complex, or functional polysome. That is, although molecularly tagged, the portion that has the biological activity of the native ribosomal protein is retained and can function in an intact ribosome to carry out translation or binding of mRNA.
  • the molecularly tagged ribosomal is expressed in a organ, tissue, cell type, or cell subtype of interest, by introducing into cells, culture, slices, or into an entire organism, a nucleic acid encoding the molecularly tagged ribosomal protein under the control of regulatory elements or transcriptional units that direct expression in the cell type or cell subtype of choice.
  • the ribosomal protein to be tagged can be from the same or different species as the cell that expresses the molecularly tagged protein.
  • the ribosome or ribosomal protein is molecularly tagged by engineering the ribosomal protein to fuse to or bind a small molecule, a protein, or peptide that is not bound by the unengineered ribosome or the ribosomal protein.
  • the nucleic acid encoding the ribosomal protein fused to the tag can be generated by routine genetic engineering methods in which a nucleotide sequence encoding the amino acid sequence for the tag sequence is engineered in frame with the nucleotide sequence encoding a ribosomal protein.
  • oligonucleotide-mediated site-directed mutagenesis or polymerase chain reaction PCR
  • other routine protocols of molecular biology see, e.g., Sambrook et al., 2001, Molecular Cloning, A Laboratory Manual, Third Edition, Cold Spring Harbor Laboratory Press, N.Y.; and Ausubel et al., 1989, Current Protocols in Molecular Biology, Green Publishing Associates and Wiley Interscience, N.Y., both of which are hereby incorporated by reference in their entireties).
  • the ribosomal protein is L10a and the tag is eGFP.
  • Nucleic acids encoding the tagged proteins can be produced using genetic engineering methods and cloning and expression vectors that are well known in the art.
  • a naturally occurring or synthetically produced nucleic acid or gene can be engineered to function as a ribosomal protein and support translation or bind (directly or indirectly) or associate with polysomal, translating ribosomal mRNA.
  • Nucleic acids encoding the ribosomal protein to be molecularly tagged may be obtained using any method known in the art. Nucleic acids may be obtained, for example, by PCR using oligonucleotide primers based upon the published sequences. Other related ribosomal (for example from other species) may be obtained by low, medium or high stringency hybridization of appropriate nucleic acid libraries using the ribosomal in hand as a probe.
  • the ribosomal protein is L10a.
  • the tagged ribosomal protein is incorporated into a ribosomal complex and is associated with one or more mRNAS, but does not bind mRNA directly.
  • a nucleic acid encoding a molecularly tagged ribosomal protein is intended for a particular expression system, in which the codon frequencies reflect the tRNA frequencies of the host cell or organism in which the protein is expressed. Codon optimization can allow for maximum protein expression by increasing the translational efficiency of a gene of interest.
  • the nucleic acid encoding a molecularly tagged ribosomal protein may be a synthetic nucleic acid in which the codons have been optimized for increased expression in the host cell in which it is produced.
  • Molecular tags can be any protein (or fragment, portion, analog or derivative thereof) that is not present or accessible in the cell of interest (or the cell fraction from which the tagged ribosomes are to be isolated, or other cells that will be contacted with the reagent that binds the tag) for which there exists a reagent (such as an antibody) or method (such as optical, fluorescence or magnetic sorting) that recognizes the tag and that is accessible to solution (and thereby, the tag).
  • a reagent such as an antibody
  • method such as optical, fluorescence or magnetic sorting
  • Tags can include those for which methods/reagents/devices exist that allow facile identification and isolation of the tagged protein, but do not, minimally, or negligibly inhibit or interfere with function of the tagged protein.
  • the tag may be an intact naturally occurring or synthetically produced protein, fragment, analog or derivative thereof of any length that permits binding to the corresponding binding reagent/method. In certain embodiments, the tag is about 8, 10, 12, 15, 18 or 20 amino acids, is less than 15, 20, 25, 30, 40 or 50 amino acids, but may be 100, 150, 200, 250, 300, 400, 500, 1000 or more amino acids in length.
  • the tag may be bound specifically by a reagent that does not otherwise bind any component of: (1) the cell of interest; or (2) a polysomal preparation of interest; or (3) whatever cellular fraction of interest is being contacted by the reagent that binds the tag.
  • the nucleotide sequence encoding a tag is preferably inserted in frame such that the tag is placed at the N- or C-terminus of the ribosomal protein, since these portions of proteins are often accessible to detection, affinity, immunological, or purification reagents.
  • the tag can be inserted into any portion of the ribosomal protein such that when the fusion protein is incorporated into an intact ribosome, ribosomal function is not compromised and the tag is accessible to the reagent/method to be used in the detection, isolation or and/or purification. That is, tagging can still allow for a functional ribosome.
  • a ribosomal protein may be molecularly tagged with a plurality of tags.
  • the tag is Green Fluorescent Protein (GFP).
  • GFP can be utilized as an optical or immunoaffinity tag for a variety of applications, all well known in the art.
  • GFP is a protein, composed of 238 amino acids (26.9 kDa), originally isolated from the jellyfish that fluoresces green when exposed to blue light (Prendergast F, Mann K (1978). “Chemical and physical properties of aequorin and the green fluorescent protein isolated from Aequorea forskálea”. Biochemistry 17 (17):3448-53; Tsien R (1998). “The green fluorescent protein”. Annu Rev Biochem 67: 509-44). The GFP from A.
  • victoria has a major excitation peak at a wavelength of 395 nm and a minor one at 475 nm. Its emission peak is at 509 nm which is in the lower green portion of the visible spectrum.
  • the GFP from the sea pansy ( Renilla reniformis ) has a single major excitation peak at 498 nm.
  • the GFP gene is frequently used as a reporter of expression (Phillips G (2001). “Green fluorescent protein—a bright idea for the study of bacterial protein localization”. FEMS Microbiol Lett 204 (1): 9-18.). In modified forms it has been used to make biosensors, and many animals have been created that express GFP.
  • the GFP gene can be introduced into organisms and maintained in their genome through breeding, or local injection with a viral vector can be used to introduce the gene.
  • a viral vector can be used to introduce the gene.
  • many bacteria, yeast and other fungal cells, plant, fly, and mammalian cells have been created using GFP as a marker.
  • the tag is a GFP mutant, variant, analog, fragment, or derivative thereof.
  • Different mutants of GFP have been engineered (Shaner N, Steinbach P, Tsien R (2005). “A guide to choosing fluorescent proteins”. Nat Methods 2 (12): 905-9).
  • One improvement was a single point mutation (S65T) reported in 1995 in Nature by Roger Tsien (Heim R, Cubitt A, Tsien R (1995). “Improved green fluorescence”. Nature 373 (6516): 663-4.)).
  • the addition of the 37° C. folding efficiency (F64L) point mutant to the scaffold yielded enhanced GFP (eGFP).
  • eGFP has an extinction coefficient (denoted a), also known as its optical cross section of 9.13 ⁇ 10-21 m 2 /molecule, also quoted as 55,000 L/(mol ⁇ cm) (Shelley R. McRae, Christopher L. Brown and Gillian R. Bushell (May 2005)). “Rapid purification of eGFP, EYFP, and ECFP with high yield and purity”. Protein Expression and Purification 41 (1): 121-127.).
  • Superfolder GFP a series of mutations that allow GFP to rapidly fold and mature even when fused to poorly folding peptides, was reported in 2006 (Pédelacq J, Cabantous S, Tran T, Terwilliger T, Waldo G (2006). “Engineering and characterization of a superfolder green fluorescent protein”. Nat Biotechnol 24 (1): 79-88).
  • the tag is enhanced GFP (eGFP).
  • Molecular tags may include both fluorescent, magnetic, epitope, radioactive or otherwise detectable tags, by way of example, and not by limitation, those listed in Table 2.
  • GFP, eGFP, mGFP, emerald GFP, derivatives and variants Green Fluorescent protein BFP, eBFP, eBFP2, Azurite, mKalama1, sapphire GFP, derivatives and variants (Blue fluorescent proteins)
  • RFP, mCherry, td-tomato, derivatives and variants red fluorescent protein
  • Bgal derivatives and variants
  • Bgalactosdiase Luc
  • CAT derivatives and variants
  • Chloramphenicol acetyltransferase human growth hormone
  • ribosomes/tagged ribosomes particularly polysomes (ribosomal clusters bound to mRNA)/tagged polysomes, from cells, cultured cells and tissues (see, e.g., Bommer et al., 1997, Isolation and characterization of eukaryotic polysomes, in Subcellular Fractionation, Graham and Rickwood (eds.), IRL Press, Oxford, pp. 280-285; incorporated herein by reference in its entirety).
  • Polysomes are interchangeably referred to as polyribosomes, ribosomal complexes or ribosomal clusters.
  • the isolated polysomes contain functional ribosomes, capable of supporting translation, association with mRNA, and/or association with translation factors.
  • the isolation method employed has one or more of the following aspects:
  • variations of the above-described general method are used to isolate membrane-associated polysomes from a total pool of polysomes. This allows for further enrichment of mRNA encoding secreted or transmembrane proteins.
  • Various methods may be used to isolate membrane-associated polysomes from cultured cells and tissue, e.g., methods that employ differential centrifugation (Hall C, Lim L. Developmental changes in the composition of polyadenylated RNA isolated from free and membrane-bound polyribosomes of the rat forebrain, analyzed by translation in vitro. Biochem J. 1981 Apr.
  • affinity methods are used to isolate or purify tagged proteins using methods well known in the art including but not limited to including chromatography, solid phase chromatography precipitation, matrices, co-immunoprecipitation, etc.
  • molecularly tagged functional ribosomes are provided, bound to mRNA, that can bind a reagent for the molecular tag.
  • the molecularly tagged ribosomes are bound to a specific reagent or affinity reagent that is bound, covalently or non-covalently, to a solid surface, such as a bead, a resin, or a chromatography resin, e.g., agarose, sepharose, and the like.
  • other methods are used with or in place of affinity purification.
  • specific polysomes can be isolated utilizing optical sorting, fluorescence-based sorting or magnetic-based sorting methods and devices.
  • polysomes are not isolated from the post-mitochondrial supernatant or even from a cell or tissue lysate before being subject to affinity purification.
  • FIG. 2 a presents a schematic to illustrate affinity purification of eGFP-tagged polysomes using anti-GFP antibody-coated beads.
  • the associated mRNA complexed with the protein may be isolated using chemical, mechanical or other methods well known in the art. For example, elution of mRNA is accomplished by addition of EDTA to buffers, which disrupts polysomes and allows isolation of bound mRNA for analysis (Schutz, et al. (1977), Nucl. Acids Res. 4:71-84; Kraus and Rosenberg (1982), Proc. Natl. Acad. Sci. USA 79:4015-4019).
  • isolated polysomes attacheded or detached from isolation matrix
  • poly A.sup.+ mRNA is preferentially isolated by virtue of its hybridization of oligodT cellulose.
  • Methods of mRNA isolation are described, for example, in Sambrook et al., 2001, Molecular Cloning, A Laboratory Manual, Third Edition, Cold Spring Harbor Laboratory Press, N.Y.; and Ausubel et al., 1989, Current Protocols in Molecular Biology, Green Publishing Associates and Wiley Interscience, N.Y., both of which are hereby incorporated by reference in their entireties.
  • Certain embodiments of the invention provide vectors, cell lines, and lines of organisms that contain nucleic acid constructs that comprise the coding sequence for a tagged ribosomal protein under the control of regulatory sequences.
  • the tagged ribosomal proteins are selectively expressed in a particular chosen cell type, cell subtype, molecular pathway, or circuit using regulatory elements naturally occurring or engineered to recapitulate a desired expression pattern.
  • Such expression is achieved by driving the expression of the tagged ribosomal protein using regulatory sequences or a transcriptional unit from a characterizing or endogenously regulated gene expressed in the chosen cell type, subtype, pathway, circuit and/or point in development.
  • a particular cell type is one that resides within a mixed population of cells, comprising a discernible group of cells sharing a common characteristic.
  • This group may be morphologically, anatomically, genetically, or functionally discernible. In other embodiments, this group may be morphologically, genetically, and developmentally indistinguishable, but be genetically distinguishable. Because of its selective expression, the population of cells may be characterized or recognized based on its positive expression of an endogenously regulated characterizing gene. Some or all of the regulatory sequences/elements may be incorporated into nucleic acids (including transgenes) to regulate the expression of tagged ribosomal protein coding sequences.
  • regulatory sequences or elements include but are not limited to enhancer sequences, insulator sequences, silencer sequences, or a combination of said sequences.
  • a gene that is not constitutively expressed, i.e., exhibits some spatial or temporal restriction in its expression pattern
  • a gene that is constitutively expressed is used as a source of a regulatory sequence.
  • a regulatory sequence is engineered or modified to achieve desired expression characteristics and patterns.
  • Regulatory regions can be whole or parts or the regulatory sequences from the loci of the genes of interest.
  • a tagged ribosomal protein for example eGFP tagged L10a
  • regulatory sequences from a medium spiny neuron-specific gene locus for example a Drd1a or Drd2 locus
  • regulatory sequences from a motor-specific gene locus for example choline acetyl transferase (Chat) locus
  • a tagged ribosomal protein for example eGFP tagged L10a
  • regulatory sequences from a cerebellar cell-specific gene loci For example loci from Pcp2, Neurod1, Grm2, Grp, Septin4, or Aldhl11 can be utilized, to drive specific expression in Purkinje cells, granule cells, golgi neurons, unipolar brush cells, Bergmann glial cells, and astrocytes, respectively.
  • An entire locus, an entire non-coding region of a locus, a portion of a locus, or a modified locus can be utilized as the regulatory sequences to drive expression of tagged ribosomal proteins in a genetically targeted, cell subtype specific manner.
  • the tagged ribosomal gene coding sequences may placed under the transcriptional control of some or all of the regulatory sequences from a particular locus such that the tagged ribosomal gene is expressed in substantially the same expression pattern as the endogenously regulated gene found in that locus in the transformed organism, or at least in an anatomical region or tissue of the organism (by way of example, in the brain, spinal cord, heart, skin, bones, head, limbs, blood, muscle, peripheral nervous system, etc. of an animal) containing the population of cells to be marked by expression of the tagged ribosomal protein gene coding sequences.
  • substantially the same expression pattern is meant that the tagged ribosomal protein gene coding sequences are expressed in at least 50%, 60%, 70% 80%, 85%, 90%, 95%, and about 100% of the cells shown to express the endogenous characterizing gene by in situ hybridization, PCR, other gene expression detection methods or functional methods familiar to those with skill in the art.
  • the regulatory sequence is, e.g., a promoter or enhancer, or any other cis or trans activating element or transcriptional unit of a characterizing gene.
  • this characterizing gene is endogenous to a host cell or host organism (or is an ortholog of an endogenous gene) and is expressed in a particular select population of cells of the organism.
  • the regulatory sequence can be derived from a human, rat, or mouse or any mammalian gene associated with specific neuronal, cellular, and metabolic pathways. In certain embodiments, a non mammalian regulatory sequence can be utilized.
  • Cis and trans, 5′ and 3′ regulatory sequences and transcriptional units from several known pathways are amenable for cell-type specific, cell subtype-specific, developmental stage-specific, temporal-specific, tissue-specific, pathway-specific, or circuit-specific expression of transgenes.
  • Examples of known pathways include but are not limited to the adrenergic or noradrenergic neurotransmitter pathway, the dopaminergic neurotransmitter pathway, the GABAergic neurotransmitter pathway, the glutaminergic neurotransmitter pathway, the glycinergic neurotransmitter pathway, the histaminergic neurotransmitter pathway, a neuropeptidergic neurotransmitter pathway, a serotonergic neurotransmitter pathway, a nucleotide receptor-specific pathway, ion channels, transcriptions factors, markers of undifferentiated or not fully differentiated cells, the sonic hedgehog signaling pathway, calcium binding, or a neurotrophic factor receptor (tables in US2005/0009028, herein incorporated by reference).
  • regulatory sequences that may be used to control expression can be derived from, include but are not limited to, the following animal transcriptional control regions that exhibit tissue specificity and that have been utilized in cell culture and transgenic animals.
  • transcriptional control regions are: elastase I gene control region, enolase promoter, insulin gene control region, immunoglobulin gene control region, mouse mammary tumor virus control region, albumin gene control region, alpha-fetoprotein gene control region, alpha 1-antitrypsin gene control region, beta.-globin gene control region, myelin basic protein gene control region, myosin light chain-2 gene control region, and gonadotropic releasing hormone gene control region.
  • the gene sequence from which the regulatory sequence derives can be protein kinase C, gamma, TH-elastin, Pax7, Eph receptors, islet-1 and Sonic hedgehog.
  • Nucleic acids to be used for regulating expression may include all or a portion of the upstream and/or downstream and 5′ and/or 3′ regulatory sequences from the naturally occurring or modified locus of a selected gene.
