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Advances in genomic study of cortical projection neurons

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Frontiers in Biology

Abstract

The mammalian neocortex gives rise to perception and initiates voluntary motor responses. The cortical laminae are comprised of six distinct cellular layers of local circuit neurons and projection neurons. To explore molecular identities of the distinct cortical projection neurons, discovery-orientated genomic approaches have been adopted. Microarray analysis of dissected cortical tissues has been applied to identify cortical layer markers. Early neuronal cells were sorted by FACS from GFPlabeled embryonic brains for gene expression profiling. Laser capture microdissection of retrograde-labeled projection neurons, when coupled with optimal RNA amplification technology, has become a valuable strategy for neuronal isolation and gene expression analysis in differentiated neurons. RNA sequencing technology is promising not only for the determination of gene expression, but also for discovery of posttranscriptional modifications of the complex neural system. There is no doubt that advances in genomic studies are opening up novel research avenues for our understanding of the cortical neuronal functions.

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References

  • Arlotta P, Molyneaux B J, Chen J, Inoue J, Kominami R, Macklis J D (2005). Neuronal subtype-specific genes that control corticospinal motor neuron development in vivo. Neuron, 45(2): 207–221

    Article  CAS  PubMed  Google Scholar 

  • Bertone P, Gerstein M, Snyder M (2005). Applications of DNA tiling arrays to experimental genome annotation and regulatory pathway discovery. Chromosome Res, 13(3): 259–274

    Article  CAS  PubMed  Google Scholar 

  • Böhm C, Newrzella D, Sorgenfrei O (2005). Laser microdissection in CNS research. Drug Discov Today, 10(17): 1167–1174

    Article  PubMed  Google Scholar 

  • Bunney W E, Bunney B G, Vawter M P, Tomita H, Li J, Evans S J, Choudary P V, Myers R M, Jones E G, Watson S J, Akil H (2003). Microarray technology: a review of new strategies to discover candidate vulnerability genes in psychiatric disorders. Am J Psychiatry, 160(4): 657–666

    Article  PubMed  Google Scholar 

  • Cahoy J D, Emery B, Kaushal A, Foo L C, Zamanian J L, Christopherson K S, Xing Y, Lubischer J L, Krieg P A, Krupenko S A, Thompson W J, Barres B A (2008). A transcriptome database for astrocytes, neurons, and oligodendrocytes: a new resource for understanding brain development and function. J Neurosci, 28(1): 264–278

    Article  CAS  PubMed  Google Scholar 

  • Chen J G, Rasin M R, Kwan K Y, Sestan N (2005). Zfp312 is required for subcortical axonal projections and dendritic morphology of deeplayer pyramidal neurons of the cerebral cortex. Proc Natl Acad Sci USA, 102(49): 17792–17797

    Article  CAS  PubMed  Google Scholar 

  • Chow N, Cox C, Callahan L M, Weimer J M, Guo L, Coleman P D (1998). Expression profiles of multiple genes in single neurons of Alzheimer’s disease. Proc Natl Acad Sci USA, 95(16): 9620–9625

    Article  CAS  PubMed  Google Scholar 

  • Clément-Ziza M, Gentien D, Lyonnet S, Thiery J P, Besmond C, Decraene C (2009). Evaluation of methods for amplification of picogram amounts of total RNA for whole genome expression profiling. BMC Genomics, 10(1): 246

    Article  PubMed  Google Scholar 

  • Colosimo M E, Brown A, Mukhopadhyay S, Gabel C, Lanjuin A E, Samuel A D, Sengupta P (2004). Identification of thermosensory and olfactory neuron-specific genes via expression profiling of single neuron types. Curr Biol, 14(24): 2245–2251

    Article  CAS  PubMed  Google Scholar 

  • Cui D, Dougherty K J, Machacek D W, Sawchuk M, Hochman S, Baro D J (2005). Divergence between motoneurons: gene expression profiling provides a molecular characterization of functionally discrete somatic and autonomic motoneurons. Physiol Genomics, 24(3): 276–289

