UNITED STATES PATENT AND TRADEMARK OFFICE
`
`_________________
`
`BEFORE THE PATENT TRIAL AND APPEAL BOARD
`_________________
`
`
`BLUEBIRD BIO, INC.,
`Petitioner
`
`v.
`
`SLOAN KETTERING INSTITUTE FOR CANCER RESEARCH,
`Patent Owner
`
`_________________
`
`Patent No. 8,058,061
`_________________
`
`
`DECLARATION OF JÖRG BUNGERT, Ph.D.
`
`
`
`
`Page 1 of 133
`
`BLUEBIRD EXHIBIT 1002
`
`

`

`Declaration of Jörg Bungert, Ph.D.
`U.S. Patent No. 8,058,061
`
`
`Table of Contents
`
`Page
`Introduction—U.S. Patent No. 8,058,061 ....................................................... 1
`I.
`Qualifications ................................................................................................... 2
`II.
`Summary of Opinions ...................................................................................... 4
`III.
`IV. Person of Ordinary Skill in the Art .................................................................. 6
`V.
`Technological Overview .................................................................................. 7
`A.
`Inherited Hemoglobin Disorders and Gene Therapies .......................... 9
`B.
`A Predicate to Gene Therapy:
`Understanding the Regulation of Hemoglobin Genes ........................ 12
`Development of Vectors for Gene Therapy ........................................ 17
`C.
`VI. Overview of the ’061 Patent .......................................................................... 21
`VII. Claim Construction ........................................................................................ 25
`VIII. The Priority Date for the ’061 Patent ............................................................ 25
`IX. Overview of the Prior Art .............................................................................. 31
`A.
`Chad M. May, “Therapeutic Hemoglobin
`Synthesis in Beta-Thalassemic Mice Expressing
`Lentivirus-Encoded Human Beta-Globin,” Cornell
`University (2001) (“May Thesis”) (Ex. 1004)..................................... 31
`Chad May, et al., “Therapeutic
`Haemoglobin Synthesis in β-Thalassaemic
`Mice Expressing Lentivirus-Encoded Human β-Globin,”
`Nature, 406(6791) (2000) (“May Article”) (Ex. 1005) ....................... 32
`C. May et al., “Lentiviral-Mediated Transfer of the
`Human β-Globin Gene and Large Locus Control Region
`Elements Permit Sustained Production of Therapeutic Levels
`of β-Globin in Long-Term Bone Marrow Chimeras,” Mol.
`Therapy, 1(5) (2000), (“May Abstract”) (Ex. 1006) ........................... 35
`D. Himanen, et al., “A Recombinant
`Sickle HemoglobinTriple Mutant With
`Independent Inhibitory Effects on Polymerization,”
`J. Biol. Chem., 271(41):25152-56 (1996) (Ex. 1047) ......................... 36
`
`B.
`
`i
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`Page 2 of 133
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`

`

`2.
`3.
`
`X. Ground 1: The May Thesis Teaches
`All of the Limitations of Claims 1, 2, 6-7, and 11 of the ’061 Patent ........... 38
`A.
`Claim 1 ................................................................................................ 38
`1.
`[1.pre] “An isolated mammalian
`hematopoietic progenitor cell or an
`isolated mammalian stem cell comprising” .............................. 38
`[1.a] “a recombinant lentiviral vector which comprises,” ........ 39
`[1.b] “a nucleic acid encoding a functional
`globin operably linked to a 3.2-kb nucleotide
`fragment which consists essentially of three
`contiguous nucleotide fragments obtainable from
`a human β-globin locus control region (LCR),” ....................... 39
`[1.c] “the three fragments being a BstXI
`and SnaBI, HS2-spanning nucleotide fragment
`of said LCR, a BamHI and HindIII, HS3-spanning
`nucleotide fragment of said LCR, and a BamHI and
`BanII, HS4-spanning nucleotide fragment of said LCR,” ........ 41
`[1.d] “said vector providing
`expression of the globin in a mammal in vivo.” ....................... 42
`Claim 2: “The cell of claim 1, wherein the mammalian
`hematopoietic progenitor cell or the stem cell is a human cell.” ........ 43
`Claim 6: “The cell of claim 1,
`wherein said functional globin is a wild-type globin.” ....................... 43
`Claim 7: “The cells of claim 1,
`wherein said functional globin is a β-globin.” .................................... 44
`Claim 11 .............................................................................................. 44
`1.
`[11.pre] “A method for making
`a mammalian hematopoietic progenitor cell or a
`mammalian stem cell composition which comprises” .............. 44
`[11.a] “(a) preparing a recombinant
`lentiviral vector comprising a nucleic acid
`encoding a functional globin operably linked to a
`3.2-kb nucleotide fragment which consists essentially
`of three contiguous nucleotide fragments obtainable
`from a human β-globin locus control region (LCR),” .............. 45
`
`Declaration of Jörg Bungert, Ph.D.
`U.S. Patent No. 8,058,061
`
`
`ii
`
`4.
`
`5.
`
`2.
`
`B.
`
`C.
`
`D.
`
`E.
`
`Page 3 of 133
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`

