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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 11/14/2025 has been entered.
Application Status
This action is written in response to applicant’s correspondence received on 5/29/2026. Claims 1-4, 6-7, 10-11, 34-39, 41-42, 44-46, and 109-112 are pending. All pending claims are currently under examination.
Any rejection of record in the previous office actions not addressed herein is withdrawn. New grounds of rejection are presented herein that were not necessitated by applicant’s amendment of the claims since the office action mailed 12/29/2025. Therefore, this action is not final.
Claim Rejections - 35 USC § 103 – New Rejection Not Necessitated by Amendment
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-4, 6-7, 34-36, 39, 41, and 109-110 are rejected under 35 U.S.C. 103 as being unpatentable over Hartl (Hartl D et al. Nucleic Acids Res. 2017 Nov 16;45(20):11607-11621, submitted in applicant’s IDS filed 5/21/2024) in view of Zheng (Zheng GX et al. Nat Commun. 2017 Jan 16;8:14049) and 10X Genomics (User guide and technical note for Chromium Single Cell 3’ v3 kit, published 2/25/2019 from 10X Genomics).
Regarding claim 1, Hartl is a research publication that teaches the use of a parallel reporter assay to identify regulatory elements with differential expression in different cell types (Title, Abstract, and see document). For instance, Harl teaches that their method is designed to analyze rod, cone, horizontal, and starburst amacrine cells (Abstract). Hartl teaches a method of identifying a regulatory element that provides selective expression in a given cell type, comprising obtaining a library of candidate regulatory elements (page 11608, left column, third paragraph, “we tested hundreds of CREs [cis-regulatory elements]”). Hartl teaches creating a library of vectors, where each vector of the library of vectors comprises a candidate regulatory element of the library of candidate regulatory elements operably linked to a transgene (page 11609, right column, first paragraph). Hartl teaches that the transgene comprises a barcode unique to the candidate regulatory element (Figure 3, and caption below Figure 3, which teaches that GFP (a transgene) was attached to a unique barcode for each regulatory element tested). Hartl teaches contacting a population of cells with the library of vectors (e.g., Figure 3A). Hartl teaches assessing the expression of the barcoded transgenes in each of the cell types to identify a barcoded transgene which is selectively expressed in the given cell type compared to other cell types of the population of cells (page 11613, right column final paragraph to page 11615, entirety, and Figures 3 and 4). Specifically, Hartl teaches that the parallel reporter assay that they used, which included a transgene with unique barcodes for the library of regulatory elements described in Figure 3 is applied to unique cell types to identify selective expression in each cell type (see page 11615, section entitled “Autonomous CRE activities in four retinal cell types,” and Figure 4). Hartl teaches correlating the identified barcode to a candidate regulatory element to identify a regulatory element that provides selective expression in the given cell type (e.g., “this effort let[sic] to the identification of a small set of short sequences showing preferential activity in different cellular subsets of the retina,” page 11618, left column, first paragraph).
Furthermore, Hartl teaches the use of a commercially available kit for single cell RNA sequencing which was used in their RNA-seq library preparation (Norgen 51800, page 11608, right column, second paragraph).
Hartl, while teaching the identification of regulatory elements expressed differentially in different cell types, does not teach that single-cell RNA sequencing was performed to obtain transcriptome data for a plurality of single cells, where the cell type is identified by the transcriptome data and not sorted by reporter or natural marker.
