WO2013173652A1 - Compositions and methods for modulating gene expression - Google Patents

Compositions and methods for modulating gene expression Download PDF

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Publication number
WO2013173652A1
WO2013173652A1 PCT/US2013/041461 US2013041461W WO2013173652A1 WO 2013173652 A1 WO2013173652 A1 WO 2013173652A1 US 2013041461 W US2013041461 W US 2013041461W WO 2013173652 A1 WO2013173652 A1 WO 2013173652A1
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WIPO (PCT)
Prior art keywords
sapiens
homo
oligonucleotide
nucleotides
single stranded
Prior art date
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Ceased
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PCT/US2013/041461
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English (en)
French (fr)
Inventor
Arthur M. Krieg
Romesh Subramanian
James Mcswiggen
Jeannie T. Lee
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
General Hospital Corp
Translate Bio Inc
Original Assignee
General Hospital Corp
RaNA Therapeutics Inc
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First worldwide family litigation filed litigation Critical https://patents.darts-ip.com/?family=49584310&utm_source=google_patent&utm_medium=platform_link&utm_campaign=public_patent_search&patent=WO2013173652(A1) "Global patent litigation dataset” by Darts-ip is licensed under a Creative Commons Attribution 4.0 International License.
Priority to EP13791343.0A priority Critical patent/EP2850189B8/en
Priority to KR1020147035191A priority patent/KR102028784B1/ko
Priority to EP18204559.1A priority patent/EP3511416A1/en
Priority to DK13791343.0T priority patent/DK2850189T3/en
Priority to CN201380037158.XA priority patent/CN104583398A/zh
Priority to US14/401,252 priority patent/US20150133362A1/en
Priority to JP2015512864A priority patent/JP2015518714A/ja
Priority to AU2013262663A priority patent/AU2013262663A1/en
Priority to CA2873809A priority patent/CA2873809A1/en
Application filed by General Hospital Corp, RaNA Therapeutics Inc filed Critical General Hospital Corp
Priority to EA201492114A priority patent/EA201492114A1/ru
Publication of WO2013173652A1 publication Critical patent/WO2013173652A1/en
Anticipated expiration legal-status Critical
Priority to US14/691,361 priority patent/US20150218560A1/en
Priority to US15/872,684 priority patent/US10837014B2/en
Ceased legal-status Critical Current

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K48/00—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P7/00—Drugs for disorders of the blood or the extracellular fluid
    • A61P7/06—Antianaemics
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/11—Antisense
    • C—CHEMISTRY; METALLURGY
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/31—Chemical structure of the backbone
    • C12N2310/315—Phosphorothioates
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/32—Chemical structure of the sugar
    • C12N2310/321—2'-O-R Modification
    • C—CHEMISTRY; METALLURGY
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/32—Chemical structure of the sugar
    • C12N2310/322—2'-R Modification
    • C—CHEMISTRY; METALLURGY
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/32—Chemical structure of the sugar
    • C12N2310/323—Chemical structure of the sugar modified ring structure
    • C12N2310/3231—Chemical structure of the sugar modified ring structure having an additional ring, e.g. LNA, ENA
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/34—Spatial arrangement of the modifications
    • C12N2310/343—Spatial arrangement of the modifications having patterns, e.g. ==--==--==--
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/35—Nature of the modification
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    • C12N2310/3517—Marker; Tag
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/35—Nature of the modification
    • C12N2310/352—Nature of the modification linked to the nucleic acid via a carbon atom
    • C12N2310/3521—Methyl
    • C—CHEMISTRY; METALLURGY
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/35—Nature of the modification
    • C12N2310/353—Nature of the modification linked to the nucleic acid via an atom other than carbon
    • C12N2310/3533—Halogen

