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    J. Anat. (2004) 204, pp311

    Anatomical Society of Great Britain and Ireland 2004

    BlackwellPublishing, Ltd.

    REVIEW

    Strategies for identifying genes that play a role in spinalcord regenerationM. Wintzer,* M. Mladinic, D. Lazarevic, C. Casseler, A. Cattaneo and J. Nicholls

    Sissa, Trieste, Italy

    Abstract

    A search for genes that promote or block CNS regeneration requires numerous approaches; for example, tests can

    be made on individual candidate molecules. Here, however, we describe methods for comprehensive identification

    of genes up- and down-regulated in neurons that can and cannot regenerate after injury. One problem concerns

    identification of low-abundance genes out of the 30 000 or so genes expressed by neurons. Another difficulty is

    knowing whether a single gene or multiple genes are necessary. When microchips and subtractive differential

    display are used to identify genes turned on or off, the numbers are still too great to test which molecules are actually

    important for regeneration. Candidates are genes coding for trophic, inhibitory, receptor and extracellular matrixmolecules, as well as unknown genes. A preparation useful for narrowing the search is the neonatal opossum. The

    spinal cord and optic nerve can regenerate after injury at 9 days but cannot at 12 days after birth. This narrow

    window allows genes responsible for the turning off of regeneration to be identified. As a next step, sites at which

    they are expressed (forebrain, midbrain, spinal cord, neurons or glia, intracellular or extracellular) must be deter-

    mined. An essential step is to characterize proteins, their levels of expression, and their importance for regenera-

    tion. Comprehensive searches for molecular mechanisms represent a lengthy series of experiments that could help

    in devising strategies for repairing injured spinal cord.

    Key words

    CNS lesions; CNS repair; molecular analysis.

    Introduction

    The adult CNS of birds and mammals has little or no

    capacity for functionally useful regeneration. Although

    it has been known since the time of Ramon y Cajal

    that some damaged CNS neurons can send out sprouts

    (Ramon y Cajal, 1928), they do not grow through lesions

    or make connections. By contrast, peripheral nerves

    regenerate successfully after injury, as do connections

    in the CNS of fish, amphibians, reptiles and invertebrates.

    To try to repair the injured spinal cord has become

    a challenging problem in neuroscience. Strategies

    employed to enhance regeneration in the mammalian

    CNS include the neutralization of potential growth

    inhibitory molecules (Caroni & Schwab, 1988; Sims &

    Gilmore, 1994; Dyer et al. 1998), the transplantation of

    cells or tissue that support axonal elongation (Bernstein-

    Goral & Bregman, 1997; McDonald et al. 1999; Ramon-

    Cueto et al. 2000; Ito et al. 2001), and the delivery of

    factors that are known to promote axonal growth,

    such as neurotrophic factors (Xu et al. 1995; Nakahara

    et al. 1996; Zhang et al. 1998). Those approaches are

    showing promising results, although the growth and

    functional recovery that can be observed are often

    limited. Knowledge of the molecules that are involved

    and the way they interact to promote or prevent

    regeneration is far from complete.

    Two different strategies

    Sustained growth of axons involves participation by

    the neuronal cell body. Axon regeneration might require

    that injured neurons up-regulate a specific set of

    Correspondence

    Dr J. Nicholls, Sissa, Via Beirut 2, Trieste 34014, Italy. E: [email protected]

    *

    Present address: Department of Neuroscience, Karolinska Institute,

    Stockholm 171 77, Sweden.

    Accepted for publication28 October 2003

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    growth-associated genes. Some of the genes that are

    up-regulated or constitutively expressed in associa-

    tion with axonal growth have been identified. Their

    products include: (1) transcription factors, such as c-jun,

    which mediates subsequent gene expression (Jenkins

    et al. 1993; Herdegen et al. 1997); (2) cytoskeletal

    proteins involved in axonal extension, such as T

    1-tubulin

    (Miller et al. 1989; Fernandes et al. 1999); (3) cell adhe-

    sion molecules, such as N-CAM involved in growth cone

    guidance (Jung et al. 1997); and (4) cytoplasmic growth

    cone proteins involved in mediating signal transduction,

    such as GAP-43 (Frey et al. 2000).

    One widely used strategy consists of testing individ-

    ual candidates for their potential to enhance fibre

    outgrowth. Such experiments aim to find the

    gene that

    will promote or prevent spinal cord regeneration as a

    first step toward a cure for injury in patients. Studying

    genes one by one can provide interesting cues as

    to their role in the process of regeneration. Because

    regenerating growth cones make complex interactions

    with their local environment, it seems unlikely that a

    single gene is responsible for promoting or preventing

    growth. For example, regeneration of spinal-cord axons

    of dorsal root ganglia occurs after transgenic expres-

    sion of GAP-43 and CAP-23 in combination, but not

    when either one of these genes was expressed on its

    own (Bomze et al. 2001). Nevertheless, the existence

    of a Mastergene switching on a specific genetic pro-

    gram cannot be excluded.

    A more ambitious approach is to make a survey of all

    the genes that are expressed in regenerating and non-

    regenerating tissue. Differentially expressed genes

    can then be fished out by comparing various samples,

    such as adult and immature spinal cord, PNS and CNS,

    injured and uninjured tissue. Such comparisons provide

    a global view of the genes that might enhance or

    inhibit neurite outgrowth.