Zheng is a research article which focuses on the profiling of different cell types using massively parallel sequencing methods (Title, Abstract, and throughout). Hartl and Zheng therefore overlap in subject matter and field of endeavor because both focus on identifying transcriptomic data and classifying cell types based on transcriptomic data/expression data. Zheng teaches that “[c]haracterizing the transcriptome of individual cells is fundamental to understanding complex biological systems. We describe a droplet-based system that enables 30 mRNA counting of tens of thousands of single cells per sample,” (Abstract). Zheng further teaches that “[s]ingle-cell RNA-sequencing (scRNA-seq) can be used to dissect transcriptomic heterogeneity that is masked in population-averaged measurements. scRNA-seq studies have led to the discovery of novel cell types and provided insights into regulatory networks during development,” (Introduction, first paragraph of page 2). Zheng therefore provides a strong motivational teaching to incorporate single cell RNA transcriptomic profiling because such strategies using single cell transcriptomics are known to be powerful methods to gain further insight into complex cell populations and to understand such complex cellular populations/systems (above). Zheng teaches that single cells were characterized and identified using single cell transcriptomic data:
“The GemCode single-cell technology can also be used for scRNA-seq of primary cells. To study immune populations within PBMCs, we obtained fresh PBMCs from a healthy donor… to identify subpopulations within the myeloid population, we further applied k-means clustering on the first 50 PCs of cluster 9 cells. At least three populations were evident: dendritic cells (characterized by the presence of FCER1A25), CD16þ monocytes and CD16_/low monocytes. Overall, these results demonstrate that our scRNA-seq method can detect all major subpopulations expected to be present a PBMC sample,” (see page 4, right column, final paragraph, to page 6, first paragraph).
Furthermore, Zheng teaches that they relied upon a cell separation technique which did not rely on reporter marker or cell surface markers prior to sequencing:
“we developed a droplet based system that enables 30 messenger RNA (mRNA) digital counting of thousands of single cells. Approximately 50% of cells loaded into the system can be captured, and up to eight samples can be processed in parallel per run. Reverse transcription takes place inside each droplet, and barcoded complementary DNAs (cDNAs) are amplified in bulk. The resulting libraries then undergo Illumina short-read sequencing. An analysis pipeline, Cell Ranger, processes the sequencing data and enables automated cell clustering. Here we first demonstrated comparable sensitivity of the system to existing droplet-based methods by performing scRNA-seq on cell lines and synthetic RNAs,” (Introduction, second paragraph).
With regards to the GEM-based (Gel Bead in Emulsion) single cell sorting method Zheng used, Zheng teaches that:
“This allowed us to discover new insights int the disease state of the host before and after transplant that were not readily achievable with traditional PCR, FACS-based analysis or any other methodology described to date,” (page 9, left column, final paragraph).
And :
“the applicability of the GemCode platform to a wide variety of cell types. The GEM-based encapsulation of single cells within the microfluidics platform reduces the need for expensive sorting equipment and complicated workflows involving large numbers of plates. The scalability and high throughput nature of the GemCode platform is achieved in two ways: hundreds to thousands of cells can be encapsulated per channel, and each chip has eight channels. Therefore, a large number of cells can be processed within a very short period of time, minimizing the perturbation of the cellular transcriptome,” (Discussion, second paragraph).
Thus, Zheng teaches a strong motivation to perform single-cell RNA sequencing to characterize transcriptomic data to identify individual cell populations, and furthermore teaches that cell separation methods which do not rely upon reporter genes or cell-specific markers, such as GEM-based separation methods, are known to be highly useful and valuable for several reasons including wide applicability across cell types, reduced expenses, high throughput and scalability, short cell processing times, and furthermore improved insights into cellular populations which are not achievable by cell-specific marker sorting methods such as FACS.
