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 .
Priority
This application claims benefit to European Patent Application No. EP 21182481.8,
filed on June 29, 2021.
Claim Status
Claims 1-17 are currently pending and under examination. Claim 1 is the only independent claim.
Drawings
The drawings are objected to under 37 CFR 1.83(a) because they fail to show Fig. 3 as described in the specification. Any structural detail that is essential for a proper understanding of the disclosed invention should be shown in the drawing. MPEP § 608.02(d). Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Claim Rejections - 35 USC § 103
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claims 1-4 and 8-17 are rejected under 35 U.S.C. 103 as being unpatentable over Oki et al. (US 2022/0251639 A1, listed on IDS as translation of WO 2020/235563 A1, published Nov. 26 2020) in view of Honda et al. (Nat. Comm., (2021) 12:4416, listed on IDS as bioRxiv published Mar. 20, 2020).
Oki is in the field of nucleic acid detection and teaches methods for detecting nucleic acids in a biological sample utilizing oligonucleotides with photolabile protective groups. Honda is a more recent extension of Oki, and teaches similar methods of photo-isolation chemistry.
In regards to claim 1, Oki teaches a plurality of oligonucleotide constructs comprising promoter regions, adapter regions, and target binding regions. (see Figs. 1 and 4, [0046] ). Oki teaches each oligonucleotide construct comprises a photoremovable molecule such as 2-(2-nitrophenyl)propyl group, 2-(2-nitrophenyl)propyloxymethyl group, 1-(2-nitrophenyl)ethyl group, and 6-nitropiperonyloxymethyl
group (NPOM), (see Figs. 1 & 4, [0049], and throughout). Oki further teaches synthesizing a complementary first strand from a template bound to the target binding regions of the oligonucleotide constructs (see [0058], [0065], and throughout). Oki also teaches scanning the sample with different light parameters that corresponding to different protecting groups used (see [0060]), and teaches using different parameters for different regions of sample (see [0065]-[0067], and throughout). While Oki doesn’t explicitly describe generating region-specific amplification templates, their follow-up paper, Honda et al., does.
Honda discloses photo-isolation chemistry for spatial transcriptome analysis, wherein focuses light is directed to selected regions of a biological sample to selectively activate and isolate nucleic acids from those regions, resulting in region-specific nucleic acid material suitable for amplification and sequencing (see Abstract, Figs. 1-5, pg. 3 para 1-2, and throughout). Honda further teaches the use of optical scanning and imaging-guided identification of regions of interest to direct light to selected regions in a predictable and reproducible manner (see Fig. 1, pg. 2 para. 4, pg. 9 paras 5 & 8). It would have been obvious to one of ordinary skill in the art at the time of filing to incorporate he photo-isolation techniques taught by Honda into the spatially selective light-directed method of Oki in order to improve spatial specificity and control over the generation of amplification templates originating from different regions of interest. One of ordinary skill in the art would have had a reasonable expectation of success in making such modification, as both Oki and Honda employ compatible light-directed processing of biological samples to generate region specific nucleic acid material.
In regards to claim 2, Oki teaches using light beams with different parameters based on the photosensitive cage molecule used (see [0065]-[0067], and throughout). One of ordinary skill in the art would recognize that using two different photoremovable groups would utilize the corresponding wavelength, time, or intensity as required by the chosen molecule.
In regards to claim 3, Oki teaches the use of photoremovable oligonucleotide constructs in which the photoremovable group is removed only using a specific wavelength of light for that group (see [0065]-[0067], and throughout).
In regards to claim 4, Oki teaches purifying the synthesized amplification templates from the biological samples (see [0062], [0101], [0106]).
In regards to claim 8, Oki teaches utilizing oligonucleotide constructs with a poly-T region (see Figs. 1-2, 4, [0004], [0055], [0066], and throughout).
In regards to claims 9 and 10, Oki teaches using a T7 promoter and T7 polymerase, reading on the limitation of an amplification template amplified with a polymerase specific to the promoter region of the oligonucleotide construct (see Fig. 1 & 4, [0004], [0048], and throughout).
In regards to claim 11, Oki teaches that the amplified amplification templates are used for sequencing, specifically Oki teaches improving upon cell expression by linear amplification and sequencing (CEL-Seq) techniques throughout the publication (see Fig. 2 & 5, [0003]-[0005], [0048], and throughout).
In regards to claim 12, While Oki and Honda teach using photo-isolation chemistry to determine expression profile of cells and subsequently the limitations of claim 1. Oki discloses scanning defined regions of interest of a biological sample with focused light to generate region-specific nucleic acid templates (see Fig. 2, 7, [0016]-[0027], [0049], [0060], and throughout). Honda further discloses optical systems for directing focused light to selected regions of a biological sample in photo-isolation workflows, including the use of optical components to steer and control the beam path to achieve spatially selective illumination (see Abstract, Figs. 1-4, pg. 2 para 4-6, pg. 3, pg. 9 para. 9- pg. 10 para.1, and throughout).
Although Oki and Honda do not explicitly describe an optical scanning unit comprising two prisms arranged in the beam path, the use of prisms as beam-directing optical elements in light-scanning systems was well known in the art. It would have been obvious to one of ordinary skill in the art at the time of filing to implement the beam-steering and scanning functions disclosed by Oki and Honda using prisms arranged in beam path as a predictable and routine optical design choice. The selection of specific optical components for directing and scanning light represents a matter of ordinary engineering optimization and does not change the underlying spatially selective illumination method. One of ordinary skill in the art would recognize prism can be used to disperse light, and that the double prism configuration can act as a tunable monochromator used to select the desired wavelength of light. It would have been obvious to one of ordinary skill in the art at the time of filing to substitute a double prism monochromator, filter cube, or digital micromirror device, to select the necessary parameters for uncaging.