    Rarity of genes involved in regeneration

    Although it may seem to be a rather simple procedure,

    in practice tracking those genes that play a part in CNS

    regeneration is like looking for a needle in a haystack;

    indeed it is worse because neither the shape of the

    needles or their numbers are known. The human brain

    and spinal cord have the greatest complexity of gene

    expression of any region of the body, reflecting the

    diverse functions of neurons and glia. Saturation and

    kinetic studies indicate that the mRNA population

    expressed by a single cell is made up of 20 00030 000

    distinct mRNAs, with approximately 99% being rare

    (Hahn & Laird, 1971; Grouse et al. 1972; Hahn et al.

    1978; Croizat et al. 1979). These 99% represent less than

    30% of the total mRNA mass. Most of the mRNA

    species that are isolated from a brain or a spinal-cord

    sample are therefore medium- to high-abundance

    transcripts. Their corresponding genes are likely to

    encode proteins necessary for basic biochemical path-

    ways, housekeeping proteins that are common to every

    cell in the body. Thus, it is reasonable to suppose that

    genes involved in the process of regeneration are of

    low abundance.

    A further dilution of the genes of interest is likely to

    occur when experiments are performed in immature

    preparations (see below). Tremendous changes in

    gene expression occur in the developing CNS. They are

    responsible for the myriad processes that may again be

    different from regeneration.

    Methods for studying differential gene

    expression

    A number of techniques have been developed in recent

    years for the identification of differentially expressed

    genes that could be involved in CNS regeneration.

    In the following we describe briefly the underlying

    principles for techniques such as: differential message

    display, serial analysis of gene expression (SAGE),

    large-scale generation of expressed sequence tags (ESTs)

    from cDNA libraries, cDNA microarray screening, and

    various subtractive hybridization strategies.

    Differential display (DD) has been widely used to

    detect and isolate genes that respond to growth

    factors, developmentally regulated genes and genes

    whose expression correlates with certain diseases

    (Pazman et al. 2000; Fu, 2002). The general strategy is to

    amplify partial cDNA sequences from subsets of mRNA

    by reverse transcription and PCR, and then to display

    these short cDNA fragments on a sequencing gel to

    obtain an mRNA fingerprint. Differential display is

    one of the most suitable methods for tracking novel

    genes (Gratsch, 2002), although the generation of false

    positives remains one of its major drawbacks (Broude,

    2002). Su et al. (1997) used this method to demonstrate

    the up-regulation of axonal transport molecules dur-

    ing motor nerve regeneration in the mouse.

    Large-scale sequencing of expressed sequence

    tags (ESTs) is another approach for studying mRNA

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    expression (Okubo et al. 1992). ESTs are randomly

    selected clones sequenced from cDNA libraries. They are

    short, partial DNA sequences, as opposed to full-length

    clones. The first collection of ESTs was initiated in 1991

    as part of the human genome project (Adams et al.

    1991). Each cDNA library is constructed from total

    RNA or poly(A)+ RNA derived from a specific tissue or

    cell, and thus the library represents genes expressed

    in the original cellular population. Overlapping EST

    sequences can be assembled, allowing the complete

    mRNA sequence to be determined. The analysis of EST

    data revealed answers to fundamental questions such

    as which genes are most abundantly expressed (e.g.

    -actin,

    - and

    -tubulin) and the amount of regional

    variation of expression within brain regions. There are

    currently over 1.5 million human EST sequences depos-

    ited in the publicly available database of ESTs provided

    by the National Center for Biotechnology Information

    (NCBI).

    Serial analysis of gene expression (SAGE) is a sequence-

    based strategy that allows the simultaneous analysis

    of a large number of transcripts (Velculescu et al. 1995;

    Scott & Chrast, 2001; Yamamoto et al. 2001). Typically,

    cDNA fragments are generated with short tags (usually

    from 8 to 11 base pairs) at the 3-end of each transcript,

    concatenated and sequenced. Analysis of tags allows

    the cataloging of thousands of genes expressed from a

    tissue source, including a quantitative estimate of gene

    expression. However, this straightforward technique

    requires high-throughput sequencing facilities. SAGE

    has been successfully applied to analyse changes in

    gene expression in hippocampus during the early epil-

    eptic phase in the rat (Hendriksen et al. 2001). Reports

    of its use to isolate genes differentially expressed

    after spinal cord injury are few to date.

    DNA microarrays represent a highly effective tool for

    studying gene expression profiles and genome compo-

    sition. The principle is to immobilize hundreds or thou-

    sands of cDNAs or nucleotides corresponding to ESTs

    or known genes on a solid support, such as nylon mem-

    brane or glass microscope slide (Lockhart et al. 1996;

    Freed & Vawter, 2001; Lobenhofer et al. 2001). To

    determine the difference in gene expression, labelled

    cDNAs or oligonucleotides are hybridized to the array.

    After hybridization and imaging, the pattern of gene

    expression is quantified. The principal advantages of

    this approach are the immediate interpretation of the

    results and the possibility of clustering genes into tem-

    poral and spatial expression patterns. One drawback is

    the difficulty in calibrating and interpreting hybridiza-

    tion signals of weakly expressed genes. Microarray

    analysis after spinal cord injury (Carmel et al. 2001;

    Fan et al. 2001) or brain injury (Matzilevich et al. 2002)

    has proven useful to describe global patterns of gene

    expression and to cluster genes into temporal and

    spatial expression groups.

    Subtractive hybridization (SH) is a valuable tech-

    nique for the isolation of differentially expressed genes.

    Although there are numerous protocols for SH, the

    principles remain the same (Diatchenko et al. 1996).