  • the regulatory sequences preferably direct expression of the tagged ribosomal protein sequences in substantially the same pattern as the endogenous characterizing gene within transgenic organism, or tissue derived therefrom. This would provide of for any and all cis- and trans-acting regulatory sequences and transcriptional units that would direct expression of the tagged ribosomal protein in an endogenous regulatory fashion.
  • a regulatory sequence can be 1 kb, 5 kb, 10 kb, 50 kb, 100 kb, 200 kb, 250 kb, 500 kb or even 1 Mb in length.
  • the nucleic acids encoding the molecularly tagged ribosomal proteins may be selectively expressed in random but distinct subsets of cells, as described in Feng et al. (2000, Imaging neuronal subsets in transgenic mice expressing multiple spectral variants of GFP, Neuron 28(1):41-51, which is hereby incorporated by reference in its entirety). Using such methods, independently generated transgenic lines may express the nucleic acids encoding the molecularly tagged ribosomal proteins in a unique pattern, perhaps pathway-specific, or circuit-specific, and although spatially separated, would all incorporate identical regulatory elements.
  • nucleotide sequences encoding the tagged ribosomal protein product may replace all or a portion of the characterizing gene coding sequences in a genomic clone/locus of the characterizing gene, leaving only all or part of the characterizing gene regulatory non-coding sequences.
  • the tagged ribosomal gene coding sequences are inserted into or replace transcribed coding or non-coding sequences of the genomic characterizing gene sequences, for example, into or replacing a region of an exon or of the 3′ UTR of the characterizing gene genomic sequence.
  • the tagged ribosomal protein gene coding sequence is inserted into or replaces a portion of the 3′ untranslated region (UTR) of the characterizing gene genomic sequence.
  • the coding sequence of the characterizing gene is mutated or disrupted to abolish characterizing gene expression from the nucleic acid construct without affecting the expression of the tagged fusion protein gene.
  • the tagged ribosomal fusion protein gene coding sequence has its own internal ribosome entry site (IRES).
  • the tagged ribosomal protein gene coding sequences are inserted using 5′ direct fusion wherein the tagged ribosomal protein gene coding sequences are inserted in-frame adjacent to the initial ATG sequence (or adjacent the nucleotide sequence encoding the first two, three, four, five, six, seven or eight amino acids of the characterizing gene protein product) of the characterizing gene, so that translation of the inserted sequence produces a fusion protein of the first methionine (or first few amino acids) derived from the characterizing gene sequence fused to the tagged ribosomal fusion protein gene protein.
  • a tagged ribosomal fusion protein gene is inserted into a separate cistron in the 5′ region of the characterizing gene genomic sequence and has an independent IRES sequence.
  • an IRES is operably linked to the tagged ribosomal fusion protein gene coding sequence to direct translation of the tagged fusion protein gene.
  • the IRES permits the creation of polycistronic mRNAs from which several proteins can be synthesized under the control of an endogenous transcriptional regulatory sequence. Such a construct is advantageous because it allows marker proteins to be produced in the same cells that express the endogenous gene (Heintz, 2000, Hum. Mol. Genet. 9(6): 937-43; Heintz et al., WO 98/59060; Heintz et al., WO 01/05962; which are incorporated herein by reference in their entireties).
  • exogenous translational control signals including, for example, the ATG initiation codon
  • the initiation codon is usually in phase with the reading frame of the desired coding sequence of the tagged ribosomal fusion protein gene to ensure translation of the entire insert.
  • exogenous translational control signals and initiation codons can be of a variety of origins, both natural and synthetic. The efficiency of expression may be enhanced by the inclusion of appropriate transcription enhancer elements, transcription terminators, etc. (see Bittner et al., 1987, Methods in Enzymol. 153: 516-44).
  • the construct can also comprise one or more selectable markers that enable identification and/or selection of recombinant vectors.
  • the selectable marker may be the tagged ribosomal fusion protein gene product itself or an additional selectable marker not necessarily tied to the expression of the characterizing gene.
  • the tagged ribosomal fusion protein gene coding sequence is embedded in the genomic sequence of the characterizing gene and is inactive unless acted on by a transactivator or recombinase, whereby expression of the tagged ribosomal fusion protein gene can then be driven by the characterizing gene regulatory sequences.
  • expression of the transactivator gene as regulated by the characterizing gene regulatory sequences, activates the expression of the tagged fusion protein gene.
  • a nucleic acid of the invention is expressed conditionally, using any type of inducible or repressible system available for conditional expression of genes known in the art, e.g., a system inducible or repressible by tetracycline (“tet system”); interferon; estrogen, ecdysone, or other steroid inducible system; Lac operator, progesterone antagonist RU486, or rapamycin (FK506).
  • t system a system inducible or repressible by tetracycline
  • a conditionally expressible nucleic acid of the invention can be created in which the coding region for the tagged ribosomal fusion protein gene (and, optionally also the characterizing gene) is operably linked to a genetic switch, such that expression of the tagged ribosomal fusion protein gene can be further regulated.
  • a genetic switch such that expression of the tagged ribosomal fusion protein gene can be further regulated.
  • this type of switch is a tetracycline-based switch.
  • the nucleic acids of the invention comprise all or a significant portion of the genomic sequence of the characterizing gene locus, at least all or a portion of the 5′ and/or 3′regulatory sequences of the characterizing endogenously regulated gene, at least sufficient sequence 5′ and/or 3′ of the characterizing gene coding sequence to direct expression of the tagged ribosomal fusion protein gene coding sequences in the same expression pattern (temporal and/or spatial) as the endogenous counterpart of the characterizing gene.
  • the nucleic acid of the invention comprises at least one exon, at least two exons, at least three exons, all but one exon, or all but two exons, of the characterizing endogenously regulated gene.
  • a binary system can be used, in which the endogenous regulatory sequence such as a promoter drives expression of a protein that then activates a second expression construct.
  • This second expression construct uses a strong regulatory sequence such as a promoter to drive expression of the tagged ribosomal fusion protein at higher levels than is possible using the endogenous regulatory region itself.
  • a particular population-specific gene drives expression of a molecular switch (e.g., a recombinase, a transactivator) in a population-specific manner. This switch then activates high-level expression though a second regulatory element regulating expression of the tagged ribosomal protein.
  • a molecular switch e.g., a recombinase, a transactivator
  • the molecularly tagged ribosomal protein coding sequence may be expressed conditionally, through the activity of a molecular switch gene which is an activator or suppressor of gene expression.
  • the second gene encodes a transactivator, e.g., tetR, a recombinase, or FLP, whose expression is regulated by the characterizing gene regulatory sequences.
  • the gene encoding the molecularly tagged ribosomal protein is linked to a conditional element, e.g., the tet promoter, or is flanked by recombinase sites, e.g., FRT sites, and may be located any where within the genome.
  • expression of the molecular switch gene as regulated by the characterizing gene regulatory sequences, activates the expression of the molecularly tagged ribosomal protein.
  • the tagged ribosomal fusion protein gene can be expressed conditionally by operably linking at least the coding region for the tagged ribosomal fusion protein gene to all or a portion of the regulatory sequences from the characterizing gene's genomic locus, and then operably linking the tagged ribosomal fusion protein gene coding sequences and characterizing gene sequences to an inducible or repressible transcriptional regulation system.
  • Transactivators in these inducible or repressible transcriptional regulation systems are designed to interact specifically with sequences engineered into the vector.
  • Such systems include those regulated by tetracycline (“tet systems”), interferon, estrogen, ecdysone, Lac operator, progesterone antagonist RU486, and rapamycin (FK506) with tet systems being particularly preferred (see, e.g., Gingrich and Roder, 1998, Annu. Rev. Neurosci. 21: 377-405; incorporated herein by reference in its entirety).
  • tet systems tetracycline
  • interferon estrogen
  • ecdysone Lac operator
  • progesterone antagonist RU486, and rapamycin FK506
  • the inducible or repressible genetic system can restrict the expression of the detectable or selectable marker either temporally, spatially, or both temporally and spatially.
  • expression of the tagged ribosomal fusion protein gene is regulated by using a recombinase system that is used to turn on or off tagged ribosomal fusion protein gene expression by recombination in the appropriate region of the genome in which the marker gene is inserted.
  • a recombinase system in which a gene that encodes a recombinase can be used to turn on or off expression of the tagged ribosomal fusion protein gene (for review of temporal genetic switches and “tissue scissors” using recombinases, see Hennighausen and Furth, 1999, Nature Biotechnol. 17: 1062-63).
  • Exclusive recombination in a selected cell type may be mediated by use of a site-specific recombinase such as Cre, FLP-wild type (wt), FLP-L or FLPe.
  • Recombination may be effected by any art-known method, e.g., the method of Doetschman et al. (1987, Nature 330: 576-78; incorporated herein by reference in its entirety); the method of Thomas et al., (1986, Cell 44: 419-28; incorporated herein by reference in its entirety); the Cre-loxP recombination system (Stemberg and Hamilton, 1981, J. Mol. Biol. 150: 467-86; Lakso et al., 1992, Proc. Natl.
  • the recombinase is highly active, e.g., the Cre-loxP or the FLPe system, and has enhanced thermostability (Rodriguez et al, 2000, Nature Genetics 25: 139-40; incorporated herein by reference in its entirety).
  • a recombinase system can be linked to a second inducible or repressible transcriptional regulation system.
  • a cell-specific Cre-loxP mediated recombination system (Gossen and Bujard, 1992, Proc. Natl. Acad. Sci. USA 89: 5547-51) can be linked to a cell-specific tetracycline-dependent time switch detailed above (Ewald et al., 1996, Science 273: 1384-1386; Furth et al. Proc. Natl. Acad. Sci. U.S.A. 91: 9302-06 (1994); St-Onge et al, 1996, Nucleic Acids Research 24(19): 3875-77; which are incorporated herein by reference in their entireties).
  • an altered cre gene with enhanced expression in mammalian cells is used (Gorski and Jones, 1999, Nucleic Acids Research 27(9): 2059-61; incorporated herein by reference in its entirety).
  • the ligand-regulated recombinase system of Kellendonk et al. (1999, J. Mol. Biol. 285: 175-82; incorporated herein by reference in its entirety) can be used.
  • the ligand-binding domain (LBD) of a receptor e.g., the progesterone or estrogen receptor, is fused to the Cre recombinase to increase specificity of the recombinase.
  • Nucleic acids comprising the characterizing gene sequences and tagged ribosomal fusion protein gene coding sequences can be obtained from any available source. In most cases, all or a portion of the characterizing gene sequences and/or the tagged ribosomal fusion protein gene coding sequences are known, for example, in publicly available databases such as GenBank, UniGene and the Mouse Genome Informatic (MGI) Database to name just a few, or in private subscription databases. With a portion of the sequence in hand, hybridization probes can be designed using highly routine methods in the art (for example filter hybridization or PCR amplification) to identify clones containing the appropriate sequences for example in a library or other source of nucleic acid.
  • MMI Mouse Genome Informatic
  • genomic clones can be identified by probing a genomic DNA library under appropriate hybridization conditions, e.g., high stringency conditions, low stringency conditions or moderate stringency conditions, depending on the relatedness of the probe to the genomic DNA being probed.
  • the characterizing gene genomic sequences are preferably in a vector that can accommodate lengths of sequence (for example, 10 kb's of sequence), such as cosmids, yeast artificial chromosomes (YACs) and bacterial artificial chromosomes (BACs), and encompass at least 50, 70, 80, 100, 120, 150, 200, 250, 300, 400, 500 or 1000 kb of sequence that comprises all or a portion of the characterizing gene sequence.
  • the larger the vector insert the more likely it is to identify a vector that contains the characterizing gene cis and trans sequences of interest.
  • the vector containing the entire genomic sequence (i.e. genomic locus) for the characterizing endogenously regulated gene is present.
  • the vector contains at least the characterizing gene sequence with the start, i.e., the most 5′ end, of the coding sequence in the approximate middle of the vector insert containing the genomic sequences and/or has at least 20 kb, 30 kb, 40 kb, 50 kb, 60 kb, 80 kb, 100 kb or 200 kb of genomic sequence on either side of the start of the characterizing gene coding sequence.
  • This can be determined by any method known in the art, for example, but not by way of limitation, by sequencing, restriction mapping, PCR amplification assays, etc.
  • the tagged ribosomal fusion protein gene can be incorporated into the characterizing gene sequence by any method known in the art for manipulating DNA.
  • homologous recombination in bacteria is used for target-directed insertion of the tagged ribosomal fusion protein gene sequence into the genomic DNA encoding the characterizing endogenously regulated gene and sufficient regulatory sequences to promote expression of the gene in its endogenous expression pattern, which characterizing gene sequences have been inserted into a vector.
  • the vector comprising the tagged ribosomal fusion protein gene and regulatory gene sequences is then introduced into the genome of a potential founder organism for generating a line of transformed organisms, using methods well known in the art, e.g., those methods described herein. Such transformed organisms are then screened for expression of the tagged ribosomal fusion protein gene coding sequences that mimics the expression of the endogenous characterizing gene.
  • Several different constructs containing nucleic acids of the invention may be introduced into several potential founder organisms and the resulting transformed organisms are then screened for the best, (e.g., highest level) and most accurate (best mimicking expression of the endogenous characterizing gene) expression of the tagged ribosomal fusion protein gene coding sequences.
  • the nucleic acid construct can be used to transform a host or recipient cell or organism using well known methods, e.g., those described herein. Transformation can be either a permanent or transient genetic change.
  • a vector is used for stable integration of the nucleic acid construct into the genome of the cell. In another aspect, the vector is maintained episomally.
  • the methods described herein provide transformed organisms, e.g., transgenic mice that express a tagged ribosomal protein within a chosen cell type.
  • BAC-mediated recombination (Yang, et al., 1997, Nat. Biotechnol. 15(9):859-865) is used to create the transformed organism.
  • Such expression is achieved by using the endogenous regulatory sequences and transcriptional units of a particular gene, wherein the expression of gene is a defining characteristic of the chosen cell type (as also described in PCT/US02/04765, entitled “Collections of Transgenic Animal Lines (Living Library)” by Serafini, published as WO 02/064749 on Aug. 22, 2002, which is incorporated by reference herein in its entirety).
  • a collection of transgenic animals expressing tagged ribosomal proteins within a set of chosen cell types is assembled, and this is often referred to as a BACarray collection.
  • a nucleic acid of the invention is inserted into a yeast artificial chromosome (YAC) (Burke et al., 1987 Science 236: 806-12; and Peterson et al., 1997, Trends Genet. 13: 61).
  • YAC yeast artificial chromosome
  • a collection of transgenic animals expressing tagged ribosomal proteins within a set of chosen cell types or subtypes is assembled, and this is often referred to as a YACarray collection.
  • the nucleic acid of the invention is inserted into another vector developed for the cloning of large segments of mammalian DNA, such as a cosmid or bacteriophage P1 (Sternberg et al., 1990, Proc. Natl. Acad. Sci. USA 87: 103-07).
  • the approximate insert size is about 30-35 kb for cosmids and 100 kb for bacteriophage P1.
  • the nucleic acid of the invention is inserted into a P-1 derived artificial chromosome (PAC) (Mejia et al., 1997, Retrofitting vectors for Escherichia coli -based artificial chromosomes (PACs and BACs) with markers for transfection studies, Genome Res. 7(2):179-86).
  • PAC P-1 derived artificial chromosome
  • the maximum insert size is about 300 kb.
  • BACs and other vectors used in the methods described here often can accommodate, and in certain embodiments comprise, large pieces of heterologous DNA such as genomic sequences.
  • Such vectors can contain an entire genomic locus, or at least sufficient sequences to confer endogenous regulatory expression pattern and to insulate the expression of coding sequences from the effect of regulatory sequences surrounding the site of integration of the nucleic acid in the genome to mimic better wild type expression.
  • entire genomic loci or portions thereof are used, few, if any, site-specific expression problems are encountered, unlike insertions of nucleic acids into smaller sequences. When insertions of nucleic acids are too large, other problems can be encountered.
  • the vector is a BAC containing genomic sequences into which a selected sequence encoding a molecular tag that has been inserted by directed homologous recombination in bacteria, e.g., by the methods of Heintz WO 98/59060; Heintz et al., WO 01/05962; Yang et al., 1997, Nature Biotechnol. 15: 859-865; Yang et al., 1999, Nature Genetics 22: 327-35; which are incorporated herein by reference in their entireties.
  • a BAC can be modified directly in a recombination-deficient E. coli host strain by homologous recombination. i.e., a cell that cannot independently support homologous recombination, e.g., Rec A.sup. ⁇ .
