EP1879448A2 - Compositions et méthodes liées au serpin spi6 - Google Patents

Compositions et méthodes liées au serpin spi6

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Publication number
EP1879448A2
EP1879448A2 EP06748251A EP06748251A EP1879448A2 EP 1879448 A2 EP1879448 A2 EP 1879448A2 EP 06748251 A EP06748251 A EP 06748251A EP 06748251 A EP06748251 A EP 06748251A EP 1879448 A2 EP1879448 A2 EP 1879448A2
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Prior art keywords
spi6
animal
activity
cell
cells
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German (de)
English (en)
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Philip G. Ashton-Rickardt
Manling Zhang
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University of Chicago
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University of Chicago
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    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
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    • C07K14/81—Protease inhibitors
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    • C07K14/811—Serine protease (E.C. 3.4.21) inhibitors
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    • G01N33/5082—Supracellular entities, e.g. tissue, organisms
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    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
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    • A01K2217/00—Genetically modified animals
    • A01K2217/07—Animals genetically altered by homologous recombination
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    • G01N2333/811—Serine protease (E.C. 3.4.21) inhibitors
    • G01N2333/8121—Serpins

Definitions

  • Proteolysis is crucial to a wide variety of cellular processes including programmed cell death (PCD), necrosis and cell differentiation.
  • PCD programmed cell death
  • necrosis and cell differentiation.
  • Homeostatic regulation of serine proteases is mainly achieved through interaction with inhibitors belonging to the Serine Protease Inhibitor (serpin) superfamily (Silverman et al., 2001). Serpins are involved in many cell metabolism states.
  • Serpin Serine Protease Inhibitor
  • compositions and methods related to serpins and cellular and organismal conditions related to serpins are disclosed.
  • FIG. 2 shows the protease specificity of Spi6.
  • A Purification of Spi6 (43kD).
  • B Inhibition of protease by S ⁇ i6 in vitro. Proteases (2OnM) were incubated with rSpi ⁇ (20OnM) over time at 37°C then assayed against labeled peptide substrate. The activity was compared with that of protease alone controls (100% activity, 0% inhibition) and the % of inhibition determined.
  • cysteine proteases the following substrates (Calbiochem, San Diego, CA) were used: cathepsin B, cathepsin L, Z-FR- /?N A; in reaction buffer (20OmM KH 2 PO 4 , 2mM EDTA, pH6.1) caspase 1, (Ac-WEHD- ⁇ NA; caspase 3, Ac- DEVD-- pNA; in reaction buffer (5OmM HEPES pH 7.4, 10OmM NaCl, 1OmM DTT, ImM EDTA, 10% glycerol, 0.1% CHAPS).
  • Figure 3 shows intrasplenic injection of DCs primes CD8 T cell expansion. Immature C57BL/6 DCs unpulsed or pulsed with the LCMV GP33 peptide (10 3 ) were injected into the spleen of C57BL/6 mice.
  • FIG. 7 shows Spi6 KO BMDCs are susceptible to CTL-induced PCD.
  • A DNA fragmentation in GP33-pulsed BMDCs (Target, T) was measured after 4 h incubation of P14 CTLs (Effector, E) over a range of E/T ratios, as described before (Matzinger, 1991). Each value is the mean of 12 determinations from
  • BMDCs from 3 mice ⁇ SEM (A) BMDCs from B6 and Spi ⁇ KO mice. (B) BMDCs from B6 with or without CMA (35nM).
  • FIG. 5 shows Spi6 KO BMDCs are no more susceptible to Fas-induced PCD than are B6 BMDCs. Cells were incubated with anti-Fas mAb (JO2) for 16h with cyclohexamide. 9. Figure 6A shows Spi6 KO BMDCs are susceptible to CTL-induced lysis. Increased CTL-induced
  • PCD of Spi6 KO gave rise to increased lysis as measured by 51 Cr-release from GP33-pulsed BMDCs after 4 h incubation with P14 CTLs.
  • Figure 6(B) show a lower number of LCMV-specific CTLs in S ⁇ i6 KO mice.
  • the absolute number of GP 33 tet + CD8 + cells is indicated for B6 and Spi6 KO mice and was determined 8 d after infection with LCMV Armstrong (2 x 10 5 PFU/mouse). 10.
  • Figure 7 shows the occurence of more PCD of LCMV-specific CTLs in Spi ⁇ KO mice. Values are the mean absolute number of 5 determinations from individual mice ⁇ SEM.
  • Figure 8 shows altered expansion and contraction of LCMV-specific CD8 T cells in Spi6 KO mice. Each value is the mean from 5 determinations from PBLs of individual mice ⁇ SEM.
  • Figure 9 shows decreased IFN- ⁇ in Spi6 KO mice. Mice were infected with LCMV then IFN- ⁇ measured in the serum over time by ELISA. Data is the mean from 4 mice ⁇ SEM.
  • Figure 10 shows lower NK cell activity against Cr-labeled tumor cells from the spleen of Spi ⁇ KO mice compared to B6 controls.
  • A The lysis of 51 Cr-labeled YAC target cells by spleen cells was measured after 4 h.
  • B Spleen cells were incubated with YAC targets for 4 h at which point they were stained with anti-DX5-PE to identify NK cells and the DNA dye YOPRO-I to identify apoptotic cells then by FCM (Opferman et al., 2001). In both parts the data is the mean from 4 separate mice ⁇ SEM.
  • Figure 11 shows the clearance of LM from Spi ⁇ KO mice. Mice were infected i.p. with LM (10 5 CFU) mice. Over time mice were killed and the spleens and livers removed and homogenized and 10-fold serial dilutions of organ homogenates plated on Trypticase-soy agar. Bacterial colonies were counted after incubation at 37° C for 24 hours. Each titer is the mean of 4 determinations on individual mice ⁇ SEM. 15.
  • Figure 12 shows decreased IFN- ⁇ in Spi ⁇ KO mice. Mice were infected with 10 5 LM and cytokine levels determined by ELISA. The data are the mean ⁇ SEM of 4 mice.
  • Figure 13 shows leukocyte numbers in Spi ⁇ KO mice. Mice were infected with 10 s LM then after 3 d the % of cells determined in the spleen by staining for phenotypic markers and FCM. The data are the mean ⁇ SEM of 4 mice. 17. Figure " ⁇ 4 snow ' s decreased LM-specific CD8 T cells in Spi6 KO mice. Mice were infected with
  • Figure 15 shows granzyme B in P14 CTLs.
  • the specific activity (units (U)/mg total protein) of enzymes was measured in GP33-specific CTLs from B6 and Grn B KO mice.
  • Figure 16 shows no granzyme B in granulocytes.
  • the specific activity (units (U)/mg total protein) of enzymes was measured in peritoneal cells from B6 and Grn B KO mice.
  • FIG. 17 shows increased uptake and killing of LM by Spi6 KO granulocytes.
  • Granulocytes were elicited by glycogen and the mice infected i.p. with LM.
  • A The titer in peritoneal cells was determined after lysis in 0.2% NP40 over time.
  • B After 2h, the titer of intracellular and extracellular LM was determined and combined to give the total titer. All data is the mean of 4 mice ⁇ SEM.
  • Figure 18 shows granulocyte function from mixed bone-marrow chimeras. Glycogen elicited granulocytes from mixed chimeras were purified by FACS (Spi6 KO CD45.1+, B6 CD45.2+) and mixed with LM in vitro. After 2h, the titer of extracellular and intracellular LM was determined and combined to give the total titer. All data is the mean of 4 mice ⁇ SEM.
  • FIG. 19 shows expression o ⁇ Spi ⁇ in CD8 + T cells.
  • B-D Gene expression was determined using real-time PCR, and is reported as a ratio compared with the control, cyclophilin A. Histograms represent individual determinations of two independent isolates (black and white), which contained cells purified from the pooled splenocytes of 5-10 mice. The expression of Spi6 and granzyme B was significantly higher in effectors and memory cells compared with naive cells. Negligible expression of MHC class //in all populations indicated the absence of contamination by APCs. * ,p ⁇ 0.05, ** , p ⁇ 0.01, *** ,p ⁇ 0.001.
  • FIG. 23 Figure 20 shows that Spi6 protects T cells specifically from granzyme B-mediated apoptosis.
  • A Jurkat clones transfected with the Spi6 cDNA or CD2 expression cassette vector (V) were incubated in the presence of sublytic concentrations of perform with (M) or without (M) granzyme B, or ( ⁇ ) in medium alone (-). Apoptosis was significantly reduced in the Jurkat clones transfected with Spi6, compared with Jurkat clones transfected with vector alone.
  • B Transfected Jurkat clones were cultured in the presence of medium alone (-), Ab against Fas (anti-Fas), or exposed to gamma-irradiation (T-IR).
  • Apoptosis initiated by these stimuli did not differ between Jurkat clones transfected with Spi6 compared with controls, indicating that S ⁇ i6 protects specifically from granzyme B-mediated apoptosis. Histograms are the mean ⁇ SEM from three determinations. * , p ⁇ 0.05.
  • Figure 21 shows the expression of Spi6 in B6 and Spi6 mice.
  • B Cells were isolated from two to four B6 and Spi6 mice (C), pooled, and the expression level of Sp ⁇ 6 determined by real-time PCR. Histograms are the mean of three determinations.
  • FIG. 25 shows enhanced memory cell development in Spi6 mice.
  • Spi6 (D), B6 ( ⁇ ), and GrnBKO (JB) mice were infected with LCMV, and memory cells detected in the spleen >180 days later by measuring ex vivo IFN-! production.
  • A, Spi6 and GrnBKO mice had significantly higher percentages of memory cells than Bt'mice.”
  • ⁇ , ' Th ' e ab'solu ⁇ e number of memory cells generated was higher in Spi6 mice than B6 mice
  • Histograms are the mean ⁇ SEM from combined experiments (n - 7-9 mice per group). * ,p ⁇ 0.05, ** ,p ⁇ 0.01, when compared with B6 mice.
  • FIG. 26 shows expression of Spi6 in CD8 + T cells increases the level of memory cells.
  • Naive CD8 + T cells from P14 and P14 x Spi6 mice, both Thyl.2 + were purified using magnetic beads and adoptively transferred to Thyl.l + congenic recipients. Recipients were infected with LCMV and more than
  • Thyl .2 The percentage of resident memory cells (Thyl .2 " ) was no different between recipients receiving P14 cells or P14 x Spi6 cells (p > 0.05).
  • FIG. 27 shows increased survival of S ⁇ i6 KO mice after bacterial infection.
  • P.aeruginosa 50ml; 0.05OD
  • FIG. 25 shows an increased bactericidal activity of Spi6 KO granulocytes.
  • Thioglycolate elicited granulocytes were harvested from the peritoneum of C57BL/6 (B6) and Spi6-deficient (Spi6 KO) mice
  • Figure 26 shows the survival of Spi6-/- mice relative to wild type mice after bacterial challenge.
  • FIG. 27 shows Spi6 is a physiologic inhibitor of elastase in mouse granulocytes.
  • Organelle and cytosolic fractions were obtained from glycogen-elicited granulocytes (Fig. 16) and the activity of elastase determined by measuring the hydrolysis of fluorescently labeled peptide substrate specific for elastase but not other related proteases (e.g. PR-3 or cathepsin G - Fig. 2B).
  • Figure 28 shows the development of neutrophils as presented in Borregaard and Cowland, 1997.
  • Figure 29 shows a method of producing Spi6 deficient mice, (a) Homologous recombination between the Spi ⁇ targeting vector and wild-type allele in ES cells as detected by altered restriction fragments [Hind Ul (H), Spel (bjj using :>'"and 3' external probes. Cre induced loxP (filled arrows) mediated excision of neo resulting in restriction fragments of altered size (kb).
  • Figure 32 shows increased GrB activity and apoptosis in Spi6 KO CTLs. Mean specific activity
  • Figure 34 shows Spi6 inhibits HNE. (a) Kinetics and (b) stocbiometry of inhibition of NE activity by rSpi ⁇ .
  • Figure 35 shows Spi6 expression in leukocytes.
  • RNA was extracted from purified cell populations and cDNA synthesized. Neutrophils were elicited from the peritoneum by injection with glycogen.
  • Cells were isolated from 3 B6 mice, pooled and real-time PCR for Spi6 and the cyclofilin A housekeeping gene performed. Histograms are the mean of 3 determinations.
  • Figure 36 shows increased NE activity in S ⁇ i6 KO neutrophils.
  • Neutrophils were harvested by lavage with PBS (ImI) of the peritoneum 4h after i.p. injection with 15% glycogen (Sigma Aldrich, St. Louis MO) then activated for 24 h with E. coli (2xlO 6 /ml) at 37 0 C .
  • FIG. 37 shows Spi6 KO neutrophils are susceptible to death.
  • (A) Death (mean % PI + ) and (B) apoptosis (mean %Y0P0R0) ⁇ SEM (n 4 mice) after stimulation in vitro with E. coli.
  • YORPRO-I detects the early onset of apoptosis be measuring changes in DNA.
  • Figure 43 shows the effect of exogenous HNE on immunity to P. aeruginosa.
  • P. aeruginosa titer ⁇ SEM
  • Figure 44 shows anti-serum that detects Spi6 in neutrophils.
  • FCM plot showing staining of glycogen-elicited neutrophils from B6 (blue histogram) or S ⁇ i6 KO mice (red histogram), with anti-rS ⁇ i6 antiserum (4 ⁇ l).
  • the secondary antibody was goat anti-rabbit IgG-APC.
  • Figure 45 shows the N-terminal sequence of the ova-family of serpins. Bold residues are charged. The hydrophobic elements are boxed. The positions of the hA and hB ⁇ -helices are indicated. The S ⁇ i6 mutants lacking hA and hB domains are indicated. Residues in lower case are those added during cloning.
  • Figure 46 shows the sequences of siRNAs. Only shown are the sense strands of RNA duplexes. Starting positions for PI9 gene (SERPINB9, accession No NM004155) is indicated. PI9 sequences were selected based on an aligorithim that optimize siRNA gene silencing based on 8 independent criteria (Reynolds et al., 2004).
  • Figure 47 shows impaired survival and function of Spi6 KO CTLs.
  • (b) Mean number gp33 + CD8 + cells ⁇ standard error of the mean (s.e.m.) (n 5 individual mice),
  • Figure 48 shows the effect of Spi6 on CTLs is dependent on GrB.
  • B6 and Spi6 KO mice were infected with LCMV Armstrong (2x10 5 pfu/mouse i.p.) then after 8d the (a) mean number of gp33 + CDS + spleen cells and (b) mean percentage YOPRO-I + of gp33 + CD8 + cells determined.
  • P14 CD8 T cells (10 4 ) were purified from B6 or Spi6 KO mice and adoptively transferred to wild-type B6 mice, then infected with LCMV clone 13 (10 6 pfu/mouse i.v.).
  • LCMV clone 13 (10 6 pfu/mouse i.v.).
  • Figure 51 shows Spi6 deficiency destabilizes lytic granules
  • (a) Distribution of the number OfGrB + granules per P14 CTL (n 300 cells). The mean values are indicated
  • (b) Effect of Z-AAD (OMe)-CMK on the number Of GrB + granules per P14 CTL ⁇ s.e.m (n 300 cells)
  • (c) Mean SA of GrA in the granule fractions of P14 CTLs ⁇ s.e.m (D 4 individual mice).
  • Figure 52 shows survival and activity of Spi6 KO neutrophils.
  • C) lysis (mean extracellular LDH activity) ⁇ SEM (n 4 mice) after stimulation in vitro with E. coli.
  • E Effect of HNE (0.12U) on E. coli titer measured after 240 min. 56.
  • Figure 53 shows the effects of Spi6 deficiency and HNE on bacterial immunity.
  • Table 3 shows cell numbers in B6 and Spi6 mice (Xl O 6 ).
  • Table 6 shows the effect of Spi6 deficiency on NE and neutrophils in the lung after P. aerginousa infection.
  • data is provided in a number of different formats, and that this data, represents endpoints and starting points, and ranges for any combination of the data points. For example, if a particular data point "10" and a particular data point 15 are disclosed, it is understood that greater than, greater than or equal to, less than, less than or equal to, and equal to 10 and 15 are considered disclosed as well as between 10 and 15. It is also understood that each unit between two particular units are also disclosed. For example, if 10 and 15 are disclosed, then 11, 12, 13, and 14 are also disclosed.
  • Primer are a subset of probes which are capable of supporting some type of enzymatic manipulation and which can hybridize with a target nucleic acid such that the enzymatic manipulation can occur.
  • a primer can be made from any combination of nucleotides or nucleotide derivatives or analogs available in the art which do not interfere with the enzymatic manipulation.
  • Probes are molecules capable of interacting with a target nucleic acid, typically in a sequence specific manner, for example through hybridization. The hybridization of nucleic acids is well understood in the art and discussed herein. Typically a probe can be made from any combination of nucleotides or nucleotide derivatives or analogs available in the art.
  • immunological memory refers to the physiological condition characterized by antigen-specific lymphocytes with the ability to provide recall responses upon future antigen experience which remain after an initial antigen experience and that cause a quicker immune response to the same antigen than a response in a similar organism which had not previously been challenged by the antigen. It is understood and herein contemplated that the lymphocytes that provide this protection can be CD4 or CD8 T-cells specific for the antigen.
  • Memory means a response of the pool of immune cells that are produced after antigen stimulation that will last for the life of an organism after antigen presentation.
  • Na ⁇ ve cell or “na ⁇ ve cells” mean a cell that has not been exposed to antigen presentation.
  • compositions and methods are related to Serpins, such as S ⁇ i6 and PI9.
  • compositions such as specific mice which overexpress Spi6, and mice which have their native Spi6 disrupted producing a knockout phenotype. These mice, both the Spi6 overexpressing mice and the Spi6 knockout mice and numerouse experiments disclosed herein with these mice have identified a number of roles for Spi6 in the general inflammation process, as well as specific roles, such as its role in Granzyme
  • Proteolysis is crucial to a wide variety of cellular processes including programmed cell death (PCD), necrosis and cell differentiation.
  • PCD programmed cell death
  • necrosis necrosis
  • cell differentiation homeostatic regulation of serine proteases is mainly achieved through interaction with inhibitors belonging to the Serine Protease Inhibitor (serpin) superfamily
  • Inhibitory serpins have a common mode of action: each contains a variable C- terminal reactive center loop (RCL) resembling the substrate of its cognate protease. On protease binding, the (RCL) is cleaved between the two residues designated Pi and P'i and it undergoes a conformational change that distorts the protease and irreversibly locks the serpin-protease complex (Silverman et al., 2001). 75.
  • CCL reactive center loop
  • Such "ovalbumin” serpins include the “ “ “ “ “ “ “ ' fiuman proleinase iMihh ⁇ s”& (FL-6), 8 (PI-8), and 9 (PI-9), plasminogen activator inhibitor 2, and the monocyte/neutrophil elastase inhibitor.
  • serpins of the family that resembles chicken ovalbumin (ova-serpins) inhibit both serine and cysteine proteases in the cytoplasm (Bird, 1998).
  • the cowpox serpin Crm A inhibits both granzyme B and caspases 1 and 8 (Komiyama et al., 1994; Quan et al., 1995; Zhou et al., 1997).
  • PI-9 is a potent granzyme B (graB) inhibitor that has an unusual
  • Pl GIu is present primarily in lymphocytes.
  • elastase inhibitors include, but are not limited to human secretory leukocyte proteinase inhibitor SLPI (SEQ ID NOS 30 and 31), mouse leukocyte proteinase inhibitor SLPI (SEQ ID NOS 36 and 37), human monocyte/neutrophils elastase inhibitor MNEI (SEQ ID NOS 41 and 42), mouse EIA (SEQ ID NOS 39 and 40), human ⁇ r antitrypsin(SEQ ID NOS 28 and 29), and mouse ⁇ r antitrypsin
  • Spi6 and PI9 are also elastase inhibitors, and so mice transgenic for elastases can also be used to screen for inhibitors of serpins.
  • Serpins characteristically act as "suicide substrates" and inactivate proteases through the formation of a 1: 1 complex (Silverman et al., 2001). However whether or not the inhibition of proteases by serpins occurs through this mechanism seems to depend on the serpin and the protease in question (Al-Khunaizi et al., 2002a; Annand-efe-al->l-999-) ⁇ «" ⁇
  • the serpins act as called “suicide inhibitors,” forming an SDS-stable complex with their target protease. They typically associate with proteases by presenting a "bait” residue, in their reactive center, that is thought to mimic the normal substrate of the enzyme.
  • the bait amino acid is called the Pl residue, with the amino acids toward the amino-terminal side of the scissile reactive center bond labeled in order PI, P2,
  • serpin-like inhibitors of granzyme B that act in a similar fashion as serpin inhibitors.
  • An example of a serpin-like inhibitor is Crm A (SEQ ID NO:24 and 25 for the gene and protein sequences respectively).
  • CrmA is a serpin-like protease encoded by cowpox virus. CrmA has been shown to be an inhibitor of granzyme B (Smith et al., 1996).
  • Substrates for the disclosed serpins can include, but are not limited to: granzyme B, cathepsin G (P28293), PR-3 (Q61096), neutrophil elastase (NP031945), mouse mast cell protein (MMCP) -1 (P11034), MMCP-2 (P15119), MMCP-3 (P21843), MMCP-4 (P21812), MMCP-5 (P21844), MMCP-8 (P43430), MMCP-9 (035164), MMCP-IO (AAK51075), or caspase 1 (P29452).
  • NK cells In addition to CTLs, natural killer (NK) cells also use the perforin/granzyme B pathway to kill tumor or virally infected cells. However, unlike CD8 T cells, NK cells can kill immediately upon encountering a target without the need for further differentiation. 83. Mast cells and basophils, which are activated by immunoglobulin E (IgE) and allergen, play a prominent role in anaphylaxis. However, they express at least three types of IgE receptor, including the high affinity IgE receptor (Fc epsilon RI).
  • IgE immunoglobulin E
  • PI9 Proteinase Inhibitor 9 (SEQ ID NOs 1 and 2, for gene and protein sequences, respectively) is a potent inhibitor of granzyme B (Sun et al., 1996).
  • Serine Protease Inhibitor 6 (Spi6) is a homologue of PI9, can also inhibit granzyme B (Sun et al., 1997a).
  • SPI6 comprises a 1.8-kilobase cDNA (SEQ ID NO:3) encoding a 374-amino acid polypeptide (SEQ ID NO:4) that is 68% identical to PI-9 (SEQ ID NO:2).
  • SEQ ID NO:3 a 1.8-kilobase cDNA
  • SEQ ID NO:4 a 374-amino acid polypeptide
  • the GIu single amino acid code -E
  • Both Spi6 and PI9 have a Cys-Cys motif in the Pl' and P2 'positions and are 69% homologous in the RCL.
  • Spi6 and PI9 refer to any protein having the functional activity of the Spi6 set forth in SEQ ID NO:4 and PI9 set forth in SEQ ID NO:2.
  • PI9 is located in the cytoplasm of cytolytic lymphocytes (CTLs and Natural. Killer (NK) cells) and activated
  • APCs such as macrophages and dendritic cells (DCs)(Bladergroen et al., 2001; Hirst et al., 2003).
  • Both PI9 and Spi6, when over expressed can protect cells from granule-mediated PCD through the inhibition of granzyme B (Medema et al., 2001a; Medema et al., 2001b ). Therefore it has been suggested that a physiological function of PI9 and Spi6 is to protect healthy cytolytic lymphocytes and DCs from "misdirected" granzyme B, which leaks into the cytoplasm during upon activation (Bird, 1999). Support for this view comes from the observation that over expression of PI9 in human CTLs increases survival and potency (Hirst et al., 2003).
  • proteases that contain homologous sequences to granzyme B that may serve as targets of Spi6.
  • proteases include: cathepsin G (P28293), PR-3 (Q61096), neutrophils elastase
  • MMCP mouse mast cell protein
  • MMCP mouse mast cell protein
  • P11034 mouse mast cell protein
  • MMCP-2 P15119
  • MMCP-3 P21843
  • MMCP-4 P21812
  • MMCP-5 P21844
  • MMCP-8 P43430
  • MMCP-9 (035164), MMCP-10 (AAK51075).
  • methods of protecting T cells from the granule exocytosis pathway of programmed cell death comprising administering a vector expressing a Spi6 nucleic acid or a PI9 nucleic acid. Also provided are methods of protecting T cells from the granule exocytosis pathway of programmed cell death, comprising administering an effective amount of SPI6 or PI9 protein, or a fragment thereof. It is understood that any means of overexpressing Spi6 or PI9 would be aid in protecting T cells from the granule exocytsis pathway of programmed cell death.
  • Cytolytic activity may also regulate the priming of CTL responses by DCs. Elimination of antigen-specific DCs by cognate CTLs and the suppression of secondary immune responses has been observed in several mouse models (Hermans et al., 2000; Loyer et al., 1999). It has been suggested that in perforin- deficient mice, DCs are protected from CTL activity and so are better able to prime the expansion of antigen-specific CD8 T cells (Badovanic et al., 2000; Loyer et al., 1999; Stepp et al., 1999).
  • the memory phase can extend for the lifetime of the host (Sprent et al., 2002), providing immunity as the result of both an increased precursor frequency of Ag-specific cells and improved function compared with naive cells (Berard et al., 2002).
  • the potency of memory responses is due to an increase in the frequency of antigen-specific lymphocytes and also to the qualitatively more effective response of memory CD8 T cells (Ahmed and
  • T-cell immunity is the sum effect of changes occurring in all three phases of the T cell response, which are priming /expansion, death and memory.
  • the induction of PCD during the contraction phase is critically dependent on another effector molecule produced by cytolytic lymphocytes - interferon - ⁇ (IFN- ⁇ )(Badovanic et al., 2000; Badovinac et al., 2004).
  • IFN- ⁇ interferon - ⁇
  • NE neutrophil elastase
  • CG cathepsin G
  • PR-3 Rao et al., 1991. While playing a protective role in host immunity, neutrophils and their serine proteases have also been implicated in numerous inflammatory diseases (Malech and Gallin, 1987). In addition to circulating serpins, intracellular ova-serpins have been implicated in the control of azurophilic granule proteases.
  • Proteinase inhibitor 6 PI6 is a potent inhibitor of CG in the cytoplasm of monocytes and neutrophils (Scott et al., 1999). In addition to granzyme B, PI9 also inhibits NE and PI9 derived peptide substrates are specifically recognized by PR-3 (Dahlen et al., 1999; Korkmaz et al., 2002).
  • granzyme B is a phenotypic marker for NK cells and CTLs
  • PMNL polymorphonuclear leukocyte
  • ADCC antibody-dependent cellular cytotoxicity
  • perform has been implicated in controlling both the expansion of activated Ag-specific cells (Badovinac et al., 2000; Badovinac et al., 2003) and the elimination of activated CD8 + T cells after viral infection (Kagi et al., 1999) in graft-vs-host disease (Spaner et al., 1999) and during chronic infection (Matloubian et al., 1999; Gallimore et al., 1998). Because perform is a vehicle for the delivery of granule toxins, thephenotypes observed in perforin-deficient mice could be due to ineffective administration of executioner proteases such as granzymes.
  • COPD chronic obstructive pulmonary diseases
  • Deficiency in ⁇ l-AT leads to a pathological increase in NE activity and neutrophil influx into the lung in humans (Gadek et al., 1981b) and mice (Martorana et al., 1993) and causes about 1-2% of all cases of COPD.
  • the neutrophil constitutes the first line of defense in protecting the host from invading bacterial and fungal pathogens. It is a highly potent cytotoxic cell and possesses an armory of antimicrobial proteins and biochemical pathways that can be used in this protective role (Bainton, 1999). Neutrophils have a relatively short half-life in the circulation of between 8-20 h and so to provide the first line of defense are produced in large numbers (40-65% of white blood cells) and are highly motile being able to leave the circulation and enter infected tissues.
  • PMCs promyelocytes
  • MPO myeloperoxidase
  • NE neurotrophil elastase
  • Cat G cathepsin G
  • PR-3 proteinase-3
  • hydrolytic enzymes and lysozyme are capable of proliferation and cell line HL-60 was originally isolated from a patient with promyelocytic leukemia (Collins et al., 1977).
  • Myelocytes (MC) accumulate large numbers of so-called specific granules (Borregaard and Cowland, 1997).
  • MMC myelocytes
  • BC band cells
  • Segm segmented cells
  • Phagocytic neutrophils confer immunity by engulfing invading microbes (Metchnikoff, 1905). It was supposed that killing was effected by the contents of cytoplasmic granules released into the phagocytic vacuole in which the microbe was encapsulated. This hypothesis was supplanted by the supposition that the killing agents were toxic"reacl ⁇ ve”oxygen species (ROS)(Mandell, 1974; Sbarra and Karnovsky, 1959), supported by the discovery of chronic granulomatous disease (CGD), a human condition characterized by profound susceptibility to bacterial and fungal infection (Gallin and Malech, 1990).
  • ROS chronic granulomatous disease
  • mice deficient in serine proteases from azurophil granules have confirmed the original supposition that the contents of cytoplasmic granules kill microbes.
  • Mice deficient in NE were susceptible to lethal infection with the gram-negative bacteria Klebsiella pneumonaie and Escherichia coli and the fungus Candida albicans, because neutrophils from these mice failed to digest the microbes after encapsulation (Belaaouaj et al., 1998; Reeves et al., 2002).
  • coli by digesting the cell wall protein Omp A (Belaaouaj et al., 2000) and can cleave Pseudomonas aeruginosa flagellin, implying that NE prevents infection by inhibiting attachment to host epithelium (Lopez-Boado et al., 2004).
  • Cat G KO mice are susceptible to gram-positive Stapliloccocus aureus infection (Reeves et al., 2002) and NE KO x Cat G KO mice are susceptible to infection with the fungi Aspergillus fumigates (Tkalcevic et al., 2000).
