Notice of Pre-AIA or AIA Status
The present application, filed on or after 16 Mar 2013, is being examined under the first inventor to file provisions of the AIA .
Claim Status
Amendments to the claims filed 27 Jul 2026 are acknowledged. Claims 18 and 24 are cancelled. Claims 19-23 and 25-49 were previously cancelled by Applicant. Claims 1-17 are pending.
Applicant’s elections without traverse of Group I, drawn to claims 1-17, and to nucleic acid as the species of agent that modulates expression of the gene that promotes clonal hematopoiesis in the reply filed 27 Jul 2026 are acknowledged.
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 1-17 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.
Where applicant acts as their own lexicographer to specifically define a term of a claim contrary to its ordinary meaning, the written description must clearly redefine the claim term and set forth the uncommon definition so as to put one reasonably skilled in the art on notice that the applicant intended to so redefine that claim term. Process Control Corp. v. HydReclaim Corp., 190 F.3d 1350, 1357, 52 USPQ2d 1029, 1033 (Fed. Cir. 1999). The abbreviation “HSPC” in claim 1 is used by the claim to mean hematopoietic stem cells while the accepted meaning is hematopoietic stem and progenitor cells. The term is indefinite because the specification does not clearly redefine the term. The specification provides than an "HSPC is a blood stem cell that is undifferentiated, proliferates indefinitely, and may mature into any of multiple mature hematopoietic cells" (par. 33) and also provides a conflicting definition, stating that
"It should be understood that an HSPC having a genomic modification associated with CH [(clonal hematopoiesis]) also encompasses any mature hematopoietic cells that differentiate from the HSPC and also have genomic modification associated with CH" (par. 33).
Therefore, the claims are indefinite because it is unclear whether the scope of the claims is limited to only hematopoietic stem cells or also includes hematopoietic progenitor cells as well as mature hematopoietic cells. Claims 2-17 are included in the rejection as the claims depend from claim 1 and do not resolve the issue. To promote compact prosecution, the claims are interpreted to mean that HSPC refers to hematopoietic stem and progenitor cells and does not include mature cell types.
Claims 1-17 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. Claim 1 recites "contacting hematopoietic stem cells (HSPCs) with an agent that modulates gene expression of a gene" in step (a) and further recites "wherein a decrease in the expression level relative to a control that the gene promotes CH" in step (c). However, changes in expression of a gene with its expression modulated by an agent merely indicates that the agent successfully modified expression of the gene and does not indicate any association clonal hematopoiesis (CH). To indicate that a gene promotes CH requires assessment of some phenotype relevant to CH that is altered by change in expression of the gene acted upon by the agent, such as those exemplified in par. 32, 60, and 71-73 of the specification. Because the method does not recite all of the necessary steps for a skilled artisan to understand how the method results in indicating that a gene promotes CH, the metes and bounds of the claim scope are unclear, rendering the claim indefinite. Claims 2-17 are included in the rejection as the claims depend from claim 1 and do not resolve the issue.
Claims 1-17 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. Claim 1 recites "culturing the contacted HSPCs with endothelial cells" in step (b). However, it is unclear how the endothelial cells contribute to identifying a gene that promotes clonal hematopoiesis (CH) as the endothelial cells are merely present but are not used or acted upon. The claim should recite an active step in which the endothelial cells are used or acted upon that indicate how the endothelial cells contribute to identifying a gene that promotes CH, such as those exemplified in par. 30 of the specification. Claims 2-17 are included in the rejection as the claims depend from claim 1 and do not resolve the issue.
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 1-17 are rejected under 35 U.S.C. § 103 as being unpatentable over Tothova (Z. Tothova, et al., Cell Stem Cell, 2017) in view of Mazzeo (C. Mazzeo, et al., Blood Cells Mol Dis, May 2021, previously cited in PTO-892 filed 27 Apr 2026).
Claim 1 is drawn to a method of identifying a gene that promotes clonal hematopoiesis (CH) by contacting hematopoietic stem and progenitor cells (HSPC) with an agent that modulates expression of a gene, wherein the HSPC comprise a genomic modification associated with CH, co-culturing the HSPC with endothelial cells, and measuring expression level of the modulated gene.