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`Declaration of Jörg Bungert, Ph.D.
`U.S. Patent No. 8,058,061
`
`
`3.
`
`4.
`
`5.
`
`6.
`
`[11.b] “the three fragments being a BstXI
`and SnaBI, HS2-spanning nucleotide fragment
`of said LCR, a BamHI and HindIII, HS3-spanning
`nucleotide fragment of said LCR, and a BamHI and
`BanII, HS4-spanning nucleotide fragment of said LCR,” ........ 46
`[11.c] “said vector providing
`expression of the globin in a mammal in vivo; and” ................ 47
`[11.d] “(b) obtaining hematopoietic progenitor
`cells or stem cells from the mammalian individual,” ............... 47
`[11.e] “and transducing the
`cells with the recombinant vector.” .......................................... 48
`XI. Ground 2: The May Thesis in Combination With Himanen Teaches
`or Suggests All of the Limitations of Claim 5 of the ’061 Patent ................. 49
`A.
`Claim 5: “The cell of claim 1,
`wherein said functional globin is a mutant globin.” ........................... 49
`XII. Ground 3: The May Article Teaches All of the Limitations of Claims
`1, 2, 6-7, and 11 of the ’061 Patent................................................................ 51
`A.
`Claim 1 ................................................................................................ 51
`1.
`[1.pre] “An isolated mammalian
`hematopoietic progenitor cell or an
`isolated mammalian stem cell comprising” .............................. 51
`[1.a] “a recombinant lentiviral vector which comprises,” ........ 52
`[1.b] “a nucleic acid encoding a functional
`globin operably linked to a 3.2-kb nucleotide
`fragment which consists essentially of three
`contiguous nucleotide fragments obtainable from
`a human β-globin locus control region (LCR),” ....................... 53
`[1.c] “the three fragments being a BstXI
`and SnaBI, HS2-spanning nucleotide fragment
`of said LCR, a BamHI and HindIII, HS3-spanning
`nucleotide fragment of said LCR, and a BamHI and
`BanII, HS4-spanning nucleotide fragment of said LCR,” ........ 55
`[1.d] “said vector providing expression of the globin in a
`mammal in vivo.” ...................................................................... 63
`
`2.
`3.
`
`4.
`
`5.
`
`iii
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`Page 4 of 133
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`

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`Declaration of Jörg Bungert, Ph.D.
`U.S. Patent No. 8,058,061
`
`
`B.
`
`C.
`
`E.
`
`2.
`
`D.
`
`Claim 2: “The cell of claim 1, wherein the mammalian
`hematopoietic progenitor cell or the stem cell is a human cell.” ........ 64
`Claim 6: “The cell of claim 1,
`wherein said functional globin is a wild-type globin.” ....................... 65
`Claim 7: “The cells of claim 1,
`wherein said functional globin is a β-globin.” .................................... 66
`Claim 11 .............................................................................................. 66
`1.
`[11.pre] “A method for making
`a mammalian hematopoietic progenitor cell or a
`mammalian stem cell composition which comprises” .............. 66
`[11.a] “(a) preparing a recombinant
`lentiviral vector comprising a nucleic acid
`encoding a functional globin operably linked to a
`3.2-kb nucleotide fragment which consists essentially
`of three contiguous nucleotide fragments obtainable
`from a human β-globin locus control region (LCR),” .............. 67
`[11.b] “the three fragments being a BstXI
`and SnaBI, HS2-spanning nucleotide fragment
`of said LCR, a BamHI and HindIII, HS3-spanning
`nucleotide fragment of said LCR, and a BamHI and
`BanII, HS4-spanning nucleotide fragment of said LCR,” ........ 68
`[11.c] “said vector providing
`expression of the globin in a mammal in vivo; and” ................ 69
`[11.d] “(b) obtaining hematopoietic progenitor
`cells or stem cells from the mammalian individual,” ............... 69
`[11.e] “and transducing the
`cells with the recombinant vector.” .......................................... 70
`XIII. Ground 4: The May Article Teaches or Suggests All of
`the Limitations of Claims 1, 2, 6, 7, and 11 of the ’061 Patent ..................... 70
`XIV. Ground 5: The May Article in Combination with Himanen Teaches
`or Suggests All of the Limitations of Claim 5 of the ’061 Patent ................. 73
`A.
`Claim 5: “The cell of claim 1,
`wherein said functional globin is a mutant globin.” ........................... 74
`
`3.
`
`4.
`
`5.
`
`6.
`
`iv
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`Page 5 of 133
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`

