DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Election/Restrictions
Applicant’s election without traverse of species 1 and 2 in the reply filed on 09/02/2025 is acknowledged. Because Applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Applicants election of the following species in the response filed 09/02/2025 is as follows:
1) An edited Hb-beta polypeptide (claim 1); Applicant elects species (ii) as recited in claim 1.
2) A guide RNA sequence (claim 9); Applicant elects species (i) as recited in claim 9.
Claims 1-4, 7-9, 12-15, and 18 are pending.
Claims 5-6, 10-11, 16-17 and 19 were previously cancelled.
Claim 1 is amended in the claims filed 09/02/2025.
Claims 1-4, 7-9, 12-15 and 18 read on the elected invention and are examined herein.
Status of Application/Amendment/Claims
Applicant's response filed September 02, 2025 has been considered. Rejections and/or objections not reiterated from the previous office action mailed October 7, 2024 are hereby withdrawn.
The following rejections and/or objections are either newly applied or are reiterated and are the only rejections and/or objections presently applied to the instant application. The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 1-4, 7-9, 12-15 and 18 are rejected under 35 U.S.C. 103 as being unpatentable over Liang et al. (Protein & Cell (2017) 8:11;811-822, as cited in the IDS filed 7/13/2021), Hoban et al (Blood (2015)125:17;1-8, as cited in the IDS filed 7/13/2021), Guadelli et al (Nature (2017)551:23(464-487, as cited in the IDS filed 7/13/2021), Viprakasit et al (Hemoglobin (2002)26;1-10), Urnov et al (US 7888121B1 2011) and Leenay et al (J Mol Biol (2017)429:2;1-25).
This is a new rejection as necessitated by the claim amendments filed 09/02/2025.
Regarding claims 1-3 and 18: Claim 1 (ii) recites the first non-wild-type codon corresponds to codon 7 in Seq ID NO:1. Figure 2 of the instant specification identifies codon 7 as the first “GAG” in the “GAGGAG” repeat.
Liang teach β-Thalassemia is caused by mutation in the HBB gene (abstract). Liang further teach a method for editing the HBB gene comprising contacting a nucleic acid molecule comprising a mutant hemoglobin B gene with the base editor BE3 to replace the mutant base (G-28) with the wildtype base (A-28). (p812 col2 ¶2 and title). Liang also teach incubating the nucleic acid molecule comprising the mutant HBB gene, the base editor, and the gRNA under conditions such that the gRNA targets the base editor to the nucleotide sequence of the first non-wild-type codon of the mutant HBB gene to a second codon within a human cell (p814 col2 ¶2).
Liang do not teach the mutant HBB gene encodes a mutant hemoglobin-β polypeptide. Liang do not teach the first non-wild-type codon corresponds to codon 7 in Seq ID NO:1, wherein the wild-type codon at this position is GAG, the first non-wild-type codon is GTG and the second non-wildtype codon is GCG. Liang do not teach the base editor is an adenine base editor.
Hoban teach sickle cell disease is characterized by a single point mutation in the seventh codon of the β-globin gene (which corresponds to the sixth codon of the instant claim), and that site-specific correction of the sickle mutation in hematopoietic stem cells would allow for permanent production of normal red blood cells (abstract). Hoban teach the edited cells are donated from donors with sickle cell disease (p2 col1 ¶3).
Hoban teach a first non-wild-type codon that corresponds to codon 7 in Seq ID No:1 is the mutated seventh codon “GTG” which is a sickle mutation (Figure 1a,c). Hoban further teach replacing the mutated seventh codon “GTG” with a corrected nucleotide sequence (Figure 1a,c).
Hoban do not teach a second non-wild-type codon is “GCG”. Hoban do not teach the base editor is an adenine base editor.
Guadelli teach adenine base editors (ABE) that convert AT to GC base pairs in genomic DNA in human cells (p464 col2 ¶1). Guadelli disclose sgRNA that directs the ABE to the γ-globin gene promoter to edit a specific base at a specific position (-198T to -198C) (p470 col1 ¶2).
Viprakasit teach that a person homozygous for “GCG” at codon six of HBB (which corresponds to codon 7 of the instant claim) is hematologically normal (abstract).
It is noted that codon numbering of Viprakasit varies by 1 number compared to numbering in the instant specification, but that codon 7 of Viprakasit encodes the first “GAG” of the “GAGGAG” of the HBB sequence and thus reads on a codon that corresponds to codon 7 in Seq ID NO:1.