Definitions

  • the invention relates to oligonucleotide based compositions, as well as methods of using oligonucleotide based compositions for treating disease.
  • aspects of the invention provide methods for selecting oligonucleotides for activating or enhancing expression of target genes.
  • the methods are particularly useful for identifying candidate oligonucleotides for activating or enhancing expression of target genes for which reduced expression or activity results in, or contributes to, disease.
  • Further aspects of the invention provide methods of selecting a set of oligonucleotides that is enriched in
  • oligonucleotides (e.g. , compared with a random selection of oligonucleotides) that activate expression of a target gene.
  • the methods may be used to establish large libraries of clinical candidates that are enriched in oligonucleotides that activate gene expression. Such libraries may be utilized, for example, to identify lead oligonucleotides for therapeutic development.
  • the methods provided are useful for establishing a broad platform of candidate oligonucleotides for targeting the expression of most known genes, including protein coding genes.
  • Further aspects provide single stranded oligonucleotides that modulate gene expression, and compositions and kits comprising the same. Methods for modulating gene expression using the single stranded oligonucleotides are also provided.
  • the invention is a method for selecting a candidate oligonucleotide for activating expression of a target gene by selecting a PRC2-associated region within a first nucleotide sequence, wherein the first nucleotide sequence maps to a position in a first chromosome between 50 kilobases upstream of a 5 '-end of the target gene and 50 kilobases downstream of a 3'-end of the target gene; determining a second nucleotide sequence that is complementary with at least 8 consecutive nucleotides of the PRC2-associated region; and selecting as the candidate oligonucleotide, a single stranded oligonucleotide comprising the second nucleotide sequence, wherein the oligonucleotide has at least one of following features: a) a sequence comprising 5'-X-Y-Z, wherein X is any nucleotide, Y is a nucleotide sequence of 6 nucleotides in
  • the single stranded oligonucleotide has only one of features a), b), c), d), and e). In some embodiments, the single stranded oligonucleotide has at least two of features a), b), c), d), and e), each independently selected. In some embodiments, the single stranded oligonucleotide has at least three of features a), b), c), d), and e), each independently selected. In some embodiments, the single stranded oligonucleotide has at least four of features a), b), c), d), and e), each independently selected. In some
  • the single stranded oligonucleotide has each of features a), b), c), d), and e).
  • the oligonucleotide has the sequence 5'X-Y-Z, in which the oligonucleotide is 8-50 nucleotides in length.
  • Y is a sequence selected from Table 3.
  • the invention is a method of selecting a set of oligonucleotides that is enriched in oligonucleotides that activate expression of a target gene, by selecting a PRC2- associated region within a first nucleotide sequence that maps to a position in a first chromosome between 50 kilobases upstream of a 5 '-end of the target gene and 50 kilobases downstream of a 3 '-end of the target gene; selecting a set of oligonucleotides, wherein each oligonucleotide in the set comprises a second nucleotide sequence that is complementary with at least 8 consecutive nucleotides of the PRC2-associated region, and has at least one of the following features: a) a sequence: 5'-X-Y-Z, wherein X is any nucleotide, Y is a nucleotide sequence of 6 nucleotides in length that is not a human seed sequence of a microRNA, and Z is
  • each of the oligonucleotides has only one of features a), b), c), d), and e). In some embodiments, each of the oligonucleotides has at least two of features a), b), c), d), and e), each independently selected. In some embodiments, each of the
  • oligonucleotides has at least three of features a), b), c), d), and e), each independently selected. In some embodiments, each of the oligonucleotides has at least four of features a), b), c), d), and e), each independently selected. In some embodiments, each of the
  • each of the oligonucleotides has the sequence 5'X-Y-Z, in which the oligonucleotide is 8-50 nucleotides in length.
  • Y is a sequence selected from Table 3.
  • the single stranded oligonucleotide or each of the oligonucleotides is up to 100, 50, 40, 30, or 20 nucleotides in length. In other embodiments the single stranded oligonucleotide or each of the oligonucleotides is 8 to 30 nucleotides in length.
  • the threshold level of sequence identity in some embodiments is 50%, 60%, 70%,
  • Y is a nucleotide sequence of 6 nucleotides in length set forth in Table 3.
  • the first chromosome is a chromosome of a first species
  • the method further comprises determining that the second nucleotide sequence is complementary to a second region of a second chromosome of a second species, the second region being located between 50 kilobases upstream of a 5 '-end of a homolog of the target gene and 50 kilobases downstream of a 3 '-end of the homolog of the target gene.
  • the second nucleotide sequence may be at least 80 % complementary to the second region of the second chromosome
  • the first nucleotide sequence maps to the strand of the first chromosome comprising the sense strand of the target gene. In other embodiments the first nucleotide sequence maps to the strand of the first chromosome comprising the antisense strand of the target gene.