  • homologous recombination in bacteria is used for target-directed insertion of a sequence encoding a molecularly tagged ribosomal protein into the genomic DNA encoding sufficient regulatory sequences (termed “characterizing gene sequences”) to promote expression of the tagged ribosomal protein in the endogenous expression pattern of the characterizing gene, which sequences have been inserted into the BAC.
  • the BAC comprising the tagged fusion protein sequence under the control/regulation of a regulatory region comprising sequences from a genomic locus of the desired characterizing gene is then recovered and introduced into the genome of a potential founder organism for a line of transformed organisms.
  • the particular nucleotide sequence that has been selected to undergo homologous recombination is contained in an independent origin based cloning vector introduced into or contained within the host cell, and neither the independent origin based cloning vector alone, nor the independent origin based cloning vector in combination with the host cell, can independently support homologous recombination (e.g., is RecA).
  • the exact method used to introduce the tagged ribosomal protein encoding sequence and to remove (or not) the RecA (or other appropriate recombination enzyme) will depend upon the nature of the BAC library used (for example, the selectable markers present on the BAC vectors) and such modifications are within the skill in the art.
  • the BAC containing the characterizing gene regulatory sequences and molecularly tagged ribosomal protein coding sequences in the desired configuration is identified, it can be isolated from the host E. coli cells using routine methods and used to make transformed organisms as described within.
  • the BAC can also be engineered or modified by “E-T cloning,” as described by Muyrers et al (1999, Nucleic Acids Res. 27(6): 1555-57, incorporated herein by reference in its entirety).
  • E-T cloning as described by Muyrers et al (1999, Nucleic Acids Res. 27(6): 1555-57, incorporated herein by reference in its entirety).
  • specific DNA may be engineered into a BAC independently of the presence of suitable restriction sites. This method is based on homologous recombination mediated by the recE and recT proteins (“ET-cloning”) (Zhang et al., 1998, Nat. Genet. 20(2): 123-28; incorporated herein by reference in its entirety).
  • a vector containing the nucleic acid encoding the regulatory sequences and the molecularly tagged fusion protein can be introduced transiently or stably into the genome of a host cell.
  • the vector can be transiently transfected wherein it is not integrated, but is maintained as an episome.
  • host cell and “recombinant host cell” are used interchangeably herein.
  • a host cell can be any prokaryotic (e.g., bacterium such as E. coli ) or eukaryotic cell (e.g., a cell from a yeast, plant, insect (e.g., Drosophila ), amphibian, amniote, or mammal, to name but a few.
  • the host cell is a human cell, a rodent cell, a mouse cell, a rat cell, a mammalian cell, an immortalized cultured cell or primary human or rodent cell.
  • the host cells are human or rodent embryonic stem cells, neuronal stem cells, hippocampal stem cells, hippocampal progenitor cells, or partially differentiated pluripotent cells, or tumor cells or cancer cells (particularly circulating cancer cells such as those resulting from leukemias and other blood system cancers).
  • Methods can utilize genetically engineered host cells that contain any of the foregoing tagged ribosomal protein coding sequences, optionally operatively associated with a regulatory element (preferably from a characterizing gene, as described above) that directs the expression of the coding sequences in the host cell. Both cDNA and genomic sequences can be cloned and expressed.
  • the host cell is recombination deficient, i.e., Rec.sup. ⁇ , and used for BAC recombination.
  • the host cell may contain more than one type of ribosomal fusion, where the fusion of the different ribosomal is to the same or different tags.
  • a single ribosomal may be fused to more than one tag, for example, at both is N-terminal and C-terminal ends.
  • a vector containing a nucleotide sequence can be introduced into the desired host cell by methods known in the art, e.g., transfection, transformation, transduction, electroporation, infection, microinjection, cell fusion, DEAE dextran, calcium phosphate precipitation, liposomes, LIPOFECTINTM, lysosome fusion, synthetic cationic lipids, use of a gene gun or a DNA vector transporter, such that the nucleotide sequence is transmitted to offspring in the line.
  • methods known in the art e.g., transfection, transformation, transduction, electroporation, infection, microinjection, cell fusion, DEAE dextran, calcium phosphate precipitation, liposomes, LIPOFECTINTM, lysosome fusion, synthetic cationic lipids, use of a gene gun or a DNA vector transporter, such that the nucleotide sequence is transmitted to offspring in the line.
  • the vector is introduced into a cultured cell.
  • the vector is introduced into a proliferating cell (or population of cells), e.g., a tumor cell, a stem cell, a blood cell, a bone marrow cell, a cell derived from a tissue biopsy, etc.
  • Particular embodiments encompass methods of introduction of the vector containing the nucleic acid, using pronuclear microinjection into the mononucleus of a mouse embryo or infection with a viral vector comprising the construct.
  • Methods of pronuclear injection into mouse embryos are well-known in the art and described in Hogan et al. 1986, Manipulating the Mouse Embryo, Cold Spring Harbor Laboratory Press, New York, N.Y. and Wagner et al., U.S. Pat. No. 4,873,191, issued Oct. 10, 1989, herein incorporated by reference in their entireties.
  • Viral methods of inserting nucleic acids are known in the art.
  • Targeted delivery can utilize lentivirus, retrovirus, adenovirus, herpes simplex virus, adeno associated virus, or any other virus amenable to gene delivery.
  • Any model organism can be engineered to express a molecularly tagged ribosome using methods well known in the art. These can include but are not limited to non-human primates, mice, rats, sheep, dogs, cows, goats, chickens, amphibians, fish, zebrafish, ( Danio rerio ), flies ( Drosophila melanogaster ), worms ( Ceanorhabditis elegans ), or yeast (or other fungi).
  • a transgenic animal is a non-human animal in which one or more of the cells of the animal includes a nucleic acid that is non-endogenous (i.e., heterologous) and is present as an extrachromosomal element in a portion of its cell or stably integrated into its germ line DNA (i.e., in the genomic sequence of most or all of its cells).
  • a transgenic animal comprises stable changes to the germline sequence.
  • Heterologous nucleic acid is introduced into the germ line of such a transgenic animal by genetic manipulation of, for example, embryos or embryonic stem cells of the host animal.
  • the heterologous nucleic acid may integrate into the genome of the founder organism by random integration. If random, the integration preferably does not knock out, e.g., insert into, an endogenous gene(s) such that the endogenous gene is not expressed or is mis-expressed.
  • the nucleic acid of the may integrate by a directed method, e.g., by directed homologous recombination (“knock-in”), Chappel, U.S. Pat. No. 5,272,071; and PCT publication No. WO 91/06667, published May 16, 1991; U.S. Pat. No. 5,464,764; Capecchi et al., issued Nov. 7, 1995; U.S. Pat. No. 5,627,059, Capecchi et al issued, May 6, 1997; U.S. Pat. No. 5,487,992, Capecchi et al., issued Jan. 30, 1996).
  • knock-in directed homologous recombination
  • Transformed organisms can be generated by random integration of a vector into the genome of the organism, for example, by pronuclear injection in an animal zygote as described above.
  • Other methods involve introducing the vector into cultured embryonic cells, for example ES cells using methods of injection or electroporation well known in the art, and then introducing the transformed cells into animal blastocysts, thereby generating a “chimeras” or “chimeric animals”, in which only a subset of cells have the altered genome.
  • Chimeras are often used for breeding purposes in order to generate the desired transgenic animal.
  • Animals having a heterozygous alteration are generated by breeding of chimeras. Male and female heterozygotes are typically bred to generate homozygous animals.
  • a transgenic founder animal can be identified based upon the presence of the nucleic acid introduced in its genome and/or expression of mRNA in tissues or cells of the animals. A transgenic founder animal can then be used to breed additional animals carrying the nucleic acid of. These transgenic animals can further be bred to other transgenic animals carrying other heterologous nucleic acids. Progeny harboring homologously recombined or integrated DNA in their germline cells can be used to breed animals in which all cells of the animal contain the homologously recombined DNA by germline transmission of the nucleic acid of interest.
  • Clones of the non-human transgenic animals described herein can also be produced according to the methods described in Wilmut et al., 1997, Nature 385: 810-13 and PCT Publication NOS. WO 97/07668 and WO 97/07669.
  • the transgenic mice may be bred and maintained using methods well known in the art.
  • the mice may be housed in an environmentally controlled facility maintained on a 10 hour dark: 14 hour light cycle. Mice are mated when they are sexually mature (6 to 8 weeks old).
  • the transgenic founders or chimeras are mated to an unmodified animal.
  • the transgenic founder or chimera is mated to C57BL/6 mice (Jackson Laboratories).
  • the chimera is mated to 129/Sv mice, which have the same genotype as the embryonic stem cells.
  • the transgenic mice are so highly inbred to be genetically identical except for sexual differences.
  • the homozygotes are tested using backcross and intercross analysis to ensure homozygosity.
  • Homozygous lines for each integration site in founders with multiple integrations are also established.
  • Brother/sister matings for 20 or more generations define an inbred strain.
  • the transgenic lines are maintained as hemizygotes.
  • individual genetically altered mouse strains are also cryopreserved rather than propagated. Methods for freezing embryos for maintenance of founder animals and transgenic lines are known in the art. Methods for reconstituting frozen embryos and bringing the embryos to term are known in the art.
  • the nucleic acid encoding the molecularly tagged ribosomal protein may be introduced into the genome of a founder plant (or embryo that gives rise to the founder plant) using methods well known in the art (Newell, 2000, Plant transformation technology. Developments and applications, Mol. Biotechnol. 16(1):53-65; Kumar and Fladung, 2001, Controlling transgene integration in plants, Trends in Plant Science 6 (4): 155-159).
  • the nucleic acid encoding the molecularly tagged ribosomal protein may be introduced into the genome of bacteria and yeast using methods described in Ausubel et al., 1989, Current Protocols in Molecular Biology, Green Publishing Associates and Wiley Interscience, N.Y., Chapters 1 and 13, respectively).
  • Potential founder organisms for a line of transformed organisms can be screened for expression of the molecularly tagged fusion protein coding sequence by ribosomes in the population of cells characterized by expression of the endogenous characterizing gene.
  • immunohistochemistry using an antibody specific for the molecular tag or a marker activated or repressed thereby is used to detect expression of the molecular tag.
  • other methods and devices are used to detect the tag, such as with the use of optics-based sorting or magnetics-based sorting.
  • Transformed organisms that exhibit appropriate expression are selected as lines of transformed organisms.
  • a collection of lines of transformed organisms that contain a selected subset of cells or a cell population expressing molecularly-tagged ribosomes is provided.
  • the collection comprises at least 2 individual lines, preferably at least 5, 10, 25, 50, 100, 500, 1000, 1500, 2000, 2500, 5000, 10,000, 15,000, or 30,000 individual lines. Each individual line is selected for the collection based on the identity of the subset of cells in which the molecularly tagged ribosomes are expressed.
  • a BACarray line related to neuronal diseases can be created. These include, but are not limited to BACarray lines specific for expression for cells involved in disease processes such as depression, obesity, anxiety, epilepsy, sleep, Parkinson's disease, ADHD, Huntington's disease, addiction, dementia, Alzheimer's disease, ALS, and the like. For example, see FIG. 1 for a representative BACarray collection specific to central nervous system diseases.
  • a BACarray collection relating to sub-regions of a tissue for example regions of the central nervous system can be created.
  • These include, but are not limited to BACarray lines specific for expression in only striatal cells (for example expression in medium spiny neurons, striatonigral and/or striatopallidal neurons), in only cerebellar cells (for example expression in Purkinje neurons, astrocytes, Bergmann glia, granule cells, etc), in only hippocampal cells (for example, expression in CA1 neurons, CA2 neurons, CA3/4 neurons, glia, astrocytes, DG neurons), in only hypothalamic cells, in only spinal cord cells, in only pineal gland cells, and the like.
  • striatal cells for example expression in medium spiny neurons, striatonigral and/or striatopallidal neurons
  • cerebellar cells for example expression in Purkinje neurons, astrocytes, Bergmann glia, granule cells, etc
  • hippocampal cells for example, expression in CA1
  • a BACarray collection relating to a particular biological function can be created. These include but are not limited to BACarray lines specific for functions related to myelination, excitatory neural transmission, motor function, migration, adhesion, infiltration, processing of noxious stimuli, processing of sensory stimuli, visual processing, auditory processing, olfactory processing, vestibular control, regulation of feeding and satiety, regulation of wakefulness and sleep, regulation of reward behavior (for example as how it relates to addictive behavior), and the like.
  • the embodiments described herein provide for translation profiling and molecular phenotyping of particular cells and/or tissues.
  • mRNA complexed in polysomes with tagged ribosomal proteins are isolated and can be analyzed by any method known in the art.
  • the translational profile of cells expressing the tagged ribosomal proteins can be analyzed by isolating the mRNA and constructing cDNA libraries or by labeling the RNA for gene expression analysis, for example by disposing the mRNA on a microarray.
  • Embodiments of this invention utilize techniques described in US 2005/0009028, which is herein incorporated in its entirety.
  • mRNA bound by the tagged ribosomal proteins may be used to produce a cDNA library and, in fact, a collection of such cell type-specific, cell-subtype specific, tissue-specific, organism-specific, disease-specific, function-specific, cDNA libraries may be generated from different populations of isolated cells.
  • Such cDNA libraries are useful to analyze gene expression, isolate and identify cell type-specific genes, splice variants and non-coding RNAs, as well as identify co-regulated gene sets for a particular cell related to a function or a disease state.
  • such cell-type specific libraries prepared from mRNA bound by, and isolated from, the tagged ribosomal proteins from treated and untreated or transgenic or otherwise manipulated cells/animals having can be used, for example in subtractive hybridization procedures, to identify genes expressed at higher or lower levels in response to a particular treatment or in a disease state as compared to untreated animals.
  • the mRNA isolated from the tagged ribosomal proteins may also be analyzed using particular microarrays generated and analyzed by methods well known in the art. Gene expression analysis using microarray technology is well known in the art. Methods for making microarrays are taught, for example, in U.S. Pat. No. 5,700,637 by Southern, U.S. Pat. No.
  • the mRNA bound by the tagged ribosomal proteins may be analyzed, for example by northern blot analysis, PCR, RNase protection, etc., for the presence of mRNAs encoding certain protein products and for changes in the presence or levels of these mRNAs depending on manipulation.
  • specific cells or cell populations that express a potential a molecularly tagged ribosomal protein are isolated from the collection and analyzed for specific protein-protein interactions or an entire protein profile using proteomics methods known in the art, for example, chromatography, mass spectroscopy, 2D gel analysis, etc.
  • assays may be used to analyze the cell population expressing the molecularly tagged ribosomal protein either in vivo, in explanted or sectioned tissue or in the isolated cells, for example, to monitor the response of the cells to a certain manipulation/treatment or candidate agent (for example, a small molecule, an antibody, a hybrid antibody, an antibody fragment, a siRNA, an antisense RNA, an aptamer, a protein, or a peptide) or to compare the response of the animals, tissue or cells to expression of the target or inhibitor thereof, with animals, tissue or cells from animals not expressing the target or inhibitor thereof.
  • a certain manipulation/treatment or candidate agent for example, a small molecule, an antibody, a hybrid antibody, an antibody fragment, a siRNA, an antisense RNA, an aptamer, a protein, or a peptide
  • the cells may be monitored, for example, but not by way of limitation, for changes in electrophysiology, physiology (for example, changes in physiological parameters of cells, such as intracellular or extracellular calcium or other ion concentration, change in pH, change in the presence or amount of second messengers, cell morphology, cell viability, indicators of apoptosis, secretion of secreted factors, cell replication, contact inhibition, etc.), morphology, etc.
  • changes in electrophysiology for example, changes in physiological parameters of cells, such as intracellular or extracellular calcium or other ion concentration, change in pH, change in the presence or amount of second messengers, cell morphology, cell viability, indicators of apoptosis, secretion of secreted factors, cell replication, contact inhibition, etc.
  • the isolated mRNA is used to probe a comprehensive expression library (see, e.g., Serafini et al., U.S. Pat. No. 6,110,711, issued Aug. 29, 2000, which is incorporated by reference herein).
  • the library may be normalized and presented in a high density array, such as a microarray.
  • a subpopulation of cells expressing a molecularly tagged ribosomal protein is identified and/or gene expression analyzed using the methods of Serafini et al., WO 99/29877 entitled “Methods for defining cell types,” which is hereby incorporated by reference in its entirety.
  • Data from such analyses may be used to generate a database of gene expression analysis for different populations of cells in the animal or in particular tissues or anatomical regions, for example, in the brain.
  • a database of gene expression analysis for different populations of cells in the animal or in particular tissues or anatomical regions, for example, in the brain.
  • bioinformatics tools such as hierarchical and non-hierarchical clustering analysis and principal components analysis, cells are “fingerprinted” for particular indications from healthy and disease-model animals or tissues, co-regulated gene sets for a particular function, and the like.
  • the methods provided herein are applicable to any cell, tissue, or organism as well as any disease or disorder.