It would have been obvious to one of ordinary skill in the art to adapt the methods of Liang drawn to a method of modifying a mutant HBB gene comprising contacting a first-non-wild-type codon with a base editor by contacting a mutant HBB gene wherein the first non-wild-type codon is “GTG”, as taught by Hoban, wherein the base editor is an adenine base editor, as taught by Guadelli, and wherein the second non-wild-type codon is ”GCG” as taught by Viprakasit.
One of ordinary skill in the art would have been motivated to modify the method taught by Liang with the teachings of Hoban, Guadelli and Viprakasit because Viprakasit teach the non-wild-type codon “GCG” does not produce a disease phenotype and thus modification of the HBB gene represents a potential cure of the disease causing mutation of the “GTG” codon 6 mutation taught by Hoban.
Furthermore, one would be motivated to use an adenine base editor to change the “GTG” codon to the “GCG” as taught by the combination of Hoban and Viprakasit because Guadelli teach adenine base editors mediate the conversion of “A·T” to “G·C” in genomic DNA with far fewer undesired products compared with standard genome editing methods, and the GTG to GCG change taught by the combination of Hoban and Viprakasit would be mediated by an adenine base editor.
One would have had a reasonable expectation of success because Liang teach base editing can specifically alter a single base in the HBB gene to correct a disease causing mutation and one of ordinary skill in the art would understand that an adenine base editor which efficiently converts “A·T” to “G·C” in a wide range of target genomic loci in in human cells efficiently and with a very high degree of product purity would have a reasonable expectation of success (p464 col2 ¶2).
Regarding claim 4: The claim refers to Seq ID NO:2. The instant specification teaches Seq ID NO:2 is the wild-type HBB amino acid sequence (p9 ln25-30).
The teachings of Liang are discussed supra. Liang also teach a mutant HBB allele with mutations occurring in promoter region. Therefore the amino acid sequence of the HBB allele would be 100% identical to the amino acid sequence of the wild-type human HBB polypeptide (SEQ ID NO: 2).
Liang do not teach the mutant HBB encodes an amino acid sequence with 90-99.5% sequence identity to SEQ ID NO: 2.
Hoban teach a first non-wild-type codon that corresponds to codon 7 in Seq ID No:1, the mutated seventh codon “GTG” which is a sickle mutation (Figure 1a,c). A nucleotide sequence encoding an amino acid sequence that is identical to wild type HBB (Seq ID No: 2), except for a single amino acid change (such as the mutated seventh codon taught by Hoban), would encode an amino acid sequence within the range of 90-99.5% sequence identity to Seq ID NO:2.
The mutation taught by Hoban is a point mutation, and thus it would be obvious to select a mutant HBB allele that encodes a highly similar amino acid sequences compared to the wild-type sequence of SEQ ID NO: 2 such as that taught by Hoban. Specifically, Hoban teach and HBB amino acid sequence with 99.32% sequence identity with Seq ID NO:2.
MPEP 2131.03 reads “when, as by a recitation of ranges or otherwise, a claim covers several compositions, the claim is ‘anticipated’ if one of them is in the prior art”.
It would have been obvious to one of ordinary skill in the art to adapt the methods of Liang drawn to producing an edited HBB gene by using an HBB gene which encodes an amino acid sequence having 90-99.5% sequence identity with wild type HBB (Seq ID NO: 2).
Hoban discloses a point mutation which is causative for sickle cell disease and the encoded amino acid shares 99.32% identity with Seq ID NO:2.
Accordingly, one of ordinary skill in the art would have been motivated to modify the teaching of Liang, which targets an HBB gene encoding a nucleic acid sequence with 100% identity with Seq ID NO:2 by targeting an HBB gene which encodes an amino acid sequence with 90-99.5% sequence identity to seq ID NO: 2 to for the purposes of correcting disease causative mutations which occur in the coding sequence of the HBB gene, such as that taught by Hoban which is causative for sickle cell disease.
One would have had a reasonable expectation of success because Liang discloses successful gene editing of the HBB gene and one of ordinary skill in the art would understand that additional nucleotide positions in the HBB gene could also be targeted with the disclosed nucleotide editing system.
Regarding claim 7: The teachings of Liang are discussed supra. Liang also teach the base editor BE2 comprises dCas9, which one of ordinary skill in the art would understand represents an impaired Cas9 mutant (p811 col2 ¶2).
Regarding claim 8: The teachings of Liang are discussed supra. Liang do not teach the base editor is an adenine deaminating editor.
Gaudelli teach a base editor is an adenosine deaminase (p471 col1 ¶2).
