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 .
Restriction/Election
Applicant’s election without traverse of Group I, drawn to claims 1-6, in the reply filed 11 May 2026 is acknowledged. Claims 7-13 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed 11 May 2026.
Claims 1-6 are considered on the merits.
Claim Interpretation
To promote compact prosecution, claim 1 is interpreted to recite "...substantially eliminating endogenous genes of a long-arm and a short-arm... "
Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. § 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
Claims 1-6 are rejected under 35 U.S.C. § 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
Claims 1-6 are rejected under 35 U.S.C. §112(b) as being incomplete for omitting essential steps, such omission amounting to a gap between the steps. See MPEP § 2172.01. The omitted step is eliminating endogenous genes from the long-arm and short-arm of a chromosome. The specification describes substantially elimination of endogenous genes of a long-arm and a short-arm (par. 29). The claim recites, "substantially eliminating an endogenous gene", but it is unclear how eliminating a single gene or a portion of a single gene can result in a human artificial chromosome vector comprising a long-arm moiety and a short-arm moiety substantially containing no endogenous genes. Claims 2-6 are included in this rejection because they depend from claim 1 and do not clarify the matter.
The term “substantially" recited in claim 1 is a relative term which renders the claim indefinite. The term “substantially” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. The specification provides that "[t]he term 'substantially' herein means that one or plural genes, for example, 30 or less, 20 or less, 10 or less, 5 or less, or 2 or less genes, excluding a causative gene causing chromosome aberration when the human cell of the present invention is used in a therapy or the like, may be contained." This definition is not limiting because the five different ranges provided are exemplary and thus do not limit the scope of the claim. It is, therefore, unclear how much of a gene or which portion of a gene must be eliminated to substantially eliminate the gene. Furthermore, it is unclear to what degree, or how many, endogenous genes must be eliminated to yield an artificial chromosome comprising substantially no endogenous genes. Claims 2-6 are included in this rejection because they depend from claim 1 and do not clarify the matter.
Regarding claim 1, the phrase "substantially eliminating an endogenous gene of a long-arm and a short-arm" is unclear. Genes are specific to unique loci that are localized to one of the two arms of a chromosome. It is, therefore, unclear how a single endogenous gene can be eliminated from both a long arm and a short arm of a chromosome. Claims 2-6 are included in this rejection because they depend from claim 1 and do not clarify the matter.
Regarding claim 2, the phrase "comprises two copies of a gene for haplo-insufficiency" is unclear. Haploinsufficiency, by definition, occurs only in a heterozygous individual and results in insufficient production of the protein encoded by the haploinsufficient gene. Furthermore, "gene for haploinsufficiency" is not an art-recognized phrase. No gene can cause haploinsufficiency as it is the absence of a copy of a gene that causes haploinsufficiency and not a function of the gene itself. It is, therefore, unclear how haploinsufficiency can arise when two copies of a gene present in a cell. Furthermore, haploinsufficiency arises due to insufficiency in endogenous genes. Given that claim 2 inherits all of the limitations of claim 1, it is unclear how two copies of a gene can be present in a chromosome comprising substantially no endogenous genes in a disomic cell.
Claim Rejections - 35 USC § 112(a)
The following is a quotation of the first paragraph of 35 U.S.C. § 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
Claims 1-6 are rejected under 35 U.S.C. § 112(a) because the specification, while being enabling for
a method for producing a human cell comprising a human artificial chromosome vector comprising:
eliminating endogenous genes from the long-arm and the short-arm in a trisomic human cell containing a trisomy of homologous human chromosomes from one of three chromosomes of the trisomy,
thereby producing a cell population containing a human cell containing a human artificial chromosome vector comprising a long-arm moiety and a short-arm moiety each substantially containing no endogenous genes, a human centromere, and a telomere, and
collecting the human cell containing the human artificial chromosome vector from the cell population,
does not reasonably provide enablement for eliminating endogenous genes from one of two homologous chromosomes in a disomic cell or from two of three homologous chromosomes in a trisomic cell. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention commensurate in scope with these claims.