  • the sensitivity afforded by the ability to interrogate an individual cell subtype in a complex heterogeneous tissue or organ system provides a resolution than can be greater than with other techniques such as whole-tissue microarrays and in situ hybridization.
  • the TRAP method of detecting one or more cell subtype-specific mRNAs/genes allows for identification of greater than 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45% and even 50% of the mRNAs/genes enriched in that cell type which are not detectable by other means such as whole-tissue microarrays or in situ hybridization.
  • the methods provided herein are applicable to any cell, tissue, or organism as well as any disease or disorder.
  • diseases are cited in, but not limited to those found in the ‘The Merck Manual of Diagnosis and Therapy’, often called simply ‘The Merck Manual’ (2006).
  • the diseases and disorders can be central nervous system disorders, peripheral nervous system disorders, and non nervous system disorders.
  • neurodegenerative diseases/disorders include, but are not limited to: alcoholism, Alexander's disease, Alper's disease, Alzheimer's disease, Amyotrophic lateral sclerosis, Ataxia telangiectasia, Batten disease (also known as Spielmeyer-Vogt-Sjogren-Batten disease), Bovine spongiform encephalopathy (BSE), Canavan disease, Cockayne syndrome, Corticobasal degeneration, Creutzfeldt-Jakob disease, Huntington's disease, HIV-associated dementia, Kennedy's disease, Krabbe's disease, Lewy body dementia, Machado-Joseph disease (Spinocerebellar ataxia type 3), Multiple sclerosis, Multiple System Atrophy, Narcolepsy, Neuroborreliosis, Parkinson's disease, Pelizaeus-Merzbacher Disease, Pick's disease, Primary lateral sclerosis, Prion diseases, Refsum's disease, Sandhoffs disease, Schilder'
  • neuropsychiatric diseases/disorders include, but are not limited to: depression, bipolar disorder, mania, obsessive compulsive disease, addiction, ADHD, schizophrenia, auditory hallucinations, eating disorders, hysteria, autism spectrum disorders and personality disorders.
  • neurodevelopmental diseases/disorders include, but are not limited to: attention deficit hyperactivity disorder (ADHD), attention deficit disorder (ADD), schizophrenia, obsessive-compulsive disorder (OCD), mental retardation, autistic spectrum disorders (ASD), cerebral palsy, Fragile-X Syndrome, Downs Syndrome, Rett's Syndrome, Asperger's syndrome, Williams-Beuren Syndrome, childhood disintegrative disorder, articulation disorder, learning disabilities (i.e., reading or arithmetic), dyslexia, expressive language disorder and mixed receptive-expressive language disorder, verbal or performance aptitude.
  • ADHD attention deficit hyperactivity disorder
  • ADD attention deficit disorder
  • OCD obsessive-compulsive disorder
  • ASD autistic spectrum disorders
  • cerebral palsy cerebral palsy
  • Fragile-X Syndrome Downs Syndrome
  • Rett's Syndrome Asperger's syndrome
  • Williams-Beuren Syndrome childhood disintegrative disorder
  • learning disabilities i.e., reading or arith
  • Diseases that can result from aberrant neurodevelopmental processes can also include, but are not limited to bi-polar disorders, anorexia, general depression, seizures, obsessive compulsive disorder (OCD), anxiety, bruixism, Angleman's syndrome, aggression, explosive outburst, self injury, post traumatic stress, conduct disorders, Tourette's disorder, stereotypic movement disorder, mood disorder, sleep apnea, restless legs syndrome, dysomnias, paranoid personality disorder, schizoid personality disorder, schizotypal personality disorder, antisocial personality disorder, borderline personality disorder, histrionic personality disorder, narcissistic personality disorder, avoidant personality disorder, dependent personality disorder, reactive attachment disorder; separation anxiety disorder; oppositional defiant disorder; dyspareunia, pyromania, kleptomania, trichotillomania, gambling, pica, neurotic disorders, alcohol-related disorders, amphetamine-related disorders, cocaine-related disorders, marijuana abuse, opioid-related disorders, phencyclidine abuse,
  • neurodevelopmental disorders can be found, for example, through the Neurodevelopmental Disorders Branch of the National Institute of Mental Health (worldwide website address at nihm.nih.gov/dptr/b2-nd.cfm).
  • the invention provides for a method to obtain a translational profile of a cell type of interest.
  • the method comprises expressing a tagged ribosomal protein under the control of a regulatory sequence specific to a gene expressed in the cell type of interest, isolating mRNAs complexed with the ribosomal protein from the cell, and identifying the mRNAs, thereby obtaining a translational profile for the cell type of interest.
  • the cell types of interest are striatonigral and striatopallidal cells.
  • L10a fused to eGFP under the control of a Drd1a or a Drd2 specific regulatory sequence is expressed and translational profiles are obtained.
  • Tables 10, 13, 17, and 18 identify genes that are translationally profiled in striatonigral and striatopallidal cells.
  • the cell type of interest are cholinergic motor neurons.
  • Ribosomal protein L10a fused to eGFP under the control of a choline acetyl transferase (chat)-specific regulatory sequence is expressed and translational profiles are obtained.
  • Table 19 identifies genes that are translationally profiled in cholinergic motor neurons.
  • the cholinergic motor neurons are spatially separated.
  • the cell type of interest are cerebellar neurons and glia, specifically Purkinje neurons and Bergmann glia.
  • Ribosomal protein L10a fused to eGFP under the control of either a Pcp2 or Septin4-specific regulatory sequence is expressed and translational profiles are obtained.
  • Table 20 identifies genes that are translationally profiled in cerebellar Purkinje neurons and Bergmann glia.
  • a gene translational profile following the manipulation of a cell, tissue or organism is obtained.
  • the method comprises manipulating a cell, tissue or organism, using the TRAP methodology to obtain a translational profile, and comparing the profiled to a reference profile from an non-manipulated cell, tissue or organism.
  • Manipulations include but are not limited to:
  • the effect of cocaine on the translational profile of dopaminergic striatonigral and striatopallidal cells is obtained.
  • the effects of acute cocaine administration and the effects of chronic cocaine administration is obtained.
  • the gene translation changes following acute cocaine treatment comprise those identified in Table 15.
  • the gene translation changes following chronic cocaine treatment comprise those identified in Table 16.
  • One embodiment of this invention is to establish a translational profile and molecular phenotype for a tissue or cell type taken from a subject to be screened for, suspected of having, or presenting with a particular disease or disorder, using the methods described herein.
  • markers associated with and/or indicative of a particular disease or disorder are identified.
  • a subject's tissue can be removed for sampling.
  • a sampling of cerebrospinal fluid (CSF) will be obtained from the subject.
  • any bodily fluid can be obtained from the subject.
  • a molecularly tagged ribosomal protein is introduced with the regulatory elements required for a cell-type specific expression.
  • the translational profile and molecular phenotype is established using the methods described herein.
  • the resulting profile and phenotype is then be compared to a profile and phenotype obtained using said methods from a subject or subjects not having or presenting with the particular disease or disorder, i.e. a reference cell, tissue or subject.
  • the results can be used for diagnostics, prognostic, or theranostic purposes in relation to a disease or disorder.
  • the disease or disorder to be detected, diagnosed, prognosed or theranosed can be any disease named herein, or previously undescribed diseases and disorders.
  • BAC-mediated expression can be utilized to drive expression of a molecularly tagged ribosomal protein in a particular cell type.
  • BACarrays have been created and collected that, based on expression of the endogenously regulated gene, have restricted patterns of expression that are directly relevant to several diseases or disorders ( FIG. 1 )
  • Another embodiment of this invention is to screen for candidate agents for modulation of a desired modulatory (antagonistic, agonistic, synergistic modulation) activity.
  • a vehicle or candidate agent is administered in a single or repeated dose to either a cell type or a subject.
  • a translational profile is established for the cell type of interest based on the methods disclosed herein.
  • the profile and phenotypes from those dosed with candidate agent are compared and related to the profile and phenotype from those dosed with a vehicle (i.e. reference sample).
  • a determination is made whether a candidate agent modulates translation and phenotype of one or more mRNA isolated from the cell type of interest, thereby screening said candidate agent for translational modulation.
  • the candidate agent may be a candidate therapeutic agent or drug.
  • the candidate agent may be a toxin.
  • the candidate agent may be but is not limited to a small molecule, an antibody, hybrid antibody or antibody fragment, a siRNA, an antisense RNA, an aptamer, a protein therapeutic, or a peptide.
  • Another aspect of this invention is to identify candidate therapeutic targets for a disease or disorder.
  • this would entail transforming a cell or creating an organism expressing a molecularly tagged ribosomal protein and exposing the cell or organism to a perturbation or stimulus.
  • mRNA transcripts selectively down regulated or up regulated would be potential targets for ameliorating the perturbation.
  • a translational profile from a cell from a subject with a disease or disorder, a cell that has been perturbed, etc will be compared to an otherwise normal or unperturbed cell. The differential translational profile will allow for identification of potential therapeutic targets.
  • any mRNA found to be upregulated in a cell type of interest associated with a disease or disorder for example in but not limited to a striatal, hippocampal, cortical, cerebellar, spinal cord, hypothalamic, pineal, retinal, auditory, olfactory, vestibular, or brain stem cell may represent a target for antagonism. That is, the protein encoded by the identified mRNA would be a therapeutic target for which antagonists could be developed.
  • the target of interest is Gpr6.
  • Gpr6 represents a target for which antagonists can be screened for and developed as a therapeutic for Parkinson's disease, due to its overexpression.
  • an mRNA found to be downregulated in a cell type of interest associated with a disease or disorder could represent a target for agonism. That is, the protein encoded by the identified mRNA would be a therapeutic target for which agonists could be developed.
  • a method for assessing whether a subject in need thereof is amenable to a therapeutic agent comprising determining a translational profile for a cell type, cell sub-type or tissue from the subject, determining if the translational profile is predictive of treatment with one or more therapeutic agents, and identifying the one or more therapeutic agents to administer to the subject.
  • a method for screening one or more therapeutic agents in a subject in need thereof comprising, administering one or more therapeutic agents to a subject, determining a translational profile for a cell type, cell sub-type or tissue from the subject, comparing the translational profile obtained to one or more reference profiles that indicate a positive or negative prognosis, and determining the treatment should continue or be modified based on the comparison.
  • a different treatment modality e.g., different therapeutic agent should be administered, such as for example, a second line drug, that is shown to be amenable to the translational profile observed for a first line drug.
  • a method to identify a co-regulated gene set for a known function or a candidate function for a novel gene comprises determining the translational profiles for a plurality of cell types that express a gene associated with a specific function, comparing the translational profiles to determine what additional genes are similarly regulated thereby identifying a co-regulated gene set involved in the function.
  • the function can be a cellular function or a cellular process.
  • the method is applied to determine a co-regulated gene set involved in myelination, excitatory neural transmission, motor function, cellular migration, cellular adhesion, cellular infiltration, processing of noxious stimuli, processing of sensory stimuli, visual processing, auditory processing, olfactory processing, vestibular control, regulation of feeding and satiety, regulation of wakefulness and sleep, or the regulation of reward behavior.
  • the method is applied to determine a co-regulated gene set involved in myelination comprising determining the translation profiles for a plurality of cells that express the myelin basic protein (Mbp).
  • the gene set comprises one or more of the genes listed in Table 9.
  • This method can be useful in identifying gene sets for known functions or candidate functions for novel gene products, since in many cases the cohorts of co-regulated genes can include genes with well known functions
  • the present invention provides kits.
  • the kit contains reagents for determining the presence, absence, and/or differential presence, of one or more markers indicative of a disease, disorder, and/or pharmacologic, genetic, or environmental manipulation.
  • the disease could be, but is not limited to a neurodegenerative, neuropsychiatric, neurodevelopmental disorder in a sample from an individual suspected of having a susceptibility to such a disease or disorder.
  • the disease or disorder is a proliferative disease such as a cancer.
  • the kit is utilized to identify co-regulated gene sets for a particular biological function. Biological functions are described herein.
  • the kit contains a customized set of clones, vectors, molecular tags from which to choose, for molecular labeling and materials such as CDs, instructions for use, and other reference guides that would allow the individual to choose the correct clone/vector for the cell type, tissue, molecular pathway, or circuit of choice.
  • the kit contains a recombinant vector encoding a nucleic acid sequence which encodes a ribosomal protein and a detectable tag operably linked to a regulatory region.
  • the kit can contain a customized BACarray clone collection relevant for a particular disease or disorder.
  • a kit in one embodiment includes a recombinant vector engineered to express a nucleic acid sequence encoding a ribosomal protein and a detectable tag operably linked to a regulatory region containing sequences endogenous to a genomic locus of a gene of interest.
  • the ribosomal protein is fused in-frame to a detectable tag.
  • the recombinant vector is a BAC.
  • the gene of interested can be selected from but is not limited to one that expresses in a striatal cell, cerebellar cell, cortical cell, hypothalamic cell, hippocampal cell, brainstem cell, and a spinal cord cell.
  • the tag is eGFP and the ribosomal protein is L10a.
  • the methodology reported here provides an enabling technology for translational profiling and molecular phenotyping. Examples allow for defining the distinguishing molecular characteristics of closely related or critical cell types. Examples also demonstrate that methods described herein can be employed to analyze physiological adaptations of specific cell types in vitro, in vivo, ex vivo, or in situ.
  • compositions and methods feature methodology, which readily and reproducibly identify translated mRNAs in any cell type or tissue of interest.
  • This methodology involves expression of a molecularly tagged ribosomal transgene, which enables tagging of polysomes for isolation, purification and identification of mRNA, in specific populations.
  • this can be achieved using Bacterial Artificial Chromosome (BAC) transgenic mice, allowing translational profiling and molecular phenotyping from whole animals.
  • BAC Bacterial Artificial Chromosome
  • mRNAs translated into protein are at one point usually attached to a ribosome or a polyribosome complex (polysomes).
  • Any tag, not limited to those named herein, fused to a ribosomal protein allows for isolation of bound mRNAS.
  • eGFP fused to the N-terminus of the large subunit ribosomal protein L10a, hereafter eGFP-L10a was utilized in this and ensuing examples, but is by no ways limiting to the tens, hundreds, thousands, or even more tag-protein combinations that can be utilized.
  • FIG. 2 (a) A schematic is presented to illustrate affinity purification of eGFP-tagged Polysomes (originating from the target cell population) using anti-GFP antibody-coated beads (Schematic in a). Fusions of Enhanced Green Fluorescent Protein (eGFP) with ribosomal proteins were screened for efficient incorporation into polysomes to provide a tag for all translated cellular mRNAs.
  • eGFP Enhanced Green Fluorescent Protein
  • the figure displays transmission electron micrographs of anti-GFP coated magnetic beads after incubation with extracts taken from HEK293T cells transfected with an empty vector (left panel) or the eGFP-L10a construct (right panel); images acquired at 50,000 ⁇ magnification, inserts enlarged by a factor of 2.3 ⁇ .
  • HEK293T cells grown on coverslips were transiently transfected, grown for two days, fixed with paraformaldehyde, and mounted with media containing 4′,6-diamidino-2phenylindo (DAPI) to stain DNA.
  • DAPI 4′,6-diamidino-2phenylindo
  • HEK293T cells transiently transfected with the eGFP-L10a transgene but not mock transfected cells HEK293T cells transfected with eGFP-L10a were homogenized in lysis buffer. The solubilized and clarified lysate was loaded onto a linear density (20-50% w/w) gradient of sucrose and centrifuged for 2 hours at 4° C. using a Beckman SW41 rotor at 40,000 r.p.m. (200,000 ⁇ g). 750 ⁇ l fractions were collected as absorbance at 254 nm was monitored with an ISCO UA-6 UV detector.
  • RNA yields from cultured cell BACarray purifications HEK293T cells were transiently transfected with eGFP (mock transfection) or eGFP-L10a constructs. Transfection efficiency was approximately 30%. Plates of different sizes were used to grow mock or eGFP-L10a-transfected cells, which is reflected in different input RNA amounts. Input and immunoprecipitated (bound) RNA were purified and the quantity and purity of RNA were determined using a Bioanalyzer 2100 (Agilent Technologies). Total RNA Total RNA Yield Transfection Bound (ng) Input (ng) (%) eGFP (Mock) 61 33,320 0.2 eGFP-L10a 6,117 56,630 10.8
  • FIG. 3 displays immunoprecipitation of translated mRNAs from transfected cells.
  • HEK293T cells were transiently transfected ( ⁇ 30% efficiency) with eGFP (mock) or eGFP-L10a constructs and grown in medium alone (no treatment, NT) or in medium supplemented with 100 ⁇ g/ml ferric ammonium citrate [pH 7.0] (iron) for 36 hours.