It would have been obvious to one of ordinary skill in the art to adapt the methods of Liang drawn to a process for producing a modified nucleic acid molecule by using an adenine deaminating editor as taught by Guadelli. Guadelli discloses a base editor that is an adenosine deaminase and successfully edits genomic DNA at a specific nucleic acid residue from T to C (p470 col1 ¶2).
Accordingly, one of ordinary skill in the art would have been motivated to modify the method as taught by Liang to for the purposes of modifying a specific genomic residue to change a A•T to G•C.
One would have had a reasonable expectation of success because Guadelli discloses the adenosine deaminase base editor successfully edits genomic DNA to change a A•T to G•C.
Regarding claim 9: The teachings of Liang are discussed supra. Liang also teach gRNA for targeting HBB-28 (A>G) (abstract).
Liang do not teach the gRNA for editing the nucleotide sequence of HBB at the codon which corresponds to codon 7 in Seq ID NO: 1 is an 18-22 nucleotide guide RNA which is complementary to a nucleotide sequence located in Seq ID NO:15 wherein the codon which corresponds to the wild-type complement of codon 7 in Seq ID NO:1 is replaced by CAC.
Urnov teach methods and compositions for targeted alteration of a genomic sequence (abstract). Urnov teach a target site for the human β-globin gene (HBB) with a CAC sequence that corresponds to the wild-type complement of codon 7 in Seq ID No:1, which is sequence 181 of Urnov. Sequence 181 of Urnov has 100% identity to seq ID NO:15 of the instant application (p87).
It would have been obvious to one of ordinary skill in the art to adapt the methods of Liang drawn to a method to edit the HBB gene using a base editor by using a gRNA to the target site as disclosed by Urnov. Urnov teach the A-T substitution causes sickle cell disease.
Accordingly, one of ordinary skill in the art would have been motivated to modify the method as taught by Liang by using a gRNA to target the sequence disclosed by Urnov to for the purposes of editing the sickle cell causing mutation in the HBB gene.
One would have had a reasonable expectation of success because Liang discloses single nucleotide changes in HBB genomic sequences and Urnov teach a target that is the well-known cause of sickle cells disease.
Regarding claim 12, 14-15: The teachings of Liang are discussed supra. Liang also teach obtaining a sample of cells from a subject wherein the cells comprise nucleic acid molecules comprising mutant HBB genes; Liang teach isolating and culturing skin fibroblast cells from a homozygous mutant patient (p814 col1 ¶2). Liang also disclose high repairing efficiency in human hematopoietic stem cells, such as with the disclosed precision base editors, will lead to new therapeutics for β-thalassemia patients (p818 col1 ¶3).
Liang do not teach introducing a population of haematopoietic stem cells comprising modified nucleic acids comprising edited HBB genes into the same or related subjects.
Wen teach obtaining a sample of haematopoietic stem cells (HSPCs) from the peripheral blood of a patient (human subject) with sickle cell disease (p7 col2 ¶1). One of ordinary skill in the art would understand that cells from a patient with sickle cell disease comprise a mutant HBB gene.
Wen teach using CRISPR/Cas9 targeted with sgRNA specifically targeting the V6G mutation which causes sickle cell disease (and corresponds to the GTG non-wild type codon 7 of Seq ID NO: 1) and successfully editing the HSPCs (p5 col1 ¶2). Wen teach autologous transplantation of the genome edited HSPCs represent a cure for sickle cell disease (p7 col1 ¶1). Autologous transplantation reads on performing the process on haematopoietic cells which have been obtained from a first subject and introducing a population of haematopoietic stem cells comprising edited HBB genes into the same subject.
Regarding claim 13: The teachings of Liang are discussed supra. Liang do not teach modifying the nucleotide sequence of one or more PAM site in the vicinity of the first non-wild-type codon.
Leenay teach Cas effector proteins rely on protospacer-adjacent motifs (PAM sequences) as the first stem in target recognition, and PAM sequences are known to vary between systems (abstract). Figure 3 teaches PAM orientation is different for different types of CRISPR-Cas systems (p20). Table 1 teaches consensus PAM sequences for some CRISPR-Cas systems (p25).
It would have been obvious to one of ordinary skill in the art to adapt the methods of Liang drawn to a method of editing an HBB gene by modifying the PAM sequence to be optimally efficient with the chosen CRISPR-Cas system because Leenay discloses PAM sequences and orientation differ depending on the chosen CRISPR-Cas system.
Accordingly, one of ordinary skill in the art would have been motivated to modify the method as taught by Liang to optimize the PAM sequence with the teachings of Leenay for the purposes of developing an effective CRISPR-Cas system with the Cas targeting protein required by the base editing system.