    Article  PubMed  Google Scholar 

  • Eberwine J (2001). Single-cell molecular biology. Nat Neurosci, 4(Suppl): 1155–1156

    Article  CAS  PubMed  Google Scholar 

  • Eberwine J, Yeh H, Miyashiro K, Cao Y, Nair S, Finnell R, Zettel M, Coleman P (1992). Analysis of gene expression in single live neurons. Proc Natl Acad Sci USA, 89(7): 3010–3014

    Article  CAS  PubMed  Google Scholar 

  • Emmert-Buck M R, Bonner R F, Smith P D, Chuaqui R F, Zhuang Z, Goldstein S R, Weiss R A, Liotta L A (1996). Laser capture microdissection. Science, 274(5289): 998–1001

    Article  CAS  PubMed  Google Scholar 

  • Espina V, Wulfkuhle J D, Calvert V S, VanMeter A, Zhou W, Coukos G, Geho D H, Petricoin E F 3rd, Liotta L A (2006). Laser-capture microdissection. Nat Protoc, 1(2): 586–603

    Article  CAS  PubMed  Google Scholar 

  • Evans S J, Choudary P V, Vawter M P, Li J, Meador-Woodruff J H, Lopez J F, Burke S M, Thompson R C, Myers R M, Jones E G, Bunney W E, Watson S J, Akil H (2003). DNA microarray analysis of functionally discrete human brain regions reveals divergent transcriptional profiles. Neurobiol Dis, 14(2): 240–250

    Article  CAS  PubMed  Google Scholar 

  • Fox R M, Von Stetina S E, Barlow S J, Shaffer C, Olszewski K L, Moore J H, Dupuy D, Vidal M, Miller D M 3rd (2005). A gene expression fingerprint of C. elegans embryonic motor neurons. BMC Genomics, 6(1): 42

    Google Scholar 

  • Geschwind D H, Levitt P (2007). Autism spectrum disorders: developmental disconnection syndromes. Curr Opin Neurobiol, 17(1): 103–111

    Article  CAS  PubMed  Google Scholar 

  • Ginsberg S D, Che S, Counts S E, Mufson E J (2006). Shift in the ratio of three-repeat tau and four-repeat tau mRNAs in individual cholinergic basal forebrain neurons in mild cognitive impairment and Alzheimer’s disease. J Neurochem, 96(5): 1401–1408

    Article  CAS  PubMed  Google Scholar 

  • Ginsberg S D, Hemby S E, Lee V M, Eberwine J H, Trojanowski J Q (2000). Expression profile of transcripts in Alzheimer’s disease tangle-bearing CA1 neurons. Ann Neurol, 48(1): 77–87

    Article  CAS  PubMed  Google Scholar 

  • Gong S, Zheng C, Doughty ML, Losos K, Didkovsky N, Schambra U B, Nowak N J, Joyner A, Leblanc G, Hatten M E, Heintz N (2003). A gene expression atlas of the central nervous system based on bacterial artificial chromosomes. Nature, 425(6961): 917–925

    Article  CAS  PubMed  Google Scholar 

  • Gray P A, Fu H, Luo P, Zhao Q, Yu J, Ferrari A, Tenzen T, Yuk D I, Tsung E F, Cai Z, Alberta J A, Cheng L P, Liu Y, Stenman J M, Valerius M T, Billings N, Kim H A, Greenberg M E, McMahon A P, Rowitch D H, Stiles C D, Ma Q (2004). Mouse brain organization revealed through direct genome-scale TF expression analysis. Science, 306(5705): 2255–2257

    Article  CAS  PubMed  Google Scholar 

  • Greenberg S A (2001). DNA microarray gene expression analysis technology and its application to neurological disorders. Neurology, 57(5): 755–761

    CAS  PubMed  Google Scholar 

  • Harel N Y, Strittmatter S M (2006). Can regenerating axons recapitulate developmental guidance during recovery from spinal cord injury? Nat Rev Neurosci, 7(8): 603–616

