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(12) United States Patent (10) Patent No.: US 9,334.313 B2 Masignani Et Al

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(12) United States Patent (10) Patent No.: US 9,334.313 B2 Masignani Et Al USOO9334.313B2 (12) United States Patent (10) Patent No.: US 9,334.313 B2 Masignani et al. (45) Date of Patent: May 10, 2016 (54) PROTEINS AND NUCLEICACIDS FROM (52) U.S. Cl. MENINGITIS/SEPSIS-ASSOCATED CPC ........... C07K 14/245 (2013.01); A61K39/0258 ESCHERICHLA COLI (2013.01); A61 K39/00 (2013.01); A61 K 2039/505 (2013.01); A6 IK 2039/523 (2013.01) (71) Applicants:Novartis Vaccines and Diagnostics Srl, (58) Field of Classification Search Siena (IT); J. Craig Venter Institute, None Inc., Rockville, MD (US) See application file for complete search history. (72) Inventors: Vega Masignani, Siena (IT); Danilo Gomes Moriel, Monteriggioni (IT): (56) References Cited Francesco Berlanda Scorza, Trento (IT): Nathalie Norais, Siena (AT): U.S. PATENT DOCUMENTS Maria Rita Fontana, Siena (IT): ck Mariagrazia Pizza, Siena (IT); Laura 7,424,370 B2 9/2008 Sachdeva et al. ............... 7O2/19 g s s 2003/O165870 A1 9, 2003 Blattner et al. Serino, Monticiano (IT): Herve Tettelin, 2004/O123343 A1 6/2004 La Rosa et al. Gaithersburg, MD (US) FOREIGN PATENT DOCUMENTS (73) Assignee: GlaxoSmithKline Biologicals SA, Rixensart (BE) EP 1342784 A1 9, 2003 WO 98.22575 A2 5, 1998 (*)c Notice:- r Subject to any disclaimer, the term of this WO 02/16439O1? 66572 A2 2/20029, 2001 patent is extended or adjusted under 35 WO O2/O5932O A2 8, 2002 U.S.C. 154(b) by 0 days. WO O2/O771.83 A2 10, 2002 WO 2004/005535 A2 1, 2004 (21) Appl. No.: 14/293,967 WO 2005, O76O10 A2 8, 2005 (22) Filed: Jun. 2, 2014 OTHER PUBLICATIONS (65) Prior Publication Data Accession: H90670; Jul 18, 2001.* US 2014/0356389 A1 Dec. 4, 2014 (Continued) Related U.S. Application Data - - - Primary Examiner — Padma V Baskar (62) Division of application No. 1 1/884.812, filed as (74) Attorney, Agent, or Firm — Morrison & Foerster LLP application No. PCT/US2006/005913 on Feb. 17, 2006, now Pat. No. 8,758,764. (60) Provisional application No. 60/654,632, filed on Feb. (57)57 ABSTRACT 18, 2005, provisional application No. 60/712,720, Disclosed herein are various open reading frames from a filed on Aug. 29, 2005. strain of E. coli responsible for neonatal meningitis (MNEC), and a Subset of these that is of particular interest for preparing (51) Int. Cl. compositions for immunizing against MNEC infections. A6 IK39/08 (2006.01) C07K I4/245 (2006.01) A61 K39/00 (2006.01) 6 Claims, 4 Drawing Sheets CX is FHE3034 HC- Gr 1,Eros 1,Esof 1,0s + . a- - - - - ,-05 + 1E--04 - 4,E+03 - - - - E-2 - H3034 E334 iHE334 FIS 80. FISQ. US 9,334.313 B2 Page 2 (56) References Cited Bernadac et al., “Escherichia coli Tol-Pal Mutants form Outer Mem brane Vesicles”, Journal of Bacteriology, vol. 180, No. 8, 1998, pp. OTHER PUBLICATIONS 4872-4878. Bonacorsi et al., “Identification of Regions of the Escherichia coli Chromosome Specific for Neonatal Meningitis Associated Strains”. Accession: D85521; Feb. 16, 2001.