Regarding claims 1-3, Tothova teaches a CRISPR library screening method for identifying genes that are drivers of clonal hematopoiesis of indeterminate potential (CHIP) (method for identifying a gene that promotes clonal hematopoiesis, claim 1) (Abstract and Introduction p. 547). Tothova teaches culturing CD34+ umbilical cord stem cells or adult CD34+ cells, populations comprising hematopoietic stem and progenitor cells (HSPC) in the presence of a pool of single guide RNAs (sgRNA) that target genes that are drivers of leukemia and/or myelodysplastic syndrome to evaluate the role of those genes in clonal hematopoiesis (contacting the HSPC with an agent that modulates expression of a gene) (Results p. 548). The sgRNA pool comprises sgRNA targeting DNMT3A, TET2, and ASXL1, genes associated with CHIP, that result in a mix of insertion and deletion mutations (indels), some of which result in in-frame mutations (wherein the HSPC comprise a genomic modification associated with clonal hematopoiesis, claim 1, wherein the genome modification is a substitution, insertion, or deletion resulting in expression of a variant of the protein in a gene, claim 2, modification of a gene encoding the proteins TET2, ASXL1, and/or DNMT3A, claim 3) (Tothova Results p. 548 and Fig. S1). Tothova further teaches sequencing cells cultured from single cell colonies for 14 days to determine how loss of function (LOF) mutations (decrease in expression level of the gene relative to a control, claim 1) induced by CRISPR-based gene editing of the genes associated with the sgRNA pool correlate with clonal expansion of the edited cells (determining an expression level of the gene in the cultured HSPC, wherein a decrease in expression level relative to a control indicates that the gene promotes clonal hematopoiesis, claim 1) (Results p. 548 and Fig. 1A-1B).
Tothova does not teach culturing the contacted HSPC with endothelial cells (EC) as required by claims 1-17.
However, Mazzeo teaches that endothelial cells contribute to neoplastic hematopoiesis in myeloproliferative neoplasms, such as clonal stem cell disorders (e.g., clonal hematopoiesis) (Introduction p. 1 and Discussion p. 5). Mazzeo further teaches that a mixed vascular microenvironment comprising wild-type and mutant bone marrow-derived endothelial cells (BMEC, claim 8) co-cultured with HSPC better models human disease ex vivo than HSPC alone (Discussion p. 5). Mazzeo further teaches that direct contact between EC and HPSC better models the contribution of mutations in EC compared to culturing HPSC in conditioned medium from EC without direct contact with EC (Results p. 4, Fig. 4, and Discussion p. 5).
Regarding claims 4-5 and 12-13, Tothova teaches administering a pool of sgRNA to the HSPC that target 11 different genes (nucleic acid, claim 4, library of agents, claim 5, library of sgRNA, claims 11-12, library of sgRNA that modulate expression of different genes in the HSPC, claim 11) (Results p. 548).
Regarding claim 6, Tothova further teaches transplanting to contacted HSPC into irradiated mice, then sequencing the cells again to determine how LOF mutations correlate to clonal hematopoiesis and found that clone comprising LOF mutations expand more readily than clones comprising non-LOF mutations (decrease in expression level of the gene relative to a control indicates that the gene promotes clonal hematopoiesis) (Results pp. 548-549 and Fig. 1C).
Regarding claims 7 and 14-17, Tothova teaches sequencing the clones at 24 h and 144 h during the in vitro culturing step (performing step (c), determining the expression level, at least twice during the culturing of the contacted HSPC, claim 7) (Results p. 548 and Fig. 1A). Tothova further teaches sequencing the contacted HSPC to determine zygosity of the induced mutations, where homozygosity results in total loss of expression of the gene (determining a copy number for an sgRNA corresponding to a gene and wherein the copy number is indicative of the expression level of the gene, claim 14) (Results p. 548). The change in the unique indel types of the HPSC clones is compared between 24 and 144 h, wherein expansion of clones with a LOF mutation indicates that the gene promotes clonal hematopoiesis (decrease in copy number relative to a control, claim 15, wherein the control copy number is determined by sequencing an aliquot of the HSPC at an earlier time point in the culturing, claim 17) (Fig. 1A). Tothova teaches contacting wild-type human HSPC (Experimental Model and Subject Details p. e3) and determination of copy number is made by calling unique indel types validated by comparison to wild-type reads in each gene (determining the control copy number in the wild-type HSPC based on the sequencing) (Experimental Model and Subject Details p. e5 and Fig. 1B and S1).
Regarding claims 9-10, Tothova teaches transient transfection of an S. pyogenes Cas9 alongside the sgRNA (HSPC express a programmable nuclease protein, claim 9, the nuclease is Cas9, claim 10) (Results p. 548).
Regarding claim 11, Tothova teaches comparing clonal expansion of wild-type cells and mutant cells in transplanted HPSC by PCR amplification of indel fractions to determine which clones preferentially expanded (wherein the control comprises an expression level of the gene in wild-type HSPCs that do not comprise the genome modification) (Results pp. 550 and 552).
Therefore, it would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to combine the method of identifying a gene that promotes clonal hematopoiesis as taught by Tothova with the method of culturing HSPC with EC as taught by Mazzeo to arrive at the claimed invention. One would be motivated to make such a combination as Mazzeo teaches that co-culture of HSPC and EC improves in vitro models of myeloproliferative neoplasms such as clonal hematopoiesis. One would have a reasonable expectation of success in making the combination as Mazzeo demonstrates that direct contact between EC and HSPC allows for studying the contribution of mutations in EC, whereas indirect contact through culturing with EC-conditioned medium is insensitive to mutational status in EC.
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, PhD
Examiner
Art Unit 1632
/Eric B Wright/Examiner, Art Unit 1632
/VALARIE E BERTOGLIO/Primary Examiner, Art Unit 1632
