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  • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
  • C12N15/09—Recombinant DNA-technology
  • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
  • C12N15/1034—Isolating an individual clone by screening libraries
  • C12N15/1051—Gene trapping, e.g. exon-, intron-, IRES-, signal sequence-trap cloning, trap vectors
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  • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
  • 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
  • C12N15/625—DNA sequences coding for fusion proteins containing a sequence coding for a signal sequence
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  • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
  • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12Q1/6844—Nucleic acid amplification reactions
  • C12Q1/6858—Allele-specific amplification
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2319/00—Fusion polypeptide
  • C07K2319/01—Fusion polypeptide containing a localisation/targetting motif
  • C07K2319/02—Fusion polypeptide containing a localisation/targetting motif containing a signal sequence
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2319/00—Fusion polypeptide
  • C07K2319/32—Fusion polypeptide fusions with soluble part of a cell surface receptor, "decoy receptors"
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2319/00—Fusion polypeptide
  • C07K2319/90—Fusion polypeptide containing a motif for post-translational modification

Definitions

• the invention relates to vectors and methods for cloning amino-terminal signal sequences. With identification of novel signal sequences, previously unidentified secreted and transmembrane proteins, especially those involved in signal transduction, can be identified.
• Growth factors are diffusable molecules that mediate intercellular communication. Growth factors include the interleukins, platelet-derived growth factor (PDGF) , epidermal growth factor (EGF) , granulocyte-macrophage colony stimulating factor (GM-CSF) , erythropoietin (EPO) , thrombopoietin (TPO) and calcitonin.
• PDGF platelet-derived growth factor
• EGF epidermal growth factor
• GM-CSF granulocyte-macrophage colony stimulating factor
• EPO erythropoietin
• TPO thrombopoietin
• Receptors include integral membrane proteins and soluble receptors.
• a common feature of these molecules of interest is the presence of a secretion leader ("signal") sequence at the N-terminus of their coding regions.
• This signal sequence encodes amino acids that direct the de novo synthesized protein into the endoplasmic reticulum or to the exterior of the cell. Because the nucleotide homology of known signal sequences is minimal or non-existent, isolation of novel signal sequences by nucleic acid hybridization is difficult, if not impossible.
• signal trapping One method for selective cloning of signal sequences (“signal trapping") has been described by K. Tashiro et al. , Science 2.51:600-03, 1993. This method featured a cDNA library containing cDNA of 400 bp average size. To generated cDNAs of 400 bp average size, the cDNA was sonicated, creating random shear of the cDNA molecules. The randomly sheared cDNA was inserted into a vector (lacking an endogenous signal sequence) capable of directing cell surface expression of Tac fusion protein, if a signal sequence was inserted in-frame in correct orientation. The presence of cell surface Tac fusion protein was microscopically detected by immunostaining with anti-Tac antibodies. After several cycles of subpooling and fluorescent microscopy detection, 6 immunologically positive cDNA clones were obtained from 600 screened clones. From these 6 clones, two new members of the intercrine ⁇ cytokine family were identified.
• the signal trap cloning method of Tashiro et al. includes the following attendant disadvantages: (1) uncontrolled, non-directional generation of small cDNA fragments through random shear; (2) cumbersome cycles of immunostaining and subpooling of individual clones; and
• 5' end of a gene comprising: preparing a plurality of DNA molecules each comprising the 5' end of a gene, wherein the 5' ends are linked to a first member of a first complementary/anti-complementary pair, thereby forming labeled 5' ends; cleaving the DNA molecules with a restriction endonuclease, thereby forming DNA fragments; exposing the DNA fragments to an opposite member of the first complementary/anti-complementary pair, whereby DNA fragments having labeled 5' ends are bound to the opposite member; and isolating DNA fragments from the first complementary/anti-complementary pair.
• the first complementary/anti-complementary pair is selected from the group consisting of a biotin/avidin pair, a receptor/ ligand pair, an antibody/epitope pair, and a sense/ antisense polynucleotide pair, with a biotin/avidin pair preferred. It is also preferred that one member of the first complementary/anti-complementary pair is immobilized on a solid phase matrix, such as a magnetic bead.
• the restriction endonuclease is a 4-cutter restriction enzyme.