  • NT no treatment
  • ferric ammonium citrate [pH 7.0] iron
  • Induction of the iron-storage protein Ferritin was seen after 36 hours of iron treatment.
  • the post-mitochondrial supernatants of untreated or iron-treated cells were loaded onto linear sucrose gradients (20-50% w/w).
  • eGFP-L10a was recovered equally well from untreated and iron-treated samples, as was all eGFP from mock samples; * indicates the presence of a light eGFP-L10a band upon longer exposure. No endogenous Rpl10a or Rpl7 was recovered in the bound (IP) fraction of mock samples, while endogenous Rpl10a and Rpl7 were both recovered in the bound (IP) fraction of untreated and iron-treated samples.
  • Antibodies were used as follows: GFP detection: JL-8, Clontech (Mountain View, Calif.), 1:2,000 in 5% non-fat milk/PBST (phosphate buffered saline-0.05% Tween-20]; Rpl7 detection: NB200-308, Novus Biologicals (Littleton, Colo.), 1:2,000 in 5% IgG-free bovine serum albumin/PBS-T; Rpl10a detection: H00004736-M01, Abnova Corporation (Taipei City, Taiwan), 1:2,000 in 5% IgG-free bovine serum albumin/PBS-T; Ferritin detection: 65077, MP Biomedicals (Solon, OH), 1:1,500 in 0.2% I-block (Applied Biosystems, Foster City, Calif.)/PBS-T; ⁇ -Actin detection: Ab8224, Abcam (Cambridge, Mass.), 1:2,500 in 5% nonfat milk/PBS-T.
  • GFP detection JL-8, Clo
  • BACarray translational profiling permits comprehensive studies of translated mRNAs in genetically defined cell populations, and their responses to physiological perturbations.
  • BACarray translational profiles for twenty four distinct and diverse CNS cell populations are presented here. Identification of cell-specific and enriched transcripts, previously not identified in whole tissue microarray studies are provided as examples to illustrate the added value of comparative analysis of these large datasets.
  • the BAC transgenic strategy has been applied (Heintz, 2004; Yang et al., 1997) to provide high resolution anatomical data and BAC vectors for the design of genetic studies of specific, morphologically defined cells in the CNS (Gong et al., 2003) (www.gensat.org).
  • Heiman et al. have reported the development of the BACarray translational profiling methodology for use in discovery of the complement of proteins synthesized in any genetically defined cell population.
  • the methodology is used to generate BACarray transgenic mice for a wide variety of anatomically and genetically defined cell types in the mammalian brain.
  • such a collection can provide a resource that will allow detailed molecular phenotyping of CNS cell types at specified developmental stages, and in response to a wide variety of pharmacological, genetic or behavioral alterations.
  • the mice and data presented confirm the generality of the BACarray approach and provide a resource for studies of the molecular bases for cellular diversity in the mammalian brain.
  • BACarray translational profiles of specific CNS cell types requires targeting of the eGFP-L10a ribosomal protein fusion to desired CNS cell types, affinity purification of polysomal RNAs from these cell types, and interrogation of the resultant mRNA populations using massively parallel analytical techniques.
  • affinity purification of polysomal RNAs from these cell types and interrogation of the resultant mRNA populations using massively parallel analytical techniques.
  • To provide a resource for comparative analysis of diverse CNS cell types, described in this examples is: the application of this strategy to generate and characterize further BACarray transgenic lines, to isolate and characterize mRNA populations from twenty four cell types targeted in these lines, to analyze these data relative to one another, and to archive and present the BACarray transgenic lines and their associated anatomic and microarray data.
  • FIG. 4 represents the BACarray strategy
  • FIGS. 5 and 6 represent engineering of BAC vectors and the creation of mice carrying BACs.
  • FIGS. 5 and 6 represent engineering of BAC vectors and the creation of mice carrying BACs.
  • FIGS. 5 and 6 represent engineering of BAC vectors and the creation of mice carrying BACs.
  • FIGS. 5 and 6 represent engineering of BAC vectors and the creation of mice carrying BACs.
  • FIGS. 5 and 6 represent engineering of BAC vectors and the creation of mice carrying BACs.
  • To tag mRNAs in specific cell types of the mouse cell specific cis and trans regulatory elements and known transcriptional units were utilized as described herein and in (Gong et al. Nature Vol 425, 2003).
  • Mouse lines with specific expression in different subsets of cells in the cerebral cortex ( FIG. 7 ) or hypothalamus ( FIG. 8 ) from BAC array lines are presented by way of example. Detailed anatomic characterization of selected BACarray transgenic mouse lines is presented below.
  • FIG. 9 Detailed anatomic studies were conducted for BACarray transgenic mouse lines as displayed in FIG. 9 .
  • transgene expression was assayed by immunohistochemistry (IHC) using an antibody against eGFP.
  • IHC data from serial coronal sections of the whole brain were collected, scanned at high resolution and mounted for inspection. All sections were processed equivalently (Neuroscience Associates) so that apparent differences in staining intensity accurately reflect differences in transgene expression level.
  • the figure shows thumbnail images for each of the 24 cell populations selected for microarray analysis, and high resolution data to illustrate the morphology evident from IHC analysis of eGFPL10a expression.
  • the regions covered in this characterization include the cerebellum (panels 1-9), the spinal cord (10), the basal forebrain and corpus striatum (11-14), the brainstem (15), and cerebral cortex (16-25).
  • BACarray lines for Purkinje cells Pcp2, panel 1
  • granule cells Neurode1, panel 2
  • Golgi neurons Grm2, panel 3
  • unipolar brush cells Grp, panel 5
  • Bergmann glia Sept4, panel 8
  • astrocytes Aldhl11, panel 9
  • Purkinje cells can be recognized in the eGFP-L10a IHC data by their large cell bodies and molecular layer dendrites, granule cells by their small size, dense packing, and location in the granule layer, and Bergmann glial cells by their morphology, radial projections, and close proximity to Purkinje cells. IHC analysis of eGFP-L10a fusion proteins in these well known cell types using these regulatory regions allow for identification of well known and previously unknown cell types.
  • the expression of the eGFP-L10a transgene from each BAC driver is regionally correct, conforming both to the literature and to the expectation given the anatomic data presented in GENSTAT and for these cell types the distribution of the eGFPL10a fusion protein, while more limited than that of soluble eGFP, is sufficient to provide enough anatomic detail to unambiguously identify these well described CNS cell types.
  • the eGFP-L10a fusion protein is detected in multiple structures within the brain.
  • An example is the characterization of fusion protein IHC in cholinergic cell populations targeted in the Chat BACarray lines. In this case expression is clear in brainstem motor neurons, spinal cord motor neurons, neurons of the corpus striatum, basal forebrain projection neurons, and neurons of the medial habenula.
  • BACarray translational profiles for four of these cholinergic cell populations were collected by separately dissecting the spinal cord, brainstem, corpus striatum and basal forebrain prior to affinity purification of the eGFPL10a tagged polysome populations.
  • the eGFP-L10a fusion protein is abundant in hippocampal CA1 cells in the Cck BACarray line, allowing translational profiling of mRNAs expressed in this cell type (panel 25). Creation of a BACarray anatomic database allows the user to browse through serial brain sections for each of the lines presented here to determine whether a cell type of interest can be analyzed in one of the BACarray lines presented in this example.
  • FIG. 10 shows that BACarray cortical pyramidal cells have the same laminar distribution as eGFP GENSTAT lines.
  • the figure shows: A) Graph (mean+/ ⁇ SE) of the distance of eGFP+ cell somas from the pial surface for the BACarray and GENSAT eGFP lines for each pyramidal cell BAC driver. The depth of the cells was consistent between both lines for each driver. B) The percentage of cells in 100 micron bins is shown as a histogram of the distribution of cell depths for each line in A. The BACarray line and eGFP line for each driver had overlapping distributions of cell depths.
  • FIG. 11 shows that in many BACarray lines, the presumed cellular identity of the targeted lines was confirmed using double immunofluorescence for the eGFP-L10a fusion protein and well characterized cell type specific markers.
  • the cell type specific markers corresponded with the BAC drivers chosen for modification (Olig2, Aldhl11, Grm2, Chat).
  • BAC drivers chosen for modification (Olig2, Aldhl11, Grm2, Chat).
  • commonly used markers which have been well characterized for specific cell types were used, as seen in panel B.
  • these studies established that BAC drivers limited expression to well-defined cell populations.
  • eGFP-L10a is found in all Pvalb positive and NeuN negative interneurons of the cerebellar molecular layer, suggesting that this line is valuable for analyses of both stellate and basket cells.
  • IF immunofluorescence
  • the eGFP-L10a transgene is expressed in a only a subset of a particular cell type.
  • the eGFP-L10a fusion protein is restricted to the subpopulation of unipolar brush cells (Nunzi et al., 2002) which are immunoreactive for Grm1 but not Calb2 (calretinin).
  • BACarray lines whose expression did not conform to readily identified cell types, were also analyzed by IF analysis to provide data concerning the broad classification of cell populations targeted. For example, in the cerebral cortex of the Cort BACarray line, Calb1 was detected in nearly 50% of eGFP-L10a positive cells, Pvalb was found in less than 5% of these cells, and Calb2 was not detected. Characterization of the fusion protein in the cortex of Pnoc BACarray mice revealed that the majority of eGFP-L10a positive cells in the superficial layers of the cerebral cortex are multipolar and are GABA positive, although some cells in deeper layers of cortex are GABA negative and appear to have a single apical dendrite.
  • the multipolar cells in this case are often positive for Calb2, but not Calb1 or Pvalb.
  • Both IHC and IF studies of the cortex of the Cck BACarray line clearly demonstrate that eGFP-L10a is detected in small neurons positive for Calb1 but not Pvalb or Calb2, as well as in pyramidal cells (data not shown), consistent with previous ISH data (www.stjudebgem.org; www.brain-map.org) (Lein et al., 2007; Magdaleno et al., 2006).
  • glial cell types In addition to neuronal cell types, three BACarray lines for glial cell types were generated which were analyzed in both cerebellar and cortical tissue. These glial cell types included astrocytes, mature oligodendrocytes, and a mixed oligodendroglial line that included mature oligodendrocytes and oligodendrocyte progenitors (also called synantocytes or polydendrocytes) (Butt et al., 2005). Astrocytes were targeted using a BAC for the gene Aldhl11 that has previously been described as astrocyte specific (Anthony and Heintz, 2007; Cahoy et al., 2008).
  • This BAC drove transgene expression in both Gfap+ (reactive) and Gfap ⁇ astrocytes, as well as Bergmann glia. It did not express in Ng2+ oligodendrocyte progenitors, nor in Cnp+ myelinating oligodendrocytes. In contrast, a BAC for the Olig2 transcription factor directed expression specifically into both the Ng2+ and Cnp+ oligodendrocyte lineage cells. Finally, a BACarray line for Cmtm5 expressed specifically, albeit weakly, in mature (Cnp+) oligodendrocytes. With these three lines, the translational profile of the three major classes of glia across the CNS can be examined.
  • Table 4 were modified as described to insert an eGFP-L10a fusion protein into the translation start site of the driver gene (Gong et al., 2002; Gong et al., 2003). Founders and subsequent generations were bred to either Swiss-Webster or c57bl/6 wildtype mice. Lines were maintained as trans-heterozygotes.
  • mice Six to twelve week old mice were euthanized with CO2 and perfused transcardially with phosphate buffered saline (PBS) pH 7.4 followed by 4% paraformaldehyde in PBS.
  • PBS phosphate buffered saline
  • DAB diaminobenzidine tetrahydrochloride
  • fixed brains were treated overnight with 20% glycerol and 2% dimethylsulfoxide to prevent freeze-artifacts.
  • Multiple brains (up to 25 per block) were embedded in a gelatin matrix using MultiBrainTM Technology (NeuroScience Associates, Knoxville, Tenn.). After curing, the block was rapidly frozen to ⁇ 70° C.
  • MultiBrainTM block was sectioned coronally at 40 microns. All sections were collected sequentially into the wells of a 4 ⁇ 6 plate filled with Antigen Preserve solution (50% PBS pH 7.0, 50% Ethylene glycol, 1% Polyvinyl Pyrrolidone).
  • the sections were incubated with a 1:75,000 solution of Goat anti-eGFP serum (Heiman et al) overnight at room temperature. Following extensive washing, the sections were incubated with biotinylated secondary antibody (Anti Goat IgG, Vector Labs, Burlingame, Calif.), washed again, and incubated with avidin-biotin-HRP (Vectastain elite ABC kit, Vector Labs, Burlingame, Calif.) according to the manufacturer's instructions. Sections were again washed and incubated with DAB and hydrogen peroxide until fully developed.
  • biotinylated secondary antibody Anti Goat IgG, Vector Labs, Burlingame, Calif.
  • avidin-biotin-HRP Vectastain elite ABC kit, Vector Labs, Burlingame, Calif.
  • GRM2/GRM3 metabotropic glutamate receptor 2&3 AB1553 Chemicon, Temecula, Ca.
  • Brains were placed in an embedding mold filled with Neg-50 embedding medium (Richard Allan Scientific, Kalamazoo, MI) for 1 hour at room temperature, and were subsequently incubated on dry ice for 1 hour to freeze the embedding medium. Brains were then transferred to and stored at ⁇ 80° C. until sectioned. 12 ⁇ m sagittal sections were cut, mounted on glass slides, and kept overnight at ⁇ 20° C., then transferred to ⁇ 80° C. until used for immunohistochemistry.
  • Sections were thawed and dried at room temperature for 20 min, washed with PBS, and incubated in 0.2% H2O2/PBS at room temperature for 30 min to quench endogenous peroxidase activity. Sections were washed with PBS, permeabilized with PBS/0.05% Tween-20, and blocked with Image-it FX signal enhancer (Invitrogen Corporation, Carlsbad, Calif.) for 30 min at room temperature. Sections were washed with PBS/0.05% Tween-20 and blocked again with 2% donkey serum/0.1% fish gelatin/PBS/0.05% Tween-20. Sections were then incubated overnight at 4° C. with primary antibodies.
  • Fresh Frozen Sections For all nuclear immunohistochemistry (Anti-Atrx, Anti-PML, Anti- ⁇ H2A.X), fresh frozen brain sections were used. For fresh frozen brain sections, BACarray mice were euthanized with CO2, decapitated, and their brains removed into ice-cold PBS. Brains were then embedded in Neg50, placed on dry ice for an hour, and stored until needed at ⁇ 80° C. Before sectioning, frozen blocks of tissue were equilibrated at ⁇ 20° C., and 16 ⁇ m sections were cut on a Leica cryostat. Slides with fresh frozen brain sections were stored at ⁇ 80° C. or ⁇ 20° C. until further use.
  • sections Prior to use, sections were allowed to air-dry at room temperature for 15 minutes, then fixed with 1% freshly made PFA in 1 ⁇ PBS for 10 minutes at room temperature. Next, slides were washed three times with 1 ⁇ PBS, and permeabilized for 10 minutes at room temperature with 0.05% Triton X-100 in PBS. After permeabilization, tissue sections were blocked using either 5% horse serum or 5% goat serum in PBS for at least one hour. Sections were incubated with primary antibodies overnight in a humidified chamber at 4° C., washed three times with PBS, and incubated at room temperature for one hour with appropriate secondary antibodies.
  • the distance from the apical tip of the soma to the pial surface was measured using the ‘straight line selection’ tool.
  • IMAGE consortium clones containing sequences from genes of interest were purchased from Open Biosystems (Table 6). Probes were synthesized by linearization of plasmid with appropriate restriction enzyme, template purification with Qiagen PCR purification kit, followed by in vitro transcription with appropriate enzyme (T3 or T7) using DIG RNA labeling kit (Roche, Basel, CH). Labeled RNA was purified with ProbeQuant G-50 microcolumns (GE Healthcare), and assayed for quality and quantity with a Bioanalyzer, following manufacturer's instructions (Agilent Technologies, Santa Clara, Calif.).
  • ISH in situ hybridization studies: ISH was conducted on 11 genes enriched in either Grm2 positive granule cell layer interneurons, or Pnoc positive neurons of cortex, using plasmids ordered from Open Biosystems. Plasmids were sequenced to confirm the accuracy and orientation of the ESTs. Plasmids were linearized with either Sal I or Eco RI and Dig labeled RNA was transcribed with either T3 or T7 polymerase to create anti-sense cRNA probe.
  • mice were processed as above, and brains were cut on cryostat into 20 micron sections and mounted onto Fisher Superfrost Plus slides. Tissue was washed, then post fixed for 20 minutes in 4% paraformaldehyde PBS, permeabilized with 0.05% Triton X100, digested with 50 ug/ml Proteinase K in TE for 10 minutes, and acetylated for 10 minutes in 0.1M TEA with 0.25% acetic anhydride.