  • the PRC2-associated region is upstream of the 5' end of the target gene and in other embodiments the PRC2-associated region is downstream of the 3' end of the target gene.
  • the PRC2-associated region may be within an intron or an exon of the target gene or the PRC2-associated region may traverse an intron-exon junction, a 5 '-UTR-exon junction or a 3 '-UTR-exon junction of the target gene.
  • the PRC2-associated region may encode an RNA that forms a secondary structure comprising at least two single stranded loops.
  • the secondary structure comprises a double stranded stem between the at least two single stranded loops.
  • the at least 8 consecutive nucleotides of the PRC2-associated region encode at least a portion of at least one or at least two of the loops or at least a portion of the double stranded stem.
  • the invention is a single stranded oligonucleotide comprising a region of complementarity that is complementary with at least 8 consecutive nucleotides of a PRC2- associated region located in a first chromosome between 50 kilobases upstream of a 5 '-end of a target gene and 50 kilobases downstream of a 3 '-end of the target gene, wherein the oligonucleotide has at least one of: a) a sequence comprising 5'-X-Y-Z, wherein X is any nucleotide, Y is a nucleotide sequence of 6 nucleotides in length that is not a human seed sequence of a microRNA, and Z is a nucleotide sequence of 1 to 23 nucleotides in length; b) a sequence that does not comprise three or more consecutive guanosine nucleotides; c) a sequence that has less than a threshold level of sequence identity with every sequence of nucleo
  • the single stranded oligonucleotide has only one of features a), b), c), d), and e). In some embodiments, the single stranded oligonucleotide has at least two of features a), b), c), d), and e), each independently selected. In some embodiments, the single stranded
  • oligonucleotide has at least three of features a), b), c), d), and e), each independently selected. In some embodiments, the single stranded oligonucleotide has at least four of features a), b), c), d), and e), each independently selected. In some embodiments, the single stranded oligonucleotide has each of features a), b), c), d), and e). In certain embodiments, the oligonucleotide has the sequence 5'X-Y-Z, in which the oligonucleotide is 8-50 nucleotides in length. In some embodiments, Y is a sequence selected from Table 3.
  • the first chromosome is a chromosome of a first species in some embodiments.
  • a sequence comprising the at least 8 consecutive nucleotides is located in a second
  • the first species may be human and the second species may be a mouse.
  • the invention also includes a single stranded oligonucleotide of 8-30 nucleotides in length, wherein the single stranded oligonucleotide is complementary with at least 8 consecutive nucleotides of a PRC2-associated region located in a chromosome between 50 kilobases upstream of a 5 '-end of a target gene and 50 kilobases downstream of a 3 '-end of the target gene, wherein the nucleotide sequence of the single stranded oligonucleotide comprises one or more nucleotide sequences selected from (X)Xxxxxx, (X)xXxxxx,
  • IncRNA long non- coding RNA
  • a single stranded oligonucleotide of 5 to 30 nucleotides in length having a region of complementarity that is complementary with at least 5 contiguous nucleotides of a long non- coding RNA (IncRNA) that regulates expression of a target gene, wherein the oligonucleotide is linked to a second oligonucleotide by a cleavable linker is provided.
  • the oligonucleotide has the structure of any of the single stranded oligonucleotides described herein.
  • IncRNA PRC2-binding long non- coding RNA
  • a single stranded oligonucleotide of 8 to 40 nucleotides in length having a region of complementarity that is complementary with at least 5 contiguous nucleotides of a long non- coding RNA (IncRNA) that regulates expression of a target gene is provided in other aspects of the invention.
  • the oligonucleotide has complementarity to the IncRNA in a region of the IncRNA that is outside of the transcribed region of the target gene.
  • IncRNA non- coding RNA
  • the IncRNA is a PRC2-associated region.
  • the PRC2-associated region has a nucleotide sequence selected from sequences Al to A193,049, Bl to B916,209, and B916,626 to B934,931. In some embodiments, the PRC2-associated region has a nucleotide sequence selected from SEQ ID NO: 1-1212.
  • the oligonucleotide may be any length. In some embodiments the oligonucleotide is up to 100, 50, 40, 30, or 20 nucleotides in length. In other embodiments the oligonucleotide is 8 to 30 nucleotides in length. In yet other embodiments the oligonucleotide is 8 to 10 nucleotides in length and all but 1, 2, or 3 of the nucleotides of the complementary sequence of the PRC2-associated region are cytosine or guanosine nucleotides.
  • the at least 8 consecutive nucleotides of the PRC2-associated region in some embodiments is in the strand of the chromosome comprising the antisense strand of the target gene and in other embodiments is in the strand of the chromosome comprising the sense strand of the target gene.
  • the PRC2-associated region is upstream of the 5' end of the target gene and in other embodiments the PRC2-associated region is downstream of the 3' end of the target gene.