• the methods further comprise, after the step of isolating DNA fragments, the additional steps of: joining the DNA fragments to a DNA segment encoding a structural protein, thereby forming a DNA fusion, wherein the DNA fusion is contained within an expression vector and operably linked to other DNA elements required for expression of the DNA fusion in a host cell; introducing the expression vector into a host cell, thereby forming an expression host cell; and culturing the expression host cell, whereby the DNA fusion is capable of being expressed.
• the structural protein is a growth factor receptor, and preferably Mpl.
• the expression vector is pSLSV-1, pSLSV-2, pSLSV-3 or combinations thereof.
• the host cell is a BaF3 cell, a Chinese hamster ovary cell, a baby hamster kidney cell, a FDC-P1 cell, or an M07e cell, with BaF3 cells preferred.
• the methods further comprise, after the step of culturing the expression host cell, the additional steps of: combining the expression host cell with a tagged reagent under conditions whereby the expression host cell is intact and the tagged reagent binds to the structural protein encoded by the DNA segment; and isolating expression host cells that bind the tagged reagent.
• the tagged reagent is a fluorescent-labeled antibody, and the step of isolating is performed using a fluorescence-activated cell sorter.
• the host cell is a factor-dependent host cell, preferably BaF3, FDC-P1, or M07e, and most preferably BaF3.
• the structural protein is directed to an exterior surface of the expression host cell and is a member of a second complementary/anti-complementary pair, whereby interaction of the structural protein with an opposite member of the second complementary/anti-complementary pair stimulates the expression host cell bearing the structural protein to proliferate.
• the second complementary/anti-complementary pair is a receptor/ligand pair
• the structural protein is Mpl, IL-4 receptor, EPO receptor or GM-CSF receptor.
• the step of culturing is conducted in the absence of a factor that the factor-dependent host cell requires for growth, and in the presence of the opposite member of the second complementary/anti-complementary pair.
• the cloning site is SEQ ID NO: 2; SEQ ID NO: 3; or SEQ ID NO: 4.
• the growth factor receptor is Mpl.
• the present invention combines the secretory function of a signal peptide with functional cloning methods to provide improved methods of identifying and cloning previously unknown signal peptides.
• the secretion leader trap cloning methods and vectors of the present invention can be advantageously used to clone, identify, and isolate cDNA segments encoding previously unknown factors (such as novel cytokines and growth factors) and previously unknown transmembrane molecules (such as novel receptors) which pass through a cell's secretory pathway.
• Previously unknown factors and receptors are also referred to as "orphan" factors and receptors.
• orphan proteins are difficult and cumbersome to clone.
• These orphan factors and receptors can be beneficially employed, however, in cell culture techniques in research and industrial settings, in studies of cell physiology and metabolism, in studies of relationships among factors, receptors, and cell lineages, and for therapeutic intervention in animals, including humans.
• secretory leader sequence and “signal (or signal peptide) sequence” are used interchangeably to denote a DNA sequence encoding a signal or secretory peptide. Signal sequences are also called leader sequences, prepro sequences and pre sequences.
• a secretory leader is an amino acid sequence that is involved in directing secretion of a mature polypeptide or protein from a cell. More specifically, a secretory leader directs translocation of a polypeptide or protein across the endoplasmic reticulum (the entry to the secretory pathway) .
• Secretory peptides are characterized by a core of hydrophobic amino acids and are typically
• amino-terminal signal sequence is used herein to denote a DNA sequence encoding signal peptide that occurs at the amino terminus of a protein.
• leader-less protein denotes a secreted structural protein wherein the protein's native, functional signal peptide (or “leader”) has been eliminated.
• the native signal peptide is eliminated through genetic manipulation of the nucleotide sequence encoding the natural signal peptide.
• receptor is used herein to denote a cell-associated protein that binds to a bioactive molecule (i.e., a ligand, which term includes hormones and growth factors) and mediates the effect of the ligand on the cell.
• a bioactive molecule i.e., a ligand, which term includes hormones and growth factors
• Receptors are characterized by a multi-domain structure comprising a ligand-binding domain and an effector domain that is typically involved in signal transduction. Binding of ligand to receptor results in a conformational change in the receptor that causes an interaction between the effector domain and other molecule (s) in the cell. This interaction in turn leads to an alteration in the metabolism of the cell.