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`2.
`3.
`
`XV. Ground 6: The May Abstract Teaches All of the Limitations of
`Claims 1, 2, 6-8, 11, and 15 of the ’061 Patent ............................................. 76
`A.
`Claim 1 ................................................................................................ 76
`1.
`[1.pre] “An isolated mammalian
`hematopoietic progenitor cell or an
`isolated mammalian stem cell comprising” .............................. 76
`[1.a] “a recombinant lentiviral vector which comprises,” ........ 77
`[1.b] “a nucleic acid encoding a functional
`globin operably linked to a 3.2-kb nucleotide
`fragment which consists essentially of three
`contiguous nucleotide fragments obtainable from
`a human β-globin locus control region (LCR),” ....................... 78
`[1.c] “the three fragments being a BstXI
`and SnaBI, HS2-spanning nucleotide fragment
`of said LCR, a BamHI and HindIII, HS3-spanning
`nucleotide fragment of said LCR, and a BamHI and
`BanII, HS4-spanning nucleotide fragment of said LCR,” ........ 79
`[1.d] “said vector providing expression of the globin in a
`mammal in vivo.” ...................................................................... 89
`Claim 2: “The cell of claim 1, wherein the mammalian
`hematopoietic progenitor cell or the stem cell is a human cell.” ........ 89
`Claim 6: “The cell of claim 1,
`wherein said functional globin is a wild-type globin.” ....................... 90
`Claim 7: “The cells of claim 1,
`wherein said functional globin is a β-globin.” .................................... 91
`Claim 8: “The cell of claim 7,
`wherein said β-globin is a human β-globin.” ...................................... 91
`Claim 11 .............................................................................................. 92
`1.
`[11.pre] “A method for making
`a mammalian hematopoietic progenitor cell or a
`mammalian stem cell composition which comprises” .............. 92
`[11.a] “(a) preparing a recombinant
`lentiviral vector comprising a nucleic acid
`encoding a functional globin operably linked to a
`
`Declaration of Jörg Bungert, Ph.D.
`U.S. Patent No. 8,058,061
`
`
`v
`
`4.
`
`5.
`
`2.
`
`B.
`
`C.
`
`D.
`
`E.
`
`F.
`
`Page 6 of 133
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`