* Infection and Immunity, vol. 68, No. 4, Apr. 2000, 8 pages. Houghten et al. (Vaccines, 1986, Edited by Fred Brown: Cold Spring Dean-Nystrom et al., “Vaccination of Pregnant Dams with Harbor Laboratory).* Intimin(0.157) Protects Suckling Piglets from Escherichia coli Holmes (Exp. Opin.Invest. Drugs, 2001, 10(3):51 1-519).* O157:H7 Infection”, Infect Immun., vol. 70, No. 5, 2002, pp. 2414 Coleman et al. (Research in Immunology, 1994: 145(1): 33-36).* 2418. Abaza et al. (Journal of Protein Chemistry, vol. 11, No. 5, 1992, pp. Gonzalez et al., "Adaptation of Signature-Tagged Mutagenesis to 433-444.* Escherichia coli K1 and the Infant-Rat Model of Invasive Disease'. European Examination Report mailed Dec. 29, 2008, for European Fems Microbiology Letters, vol. 198, No. 2, May 1, 2001, pp. 125 128. patent application No. 06748228.1, filed on Feb. 17, 2006. Houghten et al., “New Approaches to Immunization'. Vaccines 86, Extended European Search Report received for European Patent Cold Spring Harbor Laboratory, 1986, pp. 21-25. Application No. 06748228.1, mailed on Dec. 23, 2008, 4 pages. Janke et al., “A Subtractive Hybridisation Analysis of Genomic Dif International Preliminary Report on Patentability received for PCT ferences Between the Uropathogenic E. coli Strain 536 and the E. coli Patent Application No. PCT/US2006/005913, issued on Aug. 21, K-12 Strain MG 1655”, FEMS Microbiology Letters, vol. 199, No. 1, 2007.9 pages. May 2001, pp. 61-66. International Search Report and Written Opinion received for PCT Judge et al., “Plant Cell-Based Intimin Vaccine given Orally to Mice Patent Application No. PCT/US2006/005913, mailed on Feb. 15, Primed with Intimin Reduces Time of Escherichia coli O157:H7 2007, 14 pages. SheddinC in Feces”. Infection and Immunity, vol. 72, No. 1, 2008, Final Office Action received for U.S. Appl. No. 1 1/884.812, mailed pp. 168-175. on Feb. 1, 2010, 4 pages. McGuinness et al..."Class 1 Outer Membrane protein of Neisseria Non-Final Office Action received for U.S. Appl. No. 1 1/884.812, Meningitidis: Epitope Analysis of the Antigenic Diversity Between mailed on Jun. 23, 2009, 12 pages. Strains, Implications for Subtype Definition and Molecular Epide Non-Final Office Action received for U.S. Appl. No. 1 1/884.812, miology”, Mol. Microbiology, vol. 7, Feb. 1993, pp. 505-514. mailed on Sep. 23, 2013, 4 pages. McGuinness et al., “Point Mutation in Meningococcal por A Gene Notice of Allowance received for U.S. Appl. No. 1 1/884.812, mailed Associated with Increased Endemic Disease' Lancet, vol. 337, Mar. on Feb. 5, 2014, 8 pages. 1991, pp. 514-517. Accession No. 046837 2002 (or 02M9M2 or 046838 or 06BF5) or Perna et al., “Genome sequence of Enterohaemorrhagic Escherichia Science 277, 1997, pp. 1453-1474. coli O157:H7, Nature, vol. 409, No. 6819, 2001, pp. 529-533. “EBI accession No. Q8FKK3”. Version 56, Mar. 1, 2003, 2 pages. Rode et al., “Type-Specific Contributions to Chromosome Size Dif “EBI accession No. Q8X6G3, Version 71, Mar. 1, 2002, 3 pages. ferences in Escherichia coli, Infection and Immunity, vol. 67, No. 1, "Escherichia coli Pathogenicity Island V, strain 