  • PR-3 shares similar substrate specificity to NE and Cat G and is also stored in azurophil granules (Rao et al., 1991). However the requirement for PR-3 in protecting against microbial infection has yet to be examined.
  • serine proteases are primary responsible for the destruction of the bacteria. Although it is well established that serine proteases digest engulfed bacteria in phagolysomes, recently it has been shown that secreted NE can kill bacteria trapped by neutrophils in webs of extracellular fibers (Brinkmann et al., 2004). Thus, activated extracellular as well as intracellular serine proteases are important for bacterial killing.
  • COPD chronic obstructive pulmonary diseases
  • NE is clearly a major cause of COPD, recent evidence suggests that it exerts its effects by activating macrophage elastase (macrophage metalloprotein 12, MMP 12), which is required for macrophage-mediated proteolysis and matrix invasion (Shipley et al., 1996).
  • NE activates MMP12 by degrading tissue inhibitor of metalloproteinase (TIMP)-I (Okada et al., 1988), which is an inhibitor of MMP-12 (Shapiro et al., 2003).
  • TIMP tissue inhibitor of metalloproteinase
  • Serine proteases such NE stored in azurophilic granules, play a dominant role in the microbicidal activity of neutrophils by digesting phagocytosed microbes.
  • serine protease inhibitors serine protease inhibitors (serpins) protect against sepsis and other inflammatory diseases by suppressing NE activity.
  • neutrophils drive also the pathogenesis of sepsis by damaging tissue components through the action of microbicidal serine proteases.
  • neutrophil activity may be protective rather than pathological.
  • H. pylori Infection of the gastric mucosa with the gram-negative bacterium Helicobacter pylori occurs in half of the world's population (1994). In all cases, H. pylori induces gastritis and a subset of infections progress to peptic ulceration or gastric cancer (Allen, 2000; Allen, 2001). H. pylori stimulates a novel type of chronic inflammation that is characterized by a massive influx of neutrophils into the gastric mucosa and encounter bacteria in the mucus layer and at ulcer margins (Allen, 2000; Allen, 2001). The leukocytes of the innate immune system rather than lymphocytes seem to play the major role in controlling H.
  • Proteins destined for export to granules contain N-terminal secretory signal sequences, which directs synthesis to the rough endoplasmic reticulum (RER)(Blobel and Dobberstein, 1975). Sorting in the trans-Golgi network (TGN) then segregates proteins destined for the constitutive exocytosis and insertion into the plasma membrane from those that will form storage granules capable of undergoing regulated exocytosis (Sossin et al., 1990).
  • TGN trans-Golgi network
  • Storage granules are formed by aggregation of immature transport vesicles that bud off from TGN (Hartmann et al., 1995), but in neutrophils no common primary amino acid sequence structure has been identified that determines whether a protein is retained or constitutively secreted (Garwicz et al., 1995; Gullberg et al., 1995).
  • the well known targeting of glycoproteins to lysosomes via the cation-dependent and cation-independent mannose 6-phosphate receptor (Dahms et al., 1989) is not required for sorting of proteins to azurophil granules (Castanon et al., 1988; Nauseef et al., 1992).
  • NGAL Neutrophil gelatinase-associated lipocalin
  • HL-60 cells results in storage in azurophil granules (Le Cabec et al, 1996).
  • proteolytic processing affects the maturation of microbidical enzymes as well as granule volume and morphology (Stromberg et al., 1986).
  • PI9 such as the role of S ⁇ i6 or PI9 in inflammatory diseases, including the role of Spi6 in the protection of cytotoxic T-cells from self-inflicted injury and the role of Spi6 in protecting against microbial infection.
  • These cells, vectors, and animals have also elucidated new roles for SPI6 and PI9 and thus, have provide new therapeutic targets and activities.
  • transgenic non-human animals for example, disclosed are transgenic non-human animals, transgenic animal cells, and vectors comprising a disrupted Spi6 gene.
  • the transgenic non-human animals and transgenic animal cells can be a mammal or mammalian cells, respectively.
  • the transgenic non-human animal can be a mouse, a rabbit, a rat, a human, a pig, a hamster, a dog, a horse, a sheep, a goat, or any other mammal capable of transgenic manipulation.
  • cells comprising the disclosed vectors, animals comprising the disclosed cells, and animals comprising the disclosed vectors.
  • the transgenic animal cells can be any cell including, an embryonic stem cell, an embryonic germ cell, a puripotent adult stem cell, a prostate cell, testis cell, bone cell, brain cell, or muscle cell.
  • the transgenic animal cells can also comprise an immortal cell line such as a breast cell, a breast cancer cell, an ovary cell, or an ovary cancer cell.
  • the disrupted S ⁇ i6 gene can be any S ⁇ i6 gene that has a different function than an unaltered Spi6 function.
  • the disrupted Spi6 gene can be a gene that encodes a non-functional SPI6 protein.
  • the disrupted Spi6 gene can comprise a deleted exon, a point mutation, or a missense mutation.
  • the disrupted Spi6 gene can comprise a deleted exon wherein the deleted exon can be any Spi6 exon.
  • the DNA sequence of Spi6 (Accession Number AL589871; SEQ ID NO: 73) and PI9 (Accession Number AL133351; SEQ ID NO: 74) are known as are the cDNA sequence of Spi6 and PI9 are provided as SEQ ID NOs: 3 and 1, respectively and the protein sequences of Spi6 and PI9 which are provided as SEQ ID NOs: 4 and 2, respectively.
  • the disrupted Spi6 gene can comprise a deleted exon wherein the deleted exon Is exon 7.
  • Exon ' 7 contains the RCL and most of the coding region of Spi6, and thus provides a good candidate for disruption.
  • the disrupted Spi6 gene can also comprise other embodiments.
  • the disrupted Spi6 gene can also comprise a marker gene. Suitable marker genes are described below and include the E. coli lacZ gene, G418 resistance gene, HPRT, thymidine kinase, the green fluorescent protein (GFP), and the red fluorescent protein (RFP).
  • the disrupted Spi6 gene can also comprise one or more loxP sites and one or more recombinase sites.
  • the recombinase sites can flank some or all of the Spi6 exons.
  • the recombinase can be a Cre or FIp recombinase.
  • Transgenic non-human animals comprising a disrupted Spi6 gene 113.
  • transgenic non-human animals comprising a disrupted Spi6 gene.
  • the transgenic animal comprising a disrupted Spi6 gene can lack native SPI6 function or can lack native Spi6 expression.
  • the disruption of SPI6 function or Spi6 expression can lead to increased neutrophil elastase activity.
  • the disrupted Spi6 expression can also increase immunity to sepsis causing bacteria without causing inflammatory disease as well as increasing neutrophil function.
  • the neutrophil function of the transgenic animals can be greater than the neutrophil function in a non-transgenic animal.
  • the disrupted Spi6 expression can increase neutrophil recruitment to the site of infection.
  • the increase in neutrophil recruitment to the site of infection can be 2, 3, 4, 5, 6, or 7 fold higher than an animal having non-disrupted Spi6 expression.
  • the disrupted Spi6 expression can also increase the survival of the transgenic animal from septic shock induced death after infection with bacteria.
  • the bacteria can be either gram-negative or gram-positive bacteria.
  • a transgenic animal comprising a disrupted Spi6 gene can increase survival of the animal from septic shock induced death after infection with E. coli, P. aeruginosa, or L. monocytogenes.
  • transgenic non-human animals comprising a disrupted S ⁇ i6 gene wherein the amount of SPI6 produced in the animal is less than the amount of SPI6 produced in a non-transgenic animal.
  • transgenic non-human animals comprising a disrupted Spi6 gene wherein the animal has increased immunity.
  • the transgenic non-human animal can have an increased immunity to bacteria including, but not limited to, E. coli, P. aeruginosa, and L. monocytogenes.
  • transgenic non-human animals comprising a disrupted S ⁇ i6 gene wherein the granulocytes of the animal have increased bactericidal activity.
  • transgenic animals wherein infection of the transgenic animal with E. coli results in increased bactericidal activity of neutrophils than an animal not having a disrupted Spi6 gene.
  • Transgenic animal cell comprising a disrupted Spi6 gene 119.
  • transgenic animal cells comprising a disrupted Spi6 gene.
  • the transgenic animal cell can be a mammalian cell, including a human cell. Examples of other mammals are described above. F20.
  • the ⁇ ans'genic"an ⁇ mal cells comprising a disrupted S ⁇ i6 gene can lack native SPI6 function or can lack native Spi6 expression.
  • the disruption of SPI6 function or Spi6 expression can lead to increased neutrophil elastase activity.
  • the disrupted Spi6 expression can also increase immunity to sepsis causing bacteria without causing inflammatory disease as well as increasing neutrophil function.
  • the neutrophil function of the transgenic animal cells can be greater than the neutrophil function in a non- transgenic animal cell.
  • the disrupted Spi6 expression can increase neutrophil recruitment to the site of infection.
  • the increase in neutrophil recruitment to the site of infection can be 2, 3, 4, 5, 6, or 7 fold higher than an animal cell having non-disrupted Spi6 expression.
  • the disrupted S ⁇ i6 expression can also increase the survival of the transgenic animal cell from septic shock induced death after infection with bacteria.
  • the bacteria can be either gram-negative or gram- positive bacteria.
  • a transgenic animal cell comprising a disrupted Spi6 gene can increase survival of the animal from septic shock induced death after infection with E. coli, P. aeruginosa, or L. monocytogenes.
  • transgenic animal cells comprising a disrupted Spi6 gene wherein the amount of SPI6 produced in the animal is less than the amount of SPI6 produced in a non-transgenic animal cell.
  • transgenic animal cells comprising a disrupted Spi6 gene wherein the animal has increased immunity.
  • the transgenic animal cell can have an increased immunity to bacteria including, but not limited to, E. coli, P. aeruginosa, and L. monocytogenes.
  • transgenic non-human animals comprising a disrupted Spi6 gene wherein the granulocytes of the animal have increased bactericidal activity.
  • transgenic animals wherein infection of the transgenic animal with E. coli results in increased bactericidal activity of neutrophils than an animal not having a disrupted Spi6 gene.
  • vectors comprising a portion of the Spi6 gene, wherein the portion of the Spi6 gene produces a disrupted Spi6 gene, and wherein the vector can homologously recombine with the Spi6 gene.
  • a vector comprising the sequence of SEQ ID NO:72.
  • the vectors can comprise a selectable marker.
  • suitable selectable markers include, but are not limited to, dihydrofolate reductase (DHFR), thymidine kinase, neomycin, neomycin analog G418, hydromycin, and puromycin.
  • the selectable marker can be a positive or negative selection marker.
  • nucleic acid molecules produced by a process, the process comprising linking in an operative way a nucleic acid comprising the sequence of a Spi6 exon and sequence recognized by a recombinase enzyme. Further provided are cells produced by the process of transforming a cell with the nucleic acids produced by such a process.
  • Methods of gene modification and gene disruption can be used for targeted gene disruption and modification in any animal that can undergo these events.
  • Gene modification and gene disruption refer to the methods, techniques, and compositions that surround the selective removal or alteration of a gene or stretch of chromosome in an animal, such as a mammal, in a way that propagates the modification through the germ line of the mammal.
  • a cell is transformed with a vector which is designed to homologously recombine with a region of a particular chromosome contained within the cell, as for example, described herein. This homologous recombination event can produce a chromosome which has exogenous DNA introduced, for example in frame, with the surrounding DNA.
  • This type of protocol allows for very specific mutations, such as point mutations, to be introduced into the genome contained within the cell.
  • Methods for performing this type of homologous recombination are disclosed herein. 129.
  • One of the preferred characteristics of performing homologous recombination in mammalian cells is that the cells should be able to be cultured, because the desired recombination event occurs at a low frequency.
  • an animal can be produced from this cell through either stem cell technology or cloning technology.
  • stem cell technology For example, if the cell into which the nucleic acid was transfected was a stem cell for the organism, then this cell, after transfection and culturing, can be used to produce an organism which will contain the gene modification or disruption in germ line cells, which can then in turn be used to produce another animal that possesses the gene modification or disruption in all of its cells.
  • cloning technologies can be used.
  • Animals which are Spi6 or PI9 knockouts can be generated as discussed in the Examples.
  • the animals which are Spi6 or PI9 knockouts can be produced by a method comprising introducing into a non-human animal fertilized egg a recombinant nucleic acid molecule, which comprises a nucleic acid encoding a disrupted Spi6 gene whereby a transgenic animal expressing disrupted SPI6 is produced.
  • a method comprising administering a vector as described above, to an ES cell, culturing the cell, selecting a cell comprising the vector, fusing the selected cell with a blastocyst, thereby producing a chimera, incubating the chimera, and implanting the chimera into a surrogate mother to produce an offspring.
  • methods of producing an animal the methods comprising fusing the chimera produced by the method above, with another chimera, and selecting live animals homozygous for vector DNA.
  • transgenic non-human animals comprising a cell wherein the cell expresses a transgene coding for a serpin, which in certain embodiments overexpresses the serpin, such as Spi6 relative to a non-transgenic mouse. It is understood that any of the animals disclosed herein can be non-human animals.
  • transgenic animal or cell wherein the serpin is Spi6 or PI9.
  • transgenic animal or cell wherein the serpin is a serpin with at least 60% identity to Spi6, as set forth in SEQ ID NO:4.
  • transgenic animal or cell wherein the serpin is S ⁇ i6, wherein the Spi6 comprises a sequence having at least 90% identity to the sequence set forth in SEQ ID NO:4.
  • transgenic animal or cell wherein the serpin is PI9, wherein the PI9 comprises a sequence having at least 90% identity to the sequence set forth in SEQ ID NO:2.
  • transgenic animal or cell wherein the serpin is PI9, wherein the PI9 comprises a sequence having at least 90% identity to the sequence set forth in SEQ ID NO:4.
  • serpin is Spi6, wherein the Spi6 comprises a sequence in which the complete sequence hybridizes to the sequence set forth in SEQ ID NO:3, wherein the hybridization takes place at 600 mM NaCl, 60 degrees Celcius, buffered to pH 7.6.
  • transgenic animal or cell wherein the serpin is Spi6, wherein the Spi6 comprises a sequence in which the complete sequence hybridizes to the sequence set forth in SEQ ID NO: 3 after a wash of 15m M NaCl, 1.5m M Na3 citrate, 1% SDS, 65 degrees Celsius.
  • transgenic animal or cell wherein the serpin is Spi6, wherein the S ⁇ i6 comprises a sequence in which the complete sequence hybridizes to the sequence set forth in SEQ ID NO:3, wherein the hybridization takes place at 600 mM NaCl, 60 degrees Celcius, buffered to pH 7.6 and remains hybridized to the sequence set forth in SEQ ID NO:3 after a wash of 15 mM NaCl, 1.5 mM Na3 citrate, 1% SDS, at 65 degrees celius.
  • transgenic animal or cell wherein the serpin is Spi6 or PI9, wherein the Spi6 comprises a sequence as set forth in SEQ ID NO:3.
  • transgenic animal or cell wherein the serpin is Spi6 or PI9, wherein the PI9 comprises a sequence set forth in SEQ ID NO:1 144.
  • a transgenic non-human animal comprising a cell wherein the cell expresses a transgene coding for a serpin, wherein the serpin is not Crm A (SEQ ID NO:24 and 25).
  • transgenic non-human animal comprising a cell wherein the cell expresses a transgene coding for a serpin, wherein the transgene comprises sequence encoding a serpin, a promoter operably linked to the serpin, and a selectable marker.
  • transgenic non-human animal comprising a cell wherein the cell expresses a transgene coding for a serpin, wherein the serpin is a serpin having granzyme B, cathepsin G (P28293), PR-3 (Q61096), neutrophil elastase (NP031945), mouse mast cell protein (MMCP) -1 (Pl 1034), MMCP-2 (P15119), MMCP-3 (P21843), MMCP-4 (P21812), MMCP-5 (P21844), MMCP-8 (P43430), MMCP-9 (035164), MMCP-10 (AAK51075), or caspase 1 (P29452) as a substrate.
  • serpin is a serpin having granzyme B, cathepsin G (P28293), PR-3 (Q61096), neutrophil elastase (NP031945), mouse mast cell protein (MMCP) -1 (Pl 1034), MMCP-2 (P15119), MM
  • transgenic non-human animal comprising a cell wherein the cell expresses a transgene coding for a serpin, wherein the serpin is a serpin having granzyme B, cathepsin G (P28293), PR-3 (Q61096), neutrophil elastase (NP031945), mouse mast cell protein (MMCP) -1 (P11034), MMCP-2 (P15119), MMCP-3 (P21843), MMCP-4 (P21812), MMCP-5 (P21844), MMCP-8 (P43430), MMCP-9 (035164), MMCP-10 (AAK51075), or caspase 1 (P29452) as a substrate, wherein the serpin is a serpin having Granzyme B as a substrate.
  • the serpin is a serpin having Granzyme B as a substrate.
  • transgenic non-human animals comprising a cell wherein the cell expresses a transgene coding for a serpin, wherein the amount of serpin produced in the animal is more than the amount of serpin produced in a non-transgenic animal.
  • transgenic non-human animals comprising a cell wherein the cell expresses a transgene coding for a serpin, wherein the animal has increased protection against programmed cell death.
  • protect or protection can be limited to protection that provides a means for greater than 20%, 30%, 50%, 60%, 70%, 80%, or 90% increase in the number of viable of cells after 1 hour, 2 hours, 3 hours, 4 hours, 5 hours, 6, hours, 7 hours, 8 hours, 9 hours, 10, hours, 11 hours, 12 hours, 13 hours, 14 hours, 15 hours, 16 hours, 17 hours, 18 hours, 19 hours, 20 hours 21 hours, 22 hours, 23 hours,
  • transgenic non-human animals comprising a cell wherein the cell expresses a transgene coding for a serpin, wherein the transgenic non-human animal has a greater than 50% increase in number of viable of transgenic cells over the level of non-transgenic cells after a certain length of time.
  • transgenic non-human animals comprising a cell wherein the cell expresses a transgene coding for a serpin, wherein the serpin is overexpressed, and wherein the overexpression of the serpin leads to an enhanced memory cell phenotype.
  • the memory cell phenotype of the transgenic non-human animals can be enhanced 2, 3, 4, 5, 6, 7, 8, 9, or 10 fold higher than an animal not having the transgene 152.
  • transgenic non-human animals comprising a cell wherein the cell expresses a transgene coding for a serpin, wherein expression of the serpin is driven by the CD2 cassette.
  • transgenic animals or cells where CD2 drives expression in na ⁇ ve CD8 T cells but also all other T cells, and other white blood cells.
  • transgenic expression is restricted to blood cells unless a non-blood cell specific promoter is used.
  • transgenic non-human animals comprising a cell wherein the cell expresses a transgene coding for a serpin, where expression of the serpin is restricted to blood cells.
  • transgenic non-human animals comprising a cell wherein the cell expresses a transgene coding for a serpin, wherein the serpin is overexpressed in blood cells, wherein the overexpression of the serpin leads to an enhanced memory cell phenotype.
  • a transgenic animal where the serpin is overexpressed in na ⁇ ve CD8 T cells, NK cells, thymocytes, lymphocytes and phagocytic myeloid cells, wherein the overexpression of the serpin leads to an enhanced memory cell phenotype.
  • transgenic non-human animals comprising a cell wherein the cell expresses a transgene coding for a serpin, wherein the serpin is overexpressed, and wherein the overexpression of the serpin leads to an enhanced memory cell phenotype, wherein the memory is enhanced 2, 3, 4, 5, 6, 7, 8, 9, 10, fold higher than an animal not having the transgene.
  • transgenic non-human animals comprising a cell wherein the cell expresses a transgene coding for a serpin, wherein the serpin is expressed in na ⁇ ve cells at least 100, 75, 53, 50, 40, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, or
  • transgenic non-human animals comprising a cell wherein the cell expresses a transgene coding for a serpin, wherein the ratio of serpin to cyclophilin is at least 100, 75, 53, 50, 40, 31.6. 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, or 2.
  • transgenic non-human animals comprising a cell wherein the cell expresses a transgene coding for a serpin, wherein the expression of the serpin was at least 100, 75, 53, 50, 40, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5.8 5, 4, 3, or 2 fold higher in memory cells than in na ⁇ ve cells.
  • transgenic non-human animals comprising a cell wherein the cell expresses a transgene coding for a serpin, wherein the serpin expression protects T cells.
  • transgenic non-human animals comprising a cell wherein the cell expresses a transgene coding for a serpin, wherein the serpin expression protects T cells from death initiated by granzyme B delivered perform.
  • transgenic non-human animals comprising a cell wherein the cell expresses a transgene coding for a serpin, wherein the serpin expression protects T cells from granzyme B mediated apoptosis.
  • transgenic non-human animals comprising a cell wherein the cell expresses a transgene coding for a serpin, wherein the serpin expression protects T cells from death initiated by granzyme B delivered perforin, wherein the protection is greater than the protection in a non-transgenic animal. 162. Also disclosed are transgenic non-human animals comprising a cell wherein the cell expresses a transgene coding for a serpin, wherein number of memory cells is enhanced when compared to an animal without the transgene. The number of memory cells can be enhanced 2, 3, 4, 5, or 6 fold higher than an animal having non transgenic Spi6 expression. For example, disclosed are transgenic non-human animals comprising a cell wherein the cell expresses a transgene coding for a serpin, wherein number of memory cells is enhanced at least 2 fold when compared to an animal without the transgene.
  • transgenic non-human animals comprising a cell wherein the cell expresses a transgene coding for a serpin, wherein infection of the transgenic mouse with (LCMV) results in higher numbers of memory cells than an animal not having the transgene.
  • the animal not having the transgene can be a B6 mouse.
  • transgenic non-human animals comprising a cell wherein the cell expresses a transgene coding for a serpin, wherein infection of the transgenic mouse with an experimental pathogen results in higher numbers of memory cells than an animal not having the transgene.
  • mice examples include, but are not limited to Listeria moncytogenes (bacterium), influenza (virus), and herpes simplex (virus).
  • bacterium Listeria moncytogenes
  • influenza virus
  • virus herpes simplex
  • transgenic non-human animals comprising a cell wherein the cell expresses a transgene coding for a serpin, wherein infection of the transgenic mouse with an experimental pathogen results in higher numbers of memory cells than an animal not having the transgene, wherein the animal not expressing the transgene is a B6 mouse.
  • transgenic animals wherein the expression pattern of S ⁇ i6 correlates with granzyme B expression, wherein coexpression of Spi6 and granzyme B in anti-LCMV effectors is retained in resulting memory cells, wherein CD2 drives expression in hematopoietic cells, wherein the expression is highest in natural killer cells (NK cells), wherein the expression in the NK cells is is at least 10, 20, 30, 40, or 50 fold higher than in other cell types, and/or wherein the expression is highest in thymocytes, lymphocytes, or phagocytic myeloid cells. 167.
  • NK cells natural killer cells
  • transgenic non-human animals comprising a cell wherein the cell expresses a transgene coding for a serpin, wherein Spi6 is coexpressed with granzyme B in anti-LCMV effectors and expression of both is retained in resulting memory cells.
  • transgenic non-human animals comprising a cell wherein the cell expresses a transgene coding for a serpin, wherein the animal was produced by a method comprising introducing into a non-human animal fertilized egg a recombinant nucleic acid molecule, which comprises a nucleic acid encoding a serpin whereby a transgenic animal expressing the serpin is produced.
  • transgenic non-human animals comprising a cell wherein the cell expresses a transgene coding for a serpin, wherein the transgenic animal has impaired neutrophil function.
  • transgenic non-human animals comprising a cell wherein the cell expresses a transgene coding for a serpin, wherein the transgenic non-human animals hasjmpaired in vivo responses to bacteria.
  • transgenic non-human animals comprising a cell wherein the cell expresses a transgene coding for a serpin, wherein the transgenic non-human animals hasjmpaired in vivo responses to bacteria due to suppressed elastase activity in neutrophils.
  • Other Mice 172 The disclosed mice and animals can be crossed with any other mouse or animal to produce both heterozygous and homozygous, through appropriate backcrossing and breeding techniques, mice.
  • mice can be produced by crossing either the heterozygous Spi6 +/ ⁇ Pm KO P14 CD8 T or Spi6 ⁇ ' ⁇ homozygous mutant mice with another mouse, such that the newly generated mice have an identifiable phenotype.
  • Mice that can be crossed with either the heterozygous Spi6 +A Pm KO P14 CD8 T or Spi6 ⁇ ' ⁇ homozygous mutant mice can be Fc ⁇ RI KO mice (Dombrowicz et al., 1993) (Jackson Laboratory, Bar Harbor, ME)
  • the phenotypes of the crossed mice can have a combination of the phenotypes produced by each mouse individually.
  • IFN- ⁇ KO mice Jackson Laboratory, Bar Harbor, ME
  • CD8 ⁇ DCs can be purified and tested for their ability to induce the proliferation of P14 CD8 T cells.
  • Compositions that modulate Spi6/PI9 activity can be infected with LCMV and CD8 ⁇ DCs can be purified and tested for their ability to induce the proliferation of P14 CD8 T cells.
  • Inhibitors of Spi6/PI9 178 are also provided herein are methods of inhibiting Spi6 expression comprising administering an inhibitor of S ⁇ i6. Further provided herein are inhibitors of Spi6 or PI9. In certain emobodiments the inhibitors provided herein can inhibit Spi6 or PI9 expression. It is understood that the inhibition of SPI6 or PI9 with an inhibitor can be used in any of the methods disclosed herein related to SPI6 inhibition or Spi6 expression inhibition.
  • SPI6 inhibition can be achived in a variety of ways. For example, inhibition of Spi6 expression can be achieved by introducing a disrupted S ⁇ i6 gene or a SPI6 inhibitor.
  • SPI6 inhibitors include, but are not limited to, antibodies, siRNA, iRNA, aptamers, ribozymes, External guide sequences, small molecules and other compounds identified that have serpin inhibitory activity.
  • Compounds that can be used to inhibit serine protease inhibitors include, but are not limited to: WAY-140312 (See Crandall et al., 2004) XRl 853, XR334, Tiplaxtinin (See Elokdah et al., 2004), salicylic acid derivative HP129 (See Gils et al., 2002); anthram ' lic acid derivative AR-H029953XX (See
  • peptide based strategies can be used to inhibit Spi6 expression.
  • Peptide based strategies can inhibit Spi6 as described in Eitzman et al., (1995), which is hereby incorporated by reference in its entirety for its teaching of peptide based strategies can be used to inhibit expression of a target.
  • the tetradecapeptide, P1-P14 can be used to inhibit S ⁇ i6 expression.
  • Functional nucleic acids are nucleic acid molecules that have a specific function, such as binding a target molecule or catalyzing a specific reaction.
  • Functional nucleic acid molecules can be divided into the following categories, which are not meant to be limiting.
  • functional nucleic acids include antisense molecules, aptamers, ribozymes, triplex forming molecules, siRNA and iRNA, and external guide sequences.
  • the functional nucleic acid molecules can act as affectors, inhibitors, modulators, and stimulators of a specific activity possessed by a target molecule, or the functional nucleic acid molecules can possess a de novo activity independent of any other molecules.
  • siRNA, iRNA, aptamers, ribozymes, and external guide sequences directed towards PI9 or Spi6 can also be used.
  • ribozymes comprising the sequences of SEQ ID NOs: 46, 47 or 48 can be used.
  • siRNA directed towards Spi6 can be used to silence Spi6.
  • siRNA molecules with a sequence selected from a group consisting of SEQ ID NOs: 49-68 can be used.
  • siRNA molecules directed to kanamycin resistance protein, EGFP expression vector, 3' UTR of hepatitis C virus can be used as controls for comparisons.
  • siRNA molecules with a sequence selected from a group consisting of SEQ ID NOs: 69-71, respectively, can be used as controls.
  • Functional nucleic acid molecules can interact with any macromolecule, such as DNA, RNA, polypeptides, or carbohydrate chains.
  • functional nucleic acids can interact with the mRNA of Spi6 or r> TQ TM.
  • Often functional nucleic acids ' are designed to interact with other nucleic acids based on sequence homology between the target molecule and the functional nucleic acid molecule.
  • the specific recognition between the functional nucleic acid molecule and the target molecule is not based on sequence homology between the functional nucleic acid molecule and the target molecule, but rather is based on the formation of tertiary structure that allows specific recognition to take place.
  • Antisense molecules are designed to interact with a target nucleic acid molecule through either canonical or non-canonical base pairing. The interaction of the antisense molecule and the target molecule is designed to promote the destruction of the target molecule through, for example, RNAseH mediated RNA-DNA hybrid degradation. Alternatively the antisense molecule is designed to interrupt a processing function that normally would take place on the target molecule, such as transcription or replication. Antisense molecules can be designed based on the sequence of the target molecule. Numerous methods for optimization of antisense efficiency by finding the most accessible regions of the target molecule exist. Exemplary methods would be in vitro selection experiments and DNA modification studies using DMS and DEPC.
  • antisense molecules bind the target molecule with a dissociation constant (k d )less than or equal to 10 "6 , 10 "8 , 10 ⁇ 10 , or 10 "12 .
  • k d dissociation constant
  • a representative sample of methods and techniques which aid in the design and use of antisense molecules can be found in the following non- limiting list of United States patents: 5,135,917, 5,294,533, 5,627,158, 5,641,754, 5,691,317, 5,780,607, 5,786,138, 5,849,903, 5,856,103, 5,919,772, 5,955,590, 5,990,088, 5,994,320, 5,998,602, 6,005,095, 6,007,995, 6,013,522, 6,017,898, 6,018,042, 6,025,198, 6,033,910, 6,040,296, 6,046,004, 6,046,319, and 6,057,437.