• Metabolic events that are linked to receptor-ligand interactions include gene transcription, phosphorylation, dephosphorylation, increases in cyclic AMP production, mobilization of cellular calcium, mobilization of membrane lipids, cell adhesion, hydrolysis of inositol lipids and hydrolysis of phospholipids.
• Receptors can be membrane bound, cytosolic or nuclear; monomeric (e.g., thyroid stimulating hormone receptor, beta-adrenergic receptor) or multimeric (e.g., PDGF receptor, growth hormone receptor, IL-3 receptor, GM-CSF receptor, G-CSF receptor, erythropoietin receptor and IL-6 receptor) .
• Receptors are classified into families and superfamilies on the basis of conserved structural features. It is generally believed that under selective pressure for organisms to acquire new biological functions, new receptor family members arose from duplication of existing receptor genes leading to the existence of multi-gene families.
• cytokine receptor superfamily Two of the most well-known receptor superfamilies are the cytokine receptor superfamily and the seven transmembrane domain (7-TMD) receptor superfamily. Table 1 provides a partial listing of members of these three receptor superfamilies.
• cytokine receptors can be placed into one of five related families on the basis of certain structural features. All five families are characterized by the presence of an extracellular ligand binding domain and an intracellular domain that are separated by a single transmembrane sequence. Cytokine receptor structure has been reviewed by Urdal, Ann. Reports Med. Chem. 2£:221-28,
• the 7-TMD receptors are a functionally diverse group encoded by a large gene superfamily. Two characteristic features of this receptor superfamily are the presence of seven helical transmembrane domains and a cytoplasmic domain, the latter of which is believed to be responsible for coupling the receptor to G proteins. This superfamily has been reviewed by Lameh et al. , Pharm Res.
• IL-6 receptor Hematopoietin family erythropoietin receptor
• TNF (p60) receptor Other IL-2 receptor ⁇ -subunit
• Receptors are also classified on the basis of common functions.
• Table 2 presents a listing of receptor families grouped according to function. Each tyrosine kinase family is represented in Table 2 by a prototypical receptor. See Ullrich et al . , Nature 3_QL:418-25, 1984; Ullrich et al. , Nature 212. :756-61, 1985; Yaden et al . , Nature 323 :226-32. 1986; Hirai et al . , Science 2.12.:1717- 20, 1987; Sanchez-Madrid et al . , Proc . Na l . Acad. Sci. HSA _7__i:7489-93, 1982; Takeichi, Science 251:1451-55, 1991;
• Tyrosine kinase receptors EGF receptor insulin receptor PDGF receptor EPH receptor
• Cell adhesion receptors leukointegrins cadherin receptors immunoglobulin-like receptors
• Known orphan receptors include the nuclear receptors COUP- TF1/EAR3, C0UP-TF2/ARP-1, EAR-1, EAR-2, TR-2, PPARl, HNF-
• ILA insulin growth factor/tumor necrosis factor receptor family
• IRRR is a transmembrane tyrosine kinase.
• orphan tyrosine kinase-type receptors have been found in Drosophila (reviewed by Perrimon, Curr. Opin. Cell Biol. :260-66, 1994, which is incorporated herein by reference) .
• Drosophila orphan receptors are of interest because they present the opportunity for genetic, as well as biochemical, analysis. Identification of Drosophila ligands, followed by cloning by homology, provides a method for obtaining human or other animal counterparts to the Drosophila ligands.
• growth factor denotes a polypeptide that stimulates proliferation of a cell, the activity of which is mediated by a cell-surface receptor.
• growth factors include the interleukins and colony stimulating factors.
• expression vector denotes a DNA molecule, either single- or double-stranded, linear or circular, that comprises a gene of interest operably linked to other DNA sequences that provide for its expression and maintenance in a host cell.
• Expression vectors may be plasmid or virus-derived, or may contain both plasmid and viral elements.
• a DNA segment encoding a structural gene is joined to expression control sequences in an expression vector that may comprise, in addition, one or more origins of replication, one or more selectable markers, enhancers, splice signals or other elements.