Enablement is considered in view of the Wands factors (MPEP 2164.01(a)). The court in Wands states, “Enablement is not precluded by the necessity for some experimentation such as routine screening. However, experimentation needed to practice the invention must not be undue experimentation. The key word ‘undue’, not ‘experimentation.’” (Wands, 8 USPQ2d 1404). Clearly, enablement of a claimed invention cannot be predicated on the basis of quantity of experimentation required to make or use the invention. "Whether undue experimentation is needed is not a single, simple factual determination, but rather is a conclusion reached by weighing many factual considerations." (Wands, 8 USPQ2d 1404). When determining whether a specification meets the enablement requirement, some of the factors to be analyzed are: (1) the breadth of the claims, (2) the nature of the invention, (3) the state of the prior art, (4) the level of one of ordinary skill in the art, (5) the level of predictability in the art, (6) the amount of direction provided by the inventor, (7) the existence of working examples, and (8) whether the quantity of any necessary experimentation to make and use the invention based on the content of the disclosure is undue (Wands). While all of these factors are considered, those sufficient for establishing a prima facie case are discussed below.
Nature of the invention
The claims are drawn to a method of producing an artificial human chromosome vector by truncating the long and short arms of the chromosome to eliminate all but the centromere, telomeres, and a small amount of intervening genetic material that allow for insertion of exogenous genetic material.
Breadth of the claims
The claims are broad with respect to which sets of homologous chromosomes may be truncated to produce the artificial chromosome vector. Claim 1 recites elimination of endogenous genes from one of two chromosomes in a disomic pair of chromosomes in a disomic cell or from one or two of three chromosomes in a trisomic set of chromosomes in a trisomic cell. Elimination of all or most endogenous genes from one chromosome in a disomic pair of chromosomes or from two chromosomes in a trisomic set of chromosomes would result in a cell with a single intact homologous chromosome.
Existence of working examples and Amount of direction provided by the inventor
The specification provides working examples of producing an artificial chromosome vector in human induced pluripotent stem cells (iPSC) that are disomic (strain 201B7) or trisomic (strain 2767-4) for chromosome 21 (Example 6, par. 67).
The specification provides that for some genes, presence of two copies of a gene is necessary for maintaining the survival of a cell when presence of a single copy would lead to haploinsufficiency (par. 51). The specification further provides that "an exogenous gene vector carrying a gene or DNA for correcting the responsible gene may be produced..." (par. 51). However, no examples are provided for which two copies of a gene must be present for each chromosome that may be truncated.
State of the prior art and Level of predictability in the art
Abe (T. Abe, et al., Sci Rep, Sep 2021, in IDS filed 19 Mar 2024) teaches that methods for large-scale chromosome editing are well-known in the art (Introduction p. 1). Abe further teaches that "chromosome loss or large-scale truncations often result in cell lethality or severe growth defects in vertebrates" due to loss of a functional copy of a gene when a deleterious allele is present on the remaining chromosome or due to insufficient gene dosage in the remaining chromosome (i.e. haploinsufficiency) (Introduction p. 1). Abe further teaches that editing one trisomic chromosome is permissible because loss a third copy of a gene is unlikely to deleterious to the cell (Introduction p. 1). Abe further teaches correction of trisomy in the DT40 chicken B-cell line and that correction of trisomy has been accomplished in human cells (Abstract and Introduction p. 1).
Morrill (S.A. Morrill and A. Amon, PNAS, 2019) teach that about 300 genes have been identified that are haploinsufficient, but that the estimated number of such genes is much higher (Introduction. p 11866). Morrill further teaches that haploinsufficiency is extremely context dependent, and which genes are haploinsufficient in different contexts may have little overlap (Discussion p. 11870).