  • Aptamers are molecules that interact with a target molecule, preferably in a specific way.
  • aptamers are small nucleic acids ranging from 15-50 bases in length that fold into defined secondary and tertiary structures, such as stem-loops or G-quartets.
  • Aptamers can bind small molecules, such as ATP (United States patent 5,631,146) and theophiline (United States patent 5,580,737), as well as large molecules, such as reverse transcriptase (United States patent 5,786,462) and thrombin (United States patent 5,543,293).
  • Aptamers can bind very tightly with k d s from the target molecule of less than 10 ⁇ 12 M.
  • the aptamers bind the target molecule with a kd less than 10 "6 , 10 "s , 10 "10 , or 10 "12 .
  • Aptamers can bind the target molecule with a very high degree of specificity. For example, aptamers have been isolated that have greater than a 10000 fold difference in binding affinities between the target molecule and another molecule that differ at only a single position on the molecule (United States patent 5,543,293).
  • the aptamer have a k d with the target molecule at least 10, 100, 1000, 10,000, or 100,000 fold lower than the k d with a background binding molecule. It is preferred when doing the comparison for a polypeptide for example, that the background molecule be a different polypeptide.
  • the background protein could be serum albumin.
  • Ribozymes are nucleic acid molecules that are capable of catalyzing a chemical reaction, either intramolecularly or intermolecularly.
  • Ribozymes are thus catalytic nucleic acid. It is preferred that the ribozymes catalyze intermolecular reactions.
  • ribozymes that catalyze nuclease or nucleic acid polymerase type reactions which are based on ribozymes found in natural systems, such as hammerhead ribozymes, (for example, but not limited to the following United States patents: 5,334,711, 5,436,330, 5,616,466, 5,633,133, 5,646,020, 5,652,094, 5,712,384, 5,770,715, 5,856,463, 5,861,288, 5,891,683, 5,891,684, 5,985,621, 5,989,908, 5,998,193, 5,998,203, WO 9858058 by Ludwig and Sproat, WO 9858057 by Ludwig and Sproat, and WO 9718312 by Ludwig and Sproat) hairpin ribozymes (for example, but not limited to the following United States patents:
  • ribozymes that are not found in natural systems, but which have been engineered to catalyze specific reactions de novo (for example, but not limited to the following United States patents: 5,580,967, 5,688,670, 5,807,718, and 5,910,408).
  • Preferred ribozymes cleave KNA or DNA substrates, and more preferably cleave RNA substrates.
  • Ribozymes typically cleave nucleic acid substrates through recognition and binding of the target substrate with subsequent cleavage. This recognition is often based mostly on canonical or non-canonical base pair interactions.
  • Triplex forming functional nucleic acid molecules are molecules that can interact with either double-stranded or single-stranded nucleic acid. When triplex molecules interact with a target region, a structure called a triplex is formed, in which there are three strands of DNA forming a complex dependant on both Watson-Crick and Hoogsteen base-pairing. Triplex molecules are preferred because they can bind target regions with high affinity and specificity. It is preferred that the triplex forming molecules bind the target molecule with a k d less than 10 "6 , 10 "8 , 10 "10 , or 10 "12 .
  • EGSs External guide sequences
  • RNase P RNase P
  • RNAse P aids in processing transfer RNA (tRNA) within a cell.
  • Bacterial RNAse P can be recruited to cleave virtually any RNA sequence by using an EGS that causes the target RNA:EGS complex to mimic the natural tRNA substrate.
  • RNAi RNA interference
  • RNAi RNA interference
  • ds input double-stranded
  • siRNA small fragments
  • RISC RNA- induced silencing complex
  • RNAi involves the introduction by any means of double stranded RNA into the cell which triggers events that cause the degradation of a target RNA.
  • RNAi is a form of post-transcriptional gene silencing.
  • RNAi For description of making and using RNAi molecules see See, e.g., Hammond et al., Nature Rev Gen 2: 110-119 (2001); Sharp, Genes Dev 15: 485-490 (2001), Waterhouse et al., Proc. Natl. Acad. Sci. USA 95(23): 13959-13964 (1998) all of which are incorporated herein by reference in their entireties and at least form material related to delivery and making of RNAi molecules.
  • RNAi has been shown to work in a number of cells, including mammalian cells.
  • the RNA molecules which will be used as targeting sequences within the RISC complex are shorter.
  • these RNA molecules can also have overhangs on the 3' or 5' ends relative to the target RNA which is to be cleaved. These overhangs can be at least or less than or equal to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, or 20 nucleotides long.
  • RNAi works in mammalian stem cells, such as mouse ES cells.
  • antibodies is used herein in a broad sense and includes both polyclonal and monoclonal antibodies. In addition to intact immunoglobulin molecules, also included in the term “antibodies” are fragments or polymers of those immunoglobulin molecules, and human or humanized versions of immunoglobulin molecules or fragments thereof, as long as they are chosen for their ability to interact with Spi6 or PI9 such that Spi6 or PI9 are inhibited from interacting with there substrates, for example. Antibodies that bind the disclosed regions of Spi6 and PI9 involved in the interaction between Spi6 and PI9 and their substrates are also disclosed. The antibodies can be tested for their desired activity
  • the term "monoclonal antibody” as used herein refers to an antibody obtained from a substantially homogeneous population of antibodies, i.e., the individual antibodies within the population are identical except for possible naturally occurring mutations that may be present in a small subset of the antibody molecules.
  • the monoclonal antibodies herein specifically include "chimeric" antibodies in which a portion of the heavy and/or light chain is identical with or homologous to corresponding sequences in antibodies derived from a particular species or belonging to a particular antibody class or subclass, while the remainder of the chain(s) is identical with or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, as long as they exhibit the desired antagonistic activity (See, U.S. Pat. No. 4,816,567 and Morrison et al., Proc. Natl. Acad. Sd. USA, 81:6851-6855 (1984)).
  • the disclosed monoclonal antibodies can be made using any procedure which produces mono clonal antibodies.
  • disclosed monoclonal antibodies can be prepared using hybridoma methods, such as those described by Kohler and Milstein, Nature, 256:495 (1975).
  • a hybridoma method a mouse or other appropriate host animal is typically immunized with an immunizing agent to elicit lymphocytes that produce or are capable of producing antibodies that will specifically bind to the immunizing agent.
  • the lymphocytes may be immunized in vitro, e.g., using the HIV Env-CD4- co-rece ⁇ tor complexes described herein.
  • HIV Env-CD4- co-rece ⁇ tor complexes described herein.
  • the monoclonal antibodies may also be made by recombinant DNA methods, such as those described in U.S. Pat. No. 4,816,567 (Cabilly et al.).
  • DNA encoding the disclosed monoclonal antibodies can be readily isolated and sequenced using conventional procedures (e.g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of murine antibodies).
  • Libraries of antibodies or active antibody fragments can also be generated and screened using phage display techniques, e.g., as described in U.S. Patent No. 5,804,440 to Burton et al. and U.S. Patent No. 6,096,441 to
  • In vitro methods are also suitable for preparing monovalent antibodies.
  • Digestion of antibodies to produce fragments thereof, particularly, Fab fragments can be accomplished using routine techniques known in the art. For instance, digestion can be performed using papain. Examples of papain digestion are described in WO 94/29348 published Dec. 22, 1994 and U.S. Pat. No. 4,342,566.
  • Papain digestion of antibodies typically produces two identical antigen binding fragments, called Fab fragments, each with a single antigen binding site, and a residual Fc fragment. Pepsin treatment yields a fragment that has two antigen combining sites and is still capable of cross-linking antigen.
  • the fragments can also include insertions, deletions, substitutions, or other selected modifications of particular regions or specific amino acids residues, provided the activity of the antibody or antibody fragment is not significantly altered or impaired compared to the non-modified antibody or antibody fragment. These modifications can provide for some additi ⁇ naTprop'erty, sucli ' "as'i: ⁇ " remove/add amino acids capable of disulfide bonding, to increase its bio- longevity, to alter its secretory characteristics, etc. In any case, the antibody or antibody fragment must possess a bioactive property, such as specific binding to its cognate antigen.
  • Functional or active regions of the antibody or antibody fragment may be identified by mutagenesis of a specific region of the protein, followed by expression and testing of the expressed polypeptide. Such methods are readily apparent to a skilled practitioner in the art and can include site-specific mutagenesis of the nucleic acid encoding the antibody or antibody fragment. (Zoller, MJ. Curr. Opin. BiotechnoL 3:348-354, 1992).
  • antibody can also refer to a human antibody and/or a humanized antibody.
  • Many non-human antibodies e.g., those derived from mice, rats, or rabbits
  • are naturally antigenic in humans and thus can give rise to undesirable immune responses when administered to humans. Therefore, the use of human or humanized antibodies in the methods serves to lessen the chance that an antibody administered to a human will evoke an undesirable immune response.
  • the disclosed human antibodies can be prepared using any technique. Examples of techniques for human monoclonal antibody production include those described by Cole et al. (Monoclonal
  • the disclosed human antibodies can also be obtained from transgenic animals.
  • transgenic, mutant mice that are capable of producing a full repertoire of human antibodies, in response to immunization, have been described (see, e.g., Jakobovits et al., Proc. Natl. Acad. Sd. USA, 90:2551-255 (1993); Jakobovits et al., Nature, 362:255-258 (1993); Bruggermann et al., Year in Immunol, 7:33 (1993)).
  • the homozygous deletion of the antibody heavy chain joining region (J(H)) gene in these chimeric and germ-line mutant mice results in complete inhibition of endogenous antibody production, and the successful transfer of the human germ-line antibody gene array into such germ-line mutant mice results in the production of human antibodies upon antigen challenge.
  • Antibodies having the desired activity are selected using Env-CD4-co-receptor complexes as described herein.
  • Antibody humanization techniques generally involve the use of recombinant DNA technology to manipulate the DNA sequence encoding one or more polypeptide chains of an antibody molecule.
  • a humanized form of a non-human antibody is a chimeric antibody or antibody chain (or a fragment thereof, such as an Fv, Fab, Fab', or other antigen-binding portion of an antibody) which contains a portion of an antigen binding site from a non-human (donor) antibody integrated into the framework of a human (recipient) antibody.
  • a humanized antibody residues from one or more complementarity determining regions (CDRs) of a recipient (human) antibody molecule are replaced by residues from one or more CDRs of a donor (non-human) antibody molecule that is known to have desired antigen binding characteristics (.e.g., a certain level ot specilicity and affinity for the target antigen).
  • CDRs complementarity determining regions
  • donor non-human antibody molecule
  • Fv framework (FR) residues of the human antibody are replaced by corresponding non-human residues.
  • Humanized antibodies may also contain residues which are found neither in the recipient antibody nor in the imported CDR or framework sequences.
  • a humanized antibody has one or more amino acid residues introduced into it from a source which is non-human.
  • humanized antibodies are typically human antibodies in which some CDR residues and possibly some FR residues are substituted by residues from analogous sites in rodent antibodies.
  • Humanized antibodies generally contain at least a portion of an antibody constant region (Fc), typically that of a human antibody (Jones et al., Nature, 321:522-525 (1986), Reichmann et al., Nature, 332:323-327 (1988), and Presta, Curr. Opin. Struct. Biol, 2:593-596 (1992)).
  • Fc antibody constant region
  • humanized antibodies can be generated according to the methods of Winter and co-workers (Jones et al., Nature, 321:522-525 (1986), Riechmann et al., Nature, 332:323-327 (1988), Verhoeyen et al., Science, 239:1534-1536 (1988)), by substituting rodent CDRs or CDR sequences for the corresponding sequences of a human antibody.
  • Methods that can be used to produce humanized antibodies are also described in U.S. Patent No. 4,816,567 (Cabilly et al.), U.S. Patent No. 5,565,332 (Hoogenboom et al.), U.S. Patent No.
  • nucleic acid approaches for antibody delivery also exist.
  • the broadly neutralizing anti Spi6 or PI9 antibodies and antibody fragments can also be administered to patients or subjects as a nucleic acid preparation (e.g., DNA or RNA) that encodes the antibody or antibody fragment, such that the patient's or subject's own cells take up the nucleic acid and produce and secrete the encoded antibody or antibody fragment.
  • the delivery of the nucleic acid can be by any means, as disclosed herein, for example. e) Vaccines
  • Spi6 and PI9 can be used in a vaccine.
  • vaccines which decreases the number of boosters required to obtain memory cells comprising a SPI6 or PI9 protein, or a fragment thereof and a pharmaceutically acceptable excipient.
  • vaccines which decreases the number of boosters required to obtain memory cells comprising a SPI6 or PI9 protein, or a fragment thereof and a pharmaceutically acceptable excipient, further comprising a suitable adjuvant.
  • vaccines which decrease the amount of time for full memory cell response comprising a SPI6 or PI9 protein, or a fragment thereof and a pharmaceutically acceptable excipient. Also disclosed are vaccines which decrease the amount of time for full memory cell response, comprising a SPI6 or PI9 protein, or a fragment thereof and a pharmaceutically acceptable excipient, further comprising a suitable adjuvant.
  • the establishment of immunological memory is one of the goals of vaccine development. Yet, the establishment of immunological memory can take months to occur following the initial antigenic encounter. Additionally, the mere establishment of immunological memory is not necessarily sufficient to confer protection against future encounters with a pathogen or foreign antigen, as a small memory population may be overwhelmed by a pathogen. Therefore an additional goal is to establish a memory population large enough to provide the protection.
  • the sufficiency of the immunological memory can be improved through the administration of additional applications of the same or related antigens as the initial vaccine, referred to as a boost. However, multiple boosts may be required and current immunization regimens often require months between successive vaccine administrations.
  • Vaccines refer to any composition that is administered to a subject with the goal of establishing an immune response to a particular target or targets. In certain embodiments the vaccines will produce an immune response that is a protective immune response.
  • Vaccines can be, for example, prophylactic, that is, administered before a target is ever encountered, as is typically the case for Polio, measles, mumps, rubella, smallpox, chicken pox, and influenza vaccines, for example.
  • Vaccines can also be therapeutic, providing an immune response to a target that is already within a subject, for example, a vaccine to a particular cancer.
  • vaccines are administered in a single or multiple doses called immunizations and are designed to generate memory T and B-cell populations.
  • immunizations are designed to generate memory T and B-cell populations.
  • no vaccine designed to generate memory T-cells has accomplished this task with a single dose, or immunization, of the vaccine.
  • the initial immunization, or prime generates a memory T-cell population that is insufficient to provide protection against future target encounter related to the antigen. Additionally, the few memory T- cells that are generated from the initial prime can take at least 2 months and can take years to finally transform from na ⁇ ve T-cells into memory T-cells.
  • additional immunizations, or boosts comprising the same or related antigen are used to bolster the numbers of memory T-cells.
  • the memory T-cell population must be stabilized. That is, the target-specific T-cell population must have completed the transformation to memory cells and be in a steady-state.
  • a prime-boost immunization regimen can require months between immunizations creating a tremendous lag in time between when immunity to a target is desired and when it is actually achieved. The methods disclosed herein overcome these problems.
  • memory T-cells can be characterized as long-lived antigen-specific T-cells having a combination of two or more of the following markers CD44 + (positive), CDl Ia + (positive), CD43 1B ⁇ " (negative), CD62L m orLO , CD127 + (positive), and CD45RA " (negative), CD27 hi , CD122 hi , IL-15R+.
  • Memory T-cells can be divided into two major groups distinguished by the expression of CCR7 and CD62L.
  • CD62L 10 (negative) memory T-cells are referred to as "effector memory T-cells" (T EM )- These cells generally are localized in the peripheral tissues such as the liver and lungs as well as the spleen, and produce rapid effector functions, such as IFN- ⁇ production, upon stimulation.
  • CCR7 + (positive) memory T-cells generally localize m the secondary lymphoid organs such as the thymus, bone marrow, and lymph nodes, although they can also be found in peripheral tissues. These cells are referred to as “central memory T- cells” (T CM ) and provide more effective protection to the host, against at least some pathogens, through increased proliferative capacity.
  • the memory T-cells can be generated, for example, by mixing a target or antigen related to the target with dendritic cells and administering the mixture to a subject. It is understood that the disclosed methods can be used for the generation of, for example, central memory T-cells.
  • the booster immunization can comprise any antigen related to the target including, but not limited to, the same antigen supplied in the mixture provided in the prime comprising an antigen related to the target and a dendritic cell.
  • the antigen provided in the booster can be different from the antigen in the prime.
  • the antigen provided in the booster can be different than Spi6 or PI9.
  • the disclosed methods can comprise more than one boost. f) Compositions, characteristics, and relationships
  • homology and identity mean the same thing as similarity.
  • the use of the word homology is used between two non- natural sequences it is understood that this is not necessarily indicating an evolutionary relationship between these two sequences, but rather is looking at the similarity or relatedness between their nucleic acid sequences.
  • Many of the methods for determining homology between two evolutionarily related molecules are routinely applied to any two or more nucleic acids or proteins for the purpose of measuring sequence similarity regardless of whether they are evolutionarily related or not.
  • variants of genes and proteins herein disclosed typically have at least, about 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99 percent homology to the stated sequence or the native sequence.
  • the homology can be calculated after aligning the two sequences so that the homology is at its highest level.
  • a sequence recited as having a particular percent homology to another sequence refers to sequences that have the recited homology as calculated by any one or more of the calculation methods described above.
  • a first sequence has 80 percent homology, as defined herein, to a second sequence if the first sequence is calculated to have 80 percent homology to the second sequence using the Zuker calculation method even if the first sequence does not have 80 percent homology to the second sequence as calculated by any of the other calculation methods.
  • a first sequence has 80 percent homology, as defined herein, to a second sequence if the first sequence is calculated to have 80 percent homology to the second sequence using both the Zuker calculation method and the Pearson and Lipman calculation method even if the first sequence does not have 80 percent homology to the second sequence as calculated by the Smith and Waterman calculation method, the
  • a first sequence has 80 percent homology, as defined herein, to a second sequence if ' the" first sequence is calculated to have 80 percent homology to the second sequence using each of calculation methods (although, in practice, the different calculation methods will often result in different calculated homology percentages).
  • hybridization typically means a sequence driven interaction between at least two nucleic acid molecules, such as a primer or a probe and a gene.
  • Sequence driven interaction means an interaction that occurs between two nucleotides or nucleotide analogs or nucleotide derivatives in a nucleotide specific manner. For example, G interacting with C or A interacting with T are sequence driven interactions. Typically sequence driven interactions occur on the Watson-Crick face or Hoogsteen face of the nucleotide.
  • the hybridization of two nucleic acids is affected by a number of conditions and parameters known to those of skill in the art. For example, the salt concentrations, pH, and temperature of the reaction all affect whether two nucleic acid molecules will hybridize.
  • selective hybridization conditions can be defined as stringent hybridization conditions.
  • stringency of hybridization is controlled by both temperature and salt concentration of either or both of the hybridization and washing steps.
  • the conditions of hybridization to achieve selective hybridization may involve hybridization in high ionic strength solution (6X SSC or 6X SSPE) at a temperature that is about 12-25°C below the Tm (the melting temperature at which half of the molecules dissociate from their hybridization partners) followed by washing at a combination of temperature and salt concentration chosen so that the washing temperature is about 5 0 C to 20 0 C below the Tm.
  • the temperature and salt conditions are readily determined empirically in preliminary experiments in which samples of reference DNA immobilized on filters are hybridized to a labeled nucleic acid of interest and then washed under conditions of different stringencies. Hybridization temperatures are typically higher for DNA-RNA and RNA-RNA hybridizations. The conditions can be used as described above to achieve stringency, or as is known in the art. (Sambrook et al., Molecular
  • a preferable stringent hybridization condition for a DNA:DNA hybridization can be at about 68°C (in aqueous solution) in 6X SSC or 6X SSPE followed by washing at 68°C. Stringency of hybridization and washing, if desired, can be reduced accordingly as the degree of complementarity desired is decreased, and further, depending upon the G-C or A-T richness of any area wherein variability is searched for.
  • stringency of hybridization and washing can be increased accordingly as homology desired is increased, and further, depending upon the G-C or A-T richness of any area wherein high homology is desired, all as known in the art. 220.
  • Another way to define selective hybridization is by looking at the amount (percentage) of one of the nucleic acids bound to the other nucleic acid.
  • selective hybridization conditions would be when at least about, 60, 65, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, ⁇ 9 ⁇ ⁇ 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100 percent of the limiting nucleic acid is bound to the nb ⁇ -limit ⁇ ng nucleic acid.
  • the non-limiting primer is in for example, 10 or 100 or 1000 fold excess.
  • This type of assay can be performed at under conditions where both the limiting and non- limiting primer are for example, 10 fold or 100 fold or 1000 fold below their k d , or where only one of the nucleic acid molecules is 10 fold or 100 fold or 1000 fold or where one or both nucleic acid molecules are above their k d .
  • selective hybridization conditions would be when at least about, 60, 65, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100 percent of the primer is enzymatically manipulated under conditions which promote the enzymatic manipulation, for example if the enzymatic manipulation is DNA extension, then selective hybridization conditions would be when at least about 60, 65, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89,
  • nucleic acid based there are a variety of molecules disclosed herein that are nucleic acid based, including for example the nucleic acids that encode, for example, Spi6 (SEQ ID NO:3) as well as any other proteins disclosed herein, as well as various functional nucleic acids.
  • the disclosed nucleic acids are made up of for example, nucleotides, nucleotide analogs, or nucleotide substitutes. Non-limiting examples of these and other molecules are discussed herein. It is understood that for example, when a vector is expressed in a cell, that the expressed mRNA will typically be made up of A, C, G, and U.
  • an antisense molecule is introduced into a cell or cell environment through for example exogenous delivery, it is advantagous that the antisense molecule be made up of nucleotide analogs that reduce the degradation of the antisense molecule in the cellular environment.
  • a nucleotide is a molecule that contains a base moiety, a sugar moiety and a phosphate moiety. Nucleotides can be linked together through their phosphate moieties and sugar moieties creating an mternucleoside linkage, liie base moiety ot a nucleotide can De a ⁇ emn-y-yi (Aj, cytosm-i-yi ⁇ Uj, guanin-9-yl (G), uracil-1-yl (U), and thymin-1-yl (T).
  • the sugar moiety of a nucleotide is a ribose or a deoxyribose.
  • the phosphate moiety of a nucleotide is pentavalent phosphate.
  • An non-limiting example of a nucleotide would be 3'-AMP (3'-adenosine monophosphate) or 5'-GMP (5'-guanosine monophosphate). 226.
  • a nucleotide analog is a nucleotide which contains some type of modification to either the base, sugar, or phosphate moieties. Modifications to nucleotides are well known in the art and would include for example, 5-methylcytosine (5-me-C), 5-hydroxymethyl cytosine, xanthine, hypoxanthine, and 2-aminoadenine as well as modifications at the sugar or phosphate moieties.
  • Nucleotide substitutes are molecules having similar functional properties to nucleotides, but which do not contain a phosphate moiety, such as peptide nucleic acid (PNA). Nucleotide substitutes are molecules that will recognize nucleic acids in a Watson-Crick or Hoogsteen manner, but which are linked together through a moiety other than a phosphate moiety. Nucleotide substitutes are able to conform to a double helix type structure when interacting with the appropriate target nucleic acid.
  • PNA peptide nucleic acid
  • conjugates can be link other types of molecules to nucleotides or nucleotide analogs to enhance for example, cellular uptake.
  • Conjugates can be chemically linked to the nucleotide or nucleotide analogs.
  • conjugates include but are not limited to lipid moieties such as a cholesterol moiety.
  • a Watson-Crick interaction is at least one interaction with the Watson-Crick face of a nucleotide, nucleotide analog, or nucleotide substitute.
  • the Watson-Crick face of a nucleotide, nucleotide analog, or nucleotide substitute includes the C2, Nl, and C6 positions of a purine based nucleotide, nucleotide analog, or nucleotide substitute and the C2, N3, C4 positions of a pyrimidine based nucleotide, nucleotide analog, or nucleotide substitute.
  • a Hoogsteen interaction is the interaction that takes place on the Hoogsteen face of a nucleotide or nucleotide analog, which is exposed in the major groove of duplex DNA.
  • the Hoogsteen face includes the N7 position and reactive groups (NH2 or O) at the C6 position of purine nucleotides.
  • compositions including primers and probes, which are capable of interacting with the genes disclosed herein.
  • the primers are used to support DNA amplification reactions.
  • the primers will be capable of being extended in a sequence specific manner.
  • Extension of a primer in a sequence specific manner includes any methods wherein the sequence and/or composition of the nucleic acid molecule to which the primer is hybridized or otherwise associated directs or influences the composition or sequence of the product produced by the extension of the primer.
  • Extension of the primer in a sequence specific manner therefore includes, but is not limited to, PCR, DNA sequencing, DNA extension, DNA polymerization, RNA transcription, or reverse transcription. Techniques and conditions that amplify the primer in a sequence specific manner are preferred.
  • the primers are used for the DNA amplification reactions, such as PCR or direct sequencing. It is understood that in certain embodiments the primers can also be extended using non-enzymatic techniques, where for example, the nucleotides or oligonucleotides used to extend the primer are modified such that they will chemically react to extend the primer in a sequence specific manner. Typically the disclosed primers hybridize with the nucleic acid or region of the nucleic acid or they hybridize with the complement of the nucleic acid or complement of a region of the nucleic acid.
  • compositions and methods which can be used to deliver nucleic acids to cells, either in vitro or in vivo. These methods and compositions can largely be broken down into two classes: viral based delivery systems and non-viral based delivery systems.
  • the nucleic acids can be delivered through a number of direct delivery systems such as, electroporation, lipofection, calcium phosphate precipitation, plasmids, viral vectors, viral nucleic acids, phage nucleic acids, phages, cosmids, or via transfer of genetic material in cells or carriers such as cationic liposomes.
  • direct delivery systems such as, electroporation, lipofection, calcium phosphate precipitation, plasmids, viral vectors, viral nucleic acids, phage nucleic acids, phages, cosmids, or via transfer of genetic material in cells or carriers such as cationic liposomes.
  • Transfer vectors can be any nucleotide construction used to deliver genes into cells (e.g., a plasmid), or as part of a general strategy to deliver genes, e.g., as part of recombinant retrovirus or adenovirus (Ram et al. Cancer Res. 53:83-88, (1993)).
  • plasmid or viral vectors are agents that transport the disclosed nucleic acids, such as SEQ ID NO: 3 into the cell without degradation and include a promoter yielding expression of the gene in the cells into which it is delivered.
  • the vectors are derived from either a virus or a retrovirus.
  • Viral vectors are, for example, Adenovirus, Adeno-associated virus, Herpes virus, Vaccinia vims Polio virus, AIDS virus, neuronal trophic virus, Sindbis and other RNA viruses, including these viruses with ' the HIV backbone. Also preferred are any viral families which share the properties of these viruses which make them suitable for use as vectors.
  • Retroviruses include Murine Maloney Leukemia virus, MMLV, and retroviruses that express the desirable properties of MMLV as a vector.
  • Retroviral vectors are able to carry a larger genetic payload, i.e., a transgene or marker gene, than other viral vectors, and for this reason are a commonly used vector. However, they are not as useful in non-proliferating cells.
  • Adenovirus vectors are relatively stable and easy to work with, have high titers, and can be delivered in aerosol formulation, and can transfect non-dividing cells.
  • Pox viral vectors are large and have several sites for inserting genes, they are thermostable and can be stored at room temperature.
  • a preferred embodiment is a viral vector which has been engineered so as to suppress the immune response of the host organism, elicited by the viral antigens.
  • Preferred vectors of this type will carry coding regions for Interleukin 8 or 10.
  • Viral vectors can have higher transaction (ability to introduce genes) abilities than chemical or physical methods to introduce genes into cells.
  • viral vectors contain, nonstructural early genes, structural late genes, an RNA polymerase III transcript, inverted terminal repeats necessary for replication and encapsidation, and promoters to control the transcription and replication of the viral genome.
  • viruses When engineered as vectors, viruses typically have one or more of the early genes removed and a gene or gene/promotor cassette is inserted into the viral genome in place of the removed viral DNA. Constructs of this type can carry up to about 8 kb of foreign genetic material.
  • the necessary functions of the removed early genes are typically supplied by cell lines which have been engineered to express the gene products of the early genes in trans.
  • a retrovirus is an animal virus belonging to the virus family of Retroviridae, including any types, subfamilies, genus, or tropisms.
  • Retroviral vectors in general, are described by Verma, I.M., Retroviral vectors for gene transfer. In Microbiology-1985, American Society for Microbiology, pp. 229- 232, Washington, (1985), which is incorporated by reference herein. Examples of methods for using retroviral vectors for gene therapy are described in U.S. Patent Nos. 4,868,116 and 4,980,286; PCT applications WO 90/02806 and WO 89/07136; and Mulligan, (Science 260:926-932 (1993)); the teachings of which are incorporated herein by reference.
  • a retrovirus is essentially a package which has packed into it nucleic acid cargo.
  • the nucleic acid cargo carries with it a packaging signal, which ensures that the replicated daughter molecules will be efficiently packaged within the package coat.
  • a packaging signal In addition to the package signal, there are a number of molecules which are needed in cis, for the replication, and packaging of the replicated virus.
  • a retroviral genome contains the gag, pol, and env genes which are involved in the making of the protein coat. It is the gag, pol, and env genes which are typically replaced by the foreign DNA that it is to be transferred to the target cell.