• the structural gene encodes a leader- less protein, preferably a growht factor receptor, that is normally transported to the cell surface.
• the leader-less structural protein is Mpl.
• the expression vector is inserted into the host cell using conventional methods. Methods for constructing expression vectors and transfecting cultured cells are known in the art. See, for example, Levinson et al. , U.S. Patent No. 4,713,339; Hagen et al. , U.S. Patent No. 4,784,950; Palmiter et al. , U.S. Patent No. 4, 579,821 and Ringold, U.S. Patent No. 4,656,134, which are incorporated herein by reference in their entirety. For a description of genetic engineering, factor-dependent cell lines, and cell culture techniques, see pending patent application USSN 08/250,859, which is incorporated herein in its entirety.
• the claimed signal trap cloning method involves enrichment of N-terminal (i.e., 5') coding sequences.
• N-terminal i.e., 5'
• a full length, oligo-dT- primed cDNA library is 5' terminus-labeled with biotin through ligation with a biotinylated 5' PCR linker (also denoted "5' PCR primer”) .
• Biotin is used herein as an exemplary member of a complementary/anti-complementary pair.
• complementary/anti-complementary pairs include receptor/ligand pairs, antibody/antigen (or hapten or epitope) pairs, sense/antisense polynucleotide pairs, a biotin/avidin (or streptavidin) pair and the like.
• the complementary/anti- complementary pair preferably has a binding affinity of ⁇ 10 "9 M.
• the biotinylated 5 ' PCR linker contains a predetermined restriction site.
• the biotinylated 5' PCR linker contains an EcoRI site.
• the biotinylated cDNA is divided into pools, and each pool is cut with one of a panel of "4-cutter” restriction enzymes to generate small cDNA fragments.
• the term "4-cutter restriction enzyme” means a restriction enzyme having a 4 base pair (4 bp) recognition site. On average, a 4-cutter restriction enzyme will cut a sequence of cDNA approximately every 250 bp. Numerous 4-cutter restriction enzymes are commercially available; a list of representative 4-cutter restriction enzymes is provided in Table 3.
• N denotes any nucleotide
• Biotinylated 5 ' terminal fragments are isolated using avidin that has been immobilized on a solid phase matrix.
• streptavidin- conjugated magnetic beads are used.
• the solid phase matrix containing avidin-captured 5' fragments is washed, and a 3 ' PCR linker is ligated to the fragments by means of the 4-cutter-generated cohesive ends of the fragment.
• the 3' PCR linker contains a predetermined restriction site, with an Xhol restriction site particularly preferred.
• the captured cDNA fragments are then removed from the solid phase matrix using restriction sites present on the 5' and 3' PCR linkers. This 5 ' enriched cDNA preparation is then used for signal sequence library construction.
• the amount of captured cDNA can be amplified by PCR using the 5 ' and 3 ' PCR primers prior to signal sequence library construction.
• Other nucleic acid amplification methods are known in the art (see, for example, Kwoh et al . , Proc. Natl. Acad. Sci. USA ££:H73- 77, 1989; Van Gelder et al . , Proc. Natl. Acad. Sci . USA£:1663-67, 1990; Fahy et al. , PCR Meth. Appl . 1:25-33, 1991; and Kievitis et al. , J. Virol. Meth. 3_5_:273-86, 1991) , and are suitable for use in this regard.
• the claimed methods for enrichment of 5 ' signal sequence cDNAs provide the following advantages. First, depending on the amount of starting cDNA, this technique can be amenable to direct cloning or PCR- amplification/cloning of the 5' cDNA fragments. Second, digestion of full length sequences with a panel of 4- cutter restriction enzymes allows more control over fragment generation than random shear methods. Third, avidin capture of biotinylated 5 ' cDNA fragments ensures efficient enrichment of native N-terminal coding cDNAs. Fourth, by identifying the 4-cutter pool from which the cDNA fragments were obtained, specific 4-cutter-generated ends of the 5 ' enriched cDNA fragments can be ligated to an appropriate 3' linker with high efficiency.
• the known 5 ' and 3 ' linkers attached to the cDNA fragments permit directional cloning into an appropriate vector.
• the immunostaining method used by Tashiro et al . for signal sequence trap cloning is cumbersome and lacks any selection mechanism.