Additionally, as taught by 10X Genomics, GEM-based cell separation technologies are commercially available kits, and are thus a well-known methods of sorting/single-cell sequencing (see Title, Introduction, and workflow throughout). 10X Genomics further teaches that “The Chromium Single Cell Gene Expression Solution provides a comprehensive, scalable solution for gene expression profiling of hundreds to tens of thousands of cells. The Single Cell 3ʹ v3 reagents and workflow updates provide enhanced sensitivity, enabling detection of even more unique transcripts per cell,” (Introduction). Thus, 10X Genomics teaches that GEM-based microfluidic cell separation and transcriptomic sequencing such as those taught by Zheng are commercially available, well-known cell separation methods in the art, where furthermore such workflow pipelines allow for enhanced sensitivity and high scalability (above).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to modify the gene expression library construct profiling method of Hartl to include single-cell transcriptomic sequencing to identify individual cells, as taught by Zheng, as such a combination is the simple combination of known prior art elements with predictable success. Furthermore, the combination is not simply a combination of elements, the practitioner would be highly motivated to performed single-cell RNA sequencing/transcriptomics on the cell populations taught by Hartl because Zheng teaches that performing such transcriptomic analysis gives the practitioner critical knowledge with respect to the genetic expression states of the cells, where such scRNA-sequencing methods allow the practitioner to understand heterogenous cell populations at a deeper level (above). Additionally, the practitioner is motivated to use cell sorting methods such as the GEM-based microfluidic system of Zheng because Zheng teaches that such separation methods are highly desirable in terms of scalabilty, lower cost, short processing times, reduced equipment separation equipment required, as well as the ability to gain insights into cell populations which are not possible by cell marker sorting such as FACS alone (above). Furthermore, the results are predictable because Zheng teaches that their method applies to any cell type, where furthermore such GEM-based cell sorting/sequencing methods such as Chromium Single Cell 3’ v3, as taught by 10X Genomics, were commercially available kits/workflows at the time of filing.
Regarding claim 2, Hartl teaches that the regulatory element selectively increases expression of the transgene in the cell type (e.g., page 11615, right column, fourth paragraph, “revealed differences over three orders of magnitude”).
Regarding claims 3-4, Hartl teaches that a fraction of the tested regulatory elements drives detectable activity in rod cells this inherently means that some regulatory elements measured by Hartl did not drive detectable activity while some did (page 11615, right column, second paragraph). Thus, Hartl teaches that the regulatory element provides selective expression of the transgene that is at least 2-fold (claim 3) and/or 50% (claim 4) greater or less compared to expression driven by a control regulatory element in the same cell type (page 11615, right column, second paragraph). The term “control” regulatory element is not specifically restricted in the claim, and could thus reasonably be interpreted to be a negative control, where the increased expression of the above regulatory elements that are at least 2-fold or 50% greater could be compared with a negative control, and therefore read on claims 3-4.
Regarding claims 6-7, Hartl teaches that SAC and HC cells, when compared to other cell types, revealed differences of expression over three orders of magnitude (page 11615, right column, fourth paragraph). Thus, Hartl teaches that the regulatory element provides selective expression of the transgene at least 2-fold (claim 6) and/or 2% (claim 7) greater or less compared to expression of the transgene from the same regulatory element in a different cell type (page 11615, right column, fourth paragraph).
Regarding claims 34-36, Hartl teaches the viral vector AAV (Figure 3A). Furthermore, regarding claim 36, Hartl teaches that constructs were packaged in AAV serotype 8, i.e., AAV8 (page 11614, right column, final paragraph).
Regarding claim 39, Hartl teaches that they generated a catalogue of hundreds of putative regulatory elements in their methods (Abstract). Thus, Hartl teaches that the library of candidate regulatory elements comprise at least 16 candidate regulatory elements (Abstract).
Regarding claim 41, Hartl teaches that the transgene comprises a reporter gene sequence (e.g., GFP, Figure 3).
Regarding claim 109, Hartl teaches that the cells are in vivo cells in a mouse (e.g., Figure 3).
Regarding claim 110, Hartl teaches separating cells by FACS, and further that FACS-sorting relies on sorting cells based on fluorescent labeling of markers (e.g., Figure 3, page 11609, left column, third paragraph, and page 11618, left column, second paragraph). Furthermore, claim 110 simply recites that the cells are identified based upon a marker gene, where the term “marker gene” is not defined within the specification. As such, any marker gene for a given cell which is identified using transcriptomic profiling such as that performed in the method of Zheng can be viewed as a “marker gene” of that particular cell.
Claims 10-11 are rejected under 35 U.S.C. 103 as being unpatentable over Hartl (Hartl D et al. Nucleic Acids Res. 2017 Nov 16;45(20):11607-11621, submitted in applicant’s IDS filed 5/21/2024) in view of Zheng (Zheng GX et al. Nat Commun. 2017 Jan 16;8:14049) and 10X Genomics (User guide and technical note for Chromium Single Cell 3’ v3 kit, published 2/25/2019 from 10X Genomics) as applied to claims 1-4, 6-7, 34-36, 39, 41, and 109-110 above, and further in view of Cohen (Cohen SM et al. Neuron. 2016 Apr 20;90(2):292-307).