  • Retrovirus vectors typically contain a packaging signal for incorporation into the package coat, a sequence which signals the start of the gag transcription unit, elements necessary for reverse transcription, including a primer binding site to bind the tRNA primer of reverse transcription, terminal repeat sequences that guide the switch of RNA strands during DNA synthesis, a purine rich ⁇ e ⁇ nence 5' to the 3' LTR that serve as the priming site for the synthesis of the second strand of DNA syn1hes ⁇ s;''ari'd''sp'eci ' ⁇ c ' seque ⁇ ces' near the ends of the LTRs that enable the insertion ot me jj JN A state oi tne retrovirus to insert into the host genome.
  • a packaging signal for incorporation into the package coat a sequence which signals the start of the gag transcription unit, elements necessary for reverse transcription, including a primer binding site to bind the tRNA primer of reverse transcription, terminal repeat sequences that guide the switch of RNA strands during DNA synthesis, a
  • gag, pol, and env genes allow for about 8 kb of foreign sequence to be inserted into the viral genome, become reverse transcribed, and upon replication be packaged into a new retroviral particle. This amount of nucleic acid is sufficient for the delivery of a one to many genes depending on the size of each transcript. It is preferable to include either positive or negative selectable markers along with other genes in the insert.
  • a packaging cell line is a cell line which has been transfected or transformed with a retrovirus that contains the replication and packaging machinery, but lacks any packaging signal.
  • DNA of choice is transfected into these cell lines, the vector containing the gene of interest is replicated and packaged into new retroviral particles, by the machinery provided in cis by the helper cell.
  • the genomes for the machinery are not packaged because they lack the necessary signals.
  • the benefit of the use of these viruses as vectors is that they are limited in the extent to which they can spread to other cell types, since they can replicate within an initial infected cell, but are unable to form new infectious viral particles.
  • Recombinant adenoviruses have been shown to achieve high efficiency gene transfer after direct, in vivo delivery to airway epithelium, hepatocytes, vascular endothelium, CNS parenchyma and a number of other tissue sites (Morsy, J. Clin. Invest. 92:1580-1586 (1993); Kirshenbaum, J. Clin. Invest. 92:381-387 (1993); Roessler, J. Clin. Invest. 92:1085-1092 (1993); Moullier, Nature Genetics 4:154-159 (1993); La Salle, Science 259:988-990 (1993);
  • Recombinant adenoviruses achieve gene transduction by binding to specific cell surface receptors, after which the virus is internalized by receptor-mediated endocytosis, in the same manner as wild type or replication-defective adenovirus (Chardonnet and Dales, Virology 40:462-477 (1970); Brown and Burlingham, J. Virology 12:386-396 (1973); Svensson and Persson, J. Virology 55:442-449 (1985); Seth, et al., J. Virol. 51:650-655 (1984); Seth, et al., MoL Cell. Biol. 4:1528-1533 (1984); Varga et al., J. Virology 65:6061-6070 (1991); Wickham et al., Cell 73:309-319 (1993)).
  • a viral vector can be one based on an adenovirus which has had the El gene removed and these virons are generated in a cell line such as the human 293 cell line. In another preferred embodiment both the El and E3 genes are removed from the adenovirus genome. (Hi) Adeno-asscociated viral vectors
  • AAV adeno-associated virus
  • This defective parvovirus is a preferred vector because it can infect many cell types and is nonpathogenic to humans.
  • AAV type vectors can transport about 4 to 5 kb and wild type AAV is known to stably insert into chromosome 19. Vectors which contain this site specific integration property are preferred.
  • An especially preferred embodiment of this type of vector is the P4.1 C vector produced by Avigen, San Francisco, CA, which can contain the herpes simplex virus thymidine kinase gene, HSV-tk, and/or a marker gene, such as the gene encoding the green fluorescent protein, GFP.
  • the AAV contains a pair of inverted terminal repeats (ITRs) which flank at least one cassette containing a promoter which directs cell-specific expression operably linked to a heterologous gene.
  • ITRs inverted terminal repeats
  • Heterologous in this context refers to any nucleotide sequence or gene which is not native to the AAV or B19 parvovirus.
  • 6,261,834 is herein incorproated by reference for material related to the AAV vector.
  • the disclosed vectors thus provide DNA molecules which are capable of integration into a mammalian chromosome without substantial toxicity.
  • the inserted genes in viral and retroviral usually contain promoters, and/or enhancers to help control the expression of the desired gene product.
  • a promoter is generally a sequence or sequences of
  • a promoter contains core elements required for basic interaction of RNA polymerase and transcription factors, and may contain upstream elements and response elements.
  • compositions can be delivered to the target cells in a variety of ways.
  • the compositions can be delivered through electroporation, or through lipofection, or through calcium phosphate precipitation.
  • the delivery mechanism chosen will depend in part on the type of cell targeted and whether the delivery is occurring for example in vivo or in vitro.
  • compositions can comprise, in addition to the disclosed vectors for example, lipids such as liposomes, such as cationic liposomes (e.g., DOTMA, DOPE, DC-cholesterol) or anionic liposomes.
  • liposomes can further comprise proteins to facilitate targeting a particular cell, if desired.
  • Administration of a composition comprising a compound and a cationic liposome can be administered to the blood afferent to a target organ or inhaled into the respiratory tract to target cells of the respiratory tract.
  • liposomes see, e.g., Brigham et al. Am. J. Resp. Cell. MoI. Biol. 1:95-100 (1989); Feigner et al. Proc.
  • the compound can be administered as a component of a microcapsule that can be targeted to specific cell types, such as macrophages, or where the diffusion of the compound or delivery of the compound from the microcapsule is designed for a specific rate or dosage.
  • delivery of the compositions to cells can be via a variety of mechanisms.
  • delivery can be via a liposome, using commercially available liposome preparations such as LIPOFECTIN, LIPOFECTAMINE (GIBCO-BRL, Inc., Gaithersburg, MD), SUPERFECT (Qiagen, Inc. Hilden, Germany) and TRANSFECTAM (Promega Biotec,
  • nucleic acid or vector can be delivered in vivo by electroporation, the technology for which is available from Genetronics, Inc. (San Diego, CA) as well as by means of a SONOPORATION machine (ImaRx Pharmaceutical Corp., Arlington, AZ). 253.
  • the materials may be in solution, suspension (for example, incorporated into microparticles, liposomes, or cells). These may be targeted to a particular cell type via antibodies, receptors, or receptor ligands.
  • receptors are involved in pathways of endocytosis, either constitutive or ligand induced. These receptors cluster in clatnrin-coated pits, enter the cell via clathrin-coated vesicles, pass through an acidified endosome in which the receptors are sorted, and then either recycle to the cell surface, become stored intracellularly, or are degraded in lysosomes.
  • the internalization pathways serve a variety of functions, such as nutrient uptake, removal of activated proteins, clearance of macromolecules, opportunistic entry of viruses and toxins, dissociation and degradation of ligand, and receptor-level regulation. Many receptors follow more than one intracellular pathway, depending on the cell type, receptor concentration, type of ligand, ligand valency, and ligand concentration. Molecular and cellular mechanisms of receptor-mediated endocytosis has been reviewed (Brown and Greene, DNA and Cell Biology 10:6, 399-409 (1991)). 254. Nucleic acids that are delivered to cells which are to be integrated into the host cell genome, typically contain integration sequences. These sequences are often viral related sequences, particularly when viral based systems are used.
  • These viral intergration systems can also be incorporated into nucleic acids which are to be delivered using a non-nucleic acid based system of deliver, such as a liposome, so that the nucleic acid contained in the delivery system can be come integrated into the host genome.
  • Other general techniques for integration into the host genome include, for example, systems designed to promote homologous recombination with the host genome. These systems typically rely on sequence flanking the nucleic acid to be expressed that has enough homology with a target sequence within the host cell genome that recombination between the vector nucleic acid and the target nucleic acid takes place, causing the delivered nucleic acid to be integrated into the host genome.
  • These systems and the methods necessary to promote homologous recombination are known to those of skill in the art.
  • compositions can be administered in a pharmaceutically acceptable carrier and can be delivered to the subject's cells in vivo and/or ex vivo by a variety of mechanisms well known in the art (e.g., uptake of naked DNA, liposome fusion, intramuscular injection of DNA via a gene gun, endocytosis and the like).
  • cells or tissues can be removed and maintained outside the body according to standard protocols well known in the art.
  • the compositions can be introduced into the cells via any gene transfer mechanism, such as, for example, calcium phosphate mediated gene delivery, electroporation, microinjection or proteoliposomes.
  • the transduced cells can then be infused (e.g., in a pharmaceutically acceptable carrier) or homotopically transplanted back into the subject per standard methods for the cell or tissue type. Standard methods are known for transplantation or infusion of various cells into a subject.
  • the nucleic acids that are delivered to cells typically contain expression controlling systems.
  • the inserted genes in viral and retroviral systems usually contain promoters, and/or enhancers to help control the expression of the desired gene product.
  • a promoter is generally a sequence or sequences of DNA that function when in a relatively fixed location in regard to the transcription start site.
  • a promoter contains core elements required lor basic interaction of RNA polymerase and transcription factors, and may contain upstream elements and response elements.
  • Preferred promoters controlling transcription from vectors in mammalian host cells may be obtained from various sources, for example, the genomes of viruses such as: polyoma, Simian Virus 40
  • SV40 adenovirus
  • retroviruses retroviruses
  • hepatitis-B virus and most preferably cytomegalovirus
  • heterologous mammalian promoters e.g. beta actin promoter.
  • the early and late promoters of the SV40 virus are conveniently obtained as an SV40 restriction fragment which also contains the SV40 viral origin of replication (Fiers et al., Nature, 273: 113 (1978)).
  • the immediate early promoter of the human cytomegalovirus is conveniently obtained as a HindIII E restriction fragment (Greenway, PJ. et al., Gene
  • Enhancer generally refers to a sequence of DNA that functions at no fixed distance from the transcription start site and can be either 5' (Laimins, L. et al., Proc. Natl. Acad. Sci. 78: 993 (1981)) or 3' (Lusky, MX., et al., MoI. Cell Bio. 3: 1108 (1983)) to the transcription unit. Furthermore, enhancers can be within an intron (Banerji, J.L. et al., Cell 33: 729 (1983)) as well as within the coding sequence itself
  • Enhancers function to increase transcription from nearby promoters. Enhancers also often contain response elements that mediate the regulation of transcription. Promoters can also contain response elements that mediate the regulation of transcription. Enhancers often determine the regulation of expression of a gene. While many enhancer sequences are now known from mammalian genes
  • an enhancer from a eukaryotic cell virus typically one will use an enhancer from a eukaryotic cell virus for general expression.
  • Preferred examples are the SV40 enhancer on the late side of the replication origin (bp 100-270), the cytomegalovirus early promoter enhancer, the polyoma enhancer on the late side of the replication origin, and adenovirus enhancers. 261.
  • the promotor and/or enhancer may be specifically activated either by light or specific chemical events which trigger their function.
  • Systems can be regulated by reagents such as tetracycline and dexamethasone.
  • the promoter and/or enhancer region can act as a constitutive promoter and/or enhancer to maximize expression of the region of the transcription unit to be transcribed.
  • the promoter and/or enhancer region be active in all eukaryotic cell types, even if it is only expressed in a particular type of cell at a particular time.
  • a preferred promoter of this type is the CMV promoter (650 bases).
  • Other preferred promoters are SV40 promoters, cytomegalovirus (full length promoter), and retroviral vector LTR. 263. It has been shown that all specific regulatory elements can be cloned and used to construct expression vectors that are selectively expressed in specific cell types such as melanoma cells.
  • the glial fibrillary acetic protein (GFAP) promoter has been used to selectively express genes in cells of glial origin. 264!
  • Expression' vectors used in eukaryotic host cells may also contain sequences necessary for the termination of transcription which may affect mRNA expression. These regions are transcribed as polyadenylated segments in the untranslated portion of the mRNA encoding tissue factor protein. The 3' untranslated regions also include transcription termination sites. It is preferred that the transcription unit also contains a polyadenylation region. One benefit of this region is that it increases the likelihood that the transcribed unit will be processed and transported like mRNA.
  • the identification and use of polyadenylation signals in expression constructs is well established. It is preferred that homologous polyadenylation signals be used in the transgene constructs.
  • the polyadenylation region is derived from the SV40 early polyadenylation signal and consists of about 400 bases. It is also preferred that the transcribed units contain other standard sequences alone or in combination with the above sequences improve expression from, or stability of, the construct.
  • the viral vectors can include nucleic acid sequence encoding a marker product. This marker product is used to determine if the gene has been delivered to the cell and once delivered is being expressed. Marker genes include, but are not limited to the E. CoIi lacZ gene, which encodes ⁇ -galactosidase, the
  • G418 resistance gene HPRT, thymidine kinase, the green fluorescent protein (GFP), and the red fluorescent protein (RFP).
  • the marker may be a selectable marker.
  • suitable selectable markers for mammalian cells are dihydrofolate reductase (DHFR), thymidine kinase, neomycin, neomycin analog G418, hydromycin, and puromycin.
  • DHFR dihydrofolate reductase
  • thymidine kinase thymidine kinase
  • neomycin neomycin analog G418, hydromycin
  • puromycin puromycin.
  • selectable markers When such selectable markers are successfully transferred into a mammalian host cell, the transformed mammalian host cell can survive if placed under selective pressure.
  • These cells lack the ability to grow without the addition of such nutrients as thymidine or hypoxanthine. Because these cells lack certain genes necessary for a complete nucleotide synthesis pathway, they cannot survive unless the missing nucleotides are provided in a supplemented media.
  • An alternative to supplementing the media is to introduce an intact DHFR or TK gene into cells lacking the respective genes, thus altering their growth requirements. Individual cells which were not transformed with the DHFR or TK gene will not be capable of survival in non-supplemented media.
  • the second category is dominant selection which refers to a selection scheme used in any cell type and does not require the use of a mutant cell line. These schemes typically use a drug to arrest growth of a host cell. Those cells which have a novel gene would express a protein conveying drug resistance and would survive the selection. Examples of such dominant selection use the drugs neomycin, (Southern P. and Berg, P., J. Molec. Appl. Genet. 1: 327 (1982)), mycophenolic acid, (Mulligan, R.C. and Berg, P.
  • hygromycin (Sugden, B. et al., Mol. Cell. Biol. 5: 410-413 (1985)).
  • the three examples employ bacterial genes under eukaryotic control to convey resistance to the appropriate drug (J41S or neomycin (_geneticin), xgpt (mycophenolic acid) or hygromycin, respectively.
  • Others include the neomycin analog G418 and puramycin.
  • Protein variants 268 are well understood to those of skill in the art and in can involve amino acid sequence modifications. For example, amino acid sequence modifications typically fall into one or more of three classes: substitutional, insertional or deletional variants. Insertions include amino and/or carboxyl terminal fusions as well as intrasequence insertions of single or multiple amino acid residues.
  • Insertions ordinarily will be smaller insertions than those of amino or carboxyl terminal fusions, for example, on the order of one to four residues.
  • Immunogenic fusion protein derivatives such as those described in the examples, are made by fusing a polypeptide sufficiently large to confer immunogenicity to the target sequence by cross- linking in vitro or by recombinant cell culture transformed with DNA encoding the fusion. Deletions are characterized by the removal of one or more amino acid residues from the protein sequence. Typically, no more than about from 2 to 6 residues are deleted at any one site within the protein molecule.
  • variants ordinarily are prepared by site specific mutagenesis of nucleotides in the DNA encoding the protein, thereby producing DNA encoding the variant, and thereafter expressing the DNA in recombinant cell culture.
  • Techniques for making substitution mutations at predetermined sites in DNA having a known sequence are well known, for example Ml 3 primer mutagenesis and PCR mutagenesis.
  • Amino acid substitutions are typically of single residues, but can occur at a number of different locations at once; insertions usually will be on the order of about from 1 to 10 amino acid residues; and deletions will range about from 1 to 30 residues.
  • Deletions or insertions preferably are made in adjacent pairs, i.e. a deletion of 2 residues or insertion of 2 residues.
  • substitutions, deletions, insertions or any combination thereof may be combined to arrive at a final construct.
  • the mutations must not place the sequence out of reading frame and preferably will not create complementary regions that could produce secondary mRNA structure.
  • substitutional variants are those in which at least one residue has been removed and a different residue inserted in its place. Such substitutions generally are made in accordance with the following Tables 1 and 2 and are referred to as conservative substitutions.
  • Substantial changes in function or immunological identity are made by selecting that are less conservative than those in Table 2, i.e., selecting residues that differ more significantly in their effect on maintaining (a) the structure of the polypeptide backbone in the area of the substitution, for example as a sheet or helical conformation, (b) the charge or hydrophobicity of the molecule at the target site or (c) the bulk of the side chain.
  • the substitutions which in general are expected to produce the greatest changes in the protein properties will be those in which (a) a hydrophilic residue, e.g. seryl or threonyl, is substituted for (or by) a hydrophobic residue, e.g.
  • an electropositive side chain e.g., lysyl, arginyl, or histidyl
  • an electronegative residue e.g., glutamyl or aspartyl
  • the replacement of one amino acid residue with another that is biologically and/or chemically similar is known to those skilled in the art as a conservative substitution.
  • a conservative substitution would be replacing one hydrophobic residue for another, or one polar residue for another.
  • the substitutions include combinations such as, for example, GIy, Ala; VaI, He, Leu; Asp, GIu; Asn, GIn; Ser, Thr; Lys, Arg; and Phe, Tyr.
  • Such conservatively substituted variations of each explicitly disclosed sequence are included within the mosaic polypeptides provided herein.
  • Substitutional or deletional mutagenesis can be employed to insert sites for N-glycosylation (Asn-X-Thr/Ser) or O-glycosylation (Ser or Thr).
  • Deletions of cysteine or other labile residues also may be desirable.
  • Deletions or substitutions of potential proteolysis sites, e.g. Arg is accomplished for example by deleting one of the basic residues or substituting one by glutaminyl or histidyl residues.
  • Certain post-translational derivatizations are the result of the action of recombinant host cells on the expressed polypeptide. Glutaminyl and asparaginyl residues are frequently post-translationally deamidated to the corresponding glutamyl and asparyl residues. Alternatively, these residues are deamidated under mildly acidic conditions. Other post-translational modifications include hydroxylation of proline and lysine, phosphorylation of hydroxyl groups of seryl or threonyl residues, methylation of the o- amino groups of lysine, arginine, and histidine side chains (T.E. Creighton, Proteins: Structure and Molecular Properties, W. H. Freeman & Co., San Francisco pp 79-86 [1983]), acetylation of the N-terminal amine and, in some instances, amidation of the C-terminal carboxyl.
  • variants and derivatives of the disclosed proteins herein are through defining the variants and derivatives in terms of homology/identity to specific known sequences.
  • SEQ ID NO:2 sets forth a particular sequence of PI9
  • SEQ ID NO:4 sets forth a particular sequence of a Spi6 protein.
  • variants of these and other proteins herein disclosed which have at least, 70% or 75% or 80% or 85% or 90% or 95% homology to the stated sequence.
  • the homology can be calculated after aligning the two sequences so that the homology is at its highest level.
  • BESTFIT FASTA
  • TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, WI), or by inspection.
  • nucleic acids that can encode those protein sequences are also disclosed. This would include all degenerate sequences related to a specific protein sequence, i.e. all nucleic acids having a sequence that encodes one particular protein sequence as well as all nucleic acids, including degenerate nucleic acids, encoding the disclosed variants and derivatives of the protein sequences.
  • each particular nucleic acid sequence may not be written out herein, it is understood that each and every sequence is in fact disclosed and described herein through the disclosed protein sequence.
  • one of the many nucleic acid sequences that can encode the protein sequence set forth in SEQ ID NO:4 is set forth in SEQ ID NO:3.
  • Molecules can be produced that resemble peptides, but which are not connected via a natural peptide linkage.
  • Amino acid analogs and analogs and peptide analogs often have enhanced or desirable properties, such as, more economical production, greater chemical stability, enhanced pharmacological properties (half-life, absorption, potency, efficacy, etc.), altered specificity (e.g., a broad-spectrum of biological activities), reduced antigenicity, and others.
  • D-amino acids can be used to generate more stable peptides, because D amino acids are not recognized by peptidases and such.
  • Systematic substitution of one or more amino acids of a consensus sequence with a D-amino acid of the same type e.g., D-lysine in place of L-lysine
  • Cysteine residues can be used to cyclize or attach two or more peptides together.
  • compositions can also be administered in vivo in a pharmaceutically acceptable carrier.
  • pharmaceutically acceptable is meant a material that is not biologically or otherwise undesirable, i.e., the material may be administered to a subject, along with the nucleic acid or vector, without causing any undesirable biological effects or interacting in a deleterious manner with any of the other components of the pharmaceutical composition in which it is contained.
  • the carrier would naturally be selected to minimize any degradation of the active ingredient and to minimize any adverse side effects in the subject, as would be well known to one of skill in the art.
  • compositions may be administered orally, parenterally (e.g., intravenously), by intramuscular injection, by intraperitoneal injection, transdermally, extracorporeally, topically or the like, including topical intranasal administration or administration by inhalant.
  • topical intranasal administration means delivery of the compositions into the nose and nasal passages through one or both of the nares and can comprise delivery by a spraying mechanism or droplet mechanism, or through aerosolization of the nucleic acid or vector.
  • Administration of the compositions by inhalant can be through the nose or mouth via delivery by a spraying or droplet mechanism. Delivery can also be directly to any area of the respiratory system (e.g., lungs) via intubation.
  • compositions required will vary from subject to subject, depending on the species, age, weight and general condition of the subject, the severity of the allergic disorder being treated, the particular nucleic acid or vector used, its mode of administration and the like. Thus, it is not possible to specify an exact amount for every composition. However, an appropriate amount can be determined by one of ordinary skill in the art using only routine experimentation given the teachings herein.
  • Parenteral administration of the composition is generally characterized by injection.
  • Injectables can be prepared in conventional forms, either as liquid solutions or suspensions, solid forms suitable for solution of suspension in liquid prior to injection, or as emulsions.
  • a more recently revised approach for parenteral administration involves use of a slow release or sustained release system such that a constant dosage is mamM ⁇ necT''Se'e, e.g., U.S. Patent No. 3,610,795, which is incorporated by reference herein.
  • the materials may be in solution, suspension (for example, incorporated into microparticles, liposomes, or cells). These may be targeted to a particular cell type via antibodies, receptors, or receptor ligands.
  • the following references are examples of the use of this technology to target specific proteins to tumor tissue (Senter, et al., Bioconjugate Chem., 2:447-451, (1991); Bagshawe, K.D., Br. J. Cancer, 60:275- 281, (1989); Bagshawe, et al., Br. J. Cancer, 58:700-703, (1988); Senter, et al., Bioconjugate Chem., 4:3-9, (1993); Battelli, et al., Cancer Immunol.
  • Vehicles such as "stealth” and other antibody conjugated liposomes (including lipid mediated drug targeting to colonic carcinoma), receptor mediated targeting of DNA through cell specific ligands, lymphocyte directed tumor targeting, and highly specific therapeutic retroviral targeting of murine glioma cells in vivo.
  • receptors are involved in pathways of endocytosis, either constitutive or ligand induced. These receptors cluster in clathrin-coated pits, enter the cell via clathrin-coated vesicles, pass through an acidified endosome in which the receptors are sorted, and then either recycle to the cell surface, become stored intracellularly, or are degraded in lysosomes.
  • the internalization pathways serve a variety of functions, such as nutrient uptake, removal of activated proteins, clearance of macromolecules, opportunistic entry of viruses and toxins, dissociation and degradation of ligand, and receptor-level regulation. Many receptors follow more than one intracellular pathway, depending on the cell type, receptor concentration, type of ligand, ligand valency, and ligand concentration. Molecular and cellular mechanisms of receptor-mediated endocytosis has been reviewed (Brown and Greene, DNA and Cell Biology 10:6, 399-409 (1991)). (a) Pharmaceutically Acceptable Carriers
  • compositions including antibodies, can be used therapeutically in combination with a pharmaceutically acceptable carrier.
  • Suitable carriers and their formulations are described in Remington: Tfie Science and Practice of Pharmacy (19th ed.) ed. A.R. Gennaro, Mack Publishing Company, Easton, PA 1995.
  • an appropriate amount of a pharmaceutically-acceptable salt is used in the formulation to render the formulation isotonic.
  • the pharmaceutically-acceptable carrier include, but are not limited to, saline, Ringer's solution and dextrose solution.
  • the pH of the solution is preferably from about 5 to about 8, and more preferably from about 7 to about 7.5.
  • Further carriers include sustained release preparations such as semipermeable matrices of solid hydrophobic polymers containing the antibody, which matrices are in the form of shaped articles, e.g., films, liposomes or microparticles. It will be apparent to those persons skilled in the art that certain carriers may be more preferable depending upon, for instance, the route of administration and concentration of composition being administered. . ,
  • compositions may include carriers, thickeners, diluents, buffers, preservatives, surface active agents and the like in addition to the molecule of choice. Pharmaceutical compositions may also include one or more active ingredients such as antimicrobial agents, antiinflammatory agents, anesthetics, and the like. 291.
  • the pharmaceutical composition may be administered in a number of ways depending on whether local or systemic treatment is desired, and on the area to be treated. Administration may be topically (including ophthalmically, vaginally, rectally, intranasally), orally, by inhalation, or parenterally, for example by intravenous drip, subcutaneous, intraperitoneal or intramuscular injection.
  • the disclosed antibodies can be administered intravenously, intraperitoneally, intramuscularly, subcutaneously, intracavity, or transdermally.
  • Preparations for parenteral administration include sterile aqueous or non-aqueous solutions, suspensions, and emulsions.
  • non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate.
  • Aqueous carriers include water, alcoholic/aqueous solutions, emulsions or suspensions, including saline and buffered media.
  • Parenteral vehicles include sodium chloride solution, Ringer's dextrose, dextrose and sodium chloride, lactated Ringer's, or fixed oils.
  • Intravenous vehicles include fluid and nutrient replenishers, electrolyte replenishers (such as those based on Ringer's dextrose), and the like. Preservatives and other additives may also be present such as, for example, antimicrobials, anti-oxidants, chelating agents, and inert gases and the like. 293.
  • Formulations for topical administration may include ointments, lotions, creams, gels, drops, suppositories, sprays, liquids and powders. Conventional pharmaceutical carriers, aqueous, powder or oily bases, thickeners and the like may be necessary or desirable.
  • compositions for oral administration include powders or granules, suspensions or solutions in water or non-aqueous media, capsules, sachets, or tablets. Thickeners, flavorings, diluents, emulsifiers, dispersing aids or binders may be desirable..
  • compositions may potentially be administered as a pharmaceutically acceptable acid- or base- addition salt, formed by reaction with inorganic acids such as hydrochloric acid, hydrobromic acid, perchloric acid, nitric acid, thiocyanic acid, sulfuric acid, and phosphoric acid, and organic acids such as formic acid, acetic acid, propionic acid, glycolic acid, lactic acid, pyruvic acid, oxalic acid, malonic acid, succinic acid, maleic acid, and fumaric acid, or by reaction with an inorganic base such as sodium hydroxide, ammonium hydroxide, potassium hydroxide, and organic bases such as mono-, di-, trialkyl and aryl amines and substituted ethanolamines.
  • inorganic acids such as hydrochloric acid, hydrobromic acid, perchloric acid, nitric acid, thiocyanic acid, sulfuric acid, and phosphoric acid
  • organic acids such as formic acid, acetic acid, propionic acid, glyco
  • Effective dosages and schedules for administering the compositions may be determined empirically, and making such determinations is within the skill in the art.
  • the dosage ranges for the administration of the compositions are those large enough to produce the desired effect in which the symptoms and disorder are effected.
  • the dosage should not be so large as to cause adverse side effects, such as unwanted cross-reactions, anaphylactic reactions, and the like.
  • the dosage will vary with the age, condition, sex and extent of the disease in the patient, route of administration, or whether other drugs are included in the regimen, and can be determined by one of skill in the art.
  • the dosage can be adjusted by the individual physician in the event of any counterindications.
  • Dosage can vary, and can be administered in one or more dose administrations daily, for one or several days.
  • Guidance can be found in the literature for appropriate dosages for given classes of pharmaceutical products.
  • guidance in selecting appropriate doses for antibodies can be found in the literature on therapeutic uses of antibodies, e.g., Handbook of Monoclonal Antibodies, Ferrone et al, eds., Noges Publications, Park Ridge, NJ., (1985) ch. 22 and pp. 303-357; Smith et al., Antibodies in Human Diagnosis and Therapy, Haber et al., eds., Raven Press, New York (1977) pp. 365-389.
  • a typical daily dosage of the antibody used alone might range from about 1 ⁇ g/kg to up to 100 mg/kg of body weight or more per day, depending on the factors mentioned above.
  • a composition such as an antibody
  • the efficacy of the therapeutic antibody can be assessed in various ways well known to the skilled practitioner. For instance, one of ordinary skill in the art will understand that a composition, such as an antibody, disclosed herein is efficacious in treating or inhibiting Spi6 or PI9 in a subject by observing that the composition reduces bacterial load, such as Listeria moncytogenes, or prevents a further increase in bacteria, such as Listeria moncytogenes.
  • Bacteria loads such as Listeria moncytogenes
  • Bacteria loads can be measured by methods that are known in the art, for example, using polymerase chain reaction assays to detect the presence of the bacteria, such as Listeria moncytogenes, nucleic acid or antibody assays to detect the presence of bacteria, such as Listeria moncytogenes ⁇ protein in a sample (e.g., but not limited to, blood) from a subject or patient, or by measuring the level of circulating anti-bacteria antibody levels in the patient.
  • a sample e.g., but not limited to, blood
  • compositions that inhibit Spi6 or PI9 interactions disclosed herein may be administered prophylactically to patients or subjects who are at risk for bacteria infection, such as being exosed to bacteria, such as Listeria moncytogenes.