• the claimed invention provides two detection/selection improvements that are advantageously used to clone signal sequence cDNAs.
• putative signal sequence cDNAs are introduced in a directed, specific manner into an expression vector that contains a coding sequence for a leader-less protein.
• This expression vector preparation is introduced into an appropriate host cell, forming an expression host cell.
• the expression host cell is cultured under conditions that support cell growth, and that permit cell surface expression of the leader-less protein when it is operably linked to its own signal sequence.
• the previously leader-less protein (the "marker protein") can be expressed and directed to the surface of the expression host cell.
• the expression host cells are cultured for a time sufficient to enable detection of the marker protein on the cell surface.
• a reagent that (i) specifically binds to the marker protein, and (ii) is labeled with a detectable tag.
• Suitable reagents include antibodies, ligands, soluble receptors and the like.
• Detectable tags suitable for use include fluorescent, fluorescence quenching, dye and magnetic tags and the like.
• any tag that modifies the light scattering properties of the target to which it is bound is suitable for use herein.
• a preferred reagent is a fluorescent tagged anti-marker protein antibody.
• the expression host cells are then sorted according to the presence or absence of detectable tag/reagent bound at the cell surface.
• expression host cells containing a functional signal sequence are readily segregated from those in which a functional signal sequence is lacking.
• an automated machine that permits single cell examination for instance, a flow cytometer
• a fluorescence-activated flow cytometer is used to segregate cells containing a functional signal sequence.
• the leader-less protein encoded by the expression vector is a cytokine receptor or a growth factor receptor.
• the receptor is introduced into a factor-dependent cell line (the "parental cell"), cell surface expression of the receptor permits cell proliferation (i) in the presence of the receptor's corresponding cytokine or growth factor, and (ii) in the absence of the factor(s) upon which the starting cell-line is dependent.
• an expression vector preparation containing a leader-less protein and putative signal sequence cDNAs is introduced into a factor-dependent parental host cell, forming a factor-dependent expression host cell.
• This factor-dependent expression host cell is cultured in the presence of the factor necessary for parental cell proliferation.
• the selected culture conditions will otherwise support factor-dependent expression host cell growth, and will permit cell surface expression of the leader-less protein when it is operably linked to its own signal sequence.
• the factor-dependent expression host cells are cultured for a period sufficient to allow expression of the leader-less protein at the surface of cells that contain a functional signal sequence. Thereafter, the factor-dependent expression host cells are cultured under selection conditions: (i) in the absence of the factor necessary for parental cell proliferation, and (ii) in the presence of a molecule that will enable proliferation of cells that express the (formerly leader-less) protein at the cell surface. Upon continued culturing under these selection conditions, only cells that contain a functional signal sequence will survive.
• Secretion leaders that are cloned, identified, and isolated using the disclosed methods can provide alternative and/or superior secretion leaders for use as research and production tools.
• Prokaryotic, yeast, fungal, insect or mammalian secretion leaders can be discovered through use of the described techniques. For instance, these secretion peptides may display a range of secretion efficiencies and specificities.
• these methods can be used to identify one or more secretion leaders that can be used in creating suitable expression vectors for expression of heterologous proteins in such host cells.
• methods for identifying secretion leaders in the absence of a relevant bioassay can be particularly valuable tools.
• the first selection method uses automated cell sorting to isolate clones that express a detectable cell surface protein due to insertion of a functional signal sequence.
• a complex mixture of nucleic acid fragments containing putative signal sequence cDNAs are directionally cloned into an appropriate vector upstream of a nucleotide sequence encoding a leader-less structural protein that, when linked to its endogenous leader (or signal sequence) , is normally transported to the cell surface.
• marker protein in this regard is thrombopoietin receptor (i.e., Mpl) .
• Other receptors that may be suitable for use as a marker protein within the present invention include (1) receptors that "stand alone” (i.e., function/ enable cell proliferation without the presence of additional, distinct subunits) ; and (2) receptors that require the presence of one or more such subunits that are encoded by a separate, unrelated gene for the host cell's proliferative response. Examples of receptors requiring at least one additional subunit include IL-6, IL-3 and IL-4.