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`Declaration of Jörg Bungert, Ph.D.
`U.S. Patent No. 8,058,061
`
`
`3.
`
`4.
`
`3.2-kb nucleotide fragment which consists essentially
`of three contiguous nucleotide fragments obtainable
`from a human β-globin locus control region (LCR),” .............. 93
`[11.b] “the three fragments being a BstXI
`and SnaBI, HS2-spanning nucleotide fragment
`of said LCR, a BamHI and HindIII, HS3-spanning
`nucleotide fragment of said LCR, and a BamHI and
`BanII, HS4-spanning nucleotide fragment of said LCR,” ........ 94
`[11.c] “said vector providing
`expression of the globin in a mammal in vivo; and” ................ 95
`[11.d] “(b) obtaining hematopoietic progenitor
`cells or stem cells from the mammalian individual,” ............... 95
`[11.e] “and transducing the
`cells with the recombinant vector.” .......................................... 96
`Claim 15: “The method of claim 11,
`wherein said functional globin is a human β-globin.” ........................ 96
`XVI. Ground 7: The May Abstract in Combination with Himanen Teaches
`or Suggests All of the Limitations of Claim 5 of the ’061 Patent ................. 97
`A.
`Claim 5: “The cell of claim 1,
`wherein said functional globin is a mutant globin.” ........................... 97
`XVII. Conclusion ...................................................................................................100
`
`
`
`G.
`
`5.
`
`6.
`
`vi
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`Page 7 of 133
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`Declaration of Jörg Bungert, Ph.D.
`U.S. Patent No. 8,058,061
`
`
`List of Materials Considered1
`
`Ex. 1001 U.S. Patent No. 8,058,061 to Sadelain et al. (“the ’061 patent”)
`
`Ex. 1004
`
`Ex. 1005
`
`Ex. 1006
`
`May, “Therapeutic Hemoglobin Synthesis in Beta-Thalassemic
`Mice Expressing Lentivirus-Encoded Human Beta-Globin,” Cornell
`University (2001) (“the May Thesis”)
`
`May, et al., “Therapeutic Haemoglobin Synthesis in β-Thalassaemic
`Mice Expressing Lentivirus-Encoded Human β-globin,” Nature,
`406:82-86 (2000) (“the May Article”)
`
`May, et al., “Lentiviral-Mediated Transfer of the Human β-Globin
`Gene and Large Locus Control Region Elements Permit Sustained
`Production of Therapeutic Levels of β-Globin in Long-Term Bone
`Marrow Chimeras,” Mol. Therapy, 1(5):S248-49 (2000) (“the May
`Abstract”)
`
`Ex. 1007
`
`Perutz, et al., “Hemoglobin Structure and Respiratory Transport,”
`Sci. Am., 239(6): 92-125 (1978)
`
`Ex. 1008
`
`Thein & Rochette, “Disorders of Hemoglobin Structure and
`Synthesis,” in Principles of Mol. Med. 179 (Jameson, ed., 1998)
`Ex. 1009 Bank, et. al, “Disorders of Human Hemoglobin,” Science,
`207:486-93 (1980)
`
`
`1 Non-patent publication citations are to the original page numbers of the
`
`publication, and citations to U.S. patents are to the column:line number of the
`
`patents. The only exception concerns to Exs. 1032 and 1037-39, as Petitioner
`
`utilizes an asterisk (*) to denote citation to the exhibit page.
`
`vii
`
`Page 8 of 133
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`

`

`Declaration of Jörg Bungert, Ph.D.
`U.S. Patent No. 8,058,061
`
`
`Ex. 1010
`
`He & Russell, “Expression, Purification, and Characterization of
`Human Hemoglobins Gower-I (ζ2ε2), Gower-2 (α2ε2), and
`Portland-2 (ζ2β2) Assembled in Complex Transgenic-Knockout
`Mice, Blood, 97(4):1099-1105 (2001)
`Ex. 1011 Bunn, “Pathogenesis and Treatment of Sickle Cell Disease,” N.
`Engl. J. Med., 337(11):762-69 (1997)
`
`Ex. 1012
`
`Hardison, et al., “Locus Control Regions of Mammalian β-globin
`Gene Clusters: Combining Phylogenetic Analyses and
`Experimental Results to Gain Function Insights, Gene, 205:73-94
`(1997)
`
`Ex. 1013
`
`Civin, et al., “Sustained, Retransplantable, Multilineage
`Engraftment of Highly Purified Adult Human Bone Marrow Stem
`Cells In Vivo,” Blood, 88(11):4102-09 (1996)
`Ex. 1014 High, “Gene Therapy in Haematology and Oncology,” Lancet,
`356:S8 (2000)
`
`Ex. 1015
`
`Ex. 1016
`
`Ellis, et al., “Evaluation of β-globin Gene Therapy Constructs in
`Single Copy Transgenic Mice,” Nucleic Acids Res.,
`25(6):1296-1302 (1997)
`
`Li, et al., “Nucleotide Sequence of 16-Kilobase Pairs of DNA 5’ to
`the Human ε-Globin Gene,” J. Biol. Chem., 260(28):14901-10
`(1985)
`
`Ex. 1017
`
`Mishima, et al., “The DNA Deletion in an Indian δβ-thalassaemia
`Begins One Kilobase From the Aγ Globin Gene and Ends in an L1
`Repetitive Sequence,” Br. J. Haemotol., 73:375-79 (1989)
`Ex. 1018 Vosberg, “Molecular Cloning of DNA: An Introduction Into
`Techniques and Problems,” Hum. Genet. 40(1):1-72 (1977)
`Ex. 1019 Roberts, “Restriction Enzymes and Their Isoschizomers,” Nucleic
`Acids Res., 15(Suppl.):r189-r217 (1987)
`
`Ex. 1020
`
`Zufferey, et al., “Multiply Attenuated Lentiviral Vector Achieves
`Efficient Gene Delivery in Vivo,” Nature Biotech., 15:871-75
`(1997)
`
`viii
`
`Page 9 of 133
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`