Regarding claims 10 and 11, a discussion of the teachings of Hartl/Zheng is discussed above in the rejection of claim 1. Furthermore, Hartl teaches that their method was successful, and should further be expanded to other cell types (page 11619, right column, first paragraph). Hartl further teaches that their method can contribute to the goal of providing more insight into expression drivers in vivo (page 11619, left column, final paragraph). Thus, Hartl teaches that their method is useful, practical, and can target disease relevant cell types (page 11619, left and right columns).
Hartl and Zheng do not teach that the regulatory element provides selective expression in PV neurons compared to non-PV neurons such as excitatory neurons.
Cohen is a research article which teaches transcription profiling in cell types, specifically neurons (Title, Abstract, and see document). Cohen and Hartl therefore overlap in subject matter and field of endeavor because both research articles teach methods of investigating transcriptional profiles in different cell types (see documents). Cohen teaches that understanding excitation-transcription profiling is relevant to understanding disease pathology states (Abstract). Cohen further teaches that gene expression as it relates to morphological development in neurons is poorly understood, and thus teaches that there is a motivation to further understand transcription/gene expression in neurons, as this understanding would help to understand disease states (Abstract). Furthermore, Cohen teaches that expression profiles and morphological/regulatory differences exist between PV neurons and excitatory neurons (Abstract, page 2 final paragraph). Furthermore, Cohen teaches that relatively little is known about gene expression changes in interneurons (page 2, second paragraph). Additionally, Cohen teaches that understanding gene expression/excitation-transcription coupling in PV cells is critical for understanding disease states (page 13, first paragraph). Thus, Cohen teaches both PV cells and excitatory neurons, that these two cells have different transcriptional responses to external stimuli, and further that understanding transcriptional/gene expression regulation is critical to understanding disease states that are not entirely understood (Abstract, page 2 paragraphs 2-3, page 13 first paragraph).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to adapt the transcript profiling method rendered obvious by Hartl/Zheng to the PV/excitatory neurons taught by Cohen because such a combination is the simple substitution of one known element for another to obtain predictable results. In the present case, a practitioner would have simply substituted the study of the retina and interneurons of Hartl with PV/excitatory neurons taught by Cohen. Furthermore, a practitioner would be motivated to apply the method of Hartl/Zheng to PV/excitatory neurons because Cohen teaches that there is a need to understand transcription states in these two different cell populations as it would help to understand disease states (e.g., Abstract, page 2, page 13). Additionally, there is a reasonable expectation of success because Hartl has already reduced their method to practice and furthermore the method relies on elements which would also function in PV/excitatory cells (promoters, regulatory elements, reporter genes, vectors).
Claims 37 is rejected under 35 U.S.C. 103 as being unpatentable over Hartl (Hartl D et al. Nucleic Acids Res. 2017 Nov 16;45(20):11607-11621, submitted in applicant’s IDS filed 5/21/2024) and Zheng (Zheng GX et al. Nat Commun. 2017 Jan 16;8:14049) and 10X Genomics (User guide and technical note for Chromium Single Cell 3’ v3 kit, published 2/25/2019 from 10X Genomics), as applied to claims 1-4, 6-7, 34-36, 39, 41, and 109-110 above, and further in view of Inagaki (Inagaki K et al. Mol. Ther. 2006 Jul;14(1):45-53).
Regarding claim 37, a discussion of the teachings of Hartl/Zheng as they relate to claims 1 and 34-36 is given above. Hartl teaches the use of AAV serotype 8 (AAV8) vectors in their methods (e.g., page 11614, right column, first paragraph). Furthermore, Hartl teaches that their library vectors comprising AAV vectors were used in mice (Figure 3).