• proteins that are: (1) normally linked to an endogenous signal peptide; (2) expressed at the cell surface; and (3) capable of being stably bound and detected by a tagged reagent can be used as marker or structural proteins herein.
• selected marker proteins may accept longer segments of N-terminal modification than others.
• An exemplary selection vector contains a leader- less Mpl coding region.
• the leader-less Mpl cDNA was isolated by reverse transcriptase polymerase chain reaction (PCR) using standard techniques (see, for instance, pending patent application USSN 08/250,859) .
• PCR reverse transcriptase polymerase chain reaction
• this exemplary expression vector represents a set of 3 vectors that are identical except that, at the junction between the putative signal sequence and the Mpl coding sequence, the indicated Xho site has 3 frames available (“Xho(l, 2, 3 frames) ") with respect to Mpl.
• the PCR primer located at this junction (3' primer) is designed so that it will not amplify the endogenous structural protein signal sequence.
• the PCR primer located at the junction upstream of the putative signal sequence (the 5' primer) is also designed so that it will not amplify the endogenous structural protein signal sequence.
• the 5' primer is also designed so that it will not amplify the endogenous structural protein signal sequence.
• genomic DNA or cDNA from BaF3 as may be used as a template. Genomic DNA is easier and faster to isolate, but cDNA is less complex and may be more artifact-free.
• a library of putative signal sequence cDNAs inserted in an appropriate vector is introduced into host cells capable of expressing the structural protein of interest.
• Exemplary host cells include prokaryotic and eukaryotic cells, and more particularly, mammalian, yeast and insect cells. After introducing the expression vector into host cells and culturing the resultant expression host cells, these cells are combined with a tagged, detectable reagent.
• This tagged reagent is capable of binding a marker protein expressed at the cell surface.
• a preferred tagged reagent is a fluorescent-labeled antibody, with a monoclonal fluorescein isothiocyanate (FITC) -labeled anti-Mpl antibody particularly preferred.
• FITC monoclonal fluorescein isothiocyanate
• the marker protein will be expressed at the cell surface.
• An appropriate, detectably tagged reagent is combined with cultured expression host cells, and, after an appropriate period of time, the cells are separated from unbound tagged reagent. When these "washed" cells are subjected to an appropriate cell sorting procedure, only expression host cells containing a functional signal sequence will be detected and selected. For example, fluorescence- activated cell sorting can provide a quick, one-step, automated segregation of cells that contain a functional signal sequence from those that do not.
• signal sequence cDNAs of interest may be isolated clonally or en masse.
• expression host cells that contain a functional signal sequence can be cloned and expanded, and/or the signal sequence cDNA may be used as a probe or as a PCR primer to recover sufficient amounts of the cDNA of interest for sequencing.
• the totality of signal sequence DNAs can be isolated from the total population of expression host cells containing a functional signal sequence.
• a total signal trap cDNA preparation is then obtained using nucleotide sequence amplification techniques, such as PCR.
• the recovered cDNA can be recloned into the expression vector for additional cycles of enrichment. After enrichment, individual cDNA clones can be isolated for sequencing.
• the mixture of amplified cDNAs can be used as a sense primer to generate full-length cDNAs of interest. This library of full-length cDNAs can then be subjected to clonal isolation to obtain a single cDNA. Each cloned cDNA can then be sequenced, expressed and characterized.
• Any signal sequence that does not exhibit identity or significant homology to known signal sequences contained within available sequence data bases represents a fragment of a cDNA that encodes a novel secreted protein.
• new signal sequence can be used as a hybridization probe or as a PCR primer to isolate its endogenous, full-length structural coding sequence.
• novel secreted proteins such as cytokines, growth factors, and transmembrane proteins, may be cloned and identified without the need for previous development of a bioassay system specific for such protein.
• Another method for selecting functional signal sequences involves a biological selection scheme.
• Such biological selection protocol is an attractive alternative to automated cell sorting/selection, since it does not require an expensive, specialized piece of equipment (for instance, a flow cytometer) , and can be conveniently performed in most laboratory settings.
• a signal sequence cDNA library is inserted into an expression vector (as described above in Section B.I.), and this expression vector is introduced into a factor-dependent cell line.
• the expression vector encodes a leader-less structural protein.