    Article  CAS  PubMed  Google Scholar 

  • Heintz N (2000). Analysis of mammalian central nervous system gene expression and function using bacterial artificial chromosome-mediated transgenesis. Hum Mol Genet, 9(6): 937–943

    Article  CAS  PubMed  Google Scholar 

  • Hoerder-Suabedissen A, Wang W Z, Lee S, Davies K E, Goffinet A M, Rakić S, Parnavelas J, Reim K, Nicolić M, Paulsen O, Molnár Z (2009). Novel markers reveal subpopulations of subplate neurons in the murine cerebral cortex. Cereb Cortex, 19(8): 1738–1750

    Article  PubMed  Google Scholar 

  • Jiang Y M, Yamamoto M, Kobayashi Y, Yoshihara T, Liang Y, Terao S, Takeuchi H, Ishigaki S, Katsuno M, Adachi H, Niwa J, Tanaka F, Doyu M, Yoshida M, Hashizume Y, Sobue G (2005). Gene expression profile of spinal motor neurons in sporadic amyotrophic lateral sclerosis. Ann Neurol, 57(2): 236–251

    Article  CAS  PubMed  Google Scholar 

  • Johnson M B, Kawasawa Y I, Mason C E, Krsnik Z, Coppola G, Bogdanović D, Geschwind D H, Mane S M, State M W, Sestan N (2009). Functional and evolutionary insights into human brain development through global transcriptome analysis. Neuron, 62(4): 494–509

    Article  CAS  PubMed  Google Scholar 

  • Kamme F, Salunga R, Yu J, Tran D T, Zhu J, Luo L, Bittner A, Guo H Q, Miller N, Wan J, Erlander M (2003). Single-cell microarray analysis in hippocampus CA1: demonstration and validation of cellular heterogeneity. J Neurosci, 23(9): 3607–3615

    CAS  PubMed  Google Scholar 

  • Khaitovich P, Muetzel B, She X, Lachmann M, Hellmann I, Dietzsch J, Steigele S, Do H H, Weiss G, Enard W, Heissig F, Arendt T, Nieselt-Struwe K, Eichler E E, Pääbo S (2004). Regional patterns of gene expression in human and chimpanzee brains. Genome Res, 14(8): 1462–1473

    Article  CAS  PubMed  Google Scholar 

  • Kurn N, Chen P, Heath J D, Kopf-Sill A, Stephens KM, Wang S (2005). Novel isothermal, linear nucleic acid amplification systems for highly multiplexed applications. Clin Chem, 51(10): 1973–1981

    Article  CAS  PubMed  Google Scholar 

  • Leamey C A, Glendining K A, Kreiman G, Kang N D, Wang K H, Fassler R, Sawatari A, Tonegawa S, Sur M (2007). Differential gene expression between sensory neocortical areas: potential roles for Ten_m3 and Bcl6 in patterning visual and somatosensory pathways. Cereb Cortex, 18(1): 53–66

    Article  PubMed  Google Scholar 

  • Lein E S, Hawrylycz M J, Ao N, Ayres M, Bensinger A, Bernard A, Boe A F, Boguski M S, Brockway K S, Byrnes E J, Chen L, Chen L, Chen TM, Chin M C, Chong J, Crook B E, Czaplinska A, Dang C N, Datta S, Dee N R, Desaki A L, Desta T, Diep E, Dolbeare T A, Donelan M J, Dong H W, Dougherty J G, Duncan B J, Ebbert A J, Eichele G, Estin L K, Faber C, Facer B A, Fields R, Fischer S R, Fliss T P, Frensley C, Gates S N, Glattfelder K J, Halverson K R, Hart M R, Hohmann J G, Howell M P, Jeung D P, Johnson R A, Karr P T, Kawal R, Kidney J M, Knapik R H, Kuan C L, Lake J H, Laramee A R, Larsen K D, Lau C, Lemon T A, Liang A J, Liu Y, Luong L T, Michaels J, Morgan J J, Morgan R J, Mortrud M T, Mosqueda N F, Ng L L, Ng R, Orta G J, Overly C C, Pak T H, Parry S E, Pathak S D, Pearson O C, Puchalski R B, Riley Z L, Rockett H R, Rowland S A, Royall J J, Ruiz M J, Sarno N R, Schaffnit K, Shapovalova N V, Sivisay T, Slaughterbeck C R, Smith S C, Smith K A, Smith B I, Sodt A J, Stewart N N, Stumpf K R, Sunkin S M, Sutram M, Tam A, Teemer C D, Thaller C, Thompson C L, Varnam L R, Visel A, Whitlock R M, Wohnoutka P E, Wolkey C K, Wong V Y, Wood M, Yaylaoglu M B, Young R C, Youngstrom B L, Yuan X F, Zhang B, Zwingman T A, Jones A R (2007). Genome-wide atlas of gene expression in the adult mouse brain. Nature, 445(7124): 168–176