  • Chips and micro arrays 301 Disclosed are chips where at least one address is the sequences or part of the sequences set forth in any of the nucleic acid sequences disclosed herein. Also disclosed are chips where at least one address is the sequences or portion of sequences set forth in any of the peptide sequences disclosed herein.
  • chips where at least one address is a variant of the sequences or part of the sequences set forth in any of the nucleic acid sequences disclosed herein. Also disclosed are chips where at least one address is a variant of the sequences or portion of sequences set forth in any of the peptide sequences disclosed herein.
  • nucleic acids and proteins can be represented as a sequence consisting of the nucleotides of amino acids.
  • nucleotide guanosine can be represented by G or g.
  • amino acid valine can be represented by VaI or V.
  • Those of skill in the art understand how to display and express any nucleic acid or protein sequence in any of the variety of ways that exist, each of which is considered herein disclosed. Specifically contemplated herein is the display of these sequences on computer readable mediums, such as, commercially available floppy disks, tapes, chips, hard drives, compact disks, and video disks, or other computer readable mediums. Also disclosed are the binary code representations of the disclosed sequences.
  • compositions identified by screening with disclosed compositions / combinatorial chemistry (lO)Compositions identified by screening with disclosed compositions / combinatorial chemistry
  • compositions can be used as targets for any combinatorial technique to identify molecules or macromolecular molecules that interact with the disclosed compositions in a desired way.
  • the nucleic acids, peptides, and related molecules disclosed herein can be used as targets for the combinatorial approaches.
  • compositions that are identified through combinatorial techniques or screening techniques in which the compositions disclosed in SEQ ID NOS: 1, 2, 3, and 4 or portions thereof, are used as the target in a combinatorial or screening protocol. 306. It is understood that when using the disclosed compositions in combinatorial techniques or screening methods, molecules, such as macromolecular molecules, will be identified that have particular desired properties such as inhibition or stimulation or the target molecule's function.
  • the molecules identified ' Wa ⁇ sdlatM 1 WH 1 Sn 1 U 1 SIiIg the disclosed compositions, such as, Spi6 or PI9, or animlas overexpressing, for example, are also disclosed.
  • the products produced using the combinatorial or screening approaches that involve the disclosed compositions, such as, Spi6 or PI9, or animals overexpressing them are also considered herein disclosed. 307.
  • the disclosed methods for identifying molecules that inhibit the interactions between, for example, Spi6 and granzyme B can be performed using high through put means.
  • putative inhibitors can be identified using Fluorescence Resonance Energy Transfer (FRET) to quickly identify interactions.
  • FRET Fluorescence Resonance Energy Transfer
  • the underlying theory of the techniques is that when two molecules are close in space, ie, interacting at a level beyond background, a signal is produced or a signal can be quenched. Then, a variety of experiments can be performed, including, for example, adding in a putative inhibitor. If the inhibitor competes with the interaction between the two signaling molecules, the signals will be removed from each other in space, and this will cause a decrease or an increase in the signal, depending on the type of signal used. This decrease or increasing signal can be correlated to the presence or absence of the putative inhibitor. Any signaling means can be used.
  • disclosed are methods of identifying an inhibitor of the interaction between any two of the disclosed molecules comprising, contacting a first molecule and a second molecule together in the presence of a putative inhibitor, wherein the first molecule or second molecule comprises a fluorescence donor, wherein the first or second molecule, typically the molecule not comprising the donor, comprises a fluorescence acceptor; and measuring Fluorescence Resonance Energy Transfer (FRET), in the presence of the putative inhibitor and the in absence of the putative inhibitor, wherein a decrease in FRET in the presence of the putative inhibitor as compared to
  • FRET Fluorescence Resonance Energy Transfer
  • FRET measurement in its absence indicates the putative inhibitor inhibits binding between the two molecules.
  • This type of method can be performed with a cell system as well.
  • Combinatorial chemistry includes but is not limited to all methods for isolating small • molecules or macromolecules that are capable of binding either a small molecule or another macromolecule, typically in an iterative process. Proteins, oligonucleotides, and sugars are examples of macromolecules.
  • oligonucleotide molecules with a given function can be isolated from a complex mixture of random oligonucleotides in what has been referred to as "in vitro genetics" (Szostak, TIBS 19:89, 1992).
  • in vitro genetics Szostak, TIBS 19:89, 1992.
  • Combinatorial techniques are particularly suited for defining binding mt ' eractions"betw ' een”nl'61ecures and for isolating molecules that have a specific binding activity, often called aptamers when the macromolecules are nucleic acids.
  • phage display libraries have been used to isolate numerous peptides that interact with a specific target. (See for example, United States Patent No. 6,031 ,071 ; 5,824,520; 5,596,079; and 5,565,332 which are herein incorporated by reference at least for their material related to phage display and methods relate to combinatorial chemistry)
  • RNA molecule is generated in which a puromycin molecule is covalently attached to the 3 '-end of the RNA molecule.
  • An in vitro translation of this modified RNA molecule causes the correct protein, encoded by the RNA to be translated.
  • the growing peptide chain is attached to the puromycin which is attached to the RNA.
  • the protein molecule is attached to the genetic material that encodes it. Normal in vitro selection procedures can now be done to isolate functional peptides. Once the selection procedure for peptide function is complete traditional nucleic acid manipulation procedures are performed to amplify the nucleic acid that codes for the selected functional peptides. After amplification of the genetic material, new RNA is transcribed with puromycin at the 3 '-end, new peptide is translated and another functional round of selection is performed. Thus, protein selection can be performed in an iterative manner just like nucleic acid selection techniques.
  • the peptide which is translated is controlled by the sequence of the RNA attached to the puromycin.
  • This sequence can be anything from a random sequence engineered for optimum translation (i.e. no stop codons etc.) or it can be a degenerate sequence of a known RNA molecule to look for improved or altered function of a known peptide.
  • the conditions for nucleic acid amplification and in vitro translation are well known to those of ordinary skill in the art and are preferably performed as in
  • Roberts and Szostak Robots R. W. and Szostak J. W. Proc. Natl. Acad. Sci. USA, 94(23)12997-302 (1997)).
  • Cohen et al. modified this technology so that novel interactions between synthetic or engineered peptide sequences could be identified which bind a molecule of choice .
  • the benefit of this type of technology is that the selection is done in an intracellular environment.
  • the method utilizes a library of peptide molecules that attached to an acidic activation domain.
  • a peptide of choice for example an active portion of Spi6 or PI9, is attached to a DNA "Mriairtg' r aomaiiQ"cil"a'tratiscriptional activation protein, such as Gal 4.
  • Combinatorial libraries can be made from a wide array of molecules using a number of different synthetic techniques. For example, libraries containing fused 2,4-pyrimidinediones (United States patent 6,025,371) dihydrobenzopyrans (United States Patent 6,017,768and 5,821,130), amide alcohols (United States Patent 5,976,894), hydroxy-amino acid amides (United States Patent 5,972,719) carbohydrates (United States patent 5,965,719), l,4-benzodiazepin-2,5-diones (United States patent 5,962,337), cyclics (United States patent 5,958,792), biaryl amino acid amides (United States patent 5,948,696), thiophenes (United States patent 5,942,387), tricyclic Tetrahydroquinolines (United States patent 5,925,527), benzofurans (United States patent 5,919,955), isoquinolines (Un
  • Screening molecules similar to S ⁇ i6 or PI9 substrates for inhibition of Spi6 activity is a method of isolating desired compounds.
  • compositions can be used as targets for any molecular modeling technique to identify either the structure of the disclosed compositions or to identify potential or actual molecules, such as small molecules, which interact in a desired way with the disclosed compositions.
  • nucleic acids, peptides, and related molecules disclosed herein can be used as targets in any molecular modeling program or approach.
  • QUANTA performs the construction, graphic modeling and analysis of molecular structure. QUANTA allows interactive construction, modification, visualization, and analysis of the behavior of molecules with each other.
  • kits that are drawn to reagents that can be used in practicing the methods disclosed herein.
  • the kits can include any reagent or combination of reagent discussed herein or that would be understood to be required or beneficial in the practice of the disclosed methods.
  • the kits could include primers to perform the amplification reactions discussed in certain embodiments of the methods, as well as the buffers and enzymes required to use the primers as intended.
  • a kit for assessing whether a particular compound inhibits Spi6 function comprising the oligonucleotides set forth in SEQ ID Nos: 3 and 1. (12) Compositions with similar functions
  • compositions disclosed herein have-certainriunctions, such as inhibiting Spi6 or PI9.
  • Disclosed herein are certain structural requirements for performing the disclosed functions, and it is understood that there are a variety of structures which can perform the same function which are related to the disclosed structures, and that these structures will ultimately achieve the same result, for example stimulation or inhibition of Spi6 or PI9.
  • compositions can be used in a variety of ways as research tools.
  • the disclosed compositions such as the transgenic mice and knock-out mice can be used to study the mechanisms surrounding Spi6.
  • the compositions can be used for example as targets in combinatorial chemistry protocols or other screening protocols to isolate molecules that possess desired functional properties related to S ⁇ i6.
  • compositions can also be used as diagnostic tools related to diseases of the immune system, such as inflammatory diseases, as well as models of these diseases.
  • the disclosed compositions can be used as discussed herein as either reagents in micro arrays or as reagents to probe or analyze existing microarrays.
  • the disclosed compositions can be used in any known method for isolating or identifying single nucleotide polymorphisms.
  • the compositions can also be used in any method for determining allelic analysis of for example, particularly allelic analysis as it relates to Spi6 and functions.
  • the compositions can also be used in any known method of screening assays, related to chip/micro arrays.
  • the compositions can also be used in any known way of using the computer readable embodiments of the disclosed compositions, for example, to study relatedness or to perform molecular modeling analysis related to the disclosed compositions. 1 : Methods of Using Spi6 and PI9 a) Methods of Increasing Immunity to Viral Infection
  • Disclosed herein are methods of increasing immunity comprising administering a vector expressing a Spi6 nucleic acid or a PI9 nucleic acid.
  • a method of increasing immunity to viral infection comprising administering a vector expressing a Spi6 nucleic acid or a PI9 nucleic acid.
  • a method of increasing immunity to viral infection comprising administering a vector comprising a nucleic acid capable of encoding Spi6 or PI9.
  • the virus can be Lymphocytic chorioimeningitis virus, Herpes simplex virus type-1 , Herpes simplex virus type-2, Cytomegalovirus, Epstein-Barr virus, Varicella-zoster virus, Human herpesvirus 6, Human herpesvirus 7, Human herpesvirus 8, Variola virus, Vesicular stomatitis virus, Hepatitis A virus, Hepatitis B virus, Hepatitis C virus, Hepatitis D virus, Hepatitis E virus, Rhinovirus, Coronavirus, Influenza virus A, Influenza virus B, Measles virus, Polyomavirus, Human Papilomavirus, Respiratory syncytial virus, Adenovirus, Coxsackie virus, Dengue virus, Mumps virus, Poliovirus, Rabies virus, Rous sarcom
  • Spi6 in addition to suppressing the activity of cytoplasmic GrB, Spi6 also ensured the integrity of lytic granules.
  • methods of protecting the integrity of lytic granules comprising administering a vector expressing a Spi6 nucleic acid or a PI9 nucleic acid.
  • methods of protecting the integrity of lytic granules comprising administering an effective amount of SPI6 or PI9 protein, or a fragment thereof.
  • 333 Provided herein are methods of protecting against inflammatory disease comprising administering a vector expressing a Spi6 nucleic acid or a PI9 nucleic acid. Also provided herein are methods of protecting against inflammatory disease comprising administering an effective amount of SPI6 or PI9 protein, or a fragment thereof.
  • IBD inflammatory bowel disease
  • Hashimoto's disease Hashimoto's disease
  • rheumatoid arthritis graft-versus-host disease
  • Sjogren's syndrome pernicious anemia
  • Addison disease scleroderma
  • Goodpasture's syndrome ulcerative colitis
  • Crohn's disease autoimmune hemolytic anemia
  • sterility myasthenia gravis
  • myasthenia gravis multiple sclerosis
  • thrombopenia purpura insulin-dependent diabetes mellitus, allergy; asthma, atopic disease, arteriosclerosis, myocarditis, cardiomyopathy, glomerular nephritis, hypoplastic anemia, as well as "gfaft-f erSus-Mst" aM Mst-Versu's ' -graft disease.
  • a method of protecting against transplantation induced graft-versus-host and host-versus-graft disease comprising administering an effective amount of SPI6 or PI9 protein or a fragment thereof.
  • a method of protecting against transplantation induced graft-versus-host and host-versus-graft disease comprising administering a vector expressing a Spi6 nucleic acid or a PI9 nucleic acid.
  • Granzyme B-induced inflammatory diseases include, but are not limited to achalasia, early rheumatoid factor positive rheumatoid arthritis, atherosclerosis, transplant vascular disease, childhood bronchiolititis, Crohn's Disease, Ulcerative Colitis, Rasmussen's encephalitis, early rheumatoid arthritis, graft-versus-host disease, systemic lupus erythematosus, lichen sclerosus et atrophicus, and systemic sclerosis.
  • the disclosed method of protecting against inflammatory disease can also be used to dampen inflammation due to chronic infection.
  • chronic infection in COPD patients can lead to deleterious inflammation responses in the respiratory system.
  • the inflammation reaction if the inflammation reaction is completely reduced, this can help with the inflammation effects, but can create other problems with respect to bacterial immunity and the patients' ability to fight off an infection.
  • the use, of SPI6 or PI9 or active fragments, or their expression from genes can create a beneficial situation where the inflammation reaction, and for example, the neutrophil elastase activity can be dampened, but not eliminated because the SPI6 and PI9 do not completely reduce these responses and activities as discussed herein.
  • Spi6 is a potent inhibitor of Granzyme B.
  • the examples below show that Granzyme B is active in the cytoplasm and Spi6 is also expressed in the cytoplasm.
  • provided are methods of inhibiting Granzyme B activity in the cytoplasm by administering a vector expressing a Spi6 nucleic acid or a PI9 nucleic acid.
  • "'"" "'"'iPfoMW Kf bin are methods of inhibiting neutrophil elastase by administering a vector expressing a Spi6 nucleic acid or a PI9 nucleic acid. Also provided herein are methods of inhibiting neutrophil elastase by administering an effective amount of SPI6 or PI9 protein, or a fragment thereof.
  • exogenous inhibitors of neutrophil elastase would be of particular use as well.
  • exogenous inhibitors of neutrophil elastase include, but are not limited to ⁇ l-antitrysin, monocyte neutrophil elastase inhibitor (MNEI), or SLPl. These inhibitors can be added in combination with the compositions disclosed herein to decrease neutrophil elastase activity, but to not eliminate it. For example, less SLPl can be administered then what would have previously been used to achieve a reduced neutrophil elastase activity, but not to eliminate the activity.
  • the structurally novel small molecule ⁇ WAY-140312 was also shown to be a potent inactivator of PAI-I (Crandall et al., 2004). It is understood that these molecules can have cross reactivity with the other serpins, and as such these molecules can also function in certain embodiments as inhibitors of S ⁇ i6 and or PI9. Other molecules having inhibitor activity of other serpins or elastase inhibitors are also disclosed and can be used as inhibitors of Spi6 or PI9. It is understood that these and other molecules can be tested for their efficacy of inhibition, by for example, testing them in the mouse and animal models disclosed herein.
  • the disclosed animals such as mice, such as the transgenic animals, can be used to test, in vivo the activity of various molecules which either are known to have or could have Spi6 or PI9 inhibitory activity. These molecules can be tested as disclosed herein, but at least can be tested by administration of the molecule or molecules to the animal and assaying the effect the molecule has on the animal, and comparing that to, for example, a nontransgenic animal. Any of the assays for Spi6 and PI9 phenotypes of, for example, the transgenic animals discussed herein can be used to determine the effect of the molecule on
  • Disclosed are methods of identifying a candidate inhibitor of Spi6 activity comprising (a) preparing a first cell culture that overexpresses Spi ⁇ ; (b) adding the candidate inhibitor to the cell culture (c) incubating the cell culture under conditions and for a time sufficient to detect an inhibitory effect by the candidate inhibitor; and (d) determining the effect of the candidate inhibitor on the Spi6 activity.
  • Also disclosed are methods of identifying a candidate inhibitor of PI9 activity comprising (a) preparing a first cell culture that overexpresses PI9; (b) adding the candidate inhibitor to the cell culture (c) incubating the cell culture under conditions and for a time sufficient to detect an inhibitory effect by the candidate inhibitor; and (d) determining the effect of the candidate inhibitor on the PI9 activity.
  • a candidate inhibitor of PI9 can be identified by a method comprising (a) preparing a first cell culture that overexpresses Spi6; (b) adding the candidate inhibitor to the cell culture (c) incubating the cell culture under conditions and for a time sufficient to detect an inhibitory effect by the candidate inhibitor; and (d) determining the effect of the candidate inhibitor on the Spi6 activity.
  • a method of identifying a candidate inhibitor of Spi ⁇ activity comprising (a) preparing a first cell culture that overexpresses Spi ⁇ ; (b) adding the candidate inhibitor to the cell culture (c) incubating the cell culture under conditions and for a time sufficient to detect an inhibitory effect by the candidate inhibitor; and (d) determining the effect of the candidate inhibitor on the Spi ⁇ activity and further comprising assaying the cell for increased in vitro bactericidal activity of neutrophils or macrophages from
  • a method of identifying a candidate inhibitor of PI9 activity comprising (a) preparing a first cell culture that overexpresses PI9; (b) adding the candidate inhibitor to the cell culture (c) incubating the cell culture under conditions and for a time sufficient to detect an inhibitory effect by the candidate inhibitor; (d) determining the effect of the candidate inhibitor on the PI9 activity and assaying the cell for increased in vitro bactericidal activity of neutrophils or macrophages from PI9 transgenic mice.
  • a method of identifying a candidate inhibitor of Spi ⁇ activity comprising (a) preparing a transgenic non-human animal that overexpresses Spi ⁇ ; (b) administering the candidate inhibitor to the animal (c) determining the effect of the candidate inhibitor on the Spi ⁇ activity.
  • a method of identifying a candidate inhibitor of PI9 activity comprising (a) preparing a transgenic non-human animal that overexpresses PI9; (b) administering the candidate inhibitor to the animal (c) determining the - , « ⁇ + of the candidate inhibitor on the PI9 activity.
  • 3'MT - " ⁇ Al'so'tusciose ⁇ is a method of identifying a candidate inhibitor of Spi6/PI9 activity comprising (a) preparing a transgenic non-human animal that overexpresses Spi6; (b) administering the candidate inhibitor to the animal (c) determining the effect of the candidate inhibitor on the Spi6 activity, wherein the transgenic non-human animal comprises a cell wherein the cell expresses a transgene coding for a serpin.
  • a method of screening a set of candidate inhibitors of Spi6 activity comprising (a) preparing a transgenic non-human animal that overexpresses Spi6; (b) administering the set of candidate inhibitors to the animal (c) determining the effect of the set of candidate inhibitors on the S ⁇ i6 activity.
  • a method of screening a set of candidate inhibitors of PI9 activity comprising (a) preparing a transgenic non-human animal that overexpresses PI9; (b) administering the set of candidate inhibitors to the animal (c) determining the effect of the set of candidate inhibitors n the PI9 activity.
  • a method of screening a set of candidate inhibitors of Spi6 activity comprising (a) preparing a transgenic non-human animal that overexpresses Spi6; (b) administering the set of candidate inhibitors to the animal (c) determining the effect of the set of candidate inhibitors on the Spi6 activity, further comprising d) the step of subdividing the set of candidate inhibitors into subsets of candidate inhibitors, and e) testing each subset for inhibitory activity in the transgenic non-human animal that overexpresses S ⁇ i6 until a subset having the inhibitory activity is identified.
  • Also disclosed is a method of screening a set of candidate inhibitors of PI9 activity comprising (a) preparing a transgenic non-human animal that overexpresses PI9; (b) administering the set of candidate inhibitors to the animal (c) determining the effect of the set of candidate inhibitors on the PI9 activity, further comprising d) the step of subdividing the set of candidate inhibitors into subsets of candidate inhibitors, and e) testing each subset for inhibitory activity in the transgenic non-human animal that overexpresses PI9 until a subset having the inhibitory activity is identified.
  • Also disclosed is a method of screening a set of candidate inhibitors of S ⁇ i6 activity comprising (a) preparing a transgenic non-human animal that overexpresses S ⁇ i6; (b) administering the set of candidate inhibitors to the animal (c) determining the effect of the set of candidate inhibitors on the Spi6 activity, further comprising d) the step of subdividing the set of candidate inhibitors into subsets of candidate inhibitors, and e) testing each subset for inhibitory activity in the transgenic non-human animal that overexpresses Spi6 until a subset having the inhibitory activity is identified, further comprising f) the step of subdividing the identified subset of candidate inhibitors in a set of small subsets of candidate inhibitors, g) and testing each small subset of candidate inhibitors for inhibitory activity in the transgenic non-human animal that overepxresses Spi6 until a small subset having the activity is identified.
  • a method of screening a set of candidate inhibitors of PI9 activity comprising (a) preparing a transgenic non-human animal that overexpresses PI9; (b) administering the set of candidate inhibitors to the animal (c) determining the effect of the set of candidate inhibitors on the PI9 activity, further comprising d) the step of subdividing the set of candidate inhibitors into subsets of candidate inhibitors, and e) testing each subset for inhibitory activity in the transgenic non-human animal tliat 1 ove'feip ⁇ es's'es' PB 1 ttitiWsutfeet having the inhibitory activity is identified, further comprising f) the step of subdividing the identified subset of candidate inhibitors in a set of small subsets of candidate inhibitors, g) and testing each small subset of candidate inhibitors for inhibitory activity in the transgenic non-human animal that overepxresses PI9 until a small subset having the activity is identified.
  • a method of screening a set of candidate inhibitors of Spi6 activity comprising (a) preparing a transgenic non-human animal that overexpresses Spi6; (b) administering the set of candidate inhibitors to the animal (c) determining the effect of the set of candidate inhibitors on the Spi6 activity, further comprising d) the step of subdividing the set of candidate inhibitors into subsets of candidate inhibitors, and e) testing each subset for inhibitory activity in the transgenic non-human animal that overexpresses Spi6 until a subset having the inhibitory activity is identified, further comprising f) the step of subdividing the identified subset of candidate inhibitors in a set of small subsets of candidate inhibitors, g) and testing each small subset of candidate inhibitors for inhibitory activity in the transgenic non-human animal that overepxresses Spi6 until a small subset having the activity is identified, further comprising repeating steps f and g until a single candidate inhibitor having inhibitory activity is identified
  • Also disclosed is a method of screening a set of candidate inhibitors of PI9 activity comprising (a) preparing a transgenic non-human animal that overexpresses PI9; (b) administering the set of candidate inhibitors to the animal (c) determining the effect of the set of candidate inhibitors on the PI9 activity, further comprising d) the step of subdividing the set of candidate inhibitors into subsets of candidate inhibitors, and e) testing each subset for inhibitory activity in the transgenic non-human animal that overexpresses PI9 until a subset having the inhibitory activity is identified, further comprising f) the step of subdividing the identified subset of candidate inhibitors in a set of small subsets of candidate inhibitors, g) and testing each small subset of candidate inhibitors for inhibitory activity in the transgenic non-human animal that overepxresses PI9 until a small subset having the activity is identified, further comprising repeating steps f and g until a single candidate inhibitor having inhibitory activity is identified
  • a method of testing an inhibitor of Spi6 activity comprising (a) preparing a transgenic nonhuman animal that overexpresses Spi6; (b) administering the inhibitor to the animal (c) determining the effect of the inhibitor on the S ⁇ i6 activity.
  • a method of testing an inhibitor of PI9 activity comprising (a) preparing a transgenic nonhuman animal that overexpresses PI9; (b) administering the inhibitor to the animal (c) determining the effect of the inhibitor on the PI9 activity. 359.
  • Also disclosed is a method of testing an inhibitor of Spi6 activity comprising (a) preparing a transgenic nonhuman animal that overexpresses S ⁇ i6; (b) administering the inhibitor to the animal (c) determining the effect of the inhibitor on the Spi6 activity, further comprising comparing the activity of the inhibitor to the activity of a known standard.
  • a method of testing an inhibitor of PI9 activity comprising (a) preparing a transgenic nonhuman animal that overexpresses PI9; (b) administering the inhibitor to the animal (c) determining the effect of the inhibitor on the PI9 activity, further comprising comparing the activity of the inhibitor to the activity of a known standard.
  • Also'y ⁇ M ⁇ sfel-t' is a method of testing an inhibitor of Spi6 activity comprising (a) preparing a transgenic nonhuman animal that overexpresses Spi6; (b) administering the inhibitor to the animal (c) determining the effect of the inhibitor on the Spi6 activity, further comprising comparing the activity of the inhibitor to the activity of a known standard, further comprising comparing the activity of the inhibitor to the activity of the inhibitor that occurred in a previous test of the compound in the transgenic nonhuman animal.
  • Also disclosed is a method of testing an inhibitor of PI9 activity comprising (a) preparing a transgenic nonhuman animal that overexpresses PI9; (b) administering the inhibitor to the animal (c) determining the effect of the inhibitor on the PI9activity, further comprising comparing the activity of the inhibitor to the activity of a known standard, further comprising comparing the activity of the inhibitor to the activity of the inhibitor that occurred in a previous test of the compound in the transgenic nonhuman animal.
  • Granzyme B comprising administering a composition, wherein the composition expresses PI9
  • diseases caused by excess granzyme B activityjn include, but are not limited to: Graft versus Host Disease, Rheumatoid Arthritis, Systemic Lupus Erythematosis, Transplant Vascular Disease, Athrelosclerosis, Exanthematous Pustulosis, Scleroderma, Ischemic digital loss, Rasmussens Encephalitis,
  • mice were resistant to lethal infection with gram-positive L. monocytogenes
  • NE neutrophil elastase
  • HNE or NE can be administered at a concentration of 0.1 U/kg, 0.2 U/kg, 0.3 U/kg, 0.4 U/kg, 0.5 U/kg, 0.6 U/kg, 0.7 U/kg, 0.8 U/kg, 0.9 U/kg, 1.0 U/kg, 1.1 U/kg, 1.2 U/kg, 1.3 U/kg, 1.4 U/kg, 1.5 U/kg, 1.6 U/kg, 1.7 U/kg, 1.8 U/kg, 1.9 U/kg, 2.0 U/kg, 2.1 U/kg, 2.2 U/kg, 2.3 U/kg, 2.4 U/kg, 2.5 U/kg, 2.6 U/kg, 2.7 U/kg, 2.8 U/kg, 2.9 U/kg, 3.0 U/kg, 3.1 U/kg, 3.2 U/kg, 3.3 U/kg, 3.4 U/kg, or 3.5 U/kg.
  • One unit is defined as the amount of enzyme that will hydrolyze 1.0 ⁇ mol of MeO-Suc-Ala-
  • NE doses can be any disclosed herein in combination with any doses of a S ⁇ i6 inhibitor disclosed herein.
  • the bacteria can be a drug resistant bacterium.
  • drug resistant bacteria include but are not limited to: Methicillin-resistant S. aureus (MRSA), Vancomycin- resistant Enterococci (VRE), Amikacin- and ⁇ -lactam-resistant K. pneumoniae, Vancomycin-resistant Staphylococcus aureus (VRSA), Enterococcus, H. influenzae, M. tuberculosis, N. gonorrhoeae, P. falciparum, P. aeruginosa, S. dysenteriae, S. aureus, S. pneumoniae, K. pneumonia, E. coli, Salmonella.
  • the bacteria can be an extracellular bacterium.
  • extracellular bacteria include, but are not limited to: N. gonorrhoeae, N. meningitides, H. influenzae type b, ⁇ ontypeable H. influenzae, H. ducreyi, B. pertussis, P. aeruginosa, E. coli, V. cholera, H. pylori, T. pallidum, S. pneumoniae, S. aureus, S. pyogenes, S. agalactiae, C. diphtheria, C. tetani, C. perfringens.
  • a method of identifying a gene regulated by Spi6 comprising performing a microarray gene expression analysis of a Spi6 knockout mouse, wherein the gene expression analysis produces a first data set of expressed genes in the Spi6 KO mouse; performing a microarray gene expression analysis of a wild-type mouse, wherein the gene expression analysis produces a second data set of expressed genes in the wild-type mouse; comparing the first data set with the second data set; and identifying the genes in the Spi6 knockout mouse that are expressed differently than the wild-type mouse.
  • a method of identifying a gene regulated by PI9 comprising performing a microarray gene expression analysis of a PI9 knockout mouse, wherein the gene expression analysis produces a first data set of expressed genes in the PI9 KO mouse; performing a microarray gene expression analysis of a wild-type mouse, wherein the gene expression analysis produces a second data set of expressed genes in the wild-type mouse; comparing the first data set with the second data set; and identifying the genes in the PI9 knockout mouse that are expressed differently than the wild-type mouse.
  • Identification of new drugs is an important aspect of medical innovation. As discussed above, S ⁇ i6 and PI9 interact and regulate several molecules that are involved in the inflammatory system. Animals and humans alike, that lack native Spi6 or PI9 function can exhibit conditions that are characteristic of a lack of homeostatic regulation of serine proteases. As such, identifying drugs that can compensate for a lack of native Spi6 or PI9 function can be of great use.
  • Provided herein are methods of drug discovery. For example, disclosed is a method of drug discovery comprising administering a candidate drug to the Spi6 KO mouse.
  • Immunity can be immunity to bacterial infection.
  • the bacteria causing the infection can be gram positive or gram negative.
  • the bacterial infection can be in any tissue, including the lung, liver, blood, peritoneum, or spleen.