`

`Declaration of Jörg Bungert, Ph.D.
`U.S. Patent No. 8,058,061
`
`
`Ex. 1021
`
`Ex. 1022
`
`Ex. 1023
`
`Miyoshi, et al., “Transduction of Human CD34+ Cells that Mediate
`Long-Term Engraftment of NOD/SCID Mice by HIV Vectors,”
`Science, 283:682-86 (1999)
`
`Sadelain, et. al., “Generation of a High-titer Retroviral Vector
`Capable of Expressing High Levels of the Human β-Globin Gene,”
`Proc. Natl. Acad. Sci. USA, 92:6728-32 (1995)
`
`Bouhassira, et al., “Transcriptional Behavior of LCR Enhancer
`Elements Integrated at the Same Chromosomal Locus by
`Recombinase-Mediated Cassette Exchange,” Blood 90(9):3332-44
`(1997)
`
`Ex. 1024
`
`Fraser, et al., “Each Hypersensitive Site of the Human β-Globin
`Locus Control Regions Confers a Different Developmental Pattern
`of Expression on the Globin Genes,” Genes Dev., 7:106-113 (1993)
`
`Ex. 1025
`
`Engel, “Developmental Regulation of Human β-Globin Gene
`Transcription: A Switch of Loyalties?,” Trend. Genet., 9(9):304-09
`(1993)
`Ex. 1026 Roberts & Macelis, “REBASE – Restriction Enzymes and
`Methylases,” Nucleic Acids Res., 26(1):338-350 (1998)
`Ex. 1027 Roberts & Macelis, “REBASE – Restriction Enzymes and
`Methylases,” Nucleic Acids Res., 27(1):312-13 (1999)
`Ex. 1028 Roberts & Macelis, “REBASE – Restriction Enzymes and
`Methylases,” Nucleic Acids Res., 28(1):306-07 (2000)
`Ex. 1029 Roberts & Macelis, “REBASE – Restriction Enzymes and
`Methylases,” Nucleic Acids Res., 29(1):268-69 (2001)
`
`Ex. 1030
`
`Sequence Manipulation Suite (last visited October 11, 2022)
`(Website)
`Ex. 1031 Restriction Mapper, April 20, 2001 Wayback Machine Capture (last
`visited October 11, 2022) (Website)
`
`Ex. 1032
`
`Prosecution History of U.S. Patent No. 7,541,179
`(U.S. Patent Application No. 10/188,221)
`
`ix
`
`Page 10 of 133
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`

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`Declaration of Jörg Bungert, Ph.D.
`U.S. Patent No. 8,058,061
`
`
`Ex. 1033
`
`Prosecution History of the ’061 Patent
`(U.S. Patent Application No. 12/433,412)
`
`Ex. 1034 U.S. Provisional Application 60/301,861 to Sadelain
`
`Ex. 1035 U.S. Provisional Application 60/302,852 to Sadelain
`
`Ex. 1037
`
`SciMago, Nature (last visited October 11, 2022) (Website)
`
`Ex. 1038
`
`Ex. 1039
`
`SciMago, Molecular Therapy (last visited October 11, 2022
`(Website)
`
`SciMago, Journal of Biological Chemistry (last visited October 11,
`2022) (Website)
`
`Ex. 1040
`Steele, “Editorial,” Mol. Therapy, 1(5):S1 (2000)
`Ex. 1041 Glorioso, “Highlights from the Third Annual ASGT Meeting,” Mol.
`Therapy, 2(2):96-100 (2000)
`
`Ex. 1042
`
`“Author Index,” Mol. Therapy, 1(5):S345-61 (2000)
`
`Himanen, et al., “A Recombinant Sickle Hemoglobin Triple Mutant
`With Independent Inhibitory Effects on Polymerization,” J. Biol.
`Chem., 271(41):25152-56 (1996) (“Himanen”)
`
`
`Ex. 1047
`
`
`
`
`x
`
`Page 11 of 133
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`