  • Sections were prehybridized in Atlas hybridization chambers (Clontech, Mountain View, Calif.) in 5 ⁇ SSC, 2.5 ⁇ Denhardt's solution, with 500 ug/ml sheared denatured salmon sperm for 30 minutes, then hybridized overnight with labeled riboprobe. Slides were washed for 5 minutes at 65° C. with 5 ⁇ SSC, then for 1 hour with 0.2 ⁇ SSC at 68° C., and for 5 minutes at room temperature.
  • RNA quality control, amplification and hybridization were done as described by Heiman et al. For consistency across cell types, 15 ngs of total RNA were amplified for each sample.
  • mice were decapitated and the specific tissue of interest was quickly dissected from mice brains. Pooled tissue was immediately collected in ice-cold dissection buffer and homogenized in ice-cold polysome extraction buffer (10 mM HEPES [pH 7.4], 150 mM KCl, 5 mM MgCl2, 0.5 mM dithiothreitol, 100 ⁇ g/ml cycloheximide, protease inhibitors, and recombinant RNase inhibitors) using a motor-driven Teflon-glass homogenizer.
  • ice-cold polysome extraction buffer 10 mM HEPES [pH 7.4], 150 mM KCl, 5 mM MgCl2, 0.5 mM dithiothreitol, 100 ⁇ g/ml cycloheximide, protease inhibitors, and recombinant RNase inhibitors
  • NP-40 or IGEPAL EMD Biosciences, San Diego, Calif.; Sigma, St. Louis, Mo.
  • DHPC Advanti Polar Lipids, Alabaster, Ala.
  • Goat anti-GFP (custom made) coated protein G Dynal magnetic beads (Invitrogen Corporation, Carlsbad, Calif.) are added to the supernatant and the mixture was incubated at 4° C. with end-over-end rotation for 30 minutes. Beads were subsequently collected on a magnetic rack, washed three times with high-salt polysome wash buffer (10 mM HEPES [pH 7.4], 350 mM KCl, 5 mM MgCl2, 1% NP-40, 0.5 mM dithiothreitol, 100 ⁇ g/ml cycloheximide) and immediately placed in TriZol-LS reagent (Invitrogen Corporation, Carlsbad, Calif.) and chloroform to extract the bound rRNA and mRNA from polysomes.
  • high-salt polysome wash buffer (10 mM HEPES [pH 7.4], 350 mM KCl, 5 mM MgCl2, 1% NP-40, 0.5 mM di
  • RNA samples After purification of RNA samples, 1.5 ul was used for quantification using a Nanodrop spectrophotometer (NanoDrop Technologies, Wilmington, Del.). Each sample was further analyzed with a Bioanalyzer (Agilent Technologies, Santa Clara, Calif.) to ensure that the quality of each RNA sample met standard criteria and that they were comparable to each other. Specifically, all RNA samples had a 260/280 ratio (Nanodrop) of at least 1.8, and a RNA Integrity Number (Bioanalyzer) of at least 7. Moreover, the quality of the samples was visually estimated using the Bioanalyzer readout to estimate the level of potential degradation or contamination for each sample.
  • RNA from each sample was amplified, biotinylated, and fragmented with the Affymetrix two-cycle amplification kit (Affymetrix, Santa Clara, Calif.). After amplification, samples were again quantified with a Nanodrop spectrophotometer, and 20 ug of amplified RNA was fragmented following the Affymetrix protocol. Amplified and fragmented samples were analyzed with a Bioanalyzer before hybridization to Affymetrix mouse 430 2.0 microarrays. All hybridizations were done according to standard Affymetrix protocols at the Rockefeller University Genome Array Center.
  • cDNA was used for the in vitro synthesis of cRNA using the MEGAscriptT7 Kit (Ambion, Austin, Tex.).
  • cRNA 600 ng or less of clean cRNA was used in the second-cycle cDNA synthesis reaction using the SuperScript GeneChip Expression 3′-Amplification Reagents Two-Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, Calif.) and random primers (Affymetrix, Santa Clara, Calif.).
  • the cDNA was purified using the GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, Calif.). Purified cDNA was used for the in vitro synthesis of biotin-labeled cRNA using the GeneChip IVT Labeling Kit (Affymetrix, Santa Clara, Calif.).
  • cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, Calif.) and fragmented into 35-200 base pair fragments using a magnesium acetate buffer (Affymetrix, Santa Clara, Calif.).
  • Affymetrix standard spike-in controls (eukaryotic hybridization kit) were used.
  • This procedure included staining the chips with phycoerythrin-streptavidin, signal amplification by a second staining with biotinylated anti-streptavidin, and a third staining with phycoerythrin-streptavidin.
  • Mouse Genome 430 2.0 arrays were scanned using the GeneChip Scanner 3000 (Affymetrix, Santa Clara, Calif.). Three biological replicates were performed for each experiment. GeneChip CEL files were subjected to Harshlight analysis to detect if any blemishes were present on the GeneChips (http://asterion.rockefeller.edu/Harshlight/index2.html) (M. Suarez-Farinas, M. Pellegrino, K. M. Wittkowski, M. O. Magnasco, BMC Bioinformatics 6, 294 (2005)). Only GeneChips without major blemishes were used.
  • GeneChip CEL files were imported into Genespring GX 7.3.1 (Agilent Technologies, Santa Clara, Calif.), processed with the GC-RMA algorithm, and expression values on each chip were normalized to that chip's 50 th percentile. Data were filtered to eliminate genes with intensities in the lower range. Only genes where more than one sample had a normalized intensity larger than 16 (4 in log 2 scale) were kept in the analysis. Statistical analysis to determine which genes are differentially expressed in the different conditions was carried out using the Limma package from Bioconductor project (http://www.bioconductor.org).
  • MIAME compliant raw data are available from the APNRR server and GEO. Replicate array samples were normalized with quantile normalization (GCRMA). Data were filtered to remove those probesets with low signal ( ⁇ 50) from analysis, as well as those probesets identified as monoclonal background (Table 7), and replicate samples were averaged.
  • GCRMA quantile normalization
  • IP was then compared to the unbound samples from the same tissue to calculate a ratio of IP/UB as a measure of ‘enrichment’.
  • UB samples generally show little or no depletion of cell-specific RNA following IP, and UB samples from several different IPs from the same tissue were averaged for each comparison.
  • UB samples from corpus striatum (Chat line) and neostriatum (Drd1 and Drd2 lines) were normalized together. IPs were globally normalized to UBs using the Affymetrix biotinylated spike in controls, to correct for any broad biases in scanning and hybridization.
  • Table 9 contains the IP/UB values for all genes with fold change>2 and p ⁇ 0.05 by Welch's t-Test, with Benjamini and Hochberg FDR multiple testing correction, as calculated by Genespring GX version 7.3 (Agilent).
  • the corrected enrichment is the intersection of the IP/UB analysis described above with a comparison of the Bergman Glial line with the mature oligodendrocyte line, Cmtm5, using the same fold change and statistical criteria applied above.
  • the corrected enrichment is the intersection of the IP/UB enrichment described above with a comparison of Grp with the Bergman glial line, using the same criteria.
  • the ‘corrected enrichment’ was calculated by comparing granule cell IP to the average of all other cerebellar cell type IPs, using the same criteria as above.
  • Hierarchical clustering was performed in Genespring using the ‘condition tree’ function with a smoothed correlation metric on the GCRMA normalized data for the 20% of probesets with the highest coefficient of variation.
  • IP immunoprecipitation
  • TRIP translating ribosome affinity purification
  • FIG. 17 presents these data and illustrates that BACarray data are highly reproducible and cell-type specific
  • FIG. 18 presents the accuracy of this methodology to enrich for cell-specific genes.
  • the BACarray data for known cell-specific markers (positive controls) for each cell type and the BACarray data for genes known to be expressed exclusively in other cell types (negative controls) were examined.
  • Panel A shows a scatter plot of IP vs. UB for spinal cord motor neurons. Probesets for known markers of motor neurons with measurable signal on the array are clearly enriched in the IP sample, whereas probesets for glial cell-specific RNAs, that should not be present in these cells, are enriched in the UB sample.
  • the enrichment in the IP or UB sample was quantified by calculating an average ratio of IP/UB for positive and negative controls for each cell type where at least three positive controls could be found in the literature.
  • Panel B all IPs showed a clear enrichment for appropriate known markers, (Panel B, plotted in log base 2). Even for cell types with only one known marker (Pnoc positive interneurons, and Grp expressing unipolar brush cells), probesets for these genes were consistently and highly enriched in the IP.
  • the IPs with the lowest relative yield of RNA, such as those for mature oligodendrocytes (Panel B), and Cort expressing interneurons background was proportionally higher, and enrichment was less robust.
  • Novel cell-specific markers for rare cell types using the BACarray approach were identified. Eleven genes predicted by BACarray to be enriched in either the Grm2 expressing interneurons of the granule cell layer (Golgi cells), or the Pnoc expressing cells of the cerebral cortex were screened. Using confocal microscopy, double immunofluorescence for both eGFP-L10a fusion protein and the ISH probes were evaluated. For the nine genes where ISH gave clear results, all were clearly overlapping with eGFP-L10a.
  • Panel C shows that in the case of cerebellar Golgi cells, there is a great deal of overlap between eGFP-L10a expression in the BACarray line and expression of the genes chosen for this analysis. This overlap confirms the specificity of the results obtained for this and other cell types. Nonetheless, the enrichment of a particular mRNA in the IP sample cannot be used to conclude that it is exclusively expressed in the cell type labeled in the BACarray transgenic line, or that it is expressed in all cells of that type.
  • the ISH databases www.stjudebgem.org; www.brain-map.org
  • Penk1 is expressed in scattered cells in both the granular and molecular layers of the adult cerebellum.
  • RNA was used to produce cDNA with a NuGEN WT Ovation kit (NuGEN Technologies, San Carlos, Calif.) and the resulting cDNA was purified and quantified. 10 ng of cDNA was used for each real-time gene expression assay. Applied Biosystems (Foster City, Calif.) TaqMan pre-designed gene expression assays were used, following the manufacturer's instructions and using an Applied Biosystems 7900 Sequence Detection System.
  • cDNA was synthesized from 20 ng of total RNA from the three replicate IP and UB samples using M-MulV reverse transcriptase (MO253L), from New England Biolabs (Ipswich, Mass.), using oligo dT23VN as a primer, then purified with the Qiagen Quick PCR cleanup, following manufacturer's instructions (Qiagen, Valencia, Calif.).
  • PCR was performed using Bio-Rad iQ syber green supermix following manufacturer's protocols (Biorad, Hercules, Calif.), with 500 nm final concentration of each primer. Cycling and quantitation were performed using Biorad iQ5 multiplex real-time detection hardware. PCR was carried out for 45 cycles (94°, 30 seconds, 63°, 30 seconds, 72°, 30 seconds), followed by a melt curve. Each replicate was assayed in triplicate. Conditions yielding dimers, as demonstrated by melt curve and/or gel electrophoresis were excluded from further analysis.
  • Astroglial BACarray data collected from different regions of the brain are, as expected, more similar to one another and to Bergmann glia than they are to oligodendrocytes. Oligodendroglia are more similar to each other than they are to any neuronal population, etc.
  • any single cell type has fewer probesets detectable than the whole cerebellar sample, since the whole cerebellar sample represents an aggregate of different cell types.
  • comparative analysis of the sum of the probesets detectable in each of the six individual cerebellar cell types and the results obtained from whole cerebellar tissue reveals over 4000 probesets that are undetectable in the microarray from whole cerebellum. These undetectable probesets tend to represent cell-type enriched genes.
  • the translating ribosome affinity purification (TRAP) methodology can be more sensitive than microarray analysis of dissected brain regions.
  • the increased sensitivity of the translating ribosome affinity purification (TRAP) methodology results in identification of more mRNAs in each cell type, yielding a more complete picture of the translational profile for each cell type, more information.
  • the Shannon entropy was calculated for each probeset across the six whole tissue samples, and across the twenty four individual cell populations (Fuhrman et al., 2000; Shannon and Weaver, 1969). Shannon entropy is a measure of information content that describes the complexity of a signal across samples, with values ranging from 0 (low information) to 2 (high information). Data are presented in FIG. 20 . Examples of probeset with low and high information are shown in Panel B.
  • Genes with less information content tend to be those that that are more ubiquitously expressed, such as ribosomal and mitochondrial proteins. This is not to say that they do not vary—their expression can range often from two to five fold across cell types—but they vary less dramatically than the tens to thousands fold changes of many receptors and channels.
  • Table 9 is a comparative analysis of translational profiling to identify co-regulated genes that could encode the highly specialized properties of individual cell types. This analysis is can be useful in trying to identify gene sets for known functions or candidate functions for novel gene products, since in many cases these cohorts of co-regulated genes will include genes with well known functions.
  • a probeset for a gene known to be involved in myelination was selected—the myelin basic protein (Mbp). Its highest correlates were examined across all IP and UB samples.
  • FIG. 21 shows a comparative analysis of the individual cell samples to identify only those genes most highly specific for each population.
  • An iterative comparison was performed: one-by-one, each sample was compared to each other sample in the dataset, and for each population, probesets were sorted by their average ranking across these comparisons. Data were then combined and clustered by expression the top one hundred ranked probesets for each population in a heatmap (Panel A).
  • This heat map readily illustrates the extent to which distinct cell types are characterized by specific cohorts of genes. For example, cerebellar Purkinje cells are clearly distinguished by a group of genes that are not seen in any other cell types (Panel A).
  • the top twenty five most specific probesets in each cell type include probesets for both well known cell-specific markers and novel, previously uncharacterized genes.
  • Pcp2 the calcium binding protein Calb1, the scaffolding/synaptic protein Homer3, and the transcription factor Ebf2, all of which are known to be specifically expressed in Purkinje cells (Malgaretti et al., 1997; Shiraishi et al., 2004; Wang et al., 1997), are among the most highly ranked probesets in the Pcp2 BACarray list.
  • Mobp one of the most abundant components of the CNS myelin sheath (Montague et al., 2006), is prominent in the Cmtm5 myelinating oligodendrocytes' list.
  • the large number of uncharacterized genes with cell specific translation identified here provide an important resource for discovery of novel biochemical pathways operating in these cell types, or for the identification of new proteins operating in well known pathways. Finally, comparative analysis can reveal discrepancies that are not apparent from anatomical studies.
  • the most specific probesets for the Etv1 line identify several genes well-known to be expressed in lymphoid cells, suggesting that in this line the eGFP-L10a transgene may also be expressed in circulating cells in the CNS vasculature.
  • the data shown above demonstrate two important strengths of large-scale comparative analyses of BACarray data. First, molecular relationships between cell types can be easily established with hierarchical clustering; second, groups of genes that encode the biochemical functions of specific cell types can be identified using this sort of systematic comparative approach.
  • MN spinal cord motor neurons
  • MNs also express a variety of newly characterized receptors and orphan receptors.
  • BACarray data has successfully identified Grin3b as a MN specific gene encoding an NMDA subunit. This receptor was recently characterized as creating a unique glycine gated channel in MNs (Chatterton et al., 2002; Nishi et al., 2001).
  • Several other genes enriched in MNs have also been identified which potentially encode for MN specific receptors that either have not been previously characterized in MNs or are entirely unstudied. Two that are particularly interesting are the vitamin D receptor and the orphan receptor P2rxl1.
  • the cholinergic cell BACarray line was produced by placement of the eGFP-L10a transgene under the control of the choline acetyltransferase (Chat) locus, which is specifically expressed in cholinergic cells in the CNS.
  • the Chat BACarray line DW167 showed highest eGFP-L10a expression in cholinergic cells of the dorsal striatum and ventral striatum (nucleus accumbens, olfactory tubercle, and islands of Calleja), basal forebrain, brain stem, spinal cord, and medial habenula (Panel a).
  • eGFP expression was shown to be restricted to cholinergic cells in all of these structures, including motor neurons of the brain stem (Panel b), by indirect immunofluorescence staining for Chat.
  • One exception to this colocalization was in the pedunculopontine and laterodorsal tegmental nuclei, where only a minority of cholinergic cells were labeled with eGFP.
  • the Purkinje cell BACarray line DR166 was produced by placement of the eGFP-L10a transgene under the control of the Purkinje cell protein 2 (Pcp2) locus, which is specifically expressed in cerebellar Purkinje cells of the CNS (Oberdick et al., 1988).
  • the Pcp2 BACarray line showed eGFP-L10a expression that was restricted to cells that possessed a characteristic Purkinje cell morphology (Panel c).
  • FIG. 24 shows that enrichment of cell-specific positive-control genes and exclusion of known negative-control genes (glial genes), were evident for each comparison (panels a-d).
  • This example presents a study of the specific properties of the striatum.
  • This example illustrates one embodiment that can uncover unexpected molecular and physiological complexity in closely related and spatially adjacent CNS cell populations.