• Structural proteins suitable for use within this biological selection method include cell surface receptors that are capable of mediating intracellular signal transduction. It is preferred that such signal transduction directly or indirectly causes stimulation of cell proliferation.
• Preferred structural proteins in this regard include Mpl, IL-4 receptor, EPO receptor, GM-CSF receptor and the like.
• Suitable factor-dependent cell lines in this regard include growth factor-dependent myeloid and lymphoid progenitor cells. These are cells that give rise to differentiated blood cells and that are found in hematopoietic tissue, such as bone marrow, spleen and fetal liver. Myeloid and lymphoid precursors are also found in peripheral blood after treatment of an animal with cytokines.
• Preferred growth factor-dependent cell lines that can be transfected to express detectable receptors include BaF3 (Palacios and Steinmetz, Cell 41: 727-34, 1985; Mathey-Prevot et al. , Mol. Cell. Biol. £: 4133-35, 1986), FDC-P1 (Hapel et al .
• growth factor-dependent cell lines can be established according to published methods (e.g., Greenberger et al. , Leukemia Res. £: 363-75, 1984; Dexter et al. , in Baum et al. Eds. , Experimental Hematology Today , 8th Ann. Mtg. Int. Soc. Exp. Hematol. 1979, 145-56, 1980) .
• preferred factor-dependent cell lines readily take up exogenous DNA and have a known receptor subunit repertoire.
• One of ordinary skill in the art will recognize that certain characteristics of some factor-dependent cell lines may be used to select particular cell surface-expressed structural proteins as preferred marker elements in the selection vector to be employed. For instance, for a BaF3 host cell, leader-less IL-4, EPO and GM-CSF receptor coding regions may be substituted for the Mpl coding region of the selection vector.
• an EGF receptor structural gene is suitable, while a Tyro 3 receptor structural gene is not (see, for example, Stitt et al .
• TPO thrombopoietin
• cDNAs encoding functional signal sequences can be selected by growing factor-dependent expression host cells in the absence of the required factor, but in the presence of TPO.
• the factor-dependent cell line is BaF3
• the required factor for parental factor-dependent cell proliferation is IL-3.
• Factor- dependent expression host cells that do not contain a functional signal sequence cannot express Mpl at the cell surface. Therefore, if the factor required for parental cell growth is absent, these factor-dependent expression host cells that do not contain a functional signal sequence will not survive when cultured with TPO.
• Functional signal sequence cDNAs of interest may be isolated clonally or en masse from the entire surviving factor-dependent expression host cell population, as described in Section B.2., above, for fluorescence activated flow cytometry-selected cells. Both the cell sorting and biological selection methods described above permit enrichment of functional signal sequence coding regions with minimal screening.
• the invention is further illustrated by the following non-limiting examples.
• Plasmid pHZ-1 is an expression vector that may be used to express protein in mammalian cells or in a frog oocyte translation system from mRNAs that have been transcribed in vi tro .
• the pHZ-1 expression unit comprises the mouse metallothionein-1 promoter, the bacteriophage T7 promoter flanked by multiple cloning banks containing unique restriction sites for insertion of coding sequences, the human growth hormone terminator and the bacteriophage T7 terminator.
• pHZ-1 contains an E. coli origin of replication; a bacterial beta-lactamase gene; a mammalian selectable marker expression unit comprising the SV40 promoter and origin, a neomycin resistance gene and the SV40 transcription terminator.
• Xho I/Sal I cDNA fragments encoding the mature murine Mpl in each of three reading frames.
• the sequence encoding murine Mpl has been described by (see, for example, Skoda et al . , EMBQ J, 12:2645-53, 1993; Vigon et al . , Onco ⁇ ene £:2607- 15, 1993) .
• Leader-less Mpl-encoding cDNAs were isolated by PCR amplification from a full length mouse Mpl cDNA template using (i) an antisense primer containing a Sal I site (GAG GAG AAG GTC GAC TCA AGG CTG CTG CCA ATA GCT TAG; Sal I site underlined; SEQ ID NO: 1) ; and (ii) each of three sense primers containing a Xho I site in one of three reading frames with respect to the Mpl coding sequence.
• the resultant plasmids were designated as pSLSV-1, pSLSV-2 and pSLSV-3, which upon digestion with Eco RI and Xho I facilitate the cloning of leader sequences.