Hartl, while teaching AAV vectors and AAV8, does not specifically teach AAV9.
Inagaki is a research article that teaches robust systemic transduction of AAV9 vectors into mice (Title, Abstract, and see document). Inagaki teaches that AAV9 are as robust and can be more robust than AAV8 vectors in mice (Abstract). Thus, Inagaki teaches that AAV9 vectors to be used for transduction in mice is a viable and ready alternative to AAV8 vectors, and further that such AAV9 vectors may be superior to AAV8 vectors.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to substitute the AAV8 vectors used in mice taught by Hartl/Zheng with the AAV9 vectors taught by Inagaki because such a combination is the simple substitution of one known prior art element for another with predictable results. In the present case, a practitioner would have substituted the known AAV8 vector of Hartl with the AAV9 vector of Inagaki. Furthermore, Inagaki teaches that AAV9 vectors can be superior to AAV8 vectors, a teaching that would motivate a practitioner to adopt the AAV9 vectors of Inagaki (Inagaki, Abstract and see the entire document). Furthermore, because both Hartl and Inagaki concern AAV vectors used in mice to deliver vectors a practitioner would therefore have a reasonable expectation of success when combining the teachings of Hartl and Inagaki.
Claims 38 is rejected under 35 U.S.C. 103 as being unpatentable over Hartl (Hartl D et al. Nucleic Acids Res. 2017 Nov 16;45(20):11607-11621, submitted in applicant’s IDS filed 5/21/2024) Zheng (Zheng GX et al. Nat Commun. 2017 Jan 16;8:14049) and 10X Genomics (User guide and technical note for Chromium Single Cell 3’ v3 kit, published 2/25/2019 from 10X Genomics), as applied to claims 1-4, 6-7, 34-36, 39, 41, and 109-110 above, and further in view of Savy (Savy A et al. Hum Gene Ther Methods. 2017 Oct;28(5):277-289).
Regarding claim 38, the teachings of Hartl/Zheng as they relate to claims 35-36 are discussed above. Hartl teaches the use of AAV vectors (Figure 3). Hartl teaches the use of AAV8 vectors (page 11614, right column, first paragraph).
Hartl does not specifically state that the AAV vectors comprise inverted terminal repeats.
Savy is a research article that teaches the impact of inverted terminal repeats (ITRs) on AAV vectors, specifically AAV8 vectors (Title, Abstract, see document). Savy teaches that ITRs are key elements of AAVs, and that these sequences are the only sequences conserved in recombinant AAV vectors, as they allow the AAV replication, encapsidation, and long-term maintenance and expression in target cells (Abstract). Thus, Savy teaches that recombinant AAV vectors routinely use ITR sequences (Abstract).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use ITR sequences as taught by Savy with the AAV vectors taught by Hartl. A practitioner would have been motivated to include Savy’s ITR sequences in order to render functional AAV vectors, as ITRs were already known in the art to be critical elements to be included with AAV vectors a taught by Savy, and specifically AAV8 vectors taught by both Savy and Hartl (Savy Abstract, Hartl page 11614, right column, first paragraph and Figure 3).
Claims 42 and 44-46 are rejected under 35 U.S.C. 103 as being unpatentable over Hartl (Hartl D et al. Nucleic Acids Res. 2017 Nov 16;45(20):11607-11621, submitted in applicant’s IDS filed 5/21/2024), Zheng (Zheng GX et al. Nat Commun. 2017 Jan 16;8:14049), and 10X Genomics (User guide and technical note for Chromium Single Cell 3’ v3 kit, published 2/25/2019 from 10X Genomics), as applied to claims 1-4, 6-7, 34-36, 39, 41, and 109-110 above, and further in view of Swiech (Swiech L et al. Nat Biotechnol. 2015 Jan;33(1):102-6, filed with applicant’s IDS filed 5/21/2024).
Regarding claim 42, the teachings of Hartl/Zheng are discussed above. Hartl teaches that the transgene comprises a reporter gene (“GFP,” Figure 3). Hartl also teaches separating cell types transduced with AAV vectors using FACS (e.g., Figure 3).