Conclusions
The specification and the prior art provide working examples that are narrowly enabling for the invention as claimed. However, the breadth of the claims encompasses numerous non-enabled embodiments and neither the specification nor the prior art provide sufficient direction for a skilled artisan to make and/or use the full scope of the claimed invention. The art teaches that loss of large regions of a chromosome is likely to lead to cell death when truncating one of two homologous chromosomes in a disomic cell or two of three homologous chromosomes in a trisomic due to haploinsufficiency or amplification of the effect of deleterious mutations. The art further does not teach a mode by which a skilled artisan would be able to select a set of haploinsufficient genes to restore function by exogenous expression because which genes are haploinsufficient and in which contexts is unknown. The specification provides one working example of chromosome truncation in a disomic cell, but does not provide direction for how to overcome this barrier identified in the art for practicing the claimed invention on other chromosomes or in other cell types. Therefore, a skilled artisan practicing the invention as claimed would have to perform extensive experimentation to identify how many genes and in what combination must be restored by exogenous expression for each chromosome for every cell type and culture condition to practice the full scope of the claimed invention. This represents an undue burden of experimentation to a skilled artisan attempting to make and/or use the invention as claimed.
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 1-6 are rejected under 35 U.S.C. § 103 as being unpatentable over Abe (T. Abe, et al., Sci Rep, Sep 2021, in IDS filed 19 Mar 2024).
Regarding claim 1, Abe discloses a method of generating a mini-chromosome (artificial chromosome vector comprising a centromere, a telomere, and substantially no endogenous genes) in DT40 cells, a chicken B-cell line comprising a trisomy of chromosome 2 (Abstract and Introduction p. 2). Abe generates the artificial chromosome vector by "large-scale truncation of trisomic chromosome 2 by integrating two telomere repeat sequences near the centromere" to delete a 50 Mb region of the short arm and a 100 Mb region long arm (substantially eliminating), resulting in a 0.7 Mb mini-chromosome (Introduction p. 2). The resulting mini-chromosome comprises the endogenous centromere and telomeres on each end and was substantially devoid of endogenous genes (Results p. 2 and Discussion p. 10).
Regarding claim 2, the DT40 cells edited to convert one copy of trisomic chromosome 2 into a mini-chromosome comprise two intact copies of chromosome 2 and, therefore, comprise two copies numerous genes that may give rise to haploinsufficiency if one copy were to be lost.
Regarding claim 3, Abe teaches insertion of a Flip-in system to allow for site-directed insertion of auxin-inducible degron tags (inserting a sequence for site-directed DNA insertion) for negative selection of cells that do not comprise the artificial chromosome vector (Results pp. 7-8 and Discussion p. 10).
Regarding claim 4, Abe discloses insertion of exogenous telomere repeat sequences (exogenous DNA) to generate the artificial chromosome vector (Results p. 2) and insertion of green fluorescent protein (GFP, exogenous gene) into the resulting artificial chromosome vector (Results p. 6).
Regarding claim 5, the DT40 cells originated as disomic for chromosome 2, but became trisomic for chromosome 2 during establishment of the cell line in cell culture (trisomic cell artificially produced from a disomic cell) (Introduction p. 2).
Regarding claim 6, DT40 cells are a B-cell line (somatic cells) (Introduction p. 2).
The method taught by Abe is practiced chicken cells to generate a chicken artificial chromosome vector rather than human as required by claims 1-6.
However, Abe further teaches that the method of generating a mini-chromosome is applicable to correction of trisomy in other vertebrate cell types, including human cells (Introduction p. 1 and Discussion p. 10). Abe further teaches that trisomy in human cells has been corrected using similar techniques and that the method taught by Abe has been used to correct trisomy in human cells on exogenous chromosomes.
Therefore, it would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to substitute DT40 chicken cells when practicing a method of producing an artificial chromosome vector as taught by Abe for human cells as taught by Abe to arrive at the claimed invention. One would be motivated to make such a substitution as Abe teaches that the method is broadly applicable to correcting trisomy in other cultured cells, including human cells. One would have a reasonable expectation of success in making the combination as Abe teaches that trisomy correction is feasible in human cells for correcting endogenous trisomy and that the method taught by Abe has been used successfully to correct trisomy in exogenous chromosomes.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Eric B Wright whose telephone number is (571) 272-2607. The examiner can normally be reached Mo - Fr, 09:00 a.m. - 05:00 p.m. Eastern. If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Peter Paras can be reached at (571) 272-4517.
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/Eric B Wright/Examiner, Art Unit 1632
/VALARIE E BERTOGLIO/Primary Examiner, Art Unit 1632
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