    Two cDNA populations are generated from two dif-

    ferent RNA sources. For example, in suppressive PCR-

    based subtractive hybridization, adaptors are ligated

    to a tester pool of cDNA. A second pool (driver

    cDNA) is added in excess to hybridize, and only genes

    that are up-regulated in the tester pool can then be

    selectively amplified by PCR. This technique requires

    only small amounts of RNA, and is well suited for iden-

    tifying rare transcripts and novel genes. Subtractive

    hybridization is one of the most commonly used meth-

    ods for identifying differentially expressed mRNAs

    and has been successfully applied in studies of develop-

    ment, cancer, growth-factor-stimulated cells (Feng

    & Liau, 1993; Cho et al. 1998; Davidson & Swalla, 2001;

    Shridhar et al. 2002). Few laboratories have used it

    to analyse genes expressed after injury to the CNS.

    An exception is the series of subtractions made from

    regenerating identified nerve cells in the leech. Black-

    shaw and colleagues (Korneev et al. 1997) have made

    a subtractive library from regenerating Retzius cells of

    the leech, which revealed novel sequences as well as

    genes such as alpha-tubulin, synapsin and calmodulin,

    up-regulated in other species, during nerve regenera-

    tion. A remarkable feature of this study was that the

    differences in expression were analysed in individual

    identified neurons from lesioned and unlesioned nerve

    cords.

    A common feature of all methods for analysis of

    differences in gene expression is the generation of

    large amounts of data (often hundreds or thousands

    of genes). The over- or under-expressed sequences are

    then compared with sequences from public databases.

    Genome sequencing programmes carried out for sev-

    eral organisms including human and mouse have pro-

    vided an immense amount of sequence information in

    databanks. Techniques are now available for studying

    the expression profiles of previously insufficiently char-

    acterized genes.

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    Methods for selecting genes that are relevant

    for regeneration

    A major difficulty arises once the genes that are different-

    ially expressed have been identified. Which of the genes

    that stand out are actually important and how can one

    distinguish genes that play a part in regeneration from

    unrelated genes that have slipped through the subtrac-

    tion procedure? With several hundred candidates, the

    number to be tested experimentally must be narrowed

    down. Procedures for focusing on relevant genes include

    multiple screenings and hybridizations, or repeated

    experiments under various conditions and with different

    tissue samples. For example, a specific sequence may be-

    come significant if it appears in screens made of an inver-

    tebrate and a vertebrate, or in regenerating spinal cord

    and optic nerve. An interesting approach for focusing

    on putative candidates is to combine some of the tech-

    niques described above. For example, the hundreds

    of clones obtained after subtractive hybridization can

    be spotted onto microchips and can then be analysed

    using microarray procedures. This strategy has proved

    to be useful in identifying genes in the nervous system

    (Colantuoni et al. 2001; Kornblum & Geschwind, 2001;

    Dougherty & Geschwind, 2002). We describe in greater

    detail methods for narrowing the search in a later

    section devoted to work on the neonatal opossum.

    Possible discrepancies between RNA andprotein levels

    Differences in abundance of a specific mRNA between

    two samples do not necessarily reflect equivalent quantita-

    tive differences in protein levels. Although it is generally

    true that the level of a protein follows a change of

    its encoding mRNA, the extent and kinetics are often

    unpredictable. The activity of the proteins encoded by

    mRNAs is regulated at several levels beyond their mRNA

    or protein expression by their subcellular localization and

    by the extent to which they are post-translationally mod-

    ified. Neither of these parameters is revealed by measure-

    ments of mRNA abundance. Twiss et al. (2000) showed

    that under some circumstances neurons can be primed to

    rapidly regenerate injured processes independently of new

    gene expression, translating already existing messeng-

    ers. Such regulation at the level of translation would

    not be detected in assays of differential gene expression.

    Large-scale analysis similar to that made at the mRNA

    level can be undertaken directly with proteins, by

    comparing patterns obtained from two-dimensional

    (2D) protein gels. One strength of 2D gel electrophoresis

    is its ability to measure quantitatively several thousand

    proteins in a single sample, with subsequent identifica-

    tion by mass spectrometry (reviewed by Fey & Larsen,

    2001; Lilley et al. 2002). In this way one can compare quan-

    tities of proteins in related samples, such as injured and

    uninjured tissue. A major difficulty that remains is the

    detection of low-abundance proteins by 2D gels, until

    the resolution and sensitivity of the method are

    improved.

    In the near future one can expect to have available

    protein microarrays to measure the properties of

    thousands of proteins simultaneously. Proteinprotein

    interactions analysed with fluorescent probes will be

    analogous to DNA microarrays. An important applica-

    tion of this powerful technique will be to profile the

    proteins in cells under different conditions, as for example

    in regenerating and non-regenerating neurons.

    Localization in CNS of candidate genes

    relevant for regeneration

    Analysis of differential gene (or protein) expression

    is a first step in the search for genes that play a part in

    promoting or blocking regeneration. Identification

    of putative candidates does not, however, indicate at

    what sites they are expressed in the original tissue. In

    situ

    hybridization is important for answering funda-

    mental questions of distribution: Does the gene show

    a widespread expression? If not, in which areas of

    the CNS can the product be found? Is it expressed by

    neurons or by glial cells and in which structures (mem-

    branes, extracellular space, internal organelles) does

    the pattern of expression change after an injury?

    The procedure for in situ

    hybridization involves

    screening sections or the entire CNS by labelled probes

    complementary to the mRNA of interest. A risk is that

    one might discard genes that at first seem uninterest-

    ing. This is exemplified by Nogo, a member of the retic-

    ular family of transmembrane proteins. Nogo mRNA is

    widely expressed in fetal, developing and adult nervous

    system of rat and human (Josephson et al. 2001), and

    its levels of expression are not significantly changed

    after lesions to the cortex or spinal cord (Huber et al.