  • the PRC2-associated region may be within an intron or an exon of the target gene or the PRC2-associated region may traverse an intron-exon junction, a 5 '-UTR-exon junction or a 3 '-UTR-exon junction of the target gene.
  • the PRC2-associated region may encode an RNA that forms a secondary structure comprising at least two single stranded loops.
  • the secondary structure comprises a double stranded stem between the at least two single stranded loops.
  • the at least 8 consecutive nucleotides of the PRC2-associated region encode at least a portion of at least one or at least two of the loops or at least a portion of the double stranded stem.
  • the at least one nucleotide analogue results in an increase in T m of the oligonucleotide in a range of 1 to 5 °C compared with an oligonucleotide that does not have the at least one nucleotide analogue.
  • At least one nucleotide of the oligonucleotide comprises a nucleotide analogue.
  • each nucleotide of the oligonucleotide comprises a nucleotide analogue
  • the nucleotide analogue may be a 2' O-methyl or a bridged nucleotide.
  • the oligonucleotide comprises at least one ribonucleotide, at least one deoxyribonucleotide, or at least one bridged nucleotide.
  • the bridged nucleotide may be, for instance, a LNA nucleotide, a cEt nucleotide or a ENA nucleotide analogue.
  • each nucleotide of the oligonucleotide is a LNA nucleotide.
  • the nucleotides of the oligonucleotide comprise alternating nucleotide types.
  • the oligonucleotide comprises deoxyribonucleotides and 2'-fluoro-deoxyribonucleotides.
  • nucleotides of the oligonucleotide comprise alternating deoxyribonucleotides and 2'-0- methyl nucleotides. In yet other embodiments the nucleotides of the oligonucleotide comprise alternating deoxyribonucleotides and ENA nucleotide analogues or the nucleotides of the oligonucleotide comprise alternating deoxyribonucleotides and LNA nucleotides. In yet other embodiments the nucleotides of the oligonucleotide comprise alternating LNA nucleotides and 2'-0-methyl nucleotides.
  • the 5' nucleotide of the oligonucleotide may have different properties.
  • the 5' nucleotide of the oligonucleotide is a deoxyribonucleotide or a LNA nucleotide.
  • deoxyribonucleotides flanked by at least one LNA nucleotide on each of the 5' and 3' ends of the deoxyribonucleotides.
  • the single stranded oligonucleotide may also include phosphorothioate
  • nucleotide at the 3' position of the oligonucleotide has a 3' hydroxyl group. In other embodiments the nucleotide at the 3' position of the
  • oligonucleotide has a 3' thiophosphate.
  • the single stranded oligonucleotide has a biotin moiety conjugated to the 5' or 3' nucleotide.
  • the single stranded oligonucleotide has one or more of the following conjugates to either the 5' or 3' nucleotide or both: cholesterol, Vitamin A, folate, sigma receptor ligands, aptamers, peptides, such as CPP, hydrophobic molecules, such as lipids, ASGPR or dynamic polyconjugates and variants thereof.
  • composition is provided in another aspect.
  • the composition is a single stranded oligonucleotide described herein and a carrier, a buffered solution, and/or a pharmaceutically acceptable carrier.
  • the invention is a composition of a single stranded RNA
  • oligonucleotide of 8 to 20 nucleotides in length having a region of complementarity that is complementary with at least 5 contiguous nucleotides of a long non-coding RNA (IncRNA) that regulates expression of a target gene, wherein 2-19 nucleotides of the oligonucleotide are nucleotide analogues, formulated in a pharmaceutically acceptable carrier, wherein a complementary RNA oligonucleotide is not present in the composition.
  • IncRNA long non-coding RNA
  • the nucleotide analogues are selected from the group consisting of a bridged nucleotide, 2' fluoro, and 2'0-methyl nucleotide.
  • the bridged nucleotide is a LNA, ENA or cEt nucleotide.
  • the IncRNA may be transcribed from the opposite strand as the target gene in a genomic region containing the target gene.
  • the oligonucleotide has complementarity to the IncRNA in a region of the IncRNA that is transcribed from a non-coding portion of the target gene. In other embodiments the oligonucleotide has complementarity to the IncRNA in a region of the IncRNA that is outside of the transcribed region of the target gene.
  • a kit comprising a container housing any of the compositions is also provided.
  • the invention is a method of increasing expression of a target gene in a cell, by delivering a single stranded oligonucleotide described herein into the cell.
  • a method of increasing levels of a target gene in a subject by administering a single stranded oligonucleotide described herein to the subject is provided in other aspects of the invention.
  • a method of treating a condition associated with decreased levels of a target gene in a subject by administering a single stranded oligonucleotide described herein to the subject is provided in yet other aspects of the invention.
  • a method of upregulating gene expression involves contacting a cell with a single stranded RNA oligonucleotide of 8 to 30 nucleotides in length having a region of complementarity that is complementary with at least 5 contiguous nucleotides of a long non- coding RNA (IncRNA) that inhibits expression of a target gene.
  • a single stranded RNA oligonucleotide of 8 to 30 nucleotides in length having a region of complementarity that is complementary with at least 5 contiguous nucleotides of a long non- coding RNA (IncRNA) that inhibits expression of a target gene.
  • IncRNA non- coding RNA