  • the striatum is a subcortical part of the telencephalon. It is the major input station of the basal ganglia system.
  • transgenic mice containing molecularly tagged ribosomal proteins in the striatonigral and striatopallidal cells of the striatum were created using standard BACarray techniques.
  • Striatonigral and striatopallidal medium spiny neurons are intermixed, indistinguishable in somato-dendritic morphology, and of major interest due to their role in the etiology of various neurological diseases, including Parkinson's disease, schizophrenia, attention deficit hyperactivity disorder, drug addiction, and Huntington's disease. Striatonigral MSNs send projection axons directly to the output nuclei of the basal ganglia, i.e.
  • Striatonigral MSNs are known to preferentially express the dopamine D1 receptor (Drd1; Drd1a) and the neuropeptides substance P (Tac1) and dynorphin (Pdyn), while striatopallidal MSNs preferentially express the dopamine D2 receptor (Drd2), the adenosine A2a receptor (Adora2a) and the neuropeptide enkephalin (Penk) (S. Gong et al., Nature 425, 917-25 (2003)).
  • mice containing molecularly tagged ribosomal proteins in the striatonigral and striatopallidal cells of the striatum were created. Homologous recombination in bacteria was used to place eGFP-L10a under the control of either the D2 receptor (striatopallidal) or D1 receptor (striatonigral) loci in the appropriate BACs. Mouse lines were generated by pronuclear injection of engineered BACarray DNA constructs into fertilized oocytes.
  • the D2 BACarray line showed highest transgenic eGFP-L10a expression in the dorsal and ventral striatum, olfactory tubercle, and hippocampus. In addition, expression of eGFP was seen in the substantia nigra pars compacta and ventral tegmental area of this line, as expected due to D2 autoreceptor expression in dopaminergic cells (panel a).
  • the D1 BACarray line showed highest transgenic eGFP-L10a expression in the dorsal and ventral striatum, olfactory bulb, olfactory tubercle, and cortical layers 5 and 6 (panel c).
  • eGFP fluorescence revealed localization of transgenic eGFP-L10a to the nucleoli and cytoplasm (panel b).
  • eGFP co-localization with enkephalin expression was observed in striatal cells from the D2 BACarray line but not the D1 BACarray line (panels b and d), verifying correct BAC-mediated cell-type expression.
  • the polysome profile from D2 BACarray mouse striatal extract is presented in FIG. 26 as follows: Top: Post-mitochondrial striatal extract (S20) was loaded onto a linear sucrose gradient (20-50% w/w). After velocity sedimentation, fractions (direction of sedimentation noted by arrow) were collected as UV absorbance (254 nm) was measured. Bottom: gradient fractions were ethanol precipitated, resuspended in SDS-PAGE loading buffer, and Rpl7 and eGFP-L10a content were assayed by Western blotting. Velocity sedimentation analysis of polysome complexes isolated from striatal extracts for both lines of BACarray mice confirmed incorporation of the eGFP-L10a fusion protein into functional polysomes in vivo.
  • a plurality of differentially expressed genes can be identified which characterize striatonigral and striatopallidal MSNs, including all previously known markers.
  • Translation profiling and molecular Phenotyping was performed with immunoaffinity-purified mRNA from adult striatonigral or striatopallidal BACarray mice. Following two rounds of in vitro transcription, biotin-labeled antisense RNA (cRNA) was used to interrogate Affymetrix GeneChip Mouse Genome 430 2.0 arrays. For each cell type, data were collected from three independent biological replicates, each prepared from a cohort of 7 animals. Analysis of immunoaffinity-purified samples revealed no bias for mRNA length or abundance ( FIG. 27 ).
  • RefSeq lengths were plotted against D1 (a) or D2 (b) BACarray IP normalized expression values. There was no correlation observed between transcript length and IP values. Striatal expression values for all Affymetrix Genechip probe sets were obtained by total RNA arrays from wild-type striatal tissue (data not shown). These values were plotted against (c) D1 BACarray or (d) D2 BACarray IP normalized values. As expected, higher expression in total striatum (no IP, wild type mice) correlates with higher D1 or D2 BACarray IP values. The few genes that showed modest expression in total striatum but had low IP values include known non-neuronal genes.
  • qPCR assays used were Gapdh: Mm99999915_g1, Drd2: Mm00438541_m1, Gpr6: Mm01701705_s1, Lhx8: Mm00802919_m1, Gpr88: Mm02620353_s1, Trpc4: Mm00444284_m1, Tpm2: Mm00437172_g1, Eya1: Mm00438796_m1, Tac1: Mm00436880_m1, Isl1: Mm00627860_m1, Gng2: Mm00726459_s1, Chrm4: Mm00432514_s1, Drd1a: Mm02620146_s1, Crym: Mm01281258_m1, Actb: Hs99999903_m1, and Fth1: Hs01694011_s1.
  • Each assay was performed in quadruplicate and fold enrichment values were derived from the comparative Ct method (following Applied Bio
  • Adcy5 C. E. Glatt, S. H. Snyder, Nature 361, 536-8 (Feb. 11, 1993)
  • Gng7 J. B. Watson et al., J Neurosci Res 39, 108-16 (Sep. 1, 1994)
  • Rasgrp2 H. Kawasaki et al., Proc Natl Acad Sci USA 95, 13278-83 (Oct. 27, 1998)
  • Pde1b J. W. Polli, R. L. Kincaid, Proc Natl Acad Sci USA 89, 11079-83 (Nov. 15, 1992),
  • Pde10a K. Fujishige, J. Kotera, K.
  • BGEM Brain Gene Expression Map
  • striatonigral- and striatopallidal-enriched genes were searched.
  • GO terms delineate the known molecular function, biological process, as well as the cellular localization (component) for a particular gene (R. Bernardi, P. P. Pandolfi, Nat Rev Mol Cell Biol 8, 1006 (2007), while KEGG pathways summarize known molecular interaction and reaction networks.
  • the most enriched striatonigral KEGG pathways included neuroactive ligand-receptor interaction, long-term depression, and MAPK signaling pathway.
  • the most striatopallidal enriched KEGG pathways included pyrimidine metabolism, purine metabolism, and neuroactive ligand-receptor interaction. Comparison of striatonigral and striatopallidal cell data versus whole brain revealed many striatal-enriched KEGG pathways, including MAPK signaling pathway, long-term potentiation, and insulin signaling pathway.
  • Striatonigral enriched GO molecular function terms included GTPase activity, calcium ion binding, and retinal binding; striatopallidal enriched GO molecular function terms included adrenoceptor activity, calcium channel activity, and rhodopsin-like receptor activity; striatal-enriched GO terms included zinc ion binding, protein serine/threonine kinase activity, and ubiquitin-protein ligase activity.
  • Gpr6 an mRNA selectively enriched in striatopallidal neurons is Gpr6 (S. Gong et al., Nature 425, 917-25 (Oct. 30, 2003).). Gpr6 encodes a G protein-coupled receptor for the lysophospholipid sphingosine 1-phosphate (S1P) (A. Ignatov, J. Lintzel, H. J. Kreienkamp, H. C. Schaller, Biochem Biophys Res Commun 311, 329-36 (Nov. 14, 2003)).
  • S1P lysophospholipid sphingosine 1-phosphate
  • Gpr6 receptors In heterologous expression systems, S1P activation of Gpr6 receptors induces the release of Ca2+ from intracellular stores. As intracellular Ca2+ is a crucial regulator of neuronal physiology, whether selective enrichment of Gpr6 in striatopallidal neurons correlated with a differential response to S1P was investigated. To determine whether functional Gpr6 receptors were selectively expressed in striatopallidal neurons, BAC D2 striatopallidal or BAC D1 striatonigral medium spiny neurons (expressing soluble eGFP) were identified in brain slices and patch clamped ( FIG. 30 ) (M. Day et al., Nat Neurosci 9, 251-9 (February, 2006)).
  • Neurons were loaded with Alexa 594 (50 ⁇ M) to allow dendrites to be seen and with Fluo-4 (200 ⁇ M) to monitor intracellular Ca2+ concentration using 2-photon laser scanning microscopy (2PLSM). After allowing the dyes to equilibrate, neurons were imaged and a second pipette containing S1P (10 ⁇ M) was brought into close physical proximity to a dendrite, 60-80 microns from the soma (a and b).
  • Alexa 594 50 ⁇ M
  • Fluo-4 200 ⁇ M
  • 2PLSM 2-photon laser scanning microscopy
  • the Gpr6-dependent elevation of cytosolic Ca2+ seen in striatopallidal cells would be predicted to result in a decrease in threonine 34 phosphorylation of the centrally important regulatory protein DARPP-32, due to activation of the Ca2+ and calmodulin-dependent phosphatase calcineurin (A. Nishi, G. L. Snyder, A. C. Nairn, P. Greengard, J Neurochem 72, 2015-21 (May, 1999)) and/or inhibition of adenylyl cyclase type 5 (AC5; Adcy5) (C. E. Glatt, S. H. Snyder, Nature 361, 536-8 (Feb. 11, 1993); Y.
  • responses to genetic, pharmacologic or environmental changes can be analyzed effectively in single cell types using translational profiling and molecular Phenotyping methods described herein.
  • translational profiling and molecular Phenotyping methods described herein To define uncover novel physiological properties of striatal neurons, possible changes in mRNA expression of MSNs upon pharmacological perturbation of dopaminergic signaling was investigated.
  • Cocaine acts as a psychostimulant by elevating synaptic dopamine levels (M. C. Ritz, R. J. Lamb, S. R. Goldberg, M. J. Kuhar, Science 237, 1219-23 (Sep. 4, 1987); G. Di Chiara, A. Imperato, Proc Natl Acad Sci USA 85, 5274-8 (July, 1988)).
  • Adult mice were treated acutely or chronically with cocaine or saline and used for BACarray profiling of striatonigral (D1) and striatopallidal (D2) MSNs.
  • mice Manipulation of biological sample: all mice were raised under 12 h dark/12 h light conditions, housed 5 mice per cage, with food and water ad libitum. All mice used in the study were heterozygous for the eGFP-L10a transgene; mice from each line had been crossed to wild-type Swiss-Webster (Taconic Farms) four times. Four heterozygous adult BACarray females and three heterozygous adult BACarray males were used for each study. Mice used for the baseline comparison of D1 versus D2 cells were used directly from the home cage.
  • mice 7-9 weeks of age were singly housed and intraperitoneally injected at the Rockefeller University Laboratory Animal Research Center (LARC) and were moved to the laboratory approximately 16 h before the final injection.
  • LOC Rockefeller University Laboratory Animal Research Center
  • mice were injected with 100 ⁇ l saline (vehicle) once daily for eight days to habituate the mice to handling.
  • mice were injected with a test dose of 20 mg/kg cocaine or 100 ⁇ l saline and the striata were harvested 4 h after this test injection.
  • mice were injected with 20 mg/kg cocaine or 100 ⁇ l saline once daily for fifteen days and the striata were harvested 4 h after the last injection.
  • GeneChip CEL files were imported into Genespring GX 7.3.1, normalized with the GC-RMA algorithm (BACarray samples and whole brain minus striatum samples separately), and expression values on each chip were further normalized to the expression values of several positive control genes and to a constant value of 0.01.
  • a moderated two-tailed paired t-test was then performed. The p-value of the moderated t-test was adjusted for multiple hypothesis testing, controlling the false discovery rate (FDR) using the Benjamini-Hochberg procedure. Genes that had an FDR less than 0.05 (5%) and fold change larger than 2 were selected.
  • Vamp2 C. A. McClung, E. J. Nestler, Nat Neurosci 6, 1208-15 (November, 2003)
  • Kcnd2 C. A. McClung, E. J. Nestler, Nat Neurosci 6, 1208-15 (November, 2003)
  • Zfp64 C. A. McClung, E. J. Nestler, Nat Neurosci 6, 1208-15 (November, 2003)
  • GABA gamma-aminobutyric acid
  • mice were chronically treated with cocaine or vehicle (saline) and then GABA A receptor function was assayed electrophysiologically.
  • the ACSF contained the following (in mM): 126 NaCl, 3 KCl, 2 CaCl2, 1 MgCl2, 25 NaHCO3, 1.25 NaH2PO4, and 15.6 D-(+)-glucose. Unless otherwise noted, all chemicals and reagents were obtained from Sigma (St. Louis, Mo.). The slices were transferred to a holding chamber in which they were completely submerged in ACSF at 35° C. for 1 h, after which they were stored at room temperature (22° C.-23° C.) until whole-cell recording. All ACSF solutions were bubbled continuously with 95% O2 and 5% CO2 to maintain oxygenation and a pH ⁇ 7.4, and periodically checked to ensure ⁇ 300 mOsm/l.
  • Whole-cell voltage-clamp recordings were performed using standard techniques. Individual slices were transferred to a submersion-style recording chamber on Olympus Optical (Melville, N.Y.) BX50WI microscope and continuously superfused with ACSF at a rate of 2-3 ml/min at 22° C.-23° C. Whole-cell voltage-clamp recordings were performed on striatal medium spiny neurons detected in the slice with the help of an infrared-differential interference contrast (IR-DIC) video microscope with an Olympus OLY-150 camera/controller system (Olympus, Japan).
  • IR-DIC infrared-differential interference contrast
  • mIPSCs 50 ⁇ M 2-amino-5-phosphonopentanoic acid (AP-5, Tocris Cookson, Ellisville, Mo.) to block NMDA glutamate receptors, 5 ⁇ M 1,2,3,4-Tetrahydro-6-nitro2,3-dioxo-benzo 2 quinoxaline-7-sulfonamide (NBQX) to block AMPA/kainite glutamate receptors, and 1 ⁇ M tetrodotoxin (TTX, Alomone Labs, Jerusalem, Israel) to block sodium channels.
  • AP-5 2-amino-5-phosphonopentanoic acid
  • NBQX 1,2,3,4-Tetrahydro-6-nitro2,3-dioxo-benzo 2 quinoxaline-7-sulfonamide
  • TTX tetrodotoxin
  • Patch electrodes were made by pulling Sutter BF150-86-10 glass on a P-97 Flaming/Brown micropipette puller (Sutter Instrument, Novato, Calif.) and fire polished before recording. Pipette resistance was typically 2.5-4 MS2 after filling with an internal solution containing the following (in mM): 140 CsCl, 1.5 MgCl2, 10 HEPES, 0.1 BAPTA-Cs, 5 QX-314, 2 ATP-Na2, 0.4 GTP-Na2, pH 7.25-7.3 adjusted with CsOH, 270-280 mOsm/L.
  • Miniature IPSCs were recorded with a Multiclamp 700 A amplifier, a Digidata 1322A 16-bit data acquisition system, and pClamp software version 8.2 (Molecular Devices, Union City, Calif.) in gap free mode. Neurons were voltage-clamped at ⁇ 80 mV and allowed to reach a stable baseline ( ⁇ 5 min) before mIPSCs were recorded for 7 min. Mini Analysis (Synaptosoft Inc., Fort Lee, N.J.) was used to analyze mIPSC amplitude, frequency, 10-90% rise time, decay time, and non-stationary noise analysis. A threshold of 5 times the root mean square baseline noise level (commonly ⁇ 20-25 pA) was set for event detection.
  • BAC D1 Striatonigral
  • BAC D2 striatopallidal
  • eGFP 2PLSM green signals 500-550 nm were acquired from eGFP+ BAC Drd2 neurons using 810 nm excitation, while eGFP+ BAC Drd1 neurons required 900 nm excitation.
  • eGFP+ MSNs were then patched using infrared-differential interference contrast (IR-DIC) video microscopy with a Hamamatsu C2400 Newvicon camera/controller system (Hamamatsu, Japan) and a 60 ⁇ /0.9NA water-dipping lens. Patch electrodes were made by pulling BF150-86-10 glass on a P-97 Flaming/Brown micropipette puller (both from Sutter Instrument Co., Novato, Calif.).
  • IR-DIC infrared-differential interference contrast
  • the pipette resistance was ⁇ 4 M ⁇ . Seals were formed in voltage-clamp mode on the cell somas with series resistance >1 G ⁇ . After seal rupture in whole-cell configuration the series-resistance decreased to 10-15 M ⁇ .
  • Alexa 594 50 ⁇ M, Ca 2+ -insensitive red dye
  • Fluo-4 200 ⁇ M, Ca 2+ -sensitive green dye
  • eGFP fluorescence was below the threshold for detection in the dendrites and did not contribute background signal during calcium imaging
  • Thapsigargin was also added to the internal solution in some experiments to block ER-mediated Ca 2+ release.
  • the thapsigargin was initially dissolved in DMSO at a concentration of 10 mM. This stock was then diluted 1000 ⁇ in the internal recording solution. Following break in, the internal solution was allowed to approach diffusional equilibrium for at least 15 min prior to imaging. The cells were voltage clamped at ⁇ 70 mV and monitored for somatic depolarization.