    2002). From those characteristics one might exclude

    Nogo from a list of interesting candidates, and yet it is

    known to be an inhibitor of regeneration in the CNS

    (Huber & Schwab, 2000; Woolf, 2003).

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    Assessment of the functional role of unknown

    genes and proteins

    Many genes that are detected by screening of regener-

    ating and non-regenerating preparations have no known

    function. The analysis of the full-length sequence of

    such candidates with bioinformatic techniques is a first

    step towards understanding what role they might play

    in regeneration. Valuable information can be obtained

    from the gene sequence that is responsible for direct-

    ing the encoded protein to its cellular or extracellular

    location (e.g. nucleus, organelles, plasma membrane).

    Translation of the DNA sequence of a gene into the

    amino acid sequence of the encoded protein can

    provide clues to its structure and function.

    To gain further insight into the functional role of

    a candidate, numerous tests can be performed on cells

    in culture. One approach is to measure effects of a

    candidate gene on growth, either by over-expressing

    genes that promote regeneration (gain of function)

    or by blocking expression of genes that inhibit regenera-

    tion (loss of function).

    For example, immortalized cell lines such as PC12 cells

    can be engineered to produce a protein by introducing

    its coding gene into cells in culture. One method for trans-

    fecting cells is to use a gene gun, which bombards

    them with small gold particles coated with the DNA of

    interest (McAllister, 2000; Sato et al. 2000). Alterna-

    tively, genes can be delivered by trapping the DNA into

    liposomes, which are taken up by the cell (Kofler et al.

    1998), or by precipitating DNA with calcium phosphate.

    Proteins can be studied in greater detail by introducing

    the recombinant gene into cells together with green

    fluorescent protein (GFP) (reviewed by Van Roessel &

    Brand, 2002). The label makes it possible to follow the

    gene fusion product in the living cell. Specific localiza-

    tion and co-localization with other known proteins can

    provide information about the role of the protein in

    specific pathways of neurons and glial cells. For exam-

    ple, a recombinant protein expressed in a defined cell

    line may promote cell cycle arrest or loss of motility.

    Methods by which to block the expression of a gene

    include the introduction of antisense oligonucleotides

    that hybridize with the RNA in the cell and hinder their

    translation into proteins (reviewed by Lebedeva et al.

    2000; Sazani et al. 2002). Whenever they are available,

    antibodies that specifically block the action of an iden-

    tified protein can provide clear evidence for function.

    A recent effective method for silencing the expression

    of a target gene is to introduce vectors that express

    small interfering RNAs (known as siRNAs). siRNAs are

    short (about 20 nucleotides), double-stranded mole-

    cules. Once inside the cell the siRNA strands unwind

    and become associated with complementary RNA

    molecules. This provokes the cleavage and destruction of

    target mRNA and inhibition of protein synthesis by the

    cell (Scherr et al. 2003; Sorensen et al. 2003).

    A further step is modification of specific sequences to

    identify functional domains of the protein. For exam-

    ple, deletions or mutations can define regions of genes

    important for nuclear importexport or degradation.

    A two-hybrid system in yeast can also be used to pro-

    vide information about function. By this method it

    is possible to investigate proteinprotein interactions

    and to identify molecular partners (reviewed by

    Causier & Davies, 2002). The two-hybrid system exploits

    properties of transcription factors that have two sepa-

    rate functional domains. One is a DNA binding domain

    that binds to the DNA of the promoter and the other

    an activation domain that binds to the transcription

    apparatus. Each separate domain can be fused as a

    hybrid to a second protein without changing the basic

    properties of the transcription factor. When an interac-

    tion occurs, the DNA binding domain and the activa-

    tion domain of the transcription factor come close

    together and can activate transcription of a reporter

    gene encoding for a selection marker. In this way the

    protein of interest can be tested for interactions with

    several possible partners.

    Experiments performed on cells in vitro

    are indispen-

    sable to assay the role of candidate molecules and their

    possible involvement in regeneration. Observation of

    fibre outgrowth in vitro

    does not, however, imply that

    similar events will occur in the animal, let alone that

    growth will lead to functional recovery. Although most

    tests for regeneration are made in vivo

    in rats and mice,

    experiments performed in Monodelphis

    have demon-

    strated the usefulness of this mammal for studying

    regeneration.

    The opossum as a preparation for molecular

    studies of regeneration

    Properties of neonatal opossum CNS

    In the following sections we show how the approaches

    described above have been applied to the CNS of the

    newborn opossum, Monodelphis domestica.

    The emphasis

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    is on work in progress with certain clear advances but

    no defined end-point in sight.

    In newborn opossum pups the immature CNS is so

    small that it can be removed in its entirety and main-

    tained in tissue culture for up to 2 weeks (Stewart et al.

    1991; Treherne et al. 1992; Mllgard et al. 1994).

    During that time in culture, cell division goes on, the

    isolated CNS maintains reflex responses to electrical

    stimulation, and the fine structure of the nervous

    system is preserved (Nicholls et al. 1990; Eugenin &

    Nicholls, 1997). Axons regenerate rapidly and reliably

    through spinal cord lesions (Nicholls et al. 1994;

    Saunders et al. 1995; reviewed by Nicholls & Saunders,

    1996). Amino acids, transmitters and larger molecules

    such as antibodies rapidly penetrate the isolated tissue

    from the bathing fluid (Zou et al. 1991; Varga et al.