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PCT/US2013/041461 2012-05-16 2013-05-16 Compositions and methods for modulating gene expression Ceased WO2013173652A1 (en)

Priority Applications (12)

Application Number Priority Date Filing Date Title
EA201492114A EA201492114A1 (ru) 2012-05-16 2013-05-16 Композиции и способы для модулирования экспрессии генов
JP2015512864A JP2015518714A (ja) 2012-05-16 2013-05-16 遺伝子発現を調節するための組成物及び方法
EP18204559.1A EP3511416A1 (en) 2012-05-16 2013-05-16 Compositions and methods for modulating gene expression
DK13791343.0T DK2850189T3 (en) 2012-05-16 2013-05-16 COMPOSITIONS AND PROCEDURES FOR MODULATING GENEPRESSION
CN201380037158.XA CN104583398A (zh) 2012-05-16 2013-05-16 用于调节基因表达的组合物和方法
US14/401,252 US20150133362A1 (en) 2012-05-16 2013-05-16 Compositions and methods for modulating gene expression
AU2013262663A AU2013262663A1 (en) 2012-05-16 2013-05-16 Compositions and methods for modulating gene expression
EP13791343.0A EP2850189B8 (en) 2012-05-16 2013-05-16 Compositions and methods for modulating gene expression
CA2873809A CA2873809A1 (en) 2012-05-16 2013-05-16 Compositions and methods for modulating gene expression
KR1020147035191A KR102028784B1 (ko) 2012-05-16 2013-05-16 유전자 발현을 조절하기 위한 조성물 및 방법
US14/691,361 US20150218560A1 (en) 2012-05-16 2015-04-20 Compositions for modulating gene expression
US15/872,684 US10837014B2 (en) 2012-05-16 2018-01-16 Compositions and methods for modulating SMN gene family expression

Applications Claiming Priority (34)

Application Number Priority Date Filing Date Title
US201261648058P 2012-05-16 2012-05-16
US201261647858P 2012-05-16 2012-05-16
US201261647925P 2012-05-16 2012-05-16
US201261648021P 2012-05-16 2012-05-16
US201261647886P 2012-05-16 2012-05-16
US201261647949P 2012-05-16 2012-05-16
US201261648016P 2012-05-16 2012-05-16
US201261647901P 2012-05-16 2012-05-16
US201261648041P 2012-05-16 2012-05-16
US201261648051P 2012-05-16 2012-05-16
US61/648,051 2012-05-16
US61/647,901 2012-05-16
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