536', retrieved from Jan. 1999, pp. 230-236. EBI accession No. EMBL: AJ617685 Database accession, May 11, Thomas et al., “Improved Methods for Producing Outer Membrane 2004, 54 pages. Vesicles in Gram-Negative Bacteria'. Research in Microbiology, vol. "Escherichia coli strain BEN2908 pathogenicity island AGI-1, com 155, No. 6, Jul. 2004, pp. 437-446. plete sequence', retrieved from EBI accession No. Welch et al., “Extensive Mosaic Structure Revealed by the Complete EM PRO:AY395687, Oct. 24, 2003, 18 pages. Genome Sequence of Uropathogenic Escherichia coli, PNAS, vol. “RecName: Full-Putative lipoprotein acflDhomolog:Flags: Precur 99, No. 26, 2002, pp. 17020-17024. Sor, ADHKTEDSLK AAKEKIFAAF PGLKECTNPA Wu, “The Relationship Between Outer Membrane Vesicles and YHYEVNCLEY RPGTGVPVTG GMYVPQYTQ, retrieved from Pathogenicity'. Foreign Medicine (Microbiology Section), vol. 4. EBI accession No. UNIPROT:Q46837, Apr. 16, 2002, 2 pages. 2002, pp. 13-15. “Sequence Analysis of the Vibrio CholeraeacflD Gene Reveals the Zhang et al., “Molecular Epidemiologic Approaches to Urinary Tract Presence of an Overlapping Reading Frame, Orf7, which Encodes a Infection Gene Discovery in Uropathogenic Escherichia coli, Infec Protein that Shares Sequence Similarity to the FliA and FliC Products tion and Immunity, vol. 68, No. 4, Apr. 2000, pp. 2009-2015. of Salmonella'. Gene, Elsevier, Amsterdam, NL, vol. 146, No. 1, Aug. 19, 1994, pp. 79-82. * cited by examiner U.S. Patent May 10, 2016 Sheet 1 of 4 US 9,334.313 B2 FIGURE 1 - O - IHE3034 H 20 mO Ctrl. - 10 - - O O 1 2 3 4. 1,E+09 - - - --O- 1,E+08 res a - a a a a a as as a sa P. a a at a w aC a 1,E+07 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -(). as a a a at a w w at a a 1,E+06 res - M - e s - e. ( ) - - - - a w - - - w a 1,E+05 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -8 - - - - - - a .Ow is a a 1,E+04 a a a a A a a A at a a a a as a a - a . a a a a ar as a a a a a * A w a P M a war a w a as a a a w P W A a a A & e. e. Y a E+03 w w w w - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - a a a a P · w a P. p * * w w a w 1,E+02 - S - 3 -,-3- -- --G HE3034 - E3034 HE3034 FSO FSOL, FSO U.S. Patent May 10, 2016 Sheet 2 of 4 US 9,334.313 B2 FIGURE 2 timepoint -C - HE3034 a DH5 da O a FISIOL. timepoint O C o, OMV HE o p OMV DH5 c O a FSO. U.S. Patent May 10, 2016 Sheet 3 of 4 US 9,334.313 B2 FGLURIS 3 Challenge 10 7 CFU timepoint a K P roN mO ctrl. 4OOOOO 35OOOO 300000 250000 2OOOOO 15OOOO 100000 5OOOO U.S. Patent May 10, 2016 Sheet 4 of 4 US 9,334.313 B2 FIGURE 4 O 2 3. 4 timepoint a 3 P beA ma-Or Ctrl. 90000 - f 80000 - 70000 - f 60000 - 50000 40000t k 30000 - A: 2000.0 - 10000 - a"0 - I -T- - --- - 4. 5 6 7 8 9 ? US 9,334,313 B2 1. 2 PROTEINS AND NUCLECACDS FROM Most previous ExPEC vaccines have been based on cell MENINGITIS/SEPSIS-ASSOCATED lysates or on cellular structures. SOLCOUROVACTM ESCHERICHLA COLI includes ten different heat-killed bacteria including six ExPEC strains, and a successful phase II clinical trial was CROSS REFERENCE TO RELATED reported in reference 2.
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