    1995). These properties facilitate detailed analysis of

    mechanisms that promote or block regeneration.

    After a lesion to the spinal cord in the immature animal,

    regeneration is so complete that functions such as coord-

    inated walking and swimming are virtually normal

    (Saunders et al. 1998). In adult opossums, as in other

    mammals, the CNS does not regenerate. The transition

    point has been shown to occur in the early days of post-

    natal life. At 9 days of age regeneration occurs reliably.

    However, it is no longer possible in cervical spinal cord

    segments of animals aged 12 days or more. Owing to a

    rostro-caudal gradient in development, the less mature

    lumbar segments still show regeneration in animals up

    to 17 days. The narrow window of time during which

    regeneration stops being possible is particularly useful

    for studies of differences in gene expression. The space

    of time between 9 and 12 days after birth is long

    enough for expression of differences in genes of inter-

    est, yet short enough to avoid the over-representation

    of genes related to development. The presence of both

    mature (cervical) and immature (lumbar) parts in the

    spinal cord at 12 days enables one to perform addi-

    tional comparisons between regenerating and non-

    regenerating tissue of a single animal. In this way

    differences in gene expression related to regeneration

    can be analysed at different times (9 days vs. 12 days)

    and in different places (cervical vs. lumbar at 12 days).

    Analysis of genes expressed in regenerating and non-

    regenerating spinal cords

    We conducted subtractive hybridization experiments

    to detect genes that are up- or down-regulated in the

    opossum at different ages and in different parts of the

    spinal cord. Both forward and backward subtractions

    were done between cervical spinal cord at 9 days (can

    regenerate) and at 12 days (cannot regenerate). Other

    subtractions were done between 12-day lumbar (can

    regenerate) and cervical parts at the same age (cannot

    regenerate). Table 1 provides a summary of the various

    subtractions.

    cDNAs from the two first subtractions (C9C12 and

    C12C9) were cloned in E. coli, resulting in about

    3000 recombinant clones. A few clones were chosen

    at random from those libraries and sequenced. About

    half of these represented novel genes whose function

    is as yet unknown. Sequencing also revealed numerous

    interesting genes that could be involved in regenera-

    tion. They coded for transcription factors, receptors,

    signal transducing molecules, structural proteins and

    extracellular matrix proteins, among others. Other

    genes, as expected, were responsible for house-

    keeping functions (for example, enzymes and struc-

    tural proteins).

    Narrowing down the search

    To separate non-relevant genes from those involved in

    regeneration we designed experiments based on cross-

    hybridizations between different subtractions. The aim

    of those experiments was to find common clones in the

    various subtractions. All clones from a pair of subtrac-

    tive libraries were arrayed onto nylon membranes and

    hybridized with radioactively labelled probes derived

    Table 1. Subtractions to reveal genes that are differentially

    expressed in opossum spinal cord regions that do and do not

    regenerate

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    from the other subtractions. This process reduced the

    number of potentially involved genes by a factor of

    about 10. Those remaining included (among others):

    reelin, laminin receptor, TATA-box binding protein,

    MAP1b, and these were all more abundant at 9 days.

    At 12 days, genes selectively expressed included PAX-6,

    semaphorin receptor and GABA(A) receptor-associated

    protein. Novel genes were represented in both catego-

    ries. In contrast with other studies focusing on one gene

    or protein, this represents an approach based on broad

    screenings that can lead to unbiased identification

    of potentially interesting genes in the spinal cord at

    different ages.

    Comparison with other databases can help in the

    functional identification of relevant molecules. A strik-

    ing feature is that opossum gene sequences show high

    similarities to those of mouse, rat or human deposited

    in databanks. EST and microarrays are now available

    for another marsupial, the Tammar wallaby.

    What remains is to determine for each gene: the

    location of expression, its abundance, the level of

    protein and its effect on the regeneration of intact spinal

    cord axons after injury.

    Concluding remarks

    Studies of differential gene expression in injured spinal

    cord provide a picture of molecular events associated

    with processes of regeneration. Many steps, however,

    are necessary before it can be known whether this

    approach will lead to cures for patients with spinal cord

    lesions. Overoptimistic claims of cures that are just

    around the corner can have devastating consequences

    for patients with spinal cord injuries (Pearson, 2003).

    Animal tests, and extensive clinical trials for efficacy

    and side-effects involve expenditure of immense sums

    of money and large numbers of skilled manpower

    hours. It seems possible that treatments might

    arise sooner from the approach not discussed in detail

    here, namely the testing of likely molecules without

    any comprehensive screen. Although the large-scale

    screening described here may well produce no miracle

    gene, what it will do is increase basic knowledge. Our

    underlying assumption is that, just as it is easier to

    repair a watch once one knows the way it works, anal-

    ysis of mechanisms responsible for failure of regenera-

    tion in adult mammalian spinal cord will be facilitated

    by an understanding of molecular mechanisms that

    promote and inhibit neuron outgrowth.

    Acknowledgements

    We thank Dr Marco Stebel and Mr Salvatore Guarino

    for their diligent and skilled care of the animal colony.

    References

    Adams MD, Kelly JM, Gocayne JD, Dubnick M, Polymeropoulos

    MH, Xiao H, et al.

    (1991) Complementary DNA sequencing:

    expressed sequence tags and human genome project.

    Science

    252

    , 16511656.

    Bernstein-Goral H, Bregman BS

    (1997) Axotomized rubrospinal

    neurons rescued by fetal spinal cord transplants maintain

    axon collaterals to rostral CNS targets. Exp

    . Neurol

    . 148

    , 1325.