• pSLSV-1 (Frame 1) : CTC GAG GG(T) CAA GAT GTC TTC SEQ ID NO: 2 Leu Glu Gly Gin Asp Val Phe
• the underlined portions of frames 1-3 indicate a complete or partial Xhol recognition sequence.
• the " (T) " indicates substitution of thymine for the adenine present in the native Mpl signal peptide cleavage site.
• huGM-CSF human GM-CSF
• huGM-CSF mature sequence See, for instance, Wong et al . , Science 228 : 810-15, 1985.
• inserts were placed in frame in the appropriate pSLSV expression vector: (1) 1-66 huGM-CSF, wherein the insert encoded the 17 amino acid signal peptide plus 49 amino acids beyond it; (2) 1-133 huGM-CSF, wherein the insert encoded the 17 amino acid signal peptide plus 116 amino acids beyond it; and (3) 1-17 huGM-CSF, wherein the insert encoded the 17 amino acid signal peptide only.
• Negative control inserts included: (a) 18-116 huGM-CSF, wherein the insert encoded 116 amino acids beyond the signal peptide, but did not encode a signal peptide; and (b) 18-66 huGM-CSF, wherein the insert encoded 66 amino acids beyond the signal peptide, but did not encode a signal peptide.
• Another negative control inserted an ATG (met) codon next to the leaderless-Mpl coding region, to show that Mpl was not secreted in the absence of a signal peptide.
• plasmids were transfected into IL-3- dependent BaF3 cells in RPMI medium using electroporation, and 10 5 cells/ml were cultured overnight in the presence of IL-3 (5% WEHI conditioned medium) .
• the transfected BaF3 cells were plated in microtiter plates at 500 cells/well, and cultured in the presence of G418 and recombinant TPO (100 units/ml) .
• G418 selects transfectants that contain the pHZ-1 plasmid (neomycin resistance) .
• Modifications to this protocol include: (i) growing the transfectants in the presence of IL-3 for 1, 2, or 4 days before switching to TPO selection; and (ii) testing various concentrations and species of recombinant TPO. For the first, survival of TPO-dependent clones was better when the described manipulation occurred day 1 or day 2, rather than at day 4. With the second, increasing the TPO concentration may increase the sensitivity of the method, permitting more survivors to be detected.
• IL-3 rescue experiments were conducted. Transfected cells were incubated as a pool overnight in the presence of IL-3. On day 1, the cells were washed and plated in microtiter plates in the presence of TPO and G418. On day 2, 4 or 7, IL-3 was added ("IL-3 rescue") to the wells. Clones were observed with day 4 and day 7 IL-3 rescue.
• a secretion trap library is constructed by digestion of the released cDNA with Xho I, and is directionally cloned into a vector preparation consisting of equal molar amounts of Eco Rl/Xho I-digested pSLSV-1, pSLSV-2 and pSLSV-3.
• the amounts of captured cDNA fragments are limiting, they can be amplified by PCR using the 5' and 3 ' PCR primers prior to cloning into the selection vector.
• the cells are cultured in the presence of G418 and thrombopoietin, but in the absence of IL-3.
• Mpl when expressed on the surface of BaF3 cells, couples into the proliferative pathway, such that in the presence of its ligand thrombopoietin, the host cell exhibits growth independence from other exogenous growth factors (e.g., IL-3) .
• functional secretion sequences are isolated using RT-PCR from cell RNA or PCR from cell genomic DNA, employing a 5' sense primer to the vector sequence and a 3 ' antisense primer spanning the vector Xho I site.
• PCR isolation of secretion leader sequences may be performed using isolated clones of cells, or using a pool of cells in an en masse PCR reaction. Secretion leader sequences may be cloned into the selection vector for a further round of enrichment in BaF3 cells. .
• Full-length cDNA from which the secretion sequence originated can be isolated by PCR from a oligo- dT-primed cDNA library, employing a 5' sense primer synthesized to the secretion sequence and a 3 ' antisense primer directed to an anchor sequence attached to the oligo-dT cDNA synthesis primer. Alternatively, a totality of signal sequences are used as sense primer to amplify full-length cDNA en masse.

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