Regarding claims 44 and 46, Hartl teaches that the barcodes are encoded immediately beside the transgene, upstream of the poly(A) tail of the mRNA, which is within the coding region of the gene (Figure 3 and caption beneath Figure 3).
Regarding claim 45, claim 45 recites “the barcode comprises alternative codons.” According to the specification, alternative codons are simply synonymous codons that are redundant with respect to an amino acid they encode (paragraph 74 of specification). Thus, the broadest reasonable interpretation of claim 45 includes any barcode sequence that comprises codons that have redundant coding with other codons in the genetic code. Hartl teaches 15 bp barcode sequences that are random sequences (page 11608, right column, fourth paragraph). Hartl therefore inherently teaches that the barcodes comprise “alternative codons” because such barcode codons would have redundancy with other amino-acid encoding codons.
Hartl does not directly teach that the reporter gene sequence comprises the barcode (claim 44) or that the sequence encoding the nuclear binding domain comprises the barcode (claim 46).
Hartl does not teach that the reporter gene is operably linked to a sequence encoding a nuclear binding domain.
Swiech is a research article which teaches the delivery of transgenes using AAV vectors of neuronal cells (Abstract). Thus, Swiech and Hartl overlap in subject matter and field of endeavor. Swiech teaches that transgenes such as GFP are fused to nuclear binding domains in AAV-directed vector delivery, and that such domains (”KASH” domains) direct the fused GFP transgene protein to the nuclear membrane, which enables the identification of neurons which have been transduced by AAV vectors (page 102, left column, third paragraph into right column first paragraph). Swiech teaches that GFP-KASH fusions can be used in FACS cell sorting to identify cells with AAV vectors 9 (page 102, right column, final paragraph).
It would have been obvious to a person of ordinary skill in the art the effective filing date of the claimed invention to modify the GFP transgenes taught by Hartl with nuclear binding domain fusions, as taught by Swiech, because such a combination is the simple combination of known prior art elements with predictable results. In the present case, tagging transgenes with nuclear binding domains is already a known method taught by Swiech which can be used to help identify AAV-vector delivered cells in neuronal cells (Abstract, page 102). It was therefore predictable that the methods taught by Swiech would work with Hartl because Hartl taught methods to be used with AAV vectors encoding GFP (Figure 3).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to modify the barcode position taught by Hartl to be comprised either within the transgene taught by Hartl or the nuclear binding domain taught by Swiech, where such a combination would be obvious to try, where a practitioner would be choosing from a finite number of identified, predictable solutions, with a reasonable expectation of success. In the present case, a practitioner would be choosing from three regions: within the transgene, within the nuclear binding domain, or outside of these domains. The placement of a barcode is predictable in any of these locations because a barcode sequence would still function as a barcode regardless of its placement within a sequence. There is therefore a reasonable expectation that a barcodes function would not be lost if moving its location to one of the three regions of the sequence rendered obvious by Hartl and Swiech.
Claims 111-112 are rejected under 35 U.S.C. 103 as being unpatentable over Hartl (Hartl D et al. Nucleic Acids Res. 2017 Nov 16;45(20):11607-11621, submitted in applicant’s IDS filed 5/21/2024) in view of Zheng (Zheng GX et al. Nat Commun. 2017 Jan 16;8:14049) and 10X Genomics (User guide and technical note for Chromium Single Cell 3’ v3 kit, published 2/25/2019 from 10X Genomics), as applied to claims 1-4, above, and further in view of Sakaguchi (Sakaguchi M et al. Mol Biotechnol. 2014 Jul;56(7):621-30).
A discussion of Hartl and Zheng is given above concerning claims 1-4.
Regarding claims 111-112, Hartl teaches the known CAG promoter (11608, right column, first paragraph) and controls used in their experiments (Figure 2, caption) but does not teach that it is the control promoter used.