`

`I, Jörg Bungert, Ph.D., declare as follows:
`
`Declaration of Jörg Bungert, Ph.D.
`U.S. Patent No. 8,058,061
`
`
`I.
`
`Introduction—U.S. Patent No. 8,058,061
`1.
`I have been retained by bluebird bio, Inc. (“Petitioner”) to be an
`
`independent expert consultant in this proceeding before the United States Patent
`
`and Trademark Office regarding U.S. Patent No. 8,058,061 (“the ’061 patent”)
`
`(Ex. 1001), which I understand is assigned to Sloan Kettering Institute for Cancer
`
`Research (“Patent Owner”). I have been asked to consider whether: (1) whether
`
`applications to which the ’061 patent claims priority, provisional application No.
`
`60/301,861 (filed on June 29, 2001) and 60/302,852 (filed on July 2, 2001),
`
`provide adequate support for the subject matter of claims 1, 2, 5-7, and 11; (2) the
`
`May Thesis teaches all limitations of claims 1, 2, 6-7, and 11 of the ’061 patent;
`
`(3) the May Thesis in combination with Himanen teaches or suggests all the
`
`limitations of claim 5 of the ’061 patent; (4) the May Article teaches all limitations
`
`of claims 1, 2, 6-7, and 11 of the ’061 patent; (5) the May Article teaches or
`
`suggests all limitations of claims 1, 2, 6-7, and 11 of the ’061 patent; (6) the May
`
`Article in combination with Himanen teaches or suggests all the limitations of
`
`claim 5 of the ’061 patent; (7) the May Abstract teaches or suggests all limitations
`
`of claims 1, 2, 6-8, 11, and 15 of the ’061 patent; and (8) the May Abstract in
`
`combination with Himanen teaches or suggests claim 5 of the ’061 patent.
`
`1
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`Page 12 of 133
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`

`I am being compensated at my normal consulting rate of $300 per
`
`Declaration of Jörg Bungert, Ph.D.
`U.S. Patent No. 8,058,061
`
`
`2.
`
`hour. My compensation does not depend in any way on the nature of my findings,
`
`the presentation of my findings in testimony, or the outcome of this or any other
`
`proceeding. I have no other interest in this proceeding.
`
`II. Qualifications
`3. My qualifications are summarized below, and they are also set forth in
`
`more detail in my curriculum vitae, attached as Ex. 1003.
`
`4.
`
`I am a Professor in the Department of Biochemistry and Molecular
`
`Biology at the University of Florida in Gainesville, Florida. I have approximately
`
`30 years of research experience concerning globin gene regulation.
`
`5.
`
`I received a Bachelor of Science in Biology from the Christian
`
`Albrecht University of Kiel (located in Kiel, Germany) in 1986. I also obtained a
`
`Master of Science in Biology and Molecular Genetics from the Philipps University
`
`of Marburg (located in Marburg, Germany) in 1991. I then stayed on at the same
`
`institution to pursue a Ph.D. in Molecular Genetics, which I received in 1993.
`
`6.
`
`After completing my education, I worked as a Post-Doctoral Fellow in
`
`the Laboratory of Dr. James Douglas Engel at Northwestern University until 1996.
`
`I then served as a research assistant professor in the Department of Biochemistry,
`
`Molecular, and Cell Biology at Northwestern University from 1996-1998. In
`
`2
`
`Page 13 of 133
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`

`

`1998, I moved to the Department of Biochemistry and Molecular Biology at the
`
`Declaration of Jörg Bungert, Ph.D.
`U.S. Patent No. 8,058,061
`
`
`University of Florida, where I still serve as a professor.
`
`7.
`
`I have published more than 70 articles in peer-reviewed journals in
`
`my career, including several papers on analyzing how the β-globin locus control
`
`region (“LCR”) affects the transcriptional regulation and expression of the globin
`
`genes. Those articles appeared in many preeminent journals for my field,
`
`including Molecular Therapy, Nature, and the Journal of Biological Chemistry.
`
`8.
`
`Throughout my career, I have engaged with both academic and
`
`industrial researchers concerning, among other things, how the β-globin LCR
`
`operates and regulates gene expression. I have served as either chair or co-chair
`
`for the American Heart Association Study Section, have been a member of the
`
`American Society for Gene and Cell Therapy, and am presently a member of the
`
`American Society for Hematology. I have also been a reviewer for numerous
`
`journals and institutions, and an editorial board member for several refereed
`
`academic journals. Currently, I serve as the Director of the University of Florida
`
`Master of Science Program in Biochemistry and Molecular Biology.
`
`9.
`
`Over the course of my career, I have been privileged to receive
`
`several honors and awards for my research, including being selected as a member
`
`for multiple NIH study sections. I have also been recognized by the University of
`
`Florida, receiving the Exemplary Teacher Award for 17 consecutive years.
`
`3
`
`Page 14 of 133
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`