    Bomze HM, Bulsara KR, Iskandar BJ, Caroni P, Skene JH

    (2001)

    Spinal axon regeneration evoked by replacing two growth

    cone proteins in adult neurons. Nat

    . Neurosci

    . 4

    , 3843.

    Broude NE

    (2002) Trouble with differential display. Trends

    Biotechnol

    . 20

    , 181.

    Carmel JB, Galante A, Soteropoulos P, Tolias P, Young W,

    Hart RP

    (2001) Gene expression profiling of acute spinal

    cord injury reveals spreading inflammatory signals and

    neuron loss. Physiol

    . Genomics

    7

    , 201213.

    Caroni P, Schwab ME

    (1988) Antibody against Myelin-associated

    inhibitor of neurite growth neutralizes nonpermissive

    substrate properties of CNS white matter. Neuron

    1

    , 8596.

    Causier B, Davies B

    (2002) Analysing proteinprotein interac-

    tions with the yeast two-hybrid system. Plant

    . Mol

    . Biol

    . 50

    ,

    971980.

    Cho JJ, Vliagoftis H, Rumsaeng V, Metcalfe DD, Oh CK

    (1998)

    Identification and categorization of inducible mast cell

    genes in a subtraction library. Biochem. Biophys. Res.

    Commun. 242, 226230.

    Colantuoni C, Jeon OH, Hyder K, Chenchik A, Khimani AH,Narayanan V, et al. (2001) Gene expression profiling in post

    mortem Rett Syndrome brain: differential gene expression

    and patient classification. Neurobiol. Dis. 8, 847865.

    Croizat B, Berthelot F, Felsani A, Gros F (1979) Complexity of

    polyadenylated RNA in mouse whole brain and cortex. FEBS

    Lett. 103, 138143.

    Davidson B, Swalla BJ (2001) Isolation of genes involved in

    ascidian metamorphosis: epidermal growth factor signaling

    and metamorphic competence. Dev. Genes Evol. 211, 190

    194.

    Diatchenko L, Lau YF, Campbell AP, Chenchik A, Mogadam F,

    Huang B, et al. (1996) Suppression subtractive hybridization:

    a method for generating differentially regulated or tissue-

    specific cDNA probes and libraries. Proc. Natl Acad. Sci. USA

    93, 60256030.

    Dougherty JD, Geschwind DH (2002) Subtraction-coupled

    custom microarray analysis for gene discovery and gene

    expression studies in the CNS. Chem. Senses27, 293298.

    Dyer JK, Bourque JA, Steeves JD (1998) Regeneration of brain-

    stem-spinal cord axons after lesion and immunological dis-

    ruption of myelin in adult rats. Exp. Neurol. 154, 1222.

    Eugenin J, Nicholls JG (1997) Chemosensory and cholinergic

    stimulation of fictive respiration in isolated CNS of neonatal

    opossum.J. Physiol. 501, 425437.

  • 8/3/2019 M. Wintzer et al- Strategies for identifying genes that play a role in spinal cord regeneration

    8/9

    Genes for CNS regeneration, M. Wintzer et al.

    Anatomical Society of Great Britain and Ireland 2004

    10

    Fan M, Mi R, Yew DT, Chan WY

    (2001) Analysis of gene expres-

    sion following sciatic nerve crush and spinal cord hemisec-

    tion in the mouse by microarray expression profiling. Cell

    .

    Mol

    . Neurobiol

    . 21

    , 497508.

    Feng P, Liau G

    (1993) Identification of a novel serum and

    growth factor-inducible gene in vascular smooth muscle

    cells.J

    . Biol

    . Chem

    . 268

    , 93879392.

    Fernandes KJ, Fan DP, Tsui BJ, Cassar SL, Tetzlaff W

    (1999)

    Influence of the axotomy to cell body distance in rat rubro-spinal and spinal motoneurons: differential regulation of

    GAP-43, tubulins, and neurofilament-M. J

    . Comp

    . Neurol

    .

    414, 495510.

    Fey SJ, Larsen PM (2001) 2D or nor 2D. Two-dimensional gel

    electrophoresis. Curr. Opin. Chem. Biol. 5, 2633.

    Freed WJ, Vawter MP (2001) Microarrays: applications in

    neuroscience to disease, development, and repair. Resto.

    Neurol. Neurosci. 18, 5356.

    Frey D, Laux T, Xu L, Schneider C, Caroni P (2000) Shared

    and unique roles of CAP23 and GAP43 in actin regulation,

    neurite outgrowth, and anatomical plasticity. J. Cell Biol.

    149, 14431454.

    Fu Y (2002) Detection of differentially expressed genes incancer using differential display. Meth. Mol. Med. 68, 179193.

    Gratsch TE (2002) Differential display. Isolation of novel

    genes. Meth. Mol. Biol. 198, 213221.

    Grouse L, Chilton MD, McCarthy BJ (1972) Hybridization of

    ribonucleic acid with unique sequences of deoxyribonucleic

    acid. Biochemistry11, 798805.

    Hahn WE, Laird CD (1971) Transcription of nonrepeated DNA

    in mouse brain. Science173, 158161.

    Hahn WE, Van Ness J, Maxwell IH (1978) Complex population

    of mRNA sequence in large polyadenylated nuclear RNA

    molecules. Proc. Natl Acad. Sci. USA75, 55445547.

    Hendriksen H, Datson NA, Ghijsen WE, van Vliet EA, da Silva FH,

    Gorter JA, et al. (2001) Altered hippocampal gene expres-

    sion prior to the onset of spontaneous seizures in the ratpost-status epilepticus model. Eur.J. Neurosci. 14, 14751484.