  • NE serine protease neutrophil elastase
  • HNE human neutrophil elastase
  • Granulocytes both digest extracellular matrix components, as they exit the circulation and migrate to the site of infection, and digest bacteria within the phagolysosome. As such, granulocytes play a critical role the inflammatory reponse process.
  • neutrophil elastase alternative to the methods described herein related to increasing neutrophil elastase activity, provided herein are methods of inhibiting neutrophil elastase. For example, provided is a method of inhibiting neutrophil elastase comprising administering a vector expressing Spi6. Also provided is a method of inhibiting neutrophil elastase comprising administering an effective amount of SPI6 protein or a fragment thereof.
  • Methods of Treatment 389 Provided herein are methods of treating bacterial infections and sepsis in a subject. For example, provided is a method of treating a bacterial infection in a subject comprising administering to the subject an effective amount of a SPI6 inhibitor.
  • a method of treating a bacterial infection in a subject comprising introducing an effective amount of a disrupted Spi6 gene to the subject. 391. Further provided is a method of treating sepsis in a subject comprising administering to the subject an effective amount of a SPI6 inhibitor.
  • Also provided is a method of treating sepsis in a subject comprising introducing an effective amount of a disrupted Spi6 gene to the subject.
  • Serpins such as Spi6 have the propensity to form multimers, which inhibit function.
  • a mutant form of Spi6 defective in NE binding i.e. mutated or deleted RCL
  • meihWOT'tfeiatmf 1'TOte ⁇ ia ⁇ infection in a subject comprising administering to the subject an effective amount of a disfunctional SPI6 protein or a fragment thereof, wherein the dysfunctional SPI6 protein or a fragment thereof prevents native SPI6 from inhibiting neutrophil elastase function.
  • a method of treating a bacterial infection in a subject comprising administering to the subject an effective amount if an inhibitor of Spi6 in combination with human neutrophil elastase, and wherein the concentration of human neutrophil elastase is less than 1.8U/kg.
  • Also provided is a method of treating sepsis in a subject comprising administering to the subject an effective amount if an inhibitor of Spi6 in combination with human neutrophil elastase, and wherein the concentration of human neutrophil elastase is less than 1.8U/kg
  • compositions disclosed herein and the compositions necessary to perform the disclosed methods can be made using any method known to those of skill in the art for that particular reagent or compound unless otherwise specifically noted.
  • the nucleic acids such as, the oligonucleotides to be used as primers can be made using standard chemical synthesis methods or can be produced using enzymatic methods or any other known method. Such methods can range from standard enzymatic digestion followed by nucleotide fragment isolation (see for example, Sambrook et ah, Molecular Cloning: A Laboratory Manual, 2nd
  • Peptide synthesis 398 One method of producing the disclosed proteins, such as SEQ ID NO.4 is to link two or more peptides or polypeptides together by protein chemistry techniques. For example, peptides or polypeptides can be chemically synthesized using currently available laboratory equipment using either Fmoc (9-fluorenylmethyloxycarbonyl) or Boc (tert -butyloxycarbonoyl) chemistry. (Applied Biosystems, Inc., Foster City, CA). One skilled in the art can readily appreciate that a peptide or polypeptide corresponding to the disclosed proteins, for example, can be synthesized by standard chemical reactions.
  • a peptide or polypeptide can be synthesized and not cleaved from its synthesis resin whereas the other fragment of a peptide or protein can be synthesized and subsequently cleaved from the resin, thereby exposi ⁇ g"a' ⁇ ernunai grbup'Wffi ⁇ r ⁇ s functionally blocked on the other fragment.
  • peptide condensation reactions these two fragments can be covalently joined via a peptide bond at their carboxyl and amino termini, respectively, to form an antibody, or fragment thereof.
  • peptide or polypeptide is independently synthesized in vivo as described herein. Once isolated, these independent peptides or polypeptides may be linked to form a peptide or fragment thereof via similar peptide condensation reactions.
  • enzymatic ligation of cloned or synthetic peptide segments allow relatively short peptide fragments to be joined to produce larger peptide fragments, polypeptides or whole protein domains (Abrahmsen L et al., Biochemistry, 30:4151 (1991)).
  • native chemical ligation of synthetic peptides can be utilized to synthetically construct large peptides or polypeptides from shorter peptide fragments. This method consists of a two step chemical reaction (Dawson et al. Synthesis of Proteins by Native Chemical Ligation. Science, 266:776-779 (1994)).
  • the first step is the chemoselective reaction of an unprotected synthetic peptide— thioester with another unprotected peptide segment containing an amino-terminal Cys residue to give a thioester-linked intermediate as the initial covalent product. Without a change in the reaction conditions, this intermediate undergoes spontaneous, rapid intramolecular reaction to form a native peptide bond at the ligation site (Baggiolini M et al. (1992) FEBS Lett.
  • unprotected peptide segments are chemically linked where the bond formed between the peptide segments as a result of the chemical ligation is an unnatural (non-peptide) bond (Schnolzer, M et al. Science, 256:221 (1992)).
  • This technique has been used to synthesize analogs of protein domains as well as large amounts of relatively pure proteins with full biological activity (deLisle Milton RC et al., Techniques in Protein Chemistry IV. Academic Press, New York, pp. 257-267 (1992)).
  • compositions Disclosed are processes for making the compositions as well as making the intermediates leading to the compositions.
  • processes for making the compositions for example, disclosed are nucleic acids in SEQ ID NOs: 1 and 3.
  • methods for making these compositions such as synthetic chemical methods and standard molecular biology methods. It is understood that the methods of making these and the other disclosed compositions are specifically disclosed.
  • nucleic acid molecules produced by the process comprising linking in an operative way a nucleic acid comprising the sequence of Spi6 or PI9 and a sequence controlling the expression of the nucleic acid. 403. Also disclosed are nucleic acid molecules produced by the process comprising linking in an operative way a nucleic acid molecule comprising a sequence having 80% identity to a sequence set forth in SEQ ID NO:3, for example, and a sequence controlling the expression of the nucleic acid.
  • nucleic acid molecules produced by the process comprising linking in an operative way a nucleic acid molecule comprising a sequence that hybridizes under stringent hybridization conditions to a sequence set forth SEQ ID NO 3, for example, and a sequence controlling the expression of the nucleic acid 405
  • nucleic acid molecules produced by the process comprising linking in an operative way a nucleic acid molecule comprising a sequence encoding a peptide set forth m SEQ ID NO 4, for example, and a sequence controlling an expression of the nucleic acid molecule
  • nucleic acid molecules produced by the process comprising linking in an operative way a nucleic acid molecule comprising a sequence encoding a peptide having 80% identity to a peptide set forth in SEQ ID NO 4, for example, and a sequence controlling an expression of the nucleic acid molecule
  • nucleic acids produced by the process comprising linking in an operative way a nucleic acid molecule comprising a sequence encoding a peptide having 80% identity to a peptide set forth in SEQ ID NO 4, for example, wherein any change from the SEQ ID NO 4, for example, are conservative changes and a sequence controlling an expression of the nucleic acid molecule
  • any of the disclosed peptides produced by the process of expressing any of the disclosed nucleic acids Disclosed are any of the non-naturally occurring disclosed peptides produced by the process of expressing any of the disclosed nucleic acids
  • any of the disclosed peptides produced by the process of expressing any of the non-naturally disclosed nucleic acids Disclosed are any of the disclosed peptides produced by the process of expressing any of the non-naturally disclosed nucleic acids
  • animals produced by the process of transfecting a cell within the annnal with any of the nucleic acid molecules disclosed herein Disclosed are animals produced by the process of transfecting a cell within the animal any of the nucleic acid molecules disclosed herein, wherein the animal is a mammal Also disclosed are animals produced by the process of transfecting a cell within the animal any of the nucleic acid molecules disclosed herein, wherein the mammal is mouse, rat, rabbit, cow, sheep, pig, or primate
  • Animals can be housed in an approved animal care facility. Twenty-four hour-a-day veterinarian and veterinary technician consultants can be available for the time period of the project. Animals can be monitored for well being with the specifics of the animal protocol, which includes twice weekly monitoring. 414. Animals can be anesthetized by the injection of nembutal (30-70mg/kg i.p.) prior to euthanization by CO 2 . This method of euthanasia is approved by the Panel on Euthanasia of the American Veterinary Medical Association.
  • mice can be anesthetized after injection of ketamine (80 mg/kg and xylazine (10 mg/kg)). Animals can then be bled by retro-orbital bleeding.
  • Spi ⁇ - ⁇ eFic ⁇ e ⁇ mice in the C57BL/6 background were generated through ES cell technology. Standard techniques were used to generate a mutant Spi ⁇ allele in C57BL/6 ES cells (See Fig. IA). Spi ⁇ mutant alleles lack exon 7, which as well as encoding most of Spi ⁇ encompasses the functionally essential reactive center loop.
  • Cre recombinase was used to excise neo (Sun et al., 1997a).
  • Southern Blot analysis was used to identify two ES cell clones harboring mutant Spi ⁇ neo alleles (69 and 389) using 5' and 3 ' probes.
  • C57BL/6 ES cells harboring ⁇ ieSpi ⁇ ⁇ neo allele were microinjected into blastocysts from BALB/c mice and the resulting chimeras backcrossed to C57BL/6 mice.
  • Progeny derived from ES cell were identified by black coat color and screened for the mutant Spi ⁇ neo allele by Southern blots.
  • Recombinant Spi6 was generated in the pET expression system in E.coli as a fusion protein with glutathione transferase (GST), using standard procedures recommended by the manufacturer (Novagen). The GST tag was removed by factor X proteolysis and recombinant (r) Spi6 (43 kD) purified to homogeneity (Fig. 2A). Recombinant Spi6 was incubated with protease at al 0-fold molar excess for varying periods of time then the residual activity measured against labeled peptide substrates (Annand et al., 1999; Coeshott et al., 1999; Liu et al., 2003). (4) Generation of Bone Marrow Derived Dendritic Cells (BMDCs)
  • BMDCs were generated as described previously (Lutz et al., 1999). For example, bone marrow cells (10 5 /ml; 20ml) were cultured in a 10cm dish with GM-CSF for 6 days (200U/ml) then for a further 3 days ( 100U/ml), at which point the cell surface expression of CD lie and I-A b was examined for evidence of a DC-like phenotype.
  • LCMV-specific CTLs were detected in the spleen 8 days after infection by staining with H-
  • mice (Mus musculus) (C57BL/6 wild-type, C57BL/6 thyl.l congenic, C57BL/6 Spi ⁇ KO) were infected i.p. with LCMV Armstrong (2 xlO 5 PFU/ml) diluted from high titer frozen stocks in a 100-200 ⁇ l volume in PBS using a 25- G needle.
  • LCMV Armstrong (2 xlO 5 PFU/ml) diluted from high titer frozen stocks in a 100-200 ⁇ l volume in PBS using a 25- G needle.
  • mice were infected with either LCMV Armstrong (10 6
  • LCMV Armstrong clone 13 (10 ⁇ PFU/mouse i.v.).
  • recipient mice were placed in a restrainer and the tail warmed with a heat lamp to allow visualization of the tail vein, then sterilized by washing with 70% ethanol then LCMV injected into the lumen of the tail vein in a 100-200 ⁇ l volume in PBS using a 25-G needle. The spleen was removed from sacrificed mice to allow the measurement of the number of LCMV-specific CD8 T cells and LCMV using standard plaque assays on
  • mice were infected i.v. with an attenuated strain of I. monocytogenes (strain DBL-1942), diluted from freshly grown cultures in a 100-200 ⁇ l volume in PBS using a 25-G needle. Titers of LM were determined in homogenates of the spleen and liver after sacrifice. To measure recruitment of macrophages or neutrophils and obtain cells for ex vivo studies mice were infected i.p. (10 4 - 10 5 CFU/mouse). For survival experiments mice were injected i.v.
  • P14 transgenic mice were incubated with GP33 peptide (10 "7 M) and IL-2 (lOU/ml) for 3 d to give P14 CTLs (>90% P14TCR + CD8 + ).
  • Cells were lysed by sonication in hypotonic buffer (50 mM PIPES, 5OmM KCL, 5mM EGTA, 2mM MgCl 2 5mM DTT, pH 7.6) then centrifuged at 15, 000 x g for 30 min to give cytosol (supernatant) and organelle (pellet) fractions.
  • the organelle pellet was resuspended in 1% Triton X-100, 1OmM Tris.HCl, 15OmM NaCl, pH 7.6 for 30 min on ice.
  • Granulocyte function in Spi6 KO 427 Granulocytes (90% Gr-I + CDl Ib + ) were elicited in the peritoneum by glycogen injection as described previously (Lopez-Boado et al., 2004). Mice were then injected i.p. with LM (10 6 CFU).
  • spleen cells from C57BL/6 P14 or C57BL/6 Spi6KO transgenic mice can be adoptively transferred by i.v. injection to
  • DCs dendritic cells
  • recipient mice can be placed in a restrainer and the tail warmed with a heat lamp to allow visualization of the tail vein, then the tail can be sterilized by washing with 70% ethanol, and then LCMV can be injected into the lumen of the tail vein in a 100-200 ⁇ l volume in PBS using a 25-G needle.
  • C57BL/6 wild-type, or C57BL/6 Spi6 KO mice can be injected i.v. with purified mAbs (0.2-1.0 mg) to neutralize cytokines or deplete cells.
  • recipient mice can be placed in a restrainer and the tail warmed with a heat lamp to allow visualization of the tail vein, then sterilized by washing with 70% ethanol then LCMV injected into the lumen of the tail vein in a 100-200 ⁇ l volume in PBS using a 25-G needle.
  • mice can be injected i.v. with preparations of LIP-CLOD (20-80 ⁇ g CLOD/mouse; lOO ⁇ l/lOg body weight).
  • LIP-CLOD 20-80 ⁇ g CLOD/mouse; lOO ⁇ l/lOg body weight.
  • recipient mice can be placed in a restrainer and the tail warmed with a heat lamp to allow visualization of the tail vein, then sterilized by washing with 70% ethanol then LCMV injected into the lumen of the tail vein in a 100-200 ⁇ l volume in PBS using a 25-G needle.
  • C57BL/6 Spi6 KO mice can be injected with 3% thioglycollate (0.3ml/10g body weight) to induce sterile peritonitis then the recruitment of macrophages to the peritoneum measured over the course of 6 d.
  • 3% thioglycollate 0.3ml/10g body weight
  • bone-marrow can be obtained from the femur after the sacrifice of C57BL/6 wild-type, or C57BL/6 S ⁇ i6 KO mice.
  • mice can be anesthetized after injection of ketamine (80 mg/kg and xylazine (10 mg/kg)). With sterile dissecting scissors, a small incision can be made in the skin then the body wall on the side of the animal. Sterile, blunt forceps can then be used to pull out the spleen, which can be injected with cells 100-200 ⁇ l volume in PBS using a 25-G needle. Once the injection is complete, the body wall can be sutured with 2 or 3 stitches and the skin closed with wound clips. Mice can then be monitored for 48 h for signs of pain or distress (excessive grooming of wound and cessation of feeding). b) Results
  • Spi6-deficient mice 434 C57BL/6 Spi6 " ⁇ mice were generated from both lines of independently targeted ES cells.
  • Spi6 could not inhibit other granzymes, such as granzyme A (grn A) or granzyme K (grn K) nor the lysosomal cathepsins B and L.
  • granzyme A granzyme A
  • granzyme K granzyme K
  • PI9 inhibits caspase 1 (Annand et al., 1999)
  • Spi6 could not. (Fig. 2B).
  • Spi ⁇ exhibited minimal inhibition of the granulocyte proteases elastase and PR-3.
  • BMDCs bone marrow derived dendritic cells
  • BMDCs were "matured” after an additional day of culture in LPS (0.2 ⁇ g/ml), as evidenced by the up-regulation of the CDlIc and I-A b markers. The morphology of the cells was also consistent with that of DCs.
  • BMDCs from S ⁇ i6 KO mice were susceptible to PCD induced by P14 CTLs after pulsing with GP 33 (See Fig. 4A).
  • LCMV-specilic C ill's Were detected in the spleen 8 days after infection by staining with H-2D b -tetramers loaded with the GP 33 peptide antigen from LCMV then flow cytometric analysis (FCM) (Murali-Krishna et al., 1998). A lower percentage (from 8.3% in the B6 control and 1.6% in the Spi KO) and absolute number (Fig. 6B) of LCMV-specific CD8 T cells in Spi6 KO mice was observed.
  • FCM flow cytometric analysis
  • wild-type B6 controls an expansion in the number of LCMV-specific CD8 T cells to a peak after about 8 d, then a contraction over the next 2 weeks to a number in the memory phase that was stable for up to 140 days was observed (See Fig. 8).
  • NK cells provide immediate immunity through the lysis of tumor cells or infected cells and through the production of cytokines, notably IFN- ⁇ . Although they are important mediators of innate immunity they use the same granzyme B/perforin effector mechanism as CTLs do to kill target cells. Given the role of Spi6 in protecting CTLs from granzyme B -induced PCD, NK cells in S ⁇ i6 KO mice were examined.
  • the host response against Listeria is characterized by the complex interplay between the innate and adaptive components of the immune system (Harty et al., 1996). Innate effectors such as granulocytes, macrophages and NK cells play a crucial role in control of bacterial growth during the initial stages of the infection, especially in the liver (Conlan and North, 1991; Conlan and North, 1994; Dunn and
  • Granulocytes do not express granzyme B
  • KO P14 mice both of which are thyl.2 + , thyl.l " ) by magnetic bead sorting (about 97% pure).
  • the frequency of P14 CD8 T cells can be determined (typically 10-20% of CD8 T cells) and can adoptively equal numbers (i.v. injection) of P14 CD8 T cells (10 5 P14 CD8 cells typically in a population of 1-2 x 10 6 CDS T cells) from B6 P14 and S ⁇ i6 KO P14 mice to female thyl.2 " , thyl.l + C57BL/6 mice.
  • recipients can be infected with LCMV (2 x 10 5 PFU/mouse i.p.).
  • LCMV-specific donor cells can be identified by staining with anti-thyl.2, anti-CD8 antibodies and gp33/H-2D b tetramers then three color FCM on PBLs and spleen cells. This allows for a comparison of the number of LCMV-specific CD8 T cells from B6 and Spi ⁇ KO mice at the peak of the response to LCMV.
  • the donor LCMV-specific CTLs can be stained as before, but the YOPRO-I DNA-binding dye can be included.
  • C57BL/6 granzyme B KO (Gm B KO) mice (Heusel et al., 1994; Phillips et al., 2004 ), can be crossed to generate Spi6 KO P14 mice.
  • CD8 T cells can then be purified from the spleens of Grn B KO Spi6 KO P14 mice and adoptively transferred to C57BL/6 thyl.l + mice then infected with LCMV.
  • S ⁇ i6 is a physiologically relevant inhibitor of "misdirected" granzyme B in CTLs, and this can be confirmed by measuring the specific activity ofgranzyme B in the cytosol of P14 CTLs from wild- type and Spi6 KO mice.
  • cells can be lysed (60 min, on ice) in hypotonic buffer (5OmM PIPES, pH 7.6, 5OmM KCl, 5mM EGTA, 2mM MgCl 2 , 5mM DTT) then the organelle pellet and cytosol supernatant recovered by centrifugation at 15,000 x g for 10 min.
  • hypotonic buffer 5OmM PIPES, pH 7.6, 5OmM KCl, 5mM EGTA, 2mM MgCl 2 , 5mM DTT
  • the organelle pellet can then be resuspended in 1% Triton X-IOO, 1OmM Tris.HCl, pH 7.6, 15OmM NaCl for 60 min on ice before enzyme assay.
  • the activity in LCMV-specific CTLs from Grn B KO mice can be measured to control for substrate
  • Immature BMDCs from B6 and Spi6 KO mice can be pulsed with GP 33 and adoptively transferred by intrasplenic injection (range 10 3 -10 5 cells/mouse) to wild-type B6 responder mice (Fig. 3). After 7 d the number of LCMV-specific CD8 T cells can be determined in PBLs and the spleen by staining with GP33 tetramers and anti-CD8 antibody. Intrasplenic injection of un-pulsed BMDCs can be used as a negative control.
  • a role for Spi6 for DC priming can also be determined by measuring the levels of BrdU incorportion using standard procedures. As described previously (Phillips et al., 2004), mice can be given BrdU in their drinking water (0.8 mg/ml) for 1 wk then 10 6 splenocytes can be surface stained with GP33 tetramer and anti-CD8 and intracellularly stained with anti-BrdU or isotype control. The percentage of GP33 tetramer + CD8 + BMU + cells can be used as a read out for the number of LCMV-specific CD8 T cells proliferating in the spleens of Spi6 KO and B6 mice.
  • wild-type B6 mice can be infected with LCMV then after 80 d primed with GP33-pulsed BMDCs from either B6 or Spi6 KO mice.
  • the expansion of secondary GP33-specific specific CD8 T cells can be monitored in the spleen and PBLs after 5 d with GP33 tetramers and anti-CD8 antibody.
  • Spi6 KO and control mice can be infected with LCMV then after 3-5 d CD8 ⁇ + DCs can be purified (BeIz et al., 2004).
  • cell suspensions can be generated from the spleen by protease digestion and non-DC cells depleted by magnetic bead sorting (Myenthi Biotech) with the following antib ⁇ di'es:"anti-CD3; i anH-tKyl.l, anti-CD19, anti-Gr-1, and anti-Ter-199.
  • CD8 ⁇ DCs (CD8 ⁇ + CD45RA " ) can then be purified by antibody staining and FACS.
  • CD8 T cells can be purified from the spleens of Pm KO P14 mice by magnetic bead sorting, labeled with CFSE (5xlO 4 ) incubated with FACS-purified CD8 ⁇ DCs (10 4 ) in V- bottom 96 well plates. After 5 d, cultures can be analyzed for proliferation by FCM.
  • the dose of GP33 used for DC pulsing can be titrated (10 ⁇ 9 -10 ⁇ s M) to improve the ability to resolve any differences in priming efficiency between control and S ⁇ i6 KO CD8 ⁇ DC.
  • C57BL/6 IFN- ⁇ KO mice Jackson Laboratory, Bar Harbor, ME
  • CD8 ⁇ DCs can be purified and tested for their ability to induce the proliferation of P14 CD8 T cells.
  • NK cells can be depleted from C57BL/6 mice by i.v. injection of anti-NK 1.1 niAb (300 ⁇ g/mouse)( PK136 mAb ,eBiosource) which can be verified by staining with anti-NKl.l and anti-DX5 mAb and FCM (Brown et al., 2001).
  • Depleted mice can be reconstituted with NKLl + cells purified from either Spi6 KO or control mice.
  • Spleen cell suspensions can be depleted of non-NK cells by magnetic bead sorting then positively-bead sorted for NKLl + cells.
  • Intrasplenic injection can be used to deliver relatively small numbers of cells to the site of CD8 T cell priming and expansion (10 3 -10 5 per mouse).
  • P14 CD8 T cells from P14 Spi6 KO or P14 control mice (10 3 -10 4 ) can be adoptively transferred to S ⁇ i6 KO recipients, which can then be infected with LCMV. IFN- ⁇ levels can then be determined in the serum by ELISA (For example, see Fig. 9).
  • other subsets of DCs such as conventional DCs (CD45RA " CD8 ⁇ " ) or plasmacytoid DCs (CD45RA + CDSa + ) (BeIz et al., 2004) can be used to prime P14 CD8 T cells after LCMV infection. .
  • Spi6 KO and wild-type B6 mice can be infected with LCMV and then injected with CpG oligonucleotide (ODN) 1826 (25-75 ⁇ g/mouse, i.p.), to induce the production of IL-12, IFN- ⁇ and type I interferon (Krieg, 2003; Takeda et al., 2003).
  • ODN CpG oligonucleotide
  • IFN- ⁇ type I interferon
  • the increase in serum levels of IFN- ⁇ can be verified by ELISA and the contraction in the numbers of LCMV-specific CD8 T cells can also be measured.
  • B6 and Spi6 KO mice can be crossed with IFN- ⁇
  • IFN- ⁇ is the agent through which it affects CD8 T cell number contraction. If reduced levels of IFN- ⁇ are responsible for the absence of LCMV-specific CD8 T cell number contraction one can expect injection with CpG ODN 1826 will restore the contraction phase.
  • One can also measure the proportion of LCMV tetramef 1" CD8 + cells undergoing PCD can be measured by staining with YOPRO-I, which identifies cells at the early stage of apoptosis by measuring DNA condensation (Fig. 7) (Idziorek et al., 1995). This can allow one to not only examine the effect of CpG ODN 1826 on cell number but also on the induction of PCD during the contraction phase.
  • IL-7R is a marker for memory CD8 T cell-precursors (Badovinac et al., 2004; Kaech et al., 2004; Liu et al., 2004; Madakamutil et al., 2004) , during the contraction phase (about d8-22).
  • the expression of the IL-7R can be determined by staining with antibodies specific for IL-7R on GP33-specific CD8 + cells and FCM.
  • the effect of reduced levels of IFN- ⁇ in Spi6 KO mice on the frequency of memory-precursors can be tested can also be determined by injecting Spi6 KO mice with CpG ODN 1826 followed by observing the frequency of
  • IL-7R + GP33-specif ⁇ c CD8 T cells If the increase in memory-cell precursors in Spi6 KO mice is due to rescued levels of IFN- ⁇ , then one can expect that injection with CpG ODN 1826 will reduce the frequency of IL-7 + memory-cell precursors.
  • BrdU labeling as disclosed herein can be used to determine if there is an increase proliferation of LCMV-specific CD8 T from d 8 until d 22 in Spi6 KO mice
  • Another method to restore IFN- ⁇ to wild-type levels during the contraction phase by CpG ODN 1826 injection can be achieved by adoptively transfering wild-type NKl . I + cells by intrasplenic injection.
  • Ex vivo assays can also be used measure the amount of LCMV antigen available to CD8 T cells in Spi6 KO mice (Badovinac et al., 2002). For example, about 3 x 10 4 P14 CD8 T cells labeled with CFSE''c'an't)fe'ltii'kea"Wltli"abOm 3x10 6 splenocytes from LCMV infected mice. Cells can then be incubated for 12 h and for the last 6 h in the presence of brefeldin A. CFSE-labeled cells can be analyzed by intracellular staining for IFN- ⁇ then FCM.
  • P14 CD8 T cells incubated with na ⁇ ve splenocytes in the presence or absence of antigen peptide could serve as negative and positive controls respectively.
  • the percentage of IFN- ⁇ + P14 CD8 T cells can be used as a read out for the level of LCMV antigen in the spleens of Spi6 KO and B6 mice.
  • LCMV-specific CD8 T cells can also be purified from Spi6 KO and B6 mice by FACS (>98% purity) and adoptively transfered to antigen-free B6 mice.
  • Spi6 KO mice can be infected with LCMV Armstrong (2xlO 5 PFU/mouse, i.p.) and the number of memory CD8 T cells can be measured in the spleen after 80 d.
  • the number of memory CD8 T cells can be determined by quantitating the number of CD8 T cells that produce intracellular IFN-yafter ex vivo stimulation with LCMV peptide antigen (Murali-Krishna et al., 1998).
  • Spleen cells (10 6 /0.2ml/well) can be incubated with either of 3 LCMV immunodominant H-2D b -restricted antigen peptides (10 "7 M), NP 396 [FQPQNGQFI], GP33 [KAVYNFATM] and GP 276[SGVENPGGYCL] and IL-2 (lOU/ml) and after 5 h cells can be stained with antibodies specific for intracellular IFN- ⁇ and surface CD8 then FCM.
  • the level of background staining can be determined by staining with an anti-rat IgGi isotype control for the anti-IFN- ⁇ -PE antibody.
  • spleen cells (10 6 /0.2ml/well) can be stained with H-2D b -tetramer loaded with each of the three LCMV peptide antigens.
  • LCMV-specific CD8 T cells from Spi6 KO memory mice can be examined for their relative functional equivalency as described previously herein.
  • mice can be infected with LCMV as above then after 80 d the mice can be reinfected with LCMV Armstrong at a higher dose (10 6 PFU/mouse i.p.). After 5 d, the secondary CTL response to LCMV can be examined in the spleen by measuring the number of CD8 T cells specific for LCMV peptide antigens. This can be done by measuring the number of IFN- ⁇ + CD8 + cells generated after 5 hours of ex vivo stimulation with LCMV peptide antigen.
  • the clone 13 variant cannot be cleared by na ⁇ ve B6 mice (Ahmed et al., 1984; Matloubian et al., 1993). However memory B6 mice are resistant to infection with clone 13 because they harbor memory LCMV-specific CD8 T cells, which mount a vigorous recall response that clears the virus (Lau et al., 1994).
  • the functional competence of the CD8 T cell memory in Spi6 KO mice can be tested by examining their resistance to infection by clone 13.
  • B6 and Spi6 KO mice can be infected with LCMV Armstrong as above.
  • B6 and Spi6 KO mice can be reinfected with LCMV clone 13 (10 6 PFU/mouse i.v.).
  • the titer of LCMV clone 13 can be determined in the spleen using standard plaque assays on Vero cells (Ahmed et al., 1984).
  • LCMV-memory CD8 T cells For memory B6 and Spi6 KO mice the relative "" ' veness of LCMV-memory CD8 T cells can be indicated by the clearance of clone 13.
  • Direct infection ol wrurriatve' dB6 anfl 1 SpTO' EiV mice with clone 13 allows one to set the upper limit of LCMV titer in each case, from which memory-specific clearance can then be determined. More sensitive real-time PCR assay can also be used to measure LCMV clone 13.
  • Gr-I depletion studies can be performed with the RB6-8C5 mAb (eBioscience) to directly examine whether neutrophils (Gr-I + CDlIb + ) are responsible for the increased clearance of LM from Spi6 KO (Conlan and North, 1991).