Sakaguchi is a research article that focuses on the expression of transgenes from various promoters, and therefore directly overlaps in subject matter of Hartl. Furthermore, Sakaguchi teaches that the CAG promoter is a known, highly potent promoter (Abstract). Furthermore, given these properties, Sakaguchi teaches that the CAG promoter can be used as a control reference for the expression of transgenes (page 626, left column, third paragraph). Thus, the use of CAG as a reference/control promoter was already a known technique owing to the high potency/consistency of expression of the CAG promoter (page 626, left column, third paragraph, Figure 3A).
It would have been obvious to a person of ordinary skill in the art before the effective filing date to modify the method rendered obvious by Hartl/Zheng, to include CAG as a control promoter because the use of CAG as a control/reference promoter for transgene expression is already a known technique as taught by Sakaguchi. Furthermore, a practitioner would be motivated to use CAG as a control regulatory element because it is a highly potent and therefore consistent expression driver (Sakaguchi).
Response to Arguments
The Applicant’s arguments filed 5/29/2026 have been considered and are persuasive. The above 103 rejection is a new rejection in made in light of the Applicant’s arguments. Note that the above 103 rejection is made in response to the Applicant’s arguments and not necessitated by amendments. Hence, the present rejection is non-final.
Regarding the Applicant’s arguments, it is noted that the Applicant’s arguments do not completely and accurately characterize the teachings of Hartl. The Applicant asserts that Hartl “explicitly teaches that their method is tailored to identify regulatory elements that have a selection expression pattern in low abundance cel types.” This characterization is not completely accurate because, while Hartl measured two types of low abundant cells, they also measured expression patterns in high abundant cell populations:
“The retina is composed of ∼50 cell-types with specific functions for the process of vision. Identification of the cis-regulatory elements active in retinal cell-types is key to elucidate the networks controlling this diversity. Here, we combined transcriptome and epigenome profiling to map the regulatory landscape of four cell-types isolated from mouse retinas including rod and cone photoreceptors as well as rare inter-neuron populations such as horizontal and starburst amacrine cells. Integration of this information reveals sequence determinants and candidate transcription factors for controlling cellular specialization.,” (Abstract)
Furthermore, “cis-regulatory landscape” analysis (i.e., the title and focus of Hartl’s paper) is taught by Hartl for each of the four cell types, including the abundant rod and cone cells referenced by the Applicant on page 7, second paragraph, of their remarks (see Results of Harlt, where each section of the Results includes analysis of each of the four cell types). Thus, Hartl is not “explicitly” focused on only rare cell populations, where Harlt also characterized expression data/transcriptomic data from abundant cells such as rod and cone cells, where “integration of this information” reveals information about cellular specialization, to include abundant cell types (Abstract and Results) and is therefore useful. Hartl is not solely focused on rare/low abundance cell populations.
Nonetheless, the Applicant’s arguments concerning the use of the Fluidigm C1 system, as taught by Tasic and Nguyen, is persuasive. As such, the Office has reconsidered the original rejection and provides the new non-final rejection contained within this action. The present subject matter is not patentable in view of the combination of Hartl, Zheng, and 10X Genomics (103 rejection, above). In brief, Zheng teaches a strong motivation to perform single-cell RNA transcriptomic sequencing, where Zheng further teaches that such methods provide more useful data for discerning the individual transcriptomics of single cells in complex biological systems (e..g, Abstract and Introduction). Regarding the cell separation method, Zheng teaches cell separation methods such as those using Gel Bead in Emulsion technologies, where such technologies offer several advantages and would be compatible with the methods of Hartl, where Zheng further teaches that such single-cell characterizations can be superior to data gathered using FACS (see 103 rejection above).
The Applicant argues that the secondary references do not cure the deficiencies of Hartl, Tasic, and Nguyen. This argument is persuasive. However, the present rejection is based upon the combination of Hartl, Zheng, and 10X Genomics.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to DOUGLAS CHARLES RYAN whose telephone number is (571)272-8406. The examiner can normally be reached M-F 8AM - 5PM.
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/D.C.R./Examiner, Art Unit 1635
/RAM R SHUKLA/Supervisory Patent Examiner, Art Unit 1635
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