    Article  CAS  PubMed  Google Scholar 

  • Liang WS, Dunckley T, Beach T G, Grover A, Mastroeni D, Ramsey K, Caselli R J, Kukull W A, McKeel D, Morris J C, Hulette C M, Schmechel D, Reiman E M, Rogers J, Stephan D A (2008). Altered neuronal gene expression in brain regions differentially affected by Alzheimer’s disease: a reference data set. Physiol Genomics, 33(2): 240–256

    Article  CAS  PubMed  Google Scholar 

  • Lobo M K, Karsten S L, Gray M, Geschwind D H, Yang X W (2006). FACS-array profiling of striatal projection neuron subtypes in juvenile and adult mouse brains. Nat Neurosci, 9(3): 443–452

    Article  CAS  PubMed  Google Scholar 

  • Lombardino A J, Hertel M, Li X C, Haripal B, Martin-Harris L, Pariser E, Nottebohm F (2006). Expression profiling of intermingled longrange projection neurons harvested by laser capture microdissection. J Neurosci Methods, 157(2): 195–207

    Article  CAS  PubMed  Google Scholar 

  • Low L K, Cheng H J (2006). Axon pruning: an essential step underlying the developmental plasticity of neuronal connections. Philos Trans R Soc Lond B Biol Sci, 361(1473): 1531–1544

    Article  CAS  PubMed  Google Scholar 

  • Luo L, Salunga R C, Guo H, Bittner A, Joy K C, Galindo J E, Xiao H, Rogers K E, Wan J S, Jackson M R, Erlander M G (1999). Gene expression profiles of laser-captured adjacent neuronal subtypes. Nat Med, 5(1): 117–122

    Article  CAS  PubMed  Google Scholar 

  • Magdaleno S, Jensen P, Brumwell C L, Seal A, Lehman K, Asbury A, Cheung T, Cornelius T, Batten DM, Eden C, Norland SM, Rice D S, Dosooye N, Shakya S, Mehta P, Curran T (2006). BGEM: an in situ hybridization database of gene expression in the embryonic and adult mouse nervous system. PLoS Biol, 4(4): e86

    Article  PubMed  Google Scholar 

  • Marguerat S, Bähler J (2010). RNA-seq: from technology to biology. Cell Mol Life Sci, 67(4): 569–579

    Article  CAS  PubMed  Google Scholar 

  • Mirnics K, Korade Z, Arion D, Lazarov O, Unger T, Macioce M, Sabatini M, Terrano D, Douglass K C, Schor N F, Sisodia S S (2005). Presenilin-1-dependent transcriptome changes. J Neurosci, 25(6): 1571–1578

    Article  CAS  PubMed  Google Scholar 

  • Mirnics K, Middleton F A, Marquez A, Lewis D A, Levitt P (2000). Molecular characterization of schizophrenia viewed by microarray analysis of gene expression in prefrontal cortex. Neuron, 28(1): 53–67

    Article  CAS  PubMed  Google Scholar 

  • Molyneaux B J, Arlotta P, Hirata T, Hibi M, Macklis J D (2005). Fezl is required for the birth and specification of corticospinal motor neurons. Neuron, 47(6): 817–831