  • Mice can be injected with RB6-8C5 (200ug/mouse i.v.) 2 and 4 days before infection with sub-lethal doses of attenuated LM (DPL-1942) (105 -106CFU/mouse) ⁇ Brundage, 1993 #136; Conlan and North, 1994; Czuprynski et al., 1994).
  • Depletion of granulocytic myeloid cells can be verified by staining spleen cells with anti- Gr-I and CDl Ib then FCM. From d 1- 5 after infection the titer of LM can be determined in the spleen and liver by plating 10-fold serial dilutions of organ homogenates on Trypticase-soy agar. Bacterial colonies can then be counted after incubation at 37° C for 24 hours (Fig. 11).
  • LIP-CLOD The selective depletion of macrophages by LIP-CLOD, can be verified by staining splenocytes for F4/80 + CDl Ib + (macrophages) and control Gr-I + CDl Ib + cells (granulocytes) 4 d after injection and FCM. Depletion in the liver can be verified by immunohistological analysis. Mice can then be infected with LM and clearance can be measured in Spi ⁇ KO and control B6 animals. 477. One expects that LIP-CLOD treatment of B6 control mice will increase the titer of LM.
  • NK 1.1 depletion studies with the PK136 mAb can be performed to determine whether NK cells (NKLl + ) are responsible for the increased clearance of LM from S ⁇ i6 KO. (Brown et al., 2001).
  • Spi6 KO mice over a range of doses (3 x 10 3 - 10 6 CFU) with at least 5 mice for each dose. Mice can be observed in 12 hour intervals for 3 days and those that show signs of acute disease (ruffled fur, hunched posture, immobility, and apparent weight loss) can be immediately sacrificed. After initial percentage survival is determined over a range of LM doses, additional experiments can be performed with a narrower range of bacterial doses to more accurately determine LD50 values for Spi6 KO mice. The Dunnet procedure for all possible pairwise contrasts of Spi6 KO and B6 mean percentage can be used to determine statistical significance (Neighbors et al., 2001).
  • Serum levels of liver enzymes such as transaminases can be measured as an additional measure of hepatocyte damage (Koniaris et al., 2003). Since one could not detect any obvious difference in the number of granulocyte (Gr-I + CDlIb + ) subsets in the bone-marrow, blood or spleen (neutrophils, eosinophils, basophils) before or after LM infection, Spi6 does not inhibit any known protease specific to granulocytes (Fig. 2B) and mouse granulocytes do not express granzyme B, which is the only known substrate of Spi6 (Fig. 16). (24) Effect of Spi6 on sterile granulocyte recruitment
  • Spi6 KO mice can be injected i.p with 15% glycogen " "" •• UtniZffiOUsey ffi ⁇ ffi&'ttiffiOerorUiJl lt> ur-l ceils (typically, >yi% ot total cells) recruited to the peritoneum can be measured after 4 h.
  • Bone-marrow can be harvested into Hank's balanced salt solution containing 1% bovine serum albumin (BSA) and neutrophils can be purified (75-85% Gr-I + CDl Ib + ) on a discontinuous Ficoll gradient (Histopaque 1119; Sigma)(MacIvor et al., 1999).
  • BSA bovine serum albumin
  • the effect of S ⁇ i6 on phagoctosis by granulocytes can be directly examined as described previously (Maclvor et al., 1999).
  • FITC-labeled latex beads Poly Sciences, Inc
  • FCM FITC-labeled latex beads
  • neutrophils from S ⁇ i6 KO mice can be isolated (10 6 ) and examined in vitro for the killing of mid-log-phase LM (10 7 ) after 30 min (Belaaouaj et al., 1998).
  • LM can be titered by plating on Trypticase-soy agar and bacterial colonies counted after incubation at 37° C for 24 h.
  • ADCC function of granulocytes from Spi6 KO mice can be measured using classical hemolysis assays on sheep red blood cells (sRBCs) (Gagnon and Joshua, 1980).
  • sRBCs sheep red blood cells
  • sRBCs can be labeled with 51 Cr (3 x 10 4 ) and then incubated with mouse-anti-sRBC mAb (IgG 2a clone: UN-2 (Diamond et al., 1979) (ATTC).
  • ADDC activity of purified macrophages or granulocytes can then be determined after 4 h by measuring the release Of 51 Cr.
  • Spi6 KO Fc epsilon RI KO mice (Dombrowicz et al., 1993) (Jackson Laboratory, Bar Harbor, ME) can be generated and the clearance of LM can be compared with Spi6 KO mice as described previously (Takai et al., 1994).
  • the UN-2 mouse-anti-sRBC mAb was selected because antibodies of this isorype are preferentially bound by Fc ⁇ receptors expressed by neutrophils and macrophages in the mouse (Diamond et al., 1979).
  • ADCC activity can be interpreted as evidence for Spi6 controlling ADCC function of myeloid cells through the inhibition of a target protease. 487.
  • Eosinophils mediate a special type of ADCC, which could conceivably be responsible for increased ADCC of granulocytes from Spi6 KO mice. Aspects focusing on IgG-dependent ADCC of neutrophils could miss this activity. To address this one can perform a series of alternative experiments. For exampierone can IgE-dependent ADCC of eosinophils is responsible for the increased clearance of LM from Spi6 KO mice.
  • Spi6 KO Fc epsilon RI KO mice (Dombrowicz et al., 1993) (Jackson Laboratory, Bar Harbor, ME) can be generated and the clearance of LM compared with Spi6 KO mice. If one observes that deficiency in Fc ⁇ Rl diminishes the clearance of LM one can conclude that eosinophils are responsible for the increased clearance of LM in Spi6 KO mice.
  • mice can be injected with 3% thioglycollate (0.3ml/10g body weight) to induce sterile peritonitis then the recruitment of macrophages to the peritoneum can be measured over the course of 4 d by staining for F4/80 + CDl Ib + cells and FCM (Tkalcevic et al., 2000). 489.
  • bone-marrow can be plated overnight in DMEM-10% fetal calf serum
  • non-adherent cells can be cultured in 30% L929 conditioned medium for 5 d (90-95% F4/80 + CDl lb + )(Coligan et al., 1995). Phagocytic uptake of 0.9 ⁇ m-diameter FITC-labeled latex beads (Poly Sciences, Inc) from Spi6 KO mice can then be measured by FCM.
  • macrophages (10 6 ) can be examined in vitro for the killing of mid- log-phase LM (10 7 ) after 30 min and the production of bactericidal superoxide can be measured using standard procedures (Maclvor et al., 1999).
  • assays can be conducted on S ⁇ i6 KO macrophages as described elsewhere herein for granulocytes.
  • Glycogen-elicited granulocytes can be harvested (10 7 /mouse) from the peritoneum of C57BL/6 mice (99% Gr-I + CDl Ib + ).
  • B6 mice were injected i.p. with 15% glycogen (ImL) then after 4 h cells harvested and stained anti-CDl Ib-PE and Gr-I-APC mAbs and purified by FACS.
  • the % PE + APC + after FACS was 1%.
  • Staining before FACS with isotype control (IC) mAbs revealed a 99% PE + APC + after FACS.
  • Granulocytes can be resuspended in extraction buffer (1% Triton X-IOO, 1OmM Tris.HCl, pH 7.6, 15OmM NaCl, 1OmM DTT) by incubation on ice for 30 min (Fig. 16; 10 6 -2xl0 6 cells; 50-100 ⁇ g) and added to GST-S ⁇ i6-coupled agarose beads (Sigma-Aldrich; Fig. 2A) or GST-coupled agarose beads (5- lO ⁇ l; 15-30 ⁇ g coupled protein) for 90 min (250 ⁇ l) at RT while rotating.
  • extraction buffer 1% Triton X-IOO, 1OmM Tris.HCl, pH 7.6, 15OmM NaCl, 1OmM DTT
  • Beads can be centrifuged and washed 4-6 times in extraction buffer then resuspended and boiled in SDS-PAGE loading buffer (10% glycerol, 2 % SDS, 10OmM DTT, 5OmM Tris.HCl pH 6.8, 0.1 % bromophenol blue). Supernatants can be resolved by SDS-PAGE. Total protein can be visualized by silver staining, and GST-containing proteins by Western blotting with goat-anti-GST antibody (Amersham).
  • Putative complexes can be verified first by their absence from the GST-alone lane by them containing GST-Spi6 by Western blotting. The procedure can be scaled down and bands corresponding to cahdi'c ⁇ af'e"G'ST-Spi6':'"pf ⁇ tease complexes from SDS-PAGE gels stained with Coomassie blue (>O.l ⁇ g) can be excised.
  • complexes (92kD) with granzyme B (25kD) can be generated in lysates from P14 CTLs or in granulocyte lysates spiked with purified granzyme B as described previously (Medema et al., 2001a; Sun et al., 1997a).
  • the excised gel band containing the candidate GST-Spi6 protease complexes from SDS-PAGE gels stained with Coomassie blue can be subjected to protease digestion and peptide microsequencing.
  • alkylated gel protein can be digested with Lys-C (Sigma- Aldrich; enzyme protein ratio 1 :20) and then with trypsin
  • Peptides can be subjected to one dimensional reverse phase HPLC/mass spectrometry using the ABI Qstar Pulsar-i instrument. A MS/MS spectra can then be generated for each peptide (4 ions per precursor scan). Data analysis can be carried out using the Mascot platform (Matrix Science) and Spectrum Mill software platform (Agilent Technologies). The results for all proteins detected after comparison of peptide sequence data bases can then be listed by protein name and search score. The requirement for a positive identification can be that the library matches agree between search platforms and that at least 4 distinct peptides for the tentatively identified protein be present.
  • protease complexes the amount of GST-Spi6 bait or protein in lysates can be varied. In addition, the concentration of triton X-100 can be increased in the washing steps.
  • 2-D gels electrophoresis SDS-PAGE isoelectric focusing
  • GST- S ⁇ i6 protease complexes
  • co-immunoprecipitation with epitope-tagged S ⁇ i6 can be used to pull down target proteases as described previously(Liu et al., 2003).
  • immunoprecipitation with anti-FLAG mAb Sigma-Aldrich
  • the cDNA for each identified protein can then be cloned by PCR and then E. coli GST- fusion proteins can be generated kinetics and stochiometry of interaction with Spi6 can then be generated.
  • the candidate proteases (with accession numbers) identified are: cathepsin G (P28293), PR-3 (Q61096), neutrophils elastase (NP031945), mouse mast cell protein (MMCP) -1 (P11034), MMCP-2 (P15119), MMCP-3 (P21843), MMCP-4 (P21812), MMCP-5 X?2m4f, *bfiW0P- ⁇ 434yQ), MMCP-9 (035164), MMCP-IO (AAK51075). From these experiments, it has been shown that Spi6 binds the human forms of PR-3 and elastase.
  • target protease KO mice can be crossed with Spi6 KO mice. If one observes elevated activity of the target protease in Spi ⁇ KO granulocytes (Fig. 16) one can conclude that Spi ⁇ is a physiologically relevant inhibitor in vivo. If the protease is a true determinant of granulocyte function one can predict that for knock-out mice one can observe diminished LM clearance and impaired granulocyte function (i.e. recruitment, phagocytosis and bactericidal activity) as measured in vitro and ex vivo assays).
  • impaired granulocyte function i.e. recruitment, phagocytosis and bactericidal activity
  • the amount of GST-Spi6 bait or protein in lysates can be varied to enhance detection of GST-Spi6-protease complexes.
  • the controls for specificity allows the optimization of these parameters. It is likely that the amount of GST-Spi ⁇ : protease ( > 69kD) can be significantly less than unbound GST-Spi6 (69kD). If this is the case one can perform 2-D gels electrophoresis (SDS-PAGE x isoelectric focusing) for resolution.
  • Co-immunopreci ⁇ itation with epitope-tagged Spi ⁇ can also be used to detected GST-Spi6-portoease complexes through pull down assays.
  • a FLAG-tagged Spi ⁇ from NIH3T3 cells can be produced.
  • Immunoprecipitation with anti-FLAG mAb can be used to pull down complexes from detergents lysates between FLAG-S ⁇ i6 and target protease, which can then be purified as above.
  • the candidate proteases (with accession numbers) are: cathepsin G (P28293), PR-3 (Q61096), neutrophils elastase (NP031945), mouse mast cell protein (MMCP) -1 (Pl 1034), MMCP-2 (P15119), MMCP-3 (P21843), MMCP-4 (P21812), MMCP-5 (P21844), MMCP-8 (P43430), MMCP-9 (035164), MMCP-IO (AAK51075).
  • Spi ⁇ binds the human forms of PR-3 and elastase. Species variation (about 30% difference in amino acids between human and mouse) can account for the difference in binding between these proteases and Granzyme B, and the mouse homologs can be relevant targets for Spi ⁇ in mouse cells.
  • Spi6 over expression models To examine the physiological mechanism by which S ⁇ i6 controls immunity to a model virus and model bacterium a knock-out mouse model was also generated. The studies described above elucidate how the inhibition of proteases by Spi6 controls two cell biological process that are central to immune function, namely the control of T lymphocyte survival and the function of phaogocytic leukocytes. Since Spi6 is the mouse homologue of the human serpin PI9, the Spi6 KO and transgenic mice can serve as useful models to examine the roles of this class of protein to immunity and disease as well as models for testing for modulators of Spi6 or PI9.
  • Spi6 KO mice finding is particularly interesting because Spi6 KO CTLs are susceptible to PCD (Fig. 7). Spi6 can inhibit pathways of PCD that control CTL survival but do not affect the severity of the contraction phase and so does not conform to the definition of a protective factor and does not select for memory-cell precursors (Liu et al., 2004). In addition these data seem to challenge the accepted view that the size of the memory pool is proportional to the clonal burst size (Ahmed and Gray, 1996; Hou et al., 1994).
  • Spi ⁇ deficiency appears to alleviate rather than increase the severity of the contraction phase, thus S ⁇ i6 KO mice were examined for decreases in pro-apoptotic factors, which are known to induce the contraction phase, such as IFN- ⁇ (Badovanic et al., 2000; Badovinac et al., 2004). The serum levels of IFN- ⁇ in S ⁇ i6 KO mice were diminished after L. monocytogenes infection.. d) Spi6 Activity
  • Spi6-coupled agarose beads (7 ⁇ g) were incubated either alone (-) or with cytosolic extracts from wild-type (WT) or granzyme B KO (GrnBKO) P14 CTLs (10 6 cells), then boiled in SDS and DTT and resolved by SDS-PAGE. After Coomassie staining, GST-Spi6 was detected as a 69kD band.. A ⁇ 92kD protein from wild-type but not granzyme B-deficient CTLs was identified. Since the samples were boiled in SDS and reducing agent before loading it was concluded that the 92kD complex between Spi6 and granzyme B is the result of a true serpin: serine protease interaction.
  • KO granulocytes were examined for increased activity of candidate proteases.
  • Elastase is an important effector protease of granulocytes (Belaaouaj et al, 1998) and is structurally related to granzyme B (Sun et al., 1997). It was shown that elastase activity is about 3-times higher in the cytosol of S ⁇ i6 KO granulocytes compared to B6 controls. The increase in elastase activity was only evident in the cytosol, which is consistent with the intracellular location of Spi6. There was no increase in the activity of the related proteases PR-3 or cathepsin G.
  • Spi6 is a very weak inhibitor of human elastase consistent with mouse neutrophil elastase (30% difference in amino acids between human and mouse) can be a direct target of Spi6.
  • CD8 + memory T cells are derived directly from CTLs. The mechanisms underlying this transformation and the subsequent survival of memory cells are not completely understood. However, some effector molecules required by CTLs to eliminate infected cells have also been shown to control the number of Ag-specific cells.
  • memory cells express high levels of serine protease inhibitor (Spi) 6, an inhibitor of the effector molecule granzyme B, and that Spi6 can protect T cells from granzyme B- mediated apoptosis.
  • Spi serine protease inhibitor
  • Spi6 cDNA was cloned into the VA CD2 expression cassette (Zhumabekov, et al., 1995) via the Sma 1 restriction site. Spi6 cDNA was then expressed as the minimal open reading frame (1.1kb) (SEQ ID NO:43) without untranslated 5' and 3' sequences.
  • Fertilized eggs from C57BL/6 (B6) mice were microinjected with the Spi6 cDNA subcloned into the human CD2 expression cassette (Zhumabekov et al., 1995) to generate two transgenic founders, With Spi ⁇ primers: forward, 5'-GAA TTC CGG GCT GGA TTGAGA AGC C-3' (SEQ ID NO:5) and reverse, 5'-GGA TAC TGA AGA GAG AAC TCT CCC-3' (SEQ ID NO:6). Each founder was backcrossed to B6 mice to generate colonies o ⁇ Spi ⁇ Tg +/ ⁇ mice.
  • Spi6 Tg + ' + mice were crossed with P14 TCR transgenic mice (Pircher et al., 1990), which had been backcrossed onto the B6 background, to generate Pl 4 TCR M ⁇ Spi6 Tg +1" mice, which were further used to generate Pl 4 TCR +1" Spi6 Tg H+ mice by crossing with Spi ⁇ Tg* 1 * mice.
  • Spi6 Tg +f+ mice
  • Pl 4 TCR +/ ⁇ Spi6 Tg* 1 * mice mice
  • the Spi ⁇ cDNA was cloned into the 3x-Flag vector (Sigma-Aldrich, St. Louis, MO) and transfected into 293 T cells.
  • Fibroblasts transfected with 3x-Flag-S ⁇ i6 exhibited cytoplasmic staining using anti-Flag mAb, indicating that the cDNA used to generate the Spi ⁇ mice directs the production of a viable protein.
  • mice Thyl.l + congenic B6, and granzyme B cluster-deficient B6 (Heusel et al., 1994) mice were purchased from The Jackson Laboratories (Bar Harbor, ME). Mice were infected with LCMV Armstrong by i.p. injection of 2 x 10 5 PFU.
  • single cell suspensions were prepared, by depletion of erythrocytes with ammonium chloride and purification with Lympholyte-M (Cedarlane Laboratories, Hornby, Ontario, Canada), from the pooled spleens (5-10 mice) of naive or LCMV Armstrong infected B6 mice either 8 days (effector) or 50-100 days (memory) after infection.
  • Splenocytes from naive mice were FACS purified directly after staining with anti-CD8 ⁇ ' allophycocyanin and anti-CD44 PE mAbs.
  • Splenocytes from effector and memory mice were first sorted using anti-Thyl .2 magnetic beads
  • hemopoietic cell populations were purified (>95%) for real-time PCR analysis from splenocytes usingmagnetic beads conjugated to phenotypic markers (Miltenyi Biotec). Macrophages were generated from bone marrow cultured in medium containing macrophage CSF. DCs
  • each real-time PCR plate contained reactions for generating standard curves (using serial dilutions of a known quantity of cDNA generated from unsorted B6 splenocytes) for each gene being analyzed. The slope of the standard curve describes the efficiency of the real-time PCR.
  • Splenocytes &omP14 TCR + ' ' Spi ⁇ Tg-' ' Q?U),P14 TCR +I ⁇ Spi ⁇ Tg + ⁇ (P14 x Spi6, heterozygous) and Pl 4 TCR + ' ' Spi ⁇ Tg +I+ (P 14 X Spi ⁇ , homozygous) mice were depleted of erythrocytes by nium chloride and cultured for 3 days in complete medium containing human IL-2 (10 U/ml) and l GP33"'pe'f ⁇ fM ⁇ 'tlO " ""My.” "JPWSt S days, cultures (>90% activated Pl 4 TCR ⁇ / ⁇ cells) were purified using Lympholyte-M (Cedarlane Laboratories) and the RNA extracted using TRIzol Reagent (Invitrogen Life Technologies).
  • the final wash was in O.lx SSC with 0.5% SDS at 65 0 C and the membrane was exposed to film for 6 h.
  • the membrane was then stripped and reprobed with a 32 P-labeled GAPDH cDNA (SEQ ID NO:30).
  • the final wash was in 0.5x SSC with 0.5% SDS at 65°C and the membrane was exposed to film for 4 h.
  • Apoptosis assays 522 Jurkat cells (human thymoma) were cotransfected with 5 ⁇ g of either the Spi6 cDNA cloned into the CD2 expression cassette (Zhumabekov et al., 1995) or empty vector and PGK-Neo (5 ⁇ g) by electroporation (280 V, 975 ⁇ F). Transfectants were selected and cloned in 1 mg/ml G418 (Invitrogen Life Technologies) over a 3-wk period.
  • Clones were treated for 2 h with human perforin at sublytic concentrations (0.2 U/ml) and human granzyme B (2 ⁇ g/ml) (Froelich et al., 1996, Bird et al., 1998), or cultured overnight with anti-human Fas IPO-4 mAb (0.12 ⁇ g/ml) (Rokhlin et al., 1997) or subjected to gamma-irradiation (4456 rads) and apoptosis measured after 20 h.
  • Thyl .2 + by positively sorting with anti-CD8 magnetic beads (Miltenyi Biotec), then adoptively transferred (10 5 ) by i.v. injection into Thy 1.I + B6 mice. Recipients were rested for 2 days and then infected with LCMV. Thyl.2 + donor P14 or P14 x S ⁇ i6 cells were followed in the peripheral blood of recipients by staining with anti-Thyl.2 mAbs. (7) BrdU incorporation
  • mice that had received either P14 or P14 x Spi6 cells (Thyl.2 + ) were given BrdU (Sigma- Aldrich) for 1 wk in their drinking water (0.8 mg/ml) and then analyzed. Briefly, 10 6 splenocytes were surface stained using anti-Thyl .2 PE mAbs and then fixed using Cytofix/Cytoperm solution (BD Pharmingen, San Jose, CA). Fixed cells were washed once in Perm/Wash solution (BD Pharmingen, San Diego, CA).
  • Spi6 is up-regulated in effector and memory cells
  • Effectors and memory cells were isolated from the spleens of B6 mice 8 days or more than 50 days after infection with LCMV by FACS of CD8 + tetramer + cells.
  • the initial percentages and final purity of naive or tetramer 4* CD8 + T cells for na ⁇ ve cells was 99% (from 7.9%), for effector cells was 98%(from 23%), and for memory cells was 97% (from 2.5%).
  • Spi ⁇ expression One representative value for each isolate is expressed in Fig. 19B as the ratio of Spi ⁇ Xo cyclophilin.
  • Naive cells did not express high levels o ⁇ Spi ⁇ (an. average ratio of 0.6), but 8 days after LCMV infection, Ag-specific effectors had significantly up-regulated Spi6 expression (an average ratio of 11.9, p ⁇ 0.001 compared with naive cells). Therefore, separate isolates of effector cells were found to express Spi6 28.6-fold and 11 -fold higher than naive cells.
  • a third independent isolate of effector cells was also assessed for Spi6 expression and found to be 53-fold higher than naive cells (a Spi6 to cyclophilin ratio of 31.7).
  • Spi6 mice were crossed to transgenic mice expressing theP14 TCR (SEQ ID NO:34), which recognizes the GP33 peptide from LCMV(SEQ ID NO:19) in the context of H-2D b (Pircher et al., 1990).
  • Splenocytes from P14 and P14 x S ⁇ i6 mice were cultured with GP33 peptide and IL-2 for 3 days, at which time >90% of the cells have become activated P14 cells.
  • Spi6 expression was performed by real-time PCR on various hemopoietic cell populations. Endogenous expression of Spi ⁇ in B6 mice was found in all cell types tested, with MK"&gIIs"e5 ⁇ ressi ⁇ .g'tiie "" JUgnest levels (Fig.21B). The transgene increased expression of Spi6 at least 40-fold in all cell types, with the highest expression levels in thymocytes and other lymphocytes (Fig. 21C).
  • CD4 + T cells 2.8 ⁇ 0.16 2.9 ⁇ 0.16
  • CD8 + T cells 1.9 ⁇ 0.13 1.8 ⁇ 0.14
  • CD4 + T cells 5.9 ⁇ 0.5 5.6 ⁇ 0.5
  • CD8 + T cells 2.8 ⁇ 0.3 2.8 ⁇ 0.2
  • Spi6 expression was highly up-regulated in effectors and the resulting memory cells (Fig. 19B).
  • Spi6 mice were infected with LCMV and the number of memory cells that developed were quantitated.
  • Spi6 mice have elevated expression levels oiSpi ⁇ in several types of hemopoietic cells (Fig. 21). Therefore, the increase in memory cell numbers detected in Spi6 mice could be the result of enhanced priming (Wong et al., 2003) by S ⁇ i6 transgenic DCs (Medema et al., 2001b).
  • S ⁇ i6 transgenic DCs S ⁇ i6 transgenic DCs
  • LCMV LCMV and the levels of P14 memory cells determined after at least 50 days by ex vivo IFN-T production.
  • "55K 1 Gating 1 On WI .2 ⁇ or Thyl.2 + cells during FACS analysis allowed for detection of the endogenous (Thyl .2 " ) and donor (Thyl .2 + ) memory cells (CDS + IFN-I *1" ) in recipients.
  • naive CD8 + T cells from P14 and P14 X Spi6 mice, both Thyl.2 + were purified using magnetic beads and adoptively transferred to Thyl. I + congenic recipients.
  • Recipients were infected with LCMV and more than 50 days later the percentage of memory cells in recipient spleens determined by measuring ex vivo IFN-T production. FACS scans from representative recipients given P14 or P14 X Spi6 cells. Total live cells did not stain with the isotype control (IC) when stimulated with GP33 peptide, nor did they stain for IFN- ⁇ production in the absence of stimulation (No peptide).
  • Donor and recipient memory cells were CDS + IFN-T + and Thyl.2 + or Thyl .2 " , respectively. Stimulation with GP33 revealed that virtually all (91-98%) of the Thyl.2 + cells were functional CDS + IFN-T + memory cells.
  • the increased frequency of Spi6 transgenic memory cells can be due to either enhanced proliferation of memory cells containing transgenic Spi6 or to increased long-term survival.
  • Spi6 cells were given BrdU in their drinking water and 1 wk later the turnover of memory cells in the spleens of these animals determined by BrdU incorporation.
  • the frequency of P 14 and P14 x S ⁇ i6 memory cells that had divided (18 ⁇ 0.5% vs 18.1 ⁇ 0.4%) was the same, indicating that memory cells containing transgenic Spi6 appear to proliferate similarly to wild-type memory cells. This finding supports the idea that transgenic Spi ⁇ increases the long-term survival of memory cells rather than increasing proliferation.
  • the level of CD8 + memory T cells is determined by events in the expansion, contraction and memory phases of the immune response (Sprent et al., 2002). Here, it is shown that CD8 + memory T cells express elevated levels of Spi ⁇ , and that inhibition of granzyme B (by deficiency or expression of transgenic Spi ⁇ ) increases the number of CD8 + memory T cells
  • the enhanced memory cell phenotype shown in Spi6 mice (2- to 3-fold higher than B6 mice, Fig. 22) is about the same magnitude observed in other transgenic systems with higher memory cell levels, after over-expression of calcium/calmodulin kinase II and the Bcl-6 transcriptional repressor (Bui et al.,
  • Immunological memory not only requires the initial differentiation of CD8 + memory cells, but also their long-term maintenance (Sprent et al., 2002).
  • the impact of some molecules, such as the IL-15 cytokine, on memory cells is, in fact, a result of their action well past the contraction phase of CD8 + memory T cell development (Schluns et al., 2003). Consistent with previous reports (Zajac et al., 2003), persistently elevated levels of effectors or an altered contraction phase after infection of GrnBKO mice with LCMV, a phenotype mimicked in Spi6 mice was not found (Fig. 22C).
  • One of the salient qualities of memory cells is the ability to respond quickly to Ag, mediated, in part, because they have preformed granules containing toxins such as perform and granzyme B (Opferman et al., 1999, Wherry et al., 2003). It has recently been reported that this immediate response is the result of a specialized G 0 /Gi cell cycle state predisposing memory cells to rapid division upon stimulation (Veiga- Fernandes et al., 2004). At any given time, a certain percentage of the memory cell population is in cell cycle (Tough et al., 1994), and the ability of memory cells to cycle is absolutely critical to an anamnestic response (Bellier et al., 2003).
  • Spi6-deficient mice were generated. Using homologous recombination in ES cells from C57BL/6 mice (B6 mice), exon 7 of S ⁇ i6 was deleted, which encodes 60% of Spi6 and includes the critical reactive center loop (RCL), which is required for target protease inhibition. Results were confirmed via Southern blot analysis of two ES cell clones with wild-type (WT: 37) or mutant (M: 69 and 389) Spi6 neo alleles.
  • WT wild-type
  • M mutant
  • the Southern blot analysis revealed a 6.9 kb band (mutant) and a 7.2 kb band (wild-type) for both the 68 and 389 clones.
  • the 3' probe revealed a 9.8 kb band (wild-type) and a 5.8 kb band (mutant) for both the 68 and 389 clones.
  • Cre-mediated recombination the G418-resistance cassette was removed to avoid affecting the transcription of closely linked serpin genes (such as Spil 3), which may have similar functions to Spi6.
  • Spi6 is up-regulated in CTLs and overexpression can inhibit GrB-mediated apoptosis in vitro (see above and see also Phillips et al., 2004).
  • CTL response of Spi6 KO mice to infection was examined. Mice were infected with LCMV Armstrong (Phillips et al., 2004) and the attenuated DPL-1942 strain of LM, which had been engineered to express ovalbumin and generate an H-2K b -restricted peptide antigen (OVA)(Pope et al., 2001).
  • OVA H-2K b -restricted peptide antigen
  • GrA does not cleave after aspartic acids but instead is a tiyptase and cleaves after basic amino acids (Odake et al., 1991).
  • P 9 x 10 "5 ) in granule-associated GrA specific activity in Spi6 KO CTLs compared to B6 control CTLs ( Figure 33 (b)).