  • 2PLSM green and red signals were acquired using 810 nm excitation with 90 MHz pulse repetition frequency and ⁇ 250 fs pulse duration at the sample plane.
  • a second puffer pipette containing sphingosine 1-phosphate (SIP, 10 ⁇ M) was positioned for focal dendritic application.
  • SIP sphingosine 1-phosphate
  • the two-photon excitation source was a Chameleon-XR tunable laser system (705 nm to 980 nm, Coherent Laser Group, Santa Clara, Calif.). Laser average power attenuation was achieved with two Pockels cell electro-optic modulators (models 350-80 and 350-50, Con Optics, Danbury, Conn.). The two cells are aligned in series to provide enhanced modulation range for fine control of the excitation dose (0.1% steps over four decades).
  • the laser-scanned images were acquired with a Bio-Rad Radiance MPD system (Hemel Hempstead, England, UK). The fluorescence emission was collected by external or non-de-scanned photomultiplier tubes (PMTs).
  • the green fluorescence (500 to 550 nm) was detected by a bialkali-cathode PMT and the red fluorescence (570 nm to 620 nm) was collected by a multi-alkali-cathode (S20) PMT.
  • the fluorescence was acquired in 16 bit photon counting mode.
  • the laser light transmitted through the sample was collected by the condenser lens and sent to another PMT to provide a bright-field transmission image in registration with the fluorescent images.
  • the stimulation, display, and analysis software was a custom-written shareware package, WinFluor and PicViewer (John Dempster, Strathclyde University, Glasgow, Scotland; UK).
  • Cocaine treatment increased the frequency of GABA A receptor miniature inhibitory postsynaptic currents (mIPSCs) in striatonigral neurons as presented in the following figures.
  • mIPSCs GABA A receptor miniature inhibitory postsynaptic currents
  • FIG. 31 showed that cocaine treatment increased the frequency of small amplitude GABAergic mIPSCs in BAC D1 striatonigral neurons.
  • FIG. 32 showed that cocaine treatment decreased the number of GABAA channels per synapse in BAC D1 striatonigral neurons.
  • FIG. 33 showed that cocaine treatment did not alter GABAergic mIPSCs kinetics or GABAA receptor number per synapse or unitary receptor conductance in BAC D2 striatopallidal neurons. Box plot summaries showing mean mIPSCs kinetics and non-stationary noise analysis measures of individual striatopallidal neurons taken from saline-treated control and 15-day treated cocaine BAC D2.
  • the cerebellum is a region of the brain that plays a role in the integration of sensory perception and motor control.
  • the cerebellum integrates these pathways using constant feedback on body position to fine-tune motor movements (Fine E J, Ionita C C, Lohr L (2002). “The history of the development of the cerebellar examination”.
  • cerebellum also serves other functions, such as cognitive functions, including attention and the processing of language, music, and other sensory temporal stimuli (Rapp, Brenda (2001). The Handbook of Cognitive Neuropsychology: What Deficits Reveal about the Human Mind. Psychology Press, 481).
  • Ataxia is a complex of symptoms, generally involving a lack of coordination, that is often found in disease processes affecting the cerebellum.
  • the neurological examination includes assessment of gait (a broad-based gait being indicative of ataxia), finger-pointing tests and assessment of posture.
  • Structural abnormalities of the cerebellum may be identified on cross-sectional imaging.
  • Magnetic resonance imaging is the modality of choice, as computed tomography is insufficiently sensitive for detecting structural abnormalities of the cerebellum (Gilman S (1998). “Imaging the brain. Second of two parts”. N. Engl. J. Med. 338 (13): 889-96).
  • the innermost granular layer contains the cell bodies three types of cells: the numerous and tiny granule cells, the larger Golgi cells and the medium sized neuronal unipolar brush cells.
  • the middle Purkinje layer contains only one type neuron, the Purkinje cell.
  • Purkinje cells are the primary integrative neurons of the cerebellar cortex and provide its sole output.
  • Bergmann glia a type of glia also known as radial epithelial cells are astrocytes in the cerebellum that have their cell bodies in the Purkinje cell layer and processes that extend into the molecular layer, terminating with bulbous endfeet at the pial surface (Eccles J.
  • the outermost layer of the cerebellar cortex contains two types of inhibitory interneurons: the stellate and basket cells. It also contains the dendritic arbors of Purkinje neurons and parallel fiber tracts from the granule cells.
  • BACarray mice with specific expression patterns in specific cerebellar cell types can be created: expression of tagged ribosomal protein under the control of a regulatory region from the Neurod1 loci to label cerebellar granule cells; expression of tagged ribosomal protein under the control of a regulatory region from the Grm2 loci to label cerebellar inner golgi neurons; expression of tagged ribosomal protein under the control of a regulatory region from the Grp loci to label unipolar brush cells; expression of tagged ribosomal protein under the control of a regulatory region from the Pttg3 loci to label cerebellar astrocytes; and expression of tagged ribosomal protein under the control of a regulatory region from the Lypd6 loci to label stellate, basked cells.
  • Ataxia telangiectasia is a disease whose principle features includes ataxia, development of lymphocytic tumors and cerebellar degeneration (P. J. McKinnon, EMBO Rep 5, 772 (2004); F. Gumy-Pause, P. Wacker, A. P. Sappino, Leukemia 18, 238 (2004); L. Farina et al., J Comput Assist Tomogr 18, 724 (1994); F. Tavani et al., Neuroradiology 45, 315 (2003)).
  • AT is caused by recessive loss of function mutations in the gene encoding ataxia telangiectasia mutated (ATM), a ubiquitously expressed nuclear protein kinase involved in the DNA damage response and cell cycle control (K. Savitsky et al., Science 268, 1749 (1995); R. T. Abraham, Genes Dev 15, 2177 (2001); Y. Shiloh, Nat Rev Cancer 3, 155 (2003); M. F. Lavin, S. Kozlov, Cell Cycle 6, 931 (2007); S. Matsuoka et al., Science 316, 1160 (2007)).
  • Atm knockout mice display many of the characteristics of the human disorder, including sensitivity to irradiation and lymphocytic tumor formation (C.
  • ribosomes in specific cerebellar cell types in a mouse model of AT can be molecularly labeled (Doyle et al., submitted).
  • Atm ⁇ / ⁇ mice Molecular phenotyping and translational profiling of Purkinje cells in Atm knockout mice, hereafter Atm ⁇ / ⁇ mice, could reveal changes in response to the mutation. This enables the identification of genes that are differentially regulated in a cell-type specific manner, by employing the BACarray strategy and TRAP methods. Changes in response to the Atm mutation were analyzed in Purkinje cells and Bergmann glia, a specialized glial cell population with similar abundance and anatomical distribution as Purkinje cells.
  • Transgenic BACarray mice expressing the eGFP-L10a fusion protein were prepared using the Purkinje cell protein 2 (Pcp2) and Septin 4 (Sept4) BAC vectors described by the GENSAT project (www.gensat.org; S. Gong et al., Nature 425, 917 (2003)) ( FIG. 34 ).
  • BAC transgenic animals were generated using modified BAC constructs as previously described (J. Zahringer, B. S. Baliga, H. N.
  • FIG. 35 Panel A demonstrated the expression of the eGFP-L10a fusion specifically in the soma and primary dendrites of cerebellar Purkinje cells in the Pcp2 line, and panel B demonstrated its expression in Bergmann glia in the Sept4 line.
  • Microarray data were imported into Genespring GX 7.3.1 (Agilent Technologies, Santa Clara, Calif.) as GeneChip CEL files. For each experiment, Atm+/+ and Atm ⁇ / ⁇ data sets were imported together and normalized using GC RMA. For total cerebellum experiments, four replicates for each condition (Atm+/+ or Atm ⁇ / ⁇ ) were used, for the Septin4 experiments, five replicates for each condition were used, and for the Pcp2 experiments, six replicates were used for each condition. Once imported, experiments were viewed as scatter plots for further analysis.
  • Atm+/+ and Atm ⁇ / ⁇ data were further normalized per chip using the Affymetrix hybridization controls as positive control genes and divided by the constant value of 0.001.
  • data were filtered on expression with a cutoff of 25 and filtered on fold change with a cutoff of 1.5.
  • One-way ANOVA analysis was used to determine statistical significance with a p value of ⁇ 0.05.
  • Pcp2 and Sept4 BACarray transgenic animals were then crossed with Atm+/ ⁇ animals. After two generations, the Pcp2 and Sept4 BACarray constructs could be recovered in Atm+/+ or Atm ⁇ / ⁇ animals.
  • microarray data were collected from total cerebellum, from Purkinje cells and from Bergmann glial cells using 6-8 week old Pcp2 and Sept4 wt and Atm ⁇ / ⁇ BACarray mice. Lists of genes regulated in Atm ⁇ / ⁇ animals were generated by identifying all genes with expression values greater than 25 and at least a 1.5 fold difference in expression between wt and Atm ⁇ / ⁇ animals.
  • Gene Ontology (GO) analysis was performed using both DAVID (G. Dennis, Jr. et al., Genome Biol 4, P3 (2003)) and Genespring, each program essentially giving the same results. It was also essential to compare the gene lists and pertinent literature in order to completely analyze data as the GO database is incomplete.
  • Genes enriched in total cerebellum of Atm ⁇ / ⁇ animals include those involved in cell cycle control (Tacc1, Cdkn1a (p21)) and apoptosis (Cdkn1a (p21)).
  • Bergmann glial cells from Atm ⁇ / ⁇ animals are enriched in genes related to development and cellular differentiation, including BMP5.
  • Purkinje cells from Atm ⁇ / ⁇ animals are enriched in genes involved in chromatin organization, nucleotide metabolism, and transcription regulation. These include transcription factors such as Texl2, Zfpl91, Rora, Mtf2, and Mjd and genes involved in mRNA metabolism such as Ccrn41 and Ddx6. Several of these differentially regulated genes are either directly or indirectly associated with ataxia.
  • Rora is an orphan retinoic acid receptor which is mutated in the staggerer mouse mutant (B. A. Hamilton et al., Nature 379, 736 (1996)).
  • Mjd (Atxn3, Sca3) is the gene responsible for Machado-Joseph disease (Y.
  • Ddx6 is known to associate with Ataxin-2 in P-bodies, multiprotein complexes involved in mRNA degradation (U. Nonhoff et al., Mol Biol Cell 18, 1385 (2007); N. Cougot, S. Babajko, B. Seraphin, J Cell Biol 165, 31 (2004)).
  • Ccrn41 is a deadenylase which is also found in P-bodies (N. Cougot, S. Babajko, B. Seraphin, J Cell Biol 165, 31 (2004)); deadenylation is a critical first step in the degradation of mRNA by P-bodies. Over-expression of these genes could potentially either enhance neurodegeneration of Purkinje cells, or protect against it.
  • Dopamine producing (dopaminergic) neurons are present primarily in the ventral tegmental area (VTA) of the midbrain, substantia nigra pars compacta (SNc), and the arcuate nucleus of the hypothalamus.
  • Dopaminergic neurons of the SNc are particularly susceptible to neurodegeneration in Parkinson's disease (PD) and in pharmacologically-induced models of PD.
  • PD Parkinson's disease
  • the selective degeneration of the dopaminergic neurons in the substantia nigra pars compacta leads to PD but the exact cause for this nigral cell loss is still unknown.
  • the ventral tegmental area dopaminergic neurons are relatively spared in comparison.
  • a ribosomal protein e.g. L10a
  • a detectable tag whose expression is regulated by SNc and VIA-specific gene regulatory regions
  • mice with molecularly tagged ribosomal proteins are produced. These are driven by regulatory sequences for cell-type specific expression in either the SNc or VTA ( FIG. 38 ). It is expected that differentially expressed mRNAs in SNc cells will be identified as potential therapeutic targets for the amelioration of PD.
  • Dopaminergic cell loss mimicking what is seen in PD is induced with intracerebral injections of the neurotoxins 6-hydroxydopamine (6-OHDA) or 1-methyl 4-phenyl 1,2,3,6-tetrahydropyridine (MPTP) either bilaterally or unilaterally in rodents (either mice or rats).
  • 6-OHDA 6-hydroxydopamine
  • MPTP 1-methyl 4-phenyl 1,2,3,6-tetrahydropyridine
  • High-frequency stimulation of the subthalamic nucleus is one neurosurgical procedure currently available for the alleviation of motor symptoms of PD and the debilitating medication-induced dyskinesias that often accompany the disease. Stimulation of the STN is achieved by implanting deep brain stimulation (DBS) electrodes precisely in the nucleus. The striatopallidal cells of the striatum tonically inhibit the Globus Pallidus External segment (GPe) and the Sub-thalamic nucleus (STN) ( FIG. 41 ).
  • DBS deep brain stimulation
  • Gpr6 represents a target for which antagonists can be screened for and developed as a therapeutic for PD.
  • any mRNA found to be downregulated in striatopallidal cells represents a target for agonism as a therapeutic for PD.
  • hypothalamus plays a central role in several regulatory and homeostatic processes including blood pressure, body temperature, sleep, fluid and electrolyte balance, and body weight.
  • the lateral hypothalamus in particular is implicated as a feeding and satiety center. Food intake is regulated by hypothalamic neuropeptides which respond to peripheral signals. Homeostasis disrupted can lead to feeding and metabolic disorders leading to such diseases as obesity.
  • Orexin also named Hypocretin, is a excitatory neuropeptide hormone released by the lateral hypothalamus. Orexin release modulates feeding behavior, wakefulness, and energy expenditure.
  • a hypothalamic Hcrt (orexin) BACarray line has expression in the lateral hypothalamus.
  • mice with molecularly tagged ribosomal proteins are produced. These are driven by regulatory sequences for lateral hypothalamic cell-type specific expression under the control of regulatory sequences from the Hcrt (orexin) locus. By obtaining translational profiles from these animals, it is expected that targets relevant to obesity will be identified, in particular for feeding regulation.

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US10338082B2 (en) * 2014-02-14 2019-07-02 Institut Pasteur Methods for in vitro investigating mitochondrial replication dysfunction in a biological sample, kits and uses thereof, therapeutic methods against progeroid-like syndromes or symptomes and screening method for identifying particular protease inhibitor(s) and/or nitroso-redox stress scavenger compound(s)
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US10267796B2 (en) * 2010-10-25 2019-04-23 The Procter & Gamble Company Screening methods of modulating adrenergic receptor gene expressions implicated in melanogenesis
US20120197016A1 (en) * 2010-10-25 2012-08-02 The Procter & Gamble Company Screening methods of modulating adrenergic receptor gene expressions implicated in melanogenesis
WO2012145459A3 (en) * 2011-04-22 2014-05-01 International Park Of Creativity Glucose and insulin sensors and methods of use thereof
US10501815B2 (en) 2011-04-22 2019-12-10 International Park Of Creativity Glucose sensors and methods of use thereof
US9683266B2 (en) 2011-04-22 2017-06-20 International Park Of Creativity Glucose and insulin sensors and methods of use thereof
US9932644B2 (en) 2011-04-22 2018-04-03 International Park Of Creativity Glucose sensors and methods of use thereof
US9701727B2 (en) 2011-06-29 2017-07-11 The Trustees Of Columbia University In The City Of New York Inhibitor of neuronal connectivity linked to schizophrenia susceptibility and cognitive dysfunction
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US20140288097A1 (en) * 2013-02-07 2014-09-25 The Regents Of The University Of California Use of translational profiling to identify target molecules for therapeutic treatment
US20140243356A1 (en) * 2013-02-07 2014-08-28 The Regents Of The University Of California Use of translational profiling to identify target molecules for therapeutic treatment
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US11287433B2 (en) 2014-02-14 2022-03-29 Institut Pasteur Methods for in vitro investigating mitochondrial replication dysfunction in a biological sample, kits and uses thereof, therapeutic methods against progeroid-like syndromes or symptoms and screening method for identifying particular protease inhibitor(s) and/or nitroso-redox stress scavenger compound(s)
US10338082B2 (en) * 2014-02-14 2019-07-02 Institut Pasteur Methods for in vitro investigating mitochondrial replication dysfunction in a biological sample, kits and uses thereof, therapeutic methods against progeroid-like syndromes or symptomes and screening method for identifying particular protease inhibitor(s) and/or nitroso-redox stress scavenger compound(s)
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CN110582578A (zh) * 2017-02-10 2019-12-17 洛克菲勒大学 用于细胞类型特异性谱分析以鉴定药物靶标的方法
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CN113621621A (zh) * 2021-08-31 2021-11-09 河南牧业经济学院 一种靶向奶山羊CIDEa基因的小干扰RNA及其应用
CN114350705A (zh) * 2021-11-16 2022-04-15 南方医科大学 一种转基因斑马鱼在制备特异标记原始红系造血过程的动物模型中的应用

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