    Article  CAS  PubMed  Google Scholar 

  • Molyneaux B J, Arlotta P, Menezes J R L, Macklis J D (2007). Neuronal subtype specification in the cerebral cortex. Nat Rev Neurosci, 8(6): 427–437

    Article  CAS  PubMed  Google Scholar 

  • Mufson E J, Counts S E, Ginsberg S D (2002). Gene expression profiles of cholinergic nucleus basalis neurons in Alzheimer’s disease. Neurochem Res, 27(10): 1035–1048

    Article  CAS  PubMed  Google Scholar 

  • O’Leary D D, Chou S J, Sahara S (2007). Area patterning of the mammalian cortex. Neuron, 56(2): 252–269

    Article  PubMed  Google Scholar 

  • O’Leary D D, Koester S E (1993). Development of projection neuron types, axon pathways, and patterned connections of the mammalian cortex. Neuron, 10(6): 991–1006

    Article  PubMed  Google Scholar 

  • Pietersen C Y, Lim M P, Woo T U (2009). Obtaining high quality RNA from single cell populations in human postmortem brain tissue. J Vis Exp, 30(30): 1444

    PubMed  Google Scholar 

  • Polleux F, Ince-Dunn G, Ghosh A (2007). Transcriptional regulation of vertebrate axon guidance and synapse formation. Nat Rev Neurosci, 8(5): 331–340

    Article  CAS  PubMed  Google Scholar 

  • Rossner M J, Hirrlinger J, Wichert S P, Boehm C, Newrzella D, Hiemisch H, Eisenhardt G, Stuenkel C, von Ahsen O, Nave K A (2006). Global transcriptome analysis of genetically identified neurons in the adult cortex. J Neurosci, 26(39): 9956–9966

    Article  CAS  PubMed  Google Scholar 

  • Roy N S, Benraiss A, Wang S, Fraser R A, Goodman R, Couldwell WT, Nedergaard M, Kawaguchi A, Okano H, Goldman S A (2000). Promoter-targeted selection and isolation of neural progenitor cells from the adult human ventricular zone. J Neurosci Res, 59(3): 321–331

    Article  CAS  PubMed  Google Scholar 

  • Rudnicki M, Eder S, Schratzberger G, Mayer B, Meyer T W, Tonko M, Mayer G (2004). Reliability of t7-based mRNA linear amplification validated by gene expression analysis of human kidney cells using cDNA microarrays. Nephron, Exp Nephrol, 97(3): e86–e95

    Article  CAS  Google Scholar 

  • Sandberg R, Yasuda R, Pankratz D G, Carter T A, Del Rio J A, Wodicka L, Mayford M, Lockhart D J, Barlow C (2000). Regional and strainspecific gene expression mapping in the adult mouse brain. Proc Natl Acad Sci USA, 97(20): 11038–11043

    Article  CAS  PubMed  Google Scholar 

  • Schulze A, Downward J (2000). Analysis of gene expression by microarrays: cell biologist’s gold mine or minefield? J Cell Sci, 113(Pt 23): 4151–4156

    CAS  PubMed  Google Scholar 

  • Sugino K, Hempel C M, Miller M N, Hattox A M, Shapiro P, Wu C, Huang Z J, Nelson S B (2006). Molecular taxonomy of major neuronal classes in the adult mouse forebrain. Nat Neurosci, 9(1): 99–107

    Article  CAS  PubMed  Google Scholar 

  • Tudor M, Akbarian S, Chen R Z, Jaenisch R (2002). Transcriptional profiling of a mouse model for Rett syndrome reveals subtle transcriptional changes in the brain. Proc Natl Acad Sci USA, 99(24): 15536–15541

    Article  CAS  PubMed  Google Scholar 

  • van Gelder R N, von Zastrow M E, Yool A, Dement W C, Barchas J D, Eberwine J H (1990). Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc Natl Acad Sci USA, 87(5): 1663–1667

    Article  PubMed  Google Scholar 

  • Vercelli A, Repici M, Garbossa D, Grimaldi A (2000). Recent techniques for tracing pathways in the central nervous system of developing and adult mammals. Brain Res Bull, 51(1): 11–28