    Herdegen T, Skene B, Bahr M (1997) The c-jun transcription

    factor: bipotential mediator of neuronal death, survival and

    regeneration. Trends Neurosci. 20, 227231.

    Huber AB, Schwab ME (2000) Nogo-A, a potent inhibitor

    of neurite outgrowth and regeneration. Biol. Chem. 381,

    407419.

    Huber AB, Weinmann O, Brosamle C, Oertle T, Schwab ME

    (2002) Patterns of Nogo mRNA and protein expression in

    the developing and adult rat and after CNS lesions. J.

    Neurosci. 22, 35533567.

    Ito J, Murata M, Kawaguchi S (2001) Regeneration and recov-

    ery of the hearing function of the central auditory pathwayby transplants of embryonic tissue in adult rats. Exp. Neurol.

    169, 3035.

    Jenkins R, Tetzlaff W, Hunt SP (1993) Differential expression

    of immediate early genes in rubrospinal neurons following

    axotomy in rats. Eur.J. Neurosci. 5, 203209.

    Josephson A, Widenfalk J, Widmer HW, Olson L, Spenger C

    (2001) NOGO mRNA expression in adult and fetal human

    and rat nervous tissue and in weight-drop injury. Exp. Neurol.

    169, 319328.

    Jung M, Petrausch B, Stuermer CA (1997) Axon-regenerating

    retinal ganglion cells in adult rats synthesize the cell adhe-

    sion molecule L1 but not TAG-1 or SC-1. Mol. Cell. Neurosci.

    9, 116131.

    Kofler P, Wiesenhofer B, Rehrl C, Baier G, Stockhammer G,

    Humpel C (1998) Liposome-mediated gene transfer into

    established CNS cell lines, primary glial cells, and in vivo. Cell

    Transplant. 7, 175185.

    Kornblum H, Geschwind D (2001) The use of representational

    difference analysis and cDNA microarrays in neural repair

    research. Resto. Neurol. Neurosci. 18, 8994.Korneev S, Fedorov A, Collins R, Blackshaw SE, Davies JS

    (1997) A subtractive cDNA library from an identified regen-

    erating neuron is enriched in sequences up-regulated

    during nerve regeneration. Inv. Neurosci. 3, 185192.

    Lebedeva I, Benimetskaya L, Stein CA, Vilenchik M (2000)

    Cellular delivery of antisense oligonucleotides. Eur.J. Pharm.

    Biopharm. 50, 101119.

    Lilley KS, Razzaq A, Dupree P (2002) Two-dimensional gel

    electrophoresis: recent advances in sample preparation,

    detection and quantitation. Curr. Opin. Chem. Biol. 6, 4650.

    Lobenhofer EK, Bushel PR, Afshari CA, Hamadeh HK (2001)

    Progress in the application of DNA microarrays. Environ.

    Health. Perspect. 109, 881891.Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV,

    Chee MS, et al. (1996) Expression monitoring by hybridiza-

    tion to high-density oligonucleotide arrays. Nat. Biotechnol.

    14, 16751680.

    Matzilevich DA, Rall JM, Moore AN, Grill RJ, Dash PK (2002)

    High-density microarray analysis of hippocampal gene

    expression following experimental brain injury.J. Neurosci.

    Res. 67, 646663.

    McAllister AK (2000) Biolistic transfection of neurons. Sci.

    STKE2000(51), PL1.

    McDonald JW, Liu XZ, Qu Y, Mickey SK, Turetsky D, Gottlieb DI,

    et al. (1999) Transplanted embryonic stem cells survive, dif-

    ferentiate and promote recovery in adult rat spinal cord.

    Nat. Med. 5, 14101412.Miller FD, Tetzlaff W, Bisby MA, Fawcett JW, Milner RJ (1989)

    Rapid induction of the major embryonic alpha-tubulin

    mRNA, T alpha 1, during nerve regeneration in adult rats.J.

    Neurosci. 9, 14521463.

    Mllgard K, Balslev Y, Stagaard Janas M, Treherne JM,

    Saunders NR, Nicholls JG (1994) Development of spinal cord

    in the isolated CNS of a neonatal mammal (the opossum

    Monodelphis domestica) maintained in long term culture.

    J. Neurocytol. 23, 151165.

    Nakahara Y, Gage FH, Tuszynski MH (1996) Grafts of fibrob-

    lasts genetically modified to secrete NGF, BDNF, NT-3, or

    basic FGF elicit differential responses in the adult spinal

    cord. Cell Transplant. 5, 191204.Nicholls JG, Stewart RR, Erulkar SD, Saunders NR (1990)

    Reflexes, fictive respiration and cell division in the brain and

    spinal cord of the newborn opossum, Monodelphis domes-

    tica.J. Exp. Biol. 152, 115.

    Nicholls JG, Vischer H, Varga Z, Erulkar S, Saunders NR (1994)

    Repair of connections in injured neonatal and embryonic

    spinal cord in vitro. Prog. Brain. Res. 103, 263269.

    Nicholls JG, Saunders NR (1996) Regeneration of immature

    mammalian spinal cord after injury. TINS19, 229234.

    Okubo K, Hori N, Matoba R, Niiyama T, Fukushima A, Kojiima Y,

    et al. (1992) Large scale cDNA sequencing for analysis of

  • 8/3/2019 M. Wintzer et al- Strategies for identifying genes that play a role in spinal cord regeneration

    9/9

    Genes for CNS regeneration, M. Wintzer et al.