`

`Moreover, on March 1, 2020, I was given a grant for my research regarding the
`
`Declaration of Jörg Bungert, Ph.D.
`U.S. Patent No. 8,058,061
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`structure and function of the human β-globin LCR by the American Society of
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`Hematology.
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`III. Summary of Opinions
`10. The opinions expressed in this declaration are based on the documents
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`I reviewed, my professional judgment, as well as my education, experience, and
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`knowledge, including how the β-globin LCR operates and regulates gene
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`expression.
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`11.
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`In forming my opinions expressed in this declaration, I reviewed the
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`following documents and materials: (1) the ’061 patent (Ex. 1001); (2) the May
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`Thesis (Ex. 1004); (3) the May Article (Ex. 1005); (4) the May Abstract (Ex. 1006);
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`(5) Himanen (Ex. 1047); (6) the materials in the List of Materials Considered; and
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`(7) any other materials I refer to in this Declaration in support of my opinions.
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`12. My opinions are guided by how a person of ordinary skill in the art
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`(which I define in the next section) would have understood the claims and the
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`specification of the ’061 patent at the time of the alleged invention. I have been
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`asked by counsel to consider the art as of July 1, 2002, for Grounds 1 through 4,
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`Declaration of Jörg Bungert, Ph.D.
`U.S. Patent No. 8,058,061
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`and June 29, 2001, for Ground 5.2 My opinions expressed below would not change
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`if the relevant time was determined to be somewhat different (e.g., either
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`somewhat earlier or later).
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`13.
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`In my opinion: (1) the May Thesis teaches all limitations of claims 1,
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`2, 6-7, and 11 of the ’061 patent; (2) the May Thesis in combination with Himanen
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`teaches or suggests all the limitations of claim 5 of the ’061 patent; (3) the May
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`Article teaches all limitations of claims 1, 2, 6-7, and 11 of the ’061 patent; (4) the
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`May Article teaches or suggests all the limitations of claim 1, 2, 6-7, and 11 of the
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`’061 patent; (5) the May Article in combination with Himanen teaches or suggests
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`all the limitations of claim 5 of the ’061 patent; (6) the May Abstract teaches or
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`suggests all limitations of claims 1, 2, 6-8, 11, and 15 of the ’061 patent; and
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`(7) the May Abstract in combination with Himanen teaches or suggests all the
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`limitations of claim 5 of the ’061 patent
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`2 Throughout this declaration, I also rely on other documents, including for
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`background information and to show what was generally known in the field as of
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`the relevant dates. I am not citing any such document to show it teaches one or
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`more features recited in the claims of the ’061 patent (even though it may teach
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`one or more such features). Instead, I rely on the May Thesis, the May Article, the
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`May Abstract, and Himanen for the claimed features.
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`IV. Person of Ordinary Skill in the Art
`14. Based on my review of the ’061 patent, the types of problems
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`Declaration of Jörg Bungert, Ph.D.
`U.S. Patent No. 8,058,061
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`encountered in the art, prior-art solutions to those problems, the rapidity with
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`which innovations were made, the sophistication of the technology, and the
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`educational level of active workers in the field, I believe a person of ordinary skill
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`in the art at the time of the alleged invention would have had at least an advanced
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`degree (e.g., a Master’s or Ph.D.) in biochemistry, biotechnology, protein
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`chemistry, genetics, molecular and structural biology, bioengineering, or similar
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`disciplines. A person of ordinary skill in the art would have also had several years
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`of post-graduate training or related experience in one or more of these areas.
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`Based on these years of post-graduate training or related experience, a person of
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`ordinary skill in the art would have had an understanding of vector design and the
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`effect of LCR fragments on gene expression, including how the LCR regulates
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`gene expression.
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`15. All of my opinions in this declaration are from the perspective of a
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`person of ordinary skill in the art, as I have defined it here, during the relevant
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`timeframe (i.e., late 1990s-early 2000s). During this timeframe, I possessed at
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`least the qualifications of a person of ordinary skill in the art, as defined above, and
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`trained individuals who would qualify as persons of ordinary skill in the art. My
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`Declaration of Jörg Bungert, Ph.D.
`U.S. Patent No. 8,058,061
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`opinions expressed below would not change if the level of skill were determined to
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`be somewhat different (e.g., either somewhat higher or lower).