    Article  CAS  PubMed  Google Scholar 

  • Vernes S C, Newbury D F, Abrahams B S, Winchester L, Nicod J, Groszer M, Alarcón M, Oliver P L, Davies K E, Geschwind D H, Monaco A P, Fisher S E (2008). A functional genetic link between distinct developmental language disorders. N Engl J Med, 359(22): 2337–2345

    Article  CAS  PubMed  Google Scholar 

  • Visel A, Thaller C, Eichele G (2004). GenePaint.org: an atlas of gene expression patterns in the mouse embryo. Nucleic Acids Res, 32 (90001 Database issue): 552 D–556 D

    Article  Google Scholar 

  • Watakabe A, Sugai T, Nakaya N, Wakabayashi K, Takahashi H, Yamamori T, Nawa H (2001). Similarity and variation in gene expression among human cerebral cortical subregions revealed by DNA macroarrays: technical consideration of RNA expression profiling from postmortem samples. Brain Res Mol Brain Res, 88(1–2): 74–82

    Article  CAS  PubMed  Google Scholar 

  • Watson J D, Wang S, Von Stetina S E, Spencer WC, Levy S, Dexheimer P J, Kurn N, Heath J D, Miller D M 3rd (2008). Complementary RNA amplification methods enhance microarray identification of transcripts expressed in the C. elegans nervous system. BMC Genomics, 9(1): 84

    Article  PubMed  Google Scholar 

  • Wilhelm J, Muyal J P, Best J, Kwapiszewska G, Stein M M, Seeger W, Bohle RM, Fink L (2006). Systematic comparison of the T7-IVT and SMART-based RNA preamplification techniques for DNA microarray experiments. Clin Chem, 52(6): 1161–1167

    Article  CAS  PubMed  Google Scholar 

  • Wurmbach E, González-Maeso J, Yuen T, Ebersole B J, Mastaitis J W, Mobbs C V, Sealfon S C (2002). Validated genomic approach to study differentially expressed genes in complex tissues. Neurochem Res, 27(10): 1027–1033

    Article  CAS  PubMed  Google Scholar 

  • Yamamori T, Rockland K S (2006). Neocortical areas, layers, connections, and gene expression. Neurosci Res, 55(1): 11–27

    Article  CAS  PubMed  Google Scholar 

  • Yao F, Yu F, Gong L, Taube D, Rao D D, MacKenzie R G (2005). Microarray analysis of fluoro-gold labeled rat dopamine neurons harvested by laser capture microdissection. J Neurosci Methods, 143(2): 95–106

    Article  CAS  PubMed  Google Scholar 

  • Yeo G W, Xu X, Liang T Y, Muotri A R, Carson C T, Coufal N G, Gage F H (2007). Alternative splicing events identified in human embryonic stem cells and neural progenitors. PLOS Comput Biol, 3(10): 1951–1967

    Article  CAS  PubMed  Google Scholar 

  • Zapala M A, Hovatta I, Ellison J A, Wodicka L, Del Rio J A, Tennant R, Tynan W, Broide R S, Helton R, Stoveken B S, Winrow C, Lockhart D J, Reilly J F, Young W G, Bloom F E, Lockhart D J, Barlow C (2005). Adult mouse brain gene expression patterns bear an embryologic imprint. Proc Natl Acad Sci USA, 102(29): 10357–10362

    Article  CAS  PubMed  Google Scholar 

  • Zhu H, Yang Y, Gao J, Tao H, Qu C, Qu J, Chen J (2010). Area dependent expression of ZNF312 in human fetal cerebral cortex. Neurosci Res, 68(1): 73–76

    Article  CAS  PubMed  Google Scholar 

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  1. Key Laboratory of Visual Science, National Ministry of Health, and School of Optometry and Ophthalmology, Wenzhou Medical College, Zhejiang, 325027, China

    Chunsheng Qu & Jieguang Chen

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Qu, C., Chen, J. Advances in genomic study of cortical projection neurons. Front. Biol. 5, 524–531 (2010). https://doi.org/10.1007/s11515-010-0670-9

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