    Anatomical Society of Great Britain and Ireland 2004

    11

    quantitative and qualitative aspects of gene expression.

    Nat. Genet. 2, 173179.

    Pazman C, Castelli JC, Wen X, Somogyi R (2000) Large-scale

    identification of differentially expressed genes during

    neurogenesis. Neuroreport11, 719724.

    Pearson H (2003) In search of a miracle. Nature423, 112113.

    Ramon y Cajal S (1928) Degeneration and Regeneration in the

    Nervous System. London: Oxford University Press.

    Ramon-Cueto A, Cordero MI, Santos-Benito FF, Avila J (2000)Functional recovery of paraplegic rats and motor axon

    regeneration in their spinal cords by olfactory ensheathing

    glia. Neuron25, 425435.

    Sato H, Hattori S, Kawamoto S, Kudoh I, Hayashi A,

    Yamamoto I, et al. (2000) In vivo gene gun-mediated DNA

    delivery into rodent brain tissue. Biochem. Biophys. Res.

    Commun. 270, 163170.

    Saunders NR, Deal A, Knott GW, Varga ZM, Nicholls JG (1995)

    Repair and recovery following spinal cord injury in a neonatal

    marsupial (Monodelphis domestica). Clin. Exp. Pharmacol.

    Physiol. 22, 518526.

    Saunders NR, Kitchener P, Knott GW, Nicholls JG, Potter A,

    Smith TJ (1998) Development of walking, swimming andneuronal connections after complete spinal cord transection

    in the neonatal opossum, Monodelphis domestica.J. Neurosci.

    18, 339355.

    Sazani P, Vacek MM, Kole R (2002) Short-term and long-term

    modulation of gene expression by antisense therapeutics.

    Cur. Opin. Biotechnol. 13, 468472.

    Scherr M, Battmer K, Ganser A, Eder M (2003) Modulation of

    gene expression by lentiviral-mediated delivery of small

    interfering RNA. Cell Cycle2, 251257.

    Scott HS, Chrast R (2001) Global transcript expression profiling

    by Serial Analysis of Gene Expression (SAGE). Genet. Eng.

    (NY)23, 201219.

    Shridhar V, Sen A, Chien J, Staub J, Avula R, Kovats S (2002)

    Identification of underexpressed genes in early- and late-stage primary ovarian tumors by suppression subtraction

    hybridization. Cancer Res. 62, 262270.

    Sims TJ, Gilmore SA (1994) Regrowth of dorsal root axons into

    a radiation-induced glial-deficient environment in the

    spinal cord. Brain Res. 634, 113126.

    Sorensen DR, Leirdal M, Sioud M (2003) Gene silencing by

    systemic delivery of synthetic siRNAs in adult mice. J. Mol.

    Biol. 327, 761766.

    Stewart RR, Zou DJ, Treherne JM, Mllgard K, Saunders NR,

    Nicholls JG (1991) The intact central nervous system of the

    newborn opossum in long-term culture: fine structure and

    GABA-mediated inhibition of electrical activity.J. Exp. Biol.

    161, 2441.

    Su QN, Namikawa K, Toki H, Kiama H (1997) Differential

    display reveals transcriptional up-regulation of the motor

    molecules for both anterograde and retrograde axonal

    transport during nerve regeneration. Eur. J. Neurosci. 9,15421547.

    Treherne JM, Woodward SKA, Varga ZM, Ritchie JM, Nicholls

    JG (1992) Restoration of conduction and growth of axons

    through injured spinal cord of neonatal opossum in culture.

    Proc. Natl Acad. Sci. USA89, 431434.

    Twiss JL, Smith DS, Chang B, Shooter EM (2000) Translational

    control of ribosomal protein L4 is required for rapid neurite

    regeneration. Neurobiol. Dis. 7, 416428.

    Van Roessel P, Brand AH (2002) Imaging into the future:

    visualizing gene expression and protein interactions with

    fluorescent proteins. Nat. Cell Biol. 4, E15E20.

    Varga ZM, Bandlow CE, Erulkar SD, Schwab ME, Nicholls JG

    (1995) The critical period for repair of CNS of neonatal opos-sum (Monodelphis domestica) in culture: correlation with

    development of glial cells, myelin and growth-inhibitory

    molecules. Eur.J. Neurosci. 7, 21192129.

    Velculescu VE, Zhang L, Vogelstein B, Kinzler KW (1995) Serial

    analysis of gene expression. Science270, 484487.

    Woolf CJ (2003) No Nogo: wow where to go? Neuron38,

    153156.

    Xu XM, Guenard V, Kleitman N, Aebischer P, Bunge MB (1995)

    A combination of BDNF and NT-3 promotes supraspinal

    axon regeneration into Schwann cell grafts in adult rat

    thoracic spinal cord. Exp. Neurol. 134, 261272.

    Yamamoto M, Wakatsuki T, Hada A, Ryo A (2001) Use of serial

    analysis of gene expression (SAGE) technology.J. Immunol.

    Meth. 250, 4566.Zhang Y, Dijhuizen PA, Anderson PN, Lieberman AR,

    Verhaagen J (1998) NT-3 delivered by an adenoviral vector

    induces injured dorsal root axons to regenerate into the

    spinal cord of adult rats.J. Neurosci. Res. 54, 554562.

    Zou DJ, Treherne JM, Stewart RR, Saunders NR, Nicholls JG

    (1991) Regulation of GABAb receptors by histamine and

    neuronal activity in the isolated spinal cord of neonatal

    opossum in culture. Proc. R. Soc. Lond. B246, 7782.