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`V. Technological Overview
`16.
`In this section, I present a brief overview of several key technologies
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`that were widely known before June 29, 2001, and relate to the issues discussed in
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`the next section. This section is not intended to be technically comprehensive, but
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`rather provides a foundation for better understanding the ’061 patent, the prior art,
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`and certain terminology.
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`17. As a general matter, red blood cells are responsible for the critical
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`(and life-preserving) task of carrying oxygen to the body’s organs and tissues. (Ex.
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`1007 at 92.) And they will also transport carbon dioxide from the body’s organs
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`and tissues back to the lungs. (Id.) In particular, there is a protein in red blood
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`cells—hemoglobin—that is critical to this function. (Id.) Hemoglobin has a
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`tetrameric structure—meaning, it contains four subunits (also known as “globin
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`chains”). (Ex. 1008 at 179.) Each of these globin chains have a heme group with
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`an iron ion capable of binding oxygen. (Ex. 1007 at 92.) The various globin
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`chains are identified by Greek letters (e.g., α, β, γ, δ, ε, ζ) in order to differentiate
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`them. (Ex. 1008 at 179; Ex. 1009 at 486; Ex. 1012 at 73.)
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`18. There are a variety of hemoglobin types that exist. In fact, humans
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`express different hemoglobin types, such as embryonic, fetal, and adult
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`hemoglobin, at various stages of their development, with two notable switches
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`Declaration of Jörg Bungert, Ph.D.
`U.S. Patent No. 8,058,061
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`occurring: (1) from embryonic to fetal, and (2) from fetal to adult. (Ex. 1008 at
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`179; Ex. 1009 at 486; Ex. 1012 at 73.) The most common type of hemoglobin
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`found in adults is Hemoglobin A (“HbA”), which consists of two α- and two
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`β-globin chains. (Ex. 1008 at 179-80, Fig 20-1; Ex. 1009 at 486.) An illustration
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`of a red blood cell (on the right) made up of HbA hemoglobin is shown below.
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`
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`(Ex. 1011 at 762-63, Fig. 1 (adapted).)
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`19. Embryonic hemoglobin is normally found in the first several weeks of
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`gestation, and it contains two ζ-globin chains and two ε-globin chains (Hb
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`Gower-1), two α-globin chains and two ε-globin chains (Hb Gower-2), two
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`ζ-globin chains and two γ-globin chains (Hb Portland-1), or two ζ-globin chains
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`and two β-globin chains (Hb Portland-2). (Ex. 1008 at 180, Fig. 20-1; Ex. 1009 at
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`486; Ex. 1010 at 1099.) Of these, Hb Gower-1 is the primary embryonic
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`hemoglobin, while the other three are found at relatively low levels. (Ex. 1010 at
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`1099.)
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`20. Fetal hemoglobin, or Hemoglobin F (“HbF”), is normally found in
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`Declaration of Jörg Bungert, Ph.D.
`U.S. Patent No. 8,058,061
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`fetuses and newborn babies. (Ex. 1008 at 180, Fig. 20-1; Ex. 1009 at 486.) HbF
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`has the same α-globin chains as adult hemoglobin, but two γ chains instead of the
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`typical β chains. (Ex. 1008 at 180, Fig. 20-1; Ex. 1009 at 486; Ex. 1012 at 74.)
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`A.
`Inherited Hemoglobin Disorders and Gene Therapies
`21. Hemoglobin disorders, or hemoglobinopathies, are genetically
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`inherited disorders in which there is either (1) abnormal production of hemoglobin,
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`or (2) structural variation in hemoglobin. (Ex. 1008 at 179; Ex. 1009 at 487.)
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`These types of hemoglobinopathies are known as thalassemia and sickle cell
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`anemia, respectively. (Ex. 1008 at 179; Ex. 1009 at 487.) A specific example of
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`the first type is β-thalassemia. Βeta-thalassemias are hemoglobinopathies that
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`negatively impact the amount of β-globin chain produced, ultimately resulting in
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`chronic low hemoglobin production (resulting in excess α-globin, which
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`precipitates in the differentiating red blood cells and prevents maturation and
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`release of these cells into the blood stream). (Ex. 1008 at 179, 182; Ex. 1009 at
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`487.) Because patients with β-thalassemia have less hemoglobin, they also have
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`less healthy red blood cells—which in turn means less oxygen is reaching the rest
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`of the tissues in their bodies. (Ex. 1008 at 179, 182; Ex. 1009 at 487.) Low (or
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`mutant) hemoglobin or low number of red blood cells results in a condition known
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`as anemia, but β-thalassemias can also cause stunted growth, and, if untreated,
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`Declaration of Jörg Bungert, Ph.D.
`U.S. Patent No. 8,058,061
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`even death. (Ex. 1008 at 179-81; Ex. 1009 at 487.)
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`22. Hemoglobinopathies that result in a structural change of a globin
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`chain, such as sickle cell anemia, can result in chronic anemia leading to recurrent
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`episodes of severe chronic pain and tissue damage. (Ex. 1008 at 186.) Over long
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`periods of time, this can res