One would have had a reasonable expectation of success because Leenay discloses PAM consensus sequences that represent the most active PAM sequences and one of ordinary skill in the art would understand that the protein editor must be guided by the appropriate PAM sequence to comprise a functional DNA targeting system.
Response to Arguments
Response to Remarks filed 09/02/2025:
The remarks pertaining to the requirement for restriction are addressed above.
Response to Remarks filed 2/07/2025
Regarding the Request for Reconsideration:
Applicant argues the after final amendments do not require a new search. Applicant has filed an RCE and thus the argument is moot because the RCE has been filed and the claim amendments entered.
1) Regarding the Rejection under 35 U.S.C. §112(b):
Claims 1-15 were rejected as indefinite because there was no mention of the specific genomic sequence of which HBB is encoded.
The claim has been amended to include Seq ID NO: 1 as a reference sequence. This overcomes the rejection of claims 1-15 35 under U.S.C. §112(b) and the rejection is withdrawn.
2) Regarding to Applicants Traversal of the Rejection under 35 U.S.C. §103:
Applicant's arguments filed 02/07/2025 as they pertain to the current action have been fully considered.
Applicant argues that claim 1 has been amended to include the subject matter of former claim 1, and that if a skilled person were to attempt to combine the references, such combination would not result in each and every feature of claim 1 (p10 ¶3).
Applicant’s arguments, see above, filed 02/07/2025, with respect to the rejection of claim 1 under 35 U.S.C. §103 in the office action filed 10/07/2024 have been fully considered and are persuasive. Therefore, the rejection has been withdrawn.
However, upon further consideration, a new ground(s) of rejection is made in view of Liang et al. (Protein & Cell (2017) 8:11;811-822, as cited in the IDS filed 7/13/2021), Hoban et al (Blood (2015)125:17;1-8, as cited in the IDS filed 7/13/2021), Guadelli et al (Nature (2017)551:23(464-487, as cited in the IDS filed 7/13/2021), Viprakasit et al (Hemoglobin (2002)26;1-10), Urnov et al (US 7888121B1 2011) and Leenay et al (J Mol Biol (2017)429:2;1-25).
Regarding Arguments directed to Lacan:
Lacan is not relied upon in the instant action and thus Arguments direct to Lacan are considered moot.
Regarding Arguments directed to the combination of Liang and Gaudelli:
Applicant argues there was no motivation to combine Guadelli and Liang; “The skilled person, following Gaudelli, would not have edited a mutant gene or converted one mutation into another; there was simply no motivation to do this” (p17 ¶3).
Applicant acknowledges the treatments of Liang and Guadelli are successful; Applicant states “Both of these approaches were individually successful” (p14 ¶8). This statement implicitly acknowledges each method has a reasonable expectation of success
MPEP 2144.06 states: "It is prima facie obvious to combine two compositions each of which is taught by the prior art to be useful for the same purpose, in order to form a third composition to be used for the very same purpose.... [T]he idea of combining them flows logically from their having been individually taught in the prior art."
Thus the combination of Liang and Guadelli is by definition prima facie obvious and the argument is found unpersuasive.
Applicant argues the combination of Liang and Guadelli do not teach every feature of the instant claim 1 (p17 ¶3). The instant action relies upon the references Liang et al. (Protein & Cell (2017) 8:11;811-822, as cited in the IDS filed 7/13/2021), Hoban et al (Blood (2015)125:17;1-8, as cited in the IDS filed 7/13/2021), Guadelli et al (Nature (2017)551:23(464-487, as cited in the IDS filed 7/13/2021), Viprakasit et al (Hemoglobin (2002)26;1-10), Urnov et al (US 7888121B1 2011) and Leenay et al (J Mol Biol (2017)429:2;1-25). See the new rejection under 35 U.S.C. § 103 supra. Thus this argument is not found persuasive.
3) Regarding to Applicants Traversal of the Rejection under 35 U.S.C. §103:
Applicant argues against the reference WO 2016/044416 (Cost et al.) (p27 ¶5). Cost is not relied upon in the instant action and thus Arguments direct to Cost are considered moot.
4) Regarding to Applicants Traversal of the Rejection under 35 U.S.C. §103:
Applicant argues that claim 18 is dependent on claim 1 and is thus non-obvious over the prior art. This argument is unpersuasive in view of the new rejection under 35 U.S.C. §103 as discussed supra.
Conclusion
No claims are allowed.
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/ANDREA LYNNE MORRIS SPENCER/Examiner, Art Unit 1631
/JAMES D SCHULTZ/Supervisory Patent Examiner, Art Unit 1631
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