  • the human homologue of Spi6 - Proteinase inhibitor 9 (PI9)- inhibits GrB in CTLs (Sun et al., 1996) and can also inhibit NE (Dahlen et al, 1999) and is expressed in neutrophils (Hirst et al., 2003).
  • Recombinant Spi6 was generated in the pEX expression system in E. coli as a fusion protein with glutathione transferase (GST), using Standard procedures recommended by the manufacturer (Amersham, Piscataway, NJ).
  • GST tag was removed by factor X proteolysis and recombinant (r) Spi6 (43 kD) purified to homogeneity.
  • r recombinant
  • HNE human NE
  • SDS-PAGE gel stained by Coomassie blue was used to detect rSpi ⁇ (43kD).
  • NE activity was determined by measuring the hydrolysis of MeOSuc-AAPV-AMC (ImM) (Calbiochem, San Diego, CA) at 25 0 C in 2OmM Tris-HCl pH 7.4, 50OmMNaCl, 0.1% PEG.
  • ⁇ i-AT oi l -antitrypsin
  • SLPI secretory leukoprotease inhibitor
  • Spi6 is a physiological inhibitor of NE in neutrophils.
  • PBS ImI
  • E. coli E. coli (2xlO6/ml) at 37°C.
  • Cells were lysed by sonication in hypotonic buffer (50 Ml P ⁇ PESt"5UrriM 1 KCl ⁇ mM EGTA, 2mM MgC12 5mM DTT, pH 7.6) then centrifuged at 3,000 x g for 20 min to remove nuclei then 15,000 x g for 30 min to give cytosol (supernatant) and granule (pellet) fractions.
  • hypotonic buffer 50 Ml P ⁇ PESt"5UrriM 1 KCl ⁇ mM EGTA, 2mM MgC12 5mM DTT, pH 7.6
  • Spi6 acts to suppress NE in neutrophils.
  • Spi6 acts to suppress NE in neutrophils.
  • Spi6 is targeted to auzurophilic granules 563.
  • transfected HL 60 cells were seeded on wells of poly-L-Lysine coated slides then fixed and permeabilized in acetone/methanol and blocked with 10% normal horse serum in PBS for 60 min at 20 0 C.
  • Cells were stained with anti-FLAG mAb (1:1000; IgGi Sigma Aldrich, St. Louis, MO) or anti-human CD63 mAb (1:1000, Calbiochem, San Diego, CA) or rabbit anti-HNE (1 : 1000, Calbiochem, San Diego, CA) then secondary antibodies conjugated to FITC or PE then DAPI.
  • HL-60 promyelocytes as described in (Bainton, 1999; Collins et al., 1977), which is hereby incorporated by reference for its teaching of determination of intracellular locations of a gene product.
  • HL-60 cells were transiently transfected by electroporation (0.3kV; 500 ⁇ F) with Spi6 cDNA cloned into the 3 x FLAG-CMV-14 expression vector (Sigma-Aldrich, St. Louis, MO). Specifically, transfected HL 60 cells were seeded on wells of poly-L-
  • Lysine coated slides then fixed and permeabilized in acetone/methanol and blocked with 10% normal horse serum in PBS for 60 min at 20 0 C.
  • Cells were stained with anti-FLAG mAb (1:1000; IgG 1 Sigma Aldrich) or anti-human CD63 mAb (1:1000, Calbiochem) or rabbit anti-HNE (1:1000, Calbiochem) then secondary antibodies conjugated to FITC or PE then DAPI.
  • transfected HL 60 cells were seeded on wells of poly-L-Lysine coated slides then fixed and permeabilized in acetone/methanol and blocked with 10% normal horse serum in PBS for 60 min at 2O 0 C.
  • CIM revealed FLAG-tagged S ⁇ i6 not only in the cytoplasm as expected but also with azurophilic granules as indicated by co-localization with CD63 (marker for azurophil granule membrane) and NE (marker for azurophil granule matrix). i) Increased death and lysis of Spi6 KO neutrophils.
  • P. aeruginosa (4.6 xlO6 cfu/mouse), (i.n. 50 ⁇ l) P. aeruginosa ( 5 xlO7 cfu/mouse) or (i.v. 50 ⁇ l) L. monocytogenes EGDe (4 x 104 cfu/mouse) and survival measured over time. 568. Pseudonomas aeruginosa infection was performed by infecting C57BL/6 wild-type and hLP-
  • mice are dosed with HNE (1.2 -
  • L. monocytogenes is a facultative intracellular bacterium, which can escape neutrophil phagocytosis by residing in macrophages (Harty et al., 1996). Consequently, activation of macrophages by ⁇ ⁇ ⁇ produced in ThI immune reactions is critical to resolve L. monocytogenes infection. However, this mechanism is unlikely to" expla'm'tne increased clearance of L. monocytogenes in Spi6 KO mice because IFN- ⁇ levels were actually lower than in controls (Fig. 16).
  • mice were dosed with HNE then P. aeruginosa immunity measured.
  • pulse labeled cells can be re-suspended in tissue culture medium (2xlO 6 /ml) and at timed intervals up to 4 h, cells (10 7 /ml) withdrawn and subjected to homogenization and sub-cellular fractionation.
  • cells (10 s ) can be re-suspended in 0.34M sucrose, 1OmM HEPES pH 7.3, 0.3mM " 1 ⁇ ⁇ and homogenized with a Dounce homogenizer in the presence of a cocktail of protease inhibitors.
  • Unbroken ⁇ S81IS" ⁇ fod"riUb ⁇ ert.ffl be removed by centrifugation at 500 x g for 10 min then the supernatant fractionated by centrifugation at 32,000 x g for 60 min through a gradient of 20% Percoll containing 15mM HEPES pH 7.3, 0.25mM sucrose on saturated sucrose.
  • Endo H resistance indicates the conversion of Spi6 into a complex form of the N-linked oligosaccharide unit, as a measure for movement through the golgi.
  • Brefeldin A which blocks egress from the lumen of the ER to the golgi, can also be used to confirm the progress of Spi6 through the secretory pathway (Nuchtern et al., 1989).
  • HL-60 promyelocytes the same pulse-chase and sub-cellular fractionation studies on different cell lines transfected with Spi6-FLAG can be used.
  • rat basophilic/mast cell line RBL (Gullberg et al., 1995) and the mouse myeloid cell line 32D(Garwicz et al., 1995), using ⁇ -hexosaminidase as a maker for the storage granule/lysosome fractions.
  • PAI-2 like OVA, has only the minimal size to fold as a serpin and both proteins are secreted without cleavage of their signal sequences.
  • Two regions promote PAI-2 translocation (Belin et al., 1996; Belin et al., 2004): an N-terminal hydrophobic domain within the first ⁇ -helix and an internal hydrophobic domain spanning the second ⁇ -helix (hA and hB domains (Huber and Carrell, 1989).
  • Proteins can also be labeled by 35 S-methionine incorporation then resolved by SDS-PAGE and visualized by autoradiograpy.
  • S ⁇ i6 has 3 putative N-glycosylation sites (Asn-X-Ser/Thr) and so higher molecular weight glycosylated forms (secreted S- form) indicates translocation across the microsomal membrane.
  • the presence of the S-form of Spi6 can be verified by its resistance to trypsin digestion (lmg/ml; 30 min at O 0 C) in the absence of detergent. To control for the possibility that internal elements within Spi6 may interfere
  • ⁇ anslocation a fusion protein in which the yeast prepo- ⁇ -factor signal sequence precedes the complete ⁇ pio co ⁇ ing'-sequence carroe-anaiyzed.
  • Efficient translocation of tlie chimeric protein as judged by the relative intensities of N-glycosylated versus unmodified protein, can indicate the absence of inhibitory sequences within the Spi6 protein.
  • deletion mutants of Spi6 cDNA that lack either the hA (Spi ⁇ hA " ) or hB (Spi ⁇ hB " ) domains or both (Spi6hA " B ⁇ )( Figure 45), but which retain the 3 N-glycosylation sites, using standard molecular biology techniques. Briefly, PCR products encoding deletion mutants can be generated from wild-type S ⁇ i6 open reading frame template using specific primers then cloned into the pSP65 vector. After in vitro transcription/translation the proportion of S- to C-forms of Spi6 can be determined for the mutants, as described above.
  • the binding of the signal recognition protein (SRP) to Spi6 signal peptide my measuring the inhibition of Spi6 translation by the interaction can also be examined.
  • Spi6 can be translated in vitro as described, except without microsomes, and the effect of recombinant human SRP (0-20OnM; Abnova Corp., Heidelberg, Germany) on S ⁇ i6 synthesis tested.
  • SRP signal recognition protein
  • the binding of SRP to the Spi6 hA/hB deletion mutants can be measured, which allows for determination as to which hydrophobic domain of the signal sequence binds SRP.
  • the binding of Spi6 signal sequence to SRP can be compared with that of preprolactin, which binds with relatively high affinity.
  • the sections can then be double immunolabeled with rabbit anti-Spi ⁇ and mouse anti- human MPO mAb (clone MPO-7, Dako) then incubated with goat anti-rabbit IgG linked to lOnm gold and goat anti-mouse IgG linked to 5nm gold.
  • Cryosections showing expression of Spi6 within the golgi and within MPO-positive granules indicate that S ⁇ i6 is delivered to the matrix of azurophil granules through the secretory pathway.
  • the absence of expression in the golgi and association with the outside of MPO-positive granules indicate that Spi6 is a cytoplasmic peripheral protein of azurophil granules.
  • CIM with anti-Spi ⁇ antiserum can be used to localize Spi ⁇ to granules in mature glycogen-elicited neutrophils from B6 mice.
  • Cells can be fixed and permeabilized then stained with anti-Spi ⁇ antiserum and anti-rabbit IgG fluorescently labeled SecorMary attfitMIyVTffi optimal' dilutions of primary and secondary antibodies can be determined empirically.
  • Azurophil granules can be localized by counter staining with anti-CD63 (clone CLB-180, BD Pharmingen, San Jose, CA), specific granules with anti-CDllb (clone Ml/70, BD Pharmingen, San Jose, CA), gelatinase granules with anti-macrophage metalloproteinase 9 (rabbit anti-MMP9 antiserum, Abeam, Cambridge, MA ) and secretory vesicles with anti-CD35 (clone 7G6, BD Biosciences, San Jose, CA).
  • anti-CD63 clone CLB-180, BD Pharmingen, San Jose, CA
  • specific granules with anti-CDllb clone Ml/70, BD Pharmingen, San Jose, CA
  • gelatinase granules with anti-macrophage metalloproteinase 9 rabbit anti-MMP9 antiserum
  • Stained cells can be coated on poly L-lysine slide and CIM used to determine the co-localization of S ⁇ i6 with a given granule subset.
  • sub-cellular fractionation can be used to localize Spi6 in mature neutrophils as described in Kjeldsen et al., (1994). Isolation and characterization of gelatinase granules from human neutrophils. Blood 83, 1640-1649. Briefly, glycogen-elicited neutrophils can be harvested from about 10 B6 mice (10 8 /ml) and lysed by cavitation in hypotonic buffer using a nitrogen bomb (5 min at 380 psi, Parr Instruments).
  • Post-nuclear supernatant can be applied to a 3-layer Percoll gradient of densities 1.050 g/ml, 1.090 g/ml and 1.12 g/ml and centrifuged at 37, 000 xg for 30 min at 4°C to resolve the expected protein bands ⁇ - (azurophil granules), ⁇ l- (specific), ⁇ 2- (gelatinase) and ⁇ - (secretory vesicle).
  • Fractions can be assayed for marker proteins using antibodies and ELISA: anti-CD63 for azurophil, anti- CDl Ib for specific granules, anti-gelatinase B for gelatinase granules and anti-CD35 for secretory vesicles.
  • Spi6 will be assayed by IP followed by Western blotting with anti-Spi ⁇ antiserum ( Figure 44). The presence of Spi6 in fractions positive for a given marker protein indicates the localization of Spi6 to that population of granules.
  • Bone-marrow cells from B6 and Spi6 KO mice will be examined by ICS/FCM using S ⁇ i6 anti-serum (Figure 44). Staining intensity in a sub-set of B6 cells over that of Spi6 KO cells indicates Spi6 expression. Expression as early as in promyelocytes is indicative of Spi6 targeting to azurophil granules. Absence from promyelocytes and expression in myelocytes and later forms is indicative of targeting to specific/gelatinase granules. Expression of Spi6 in only mature segmented cells is consistent with localization to secretory granules. (7) Association of Spi6 with NE during bacterial killing
  • Spi6 is delivered to NE-positive phagolysosomes by the fusion of either specific granules, gelatinase granules or secretory vesicles with azurophil granules can also be examined.
  • Neutrophils can be incubated with flouresecently-labeled E. coli as described in Belaaouaj et al., (1998), which is hereby incorporated by reference in its entirety for its teaching of incubating neutrophils with flouresecently-labeled E. coli. ( Figure 36).
  • Spi6 can then be localized with NE and other granule markers during the fusion of granules to form the phagolysosome using CIM as described elsewhere herein.
  • the phagolysosome can be identified as the compartment containing labeled bacteria and NE.
  • deletion mutants of Spi6 lacking the RCL region can be generated, which is required for interaction with a target protease.
  • the deletion mutants can be expressed in HL-60 cells and the effect on the targeting of Spi6 to azurophil granules determined as described above.
  • KO neutrophils can be measured.
  • Azurophil granules can be visualized by staining for anti-CD63 and CIM (see above).
  • the number of MPO-positive granules can be measured by cyto-chemical staining for peroxidase then CIM as described in Bainton et al., (1971), which is hereby incorporated by reference in its entirety for its teaching of measuring MPO-positive granules by cyto- chemical staining for peroxidase then CIM.
  • cytoplasm of the azurophil granules can be examined for increased NE activity by enzyme assay ( Figure 36) on cytoplasmic fractions from Percoll density centrifugation (see elsewhere herein).
  • Figure 36 enzyme assay
  • a decrease in the level of azurophil granules in Spi6 KO neutrophils is indicative of a requirement for Spi6 in ensuring granule stability.
  • Spi6 KO mice can be crossed to generate Spi6 KO x NE KO, Spi6 KO x Cat G KO and Spi6 KO x PR-3 KO. The killing of S. aurues in double KO mice can then be compared with B6 wild-type controls, as well as Spi6 KO and NE KO, Cat G KO and PR-3 KO.
  • Glycogen-elicited neutrophils (2x10 6 ) can be incubated with S. aurues (2x10 5 ) and the number of viable bacteria measured for up to 6 h, by titering colony forming units (cm) overnight on LB plates. In addition, it can be determined whether Spi6 KO neutrophils exhibit increased S. aurues killing and whether it can be abolished by either Cat G or PR-3 deficiency.
  • the survival of Spi6 KO and azurophil serine proteases KO mice after infection with S. aureus can also be determined.
  • Age, sex and weight match B6 and KO mice can be infected (i.v.) with S. aureus (2-6 x 10 5 cfu/mouse) and the survival of mice and and titer in the spleen and liver measured every 12 h for up to 7 d.
  • C57BL/6 wild-type and C57BL/6 Spi6 KO, NE KO, Cat G KO, Spi ⁇ KO x NE KO, Spi6 KO x Cat G KO, Spi6 KO x PR-3 KO mice can be infected i.v. by tail vein injection (lOO ⁇ l in PBS, 25 gauge needle) with S. aureus (NCTC 12981) cells (2-6 x 105 cfu) and survival monitored every 12 h for 7 d. Mice that show signs of acute disease (ruffled fur, hunched posture, immobility, and apparent weight loss) are immediately sacrificed. For i.v.
  • recipient mice can be placed in a restrainer and the tail warmed with a heat lamp to allow visualization of the tail vein, then sterilized by washing with 70% ethanol.
  • Bacteria were titered from the liver and spleen of euthanized mice by standard overnight LB plate assay. In each survival experiment at least 20 mice are used to achieve statistical significance. These experiments address the role of Spi6 and its target protease in neutrophil immunity to gram-positive bacteria. c; ""D'eter'mine if other azurophil proteases are also inhibited by Spi6.
  • L. monocytogenes is a facultative intracellular bacterium, neutrophils are critical for the early control of infection of hepatocytes by killing extracellular bacteria. Therefore the increased resistance of Spi6 KO to L. monocytogenes can be due to increased activity of NE or other putative substrates of Spi6. a) Requirement for azurophil proteases immunity to L .monocytogenes
  • Glycogen-elicited neutrophils (2xlO 5 ) from B6 and Spi6 KO x serine protease (NE, Cat G and PR-3) KO mice can be incubated with L. monocytogenes (2 xlO 6 ) and the number of viable bacteria "measure'd i ⁇ r " ⁇ pi't ⁇ b n"; Dy ti ⁇ ermg overnight on brain-heart infusion agar plates ( Figure 41(c)).
  • the specific activity of NE, Cat G and PR-3 in neutrophils activated with L. monocytogenes can be measured as described elsewhere herein.
  • Example 7 Macrophage function in Spi6 KO mice 601.
  • L. monocytogenes is a facultative intracellular bacterium, which can escape neutrophil phagocytosis by residing in macrophages. Consequently, activation of macrophages by IFN- ⁇ produced in ThI immune reactions is critical to resolve L. monocytogenes infection. This mechanism is unlikely to explain the increased clearance of L. monocytogenes in S ⁇ i6 KO mice because IFN- ⁇ levels were actually lower than controls ( Figure 42).
  • NE can degrade tissue inhibitor of metalloproteinase (TIMP)-I, which is an inhibitor of MMP-12.
  • TRIP tissue inhibitor of metalloproteinase
  • Macrophages can be depleted from S ⁇ i6 KO mice by liposome-encapsulated clondrate (Lip- CLOD) induced apoptosis as described in Van Rooijen, (1989),which is hereby incorporated by reference in its entirety for its teaching of such.. Briefly, C57BL/6 wild-type and C57BL/6 Spi6 KO mice are injected i.v. with preparations of LIP-CLOD (20-80 ⁇ g CLOD/mouse; lOO ⁇ l/lOg body weight).
  • Lip-CLOD-depletion has been broadly used in different experimental models to investigate splenic and hepatic macrophage function.
  • Liposomes containing clodronate (dichlorormethylene) can be prepared using standard procedures and i.v. injected into mice (20-80 ⁇ g CLOD/mouse; lOO ⁇ l/lOg body weight). Pilot experiments to optimize the selective depletion of macrophages by Lip-CLOD can be conducted, which can be verified by staining splenocytes for F4/80 + CDl Ib + (macrophages) and control Gr-I + CDl Ib + cells (granulocytes) 4 d after injection and FCM. Depletion in the liver can be verified by immunohistological analysis. Mice can then be infected with L. monocytogenes and clearance measured in Spi6KO and control B6 animals ( Figure 41 (c)).
  • the biochemical basis for the increased recruitment of macrophages in Spi6 KO mice can also be examined by infecting mice with L. monocytogenes and macrophages can be purified from perfused liver by magnetic bead sorting with anti-F4/60 beads (Miltenyi Biotech, Auburn, CA). MMP-12 activity can be determined in macrophages by measuring the degradation of elastin. Briefly, Macrophages (10 6 /ml) are cultured on plates coated with 3 H-labeled elastin (Elastin Products, Owensville, Missouri) for 3 days and the amount of elastin degraded measured by determining the production of solubilized 3 H-elastin in the medium. o ⁇ o.
  • wnetner invir-i is degraded by increased NE activity can be examined by measuring TIMP- 1 activity by reverse zymography in macrophages after L. monocytogenes infection. Briefly, macrophage protein extracts are resolved by PAGE in gelatin (Elastin Products, Owensville, Missouri) (lmg/ml) then incubated in 2.5% Triton X-IOO for 30 min then overnight in 5OmM Tris.HCl pH 8.0, 5mM CaCi 2 ImM ZnCl 2 at 37 0 C with rat uterine explant conditioned medium as a source of MMPs. TIMP-I will protect gelatin from degradation by inhibiting MMP- 12 and so a band of gelatin at 27kD after staining with 0.125% Coomassie blue is present.
  • Helicobacter pylori stimulates a novel form of chronic inflammation that is characterized by a massive influx of neutrophils into the gastric mucosa leading to gastritis, peptic ulceration and in some cases gastric cancer.
  • mice (6-8 w old) can be infected with H. felis (0.5-1.0 x 10 9 ) (ATCC 49179) by gastric intubation on 3 consecutive days as described in Blanchard et al., (1995); Mohammadi et al., (1996); and Walker et al., (2002), all of whih are hereby incorporated by reference for their teachings of such techniques.
  • mice can be infected with H. felis (0.5-1.0 x 10 9 ) (ATCC 49179) in 0.5ml Columbia broth by gastric intubation on 3 consecutive days. Mice are anesthetized and a polypropylene tube inserted down the oesophegus into the stomach. An attached syringe is used to inject the bacteria. Mice are sacrificed from 2 w up until 1Ow after infection and the stomach subjected to histopathological analysis. Mice that show signs of acute disease (ruffled fur, hunched posture, immobility, and apparent weight loss) are immediately sacrificed.
  • stomachs of mice are histologically evaluated for inflammation and the level of H. felis. Briefly, strips of the entire curvature of the stomach are cut, fixed in 10% buffered formalin and embedded in paraffin. Sections can then be stained with H&E and Giesma reagents. Gastric sections can be evaluated.in a blinded fashion according to the following criteria.
  • the extent of inflammation can be determined and expressed as the percentage of the mucosal surface involved in inflammation.
  • the frequency of crypt abscesses can be determined as evidence for chronic gastritis.
  • the following cellular components of the inflammatory infiltrate can be graded from 0 to 3: mononuclear cells, polymorphonuclear cells and plasma cells.
  • H.felis does not reliably form discrete colonies and so is difficult to titer by plating on culture dishes. The extent of infection by measuring the average number of H.felis positive glands/cm observed in
  • H. felis can be identified as characteristically curved and confirmed by urease assays after culturing on Columbia agar (Difco) containing 7% horse blood under microaerophilic conditions for 4 d. Both fundus and antrum of the stomach can be scored and averaged to give one value for bacterial infection of each mouse. Sufficient numbers of mice (n > 10) from each group can be examined to give statistically significant results.
  • B6 and Spi6 KO mice can be infected with H. felis then from 1 week until at least 8 weeks evaluated for inflammation and the level of H. felis.
  • H. pylori infects the gastric mucosa of half the adult population worldwide (1994) and the incidence of antibiotic resistant forms is on the rise. Therefore there is need for alternative cures for diseases such as gastritis and peptic ulcers that are caused by H. pylori.
  • PI9 the human homologue of Spi6 also inhibits NE and is expressed in neutrophils.
  • Whether suppression of NE activity can alleviate disease in PI9 transgenic mice can be determined by amplifying the PI9 open reading frame from PI9 cDNAand cloning the PI9 open reading frame into the 3 x FLAG-CMV-14 expression vector (Sigma Aldrich, St. Louis, MO). DNA encoding PI9 with a C-terminal 3 x FLAG epitope tag can then be cloned into the Eco RI-Bam HI sites of the human lysozyme promoter (hLP) expression cassette, which directs expression in activated neutrophils and macrophages. Tl ⁇ -Fr ⁇ 'transcription is then driven by the proximal promoter of the human lysozyme gene (3.5kB) and terminated by stop sequences provided by human growth hormone gene (2.5kB).
  • hLP human lysozyme promoter
  • mice One-cell embryos from C57BL/6 mice will be microinjected with hLP- PI9-FLAG DNA and implanted into the oviducts of pseudo-pregnant recipients.
  • Transgenic mice can be identified by Southern blots of DNA from tail biopsies probed with hLP-PI9- FLAG DNA. Independent lines of heterozygous hLP-PI9-FLAG mice can be generated by backcrossing to wild-type C57BL/6 mice.
  • C57BL/6 wild-type and C57BL/6 Spi6 KO, NE KO, Cat G KO, Spi6KO x NE KO, Spi6 KO x Cat G KO, S ⁇ i6 KO x PR-3 KO mice can be injected i.p with 15% glycogen in PBS (lml/mouse) using a 20-gauge needle and neutrophils harvested by peritoneal lavage with HBBS after 4 h.
  • neutrophils can be used to examine the granule association of endogenous Spi6 in neutrophils, the suppression of extracellular NE by Spi6 and the role of Spi6 in the killing of gram-positive Staphloccocus aureus in vitro.
  • hLP-PI9-FLAG transgenic mice can be infected with H. felis and bacterial clearance and inflammatory disease can be observed. Additionally, hLP-PI9-FLAG transgenic x NE KO mice can be observed.
  • siRNAs small inhibitory RNAs
  • Figure 46 the ability of candidate siRNAs (PI9 1-5) (Dharmacon) to knock down PI9 expression in glycogen-elicited neutrophils from hLP-PI9-FLAG transgenic mice can also be examined. Briefly, neutrophils (2.5 x 10 5 cells) can be transfected with siRNAs (1-10OmM) using oligofectamine (Invitrogen, Carlsbad, California) and PI9 expression assayed after 24 h. To control for the specificity of PI9 gene silencing irrelevant control (1-3) siRNAs can also be tested (Figure 46).
  • siRNAs can modulate gene expression Ol neutroprms a ⁇ er ⁇ eiivery to adult mice. This technology can be exploited to knock-down PI9 expression in neutrophils infiltrating the gastric mucosa.
  • hLP-PI9-FLAG transgenic mice (8-10 w old, 20-25 g) can be infected with H.felis.
  • PI9-specific siRNA 50 ⁇ g can then be delivered to mucosal surfaces by gastric intubation.
  • the efficacy of delivery of FITC-labeled siRNA can be assessed by CIM analysis of mucosal neutrophils.
  • the reduction of PI9 expression in infiltrating neutrophils can then be assessed by immunohistochemistry on stomach sections and ICS/FCM of disaggregated tissue, using either anti-PI9 antibody or anti-FLAG mAb.
  • the specificity of PI9 gene silencing can be controlled using irrelevant control (1-3) siRNAs ( Figure 46). To confirm that any affect of PI9 silencing is through increased NE activity the experiments in hLP-PI9-FLAG transgenic x NE KO mice can be repeated. 623.
  • the 'hydrodynamic transfer method' can be used to deliver siRNA to the circulation (i.v. injection about 1ml PBS). Intravenous injection of siRNA with cationic liposomes can also be considered if it improves the efficiency of delivery. Alternatively, i.p. injection can also prove to be an effective means to deliver to circulation and stomach.
  • pre-optimized pooled siRNAs Smart pool reagent, Dharmacon Inc., Chicago, IL
  • Smart pool reagent Dharmacon Inc., Chicago, IL
  • Example 9 Translation of studies into cures for pneumonia caused by bacterial infection.
  • B6 and MMP 12 KO mice can be infected with P. aeruginosa then after 4 h instilled with HNE (0-7U/kg) (Figure 43). Survival can then be examined every 12 h for 96 h. Bacterial titer, NE activity and leukocyte numbers can be measured in the BAL mice. The lungs of survivors can be measured for signs of gross pathology using standard histological techniques.
  • hLP-PI9-FLAG transgenic mice are infected with P. aeruginosa then siRNA (50 ⁇ g) is delivered by intranasal injection in PBS. Every 12 h for 96 h the expression of FLAG-PI9 is measured in neutrophils from the BAL to determine the optimal conditions to knock-down PI9 expression.
  • the delivery of siRNA and ablation of gene expression in lung neutrophils has been achieved by others using this protocol, see for example Lomas-Neira et al., (2005), which is hereby incorporated by reference in its entirety for its teaching of delivery of siRNA and ablation of gene expression in lung neutrophils. 10.
  • Serine protease inhibitor 6 protects cytotoxic T cells from self-inflicted injury by ensuring the integrity of lytic granules a) Methods
  • Spi6 locus (Serpin b9) from a bacterial artificial chromosome (BAC) library (129/Sv strain RPCI-22, Res Gen).
  • the 5 ' homology region (4.1 kb Sac //- Kpn I fragment) and the 3 ' homology region (3.6 kb Not I— Xlio I fragment) were cloned on either side of the neo gene (1.8 kb Kpn I- Not I fragment) flanked by loxP recombination sites (Kuhn et al., 1995).
  • C57BL/6 ES cells (Ware et al., 2003) were transfected with targeting vector (50 ⁇ g).
  • DNA from G418 resistant clones was digested with Spe /and Hind III and hybridized with probes to detect wild-type (5'- 7.6kb, 3'- 9.8kb) and mutant alleles (5'-6.9 kb, 3'-5.8 kb).
  • ES cells from targeted clones (2/398) were transfected (30 ⁇ g) with Cre (pBS185, Invitrogen, Carlsbad, California) and excision of the neo after loxP site-specific recombination was detected by the presence of a 5.8kb band after blotting with 5'- probe (Kuhn et al., 1995).
  • C57BL/6 ES cells were microinjected into BALB/c blastocysts to produce chimeric mice, which were then backcrossed against wild-type C57BL/6 mice (Jackson Laboratory, Bar Harbor, ME).
  • C57BL/6 Spi6 +/ ⁇ mice from 2 independently targeted ES cell clones were intercrossed to generate C57BL/6 Spi6 ⁇ f ⁇ mice (S ⁇ i6 KO mice), which were born at a Mendelian frequency.

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Abstract

La présente invention concerne des compositions et des procédés se rapportant aux serpines, et leur fonction, ainsi que des procédés se rapportant à des mécanismes dépendant des serpines.
EP06748251A 2005-02-25 2006-02-24 Compositions et méthodes liées au serpin spi6 Withdrawn EP1879448A2 (fr)

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US9518107B2 (en) 2010-08-31 2016-12-13 Yissum Research Development Company Of The Hebrew University Of Jerusalem, Ltd. Pharmaceutical compositions containing polypeptides derived from α-1 antitrypsin and methods of use thereof
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