In regards to claims 13 and 14, Honda discloses methods wherein the biological sample is stained and imaged prior to directing the light beams to regions of interest (see Fig. 1, pg. 5 para. 3-4, pg. 9 para 5 & 8). Honda further teaches selecting regions based on image data and directing focused light to those selected regions to selectively activate or isolate nucleic acids (see Fig. 1, pg. 9 para. 5 and 8). Honda describes integrating imaging data with photo-isolation workflows to enable precise spatial targeting of light to defined tissues regions (see pg. 9 para 1 and throughout). In such systems, regions identified in image data are translated into corresponding coordinates within a scanning coordinate system to enable directing the light beam to the selected spatial locations.
It would have been prima facie obvious to one of ordinary skill in the art at the time of filing to modify the spatially selective light-directed method of Oki to incorporate the imaging-guided region identification and targeting approach taught by Honda, including staining and imaging a biological sample to identify regions of interest and generating corresponding scanning coordinates to direct light beams to those regions. Such integration represents a predictable and routine implementation of image-guided optical scanning techniques in spatial transcriptomic workflows, and one of ordinary skill in the art would have had a reasonable expectation of success in making such a modification.
In regards to claims 15-17, as set forth in the rejection of claim 1, Oki in view of Honda teach or suggest a method for spatially selective light-directed processing of a biological sample to generate region-specific nucleic acid templates. The system recited in claim 15 is directed to performing the method of claim 1 and therefore requires the structural components capable of carrying out the previously discussed steps. Oki discloses directing focused light to defined regions of interest within a biological sample, which necessarily requires a light-delivery and scanning unit capable of scanning first and second regions of interest with respective light beams. Honda disclose imaging biological samples to identify regions of interest and integrating imaging systems with light-directed spatial processing workflows. It would have been obvious to one of ordinary skill in the art to provide the spatially selective system of Oki with an imaging unit as taught by Honda and to configure the system to scan first and second regions of interest using respective light beams in order to enable imaging-guided spatial targeting.
With respect to claim 16, configuring the scanning unit to generate light beams having differing light parameters such as wavelength, intensity, or exposure duration represents predictable and routine implementation of optical scanning systems as discussed in connection with claim 1.
In regards to claim 17, although Oki and Honda do not explicitly describe the scanning unit as comprising two prisms arranged in the beam path, the use of prisms as beam-directing optical elements in light scanning systems was well known in the art. Implementing the beam-steering function using prisms arranged in the beam path represents a predictable optical design choice that does not alter the fundamental operation of the system.
Claims 1-17 are rejected under 35 U.S.C. 103 as being unpatentable over Oki et al. (US 2022/0251639 A1, listed on IDS as translation of WO 2020/235563 A1, published Nov. 26 2020) in view of Honda et al. (Nat. Comm., (2021) 12:4416) as applied to claims 1-4, 8-17 above and included here for reasons supra, and further in view of Eberwine et al. (US 2017/0253876 A1, published Sep. 7, 2017) and Pirrung et al. (Bioconjugate Chem., 1996, 7, 317-321).
Eberwine, like Oki and Honda, is in the field of nucleic acid detection, and likewise teaches methods and compositions utilizing oligonucleotides with photolabile molecules to spatially isolate molecules of interest, while Pirrung discloses methods for spatially defined immobilization of affinity tags useful in biochip generation.
In regards to claim 5, while Oki in view of Honda disclose generating region-specific nucleic acid material from a biological sample using spatially selective light exposure. Eberwine further discloses oligonucleotide-based workflows for spatial transcriptomic analysis in which oligonucleotide constructs are modified to include affinity reagents, such as biotin, and are subsequently isolated or enriched by affinity capture, for example using streptavidin-based pull-down, to facilitate downstream amplification, sequencing and analysis. Eberwine further teaches that such affinity-tagged oligonucleotide constructs may be used to recover nucleic acid templates corresponding to defined regions of a biological sample (see Abstract, Figs. 4, 17, 19-20, & 22, [0049], [0195]-[0196], and throughout). Accordingly, it would have been obvious to one of ordinary skill in the art at the time of filing, to modify the oligonucleotide constructs used in spatially selective methods of Oki as applied in photo-controlled spatial workflows such as those taught by Honda to include affinity reagents on the first and second oligonucleotide constructs, as taught by Eberwine in order to facilitate downstream handling or isolation of region-specific amplification templates.
In regards to claims 6 and 7, as outlined above, Oki in view of Honda and Eberwine disclose oligonucleotide constructs comprising affinity reagents, such as biotin, that enables selective isolation of spatially-selective, region specific, nucleic acid templates by affinity capture. However, neither Oki, Honda nor Eberwine explicitly teach that the photoremovable cage molecule is bound directly to the affinity reagent.
Pirrung discloses methods for spatially defined immobilization of biomolecules using caged biotin, wherein a photoremovable protecting group is bound directly to the biotin moiety, thereby preventing streptavidin binding until removal of the cage by light exposure. Pirrung further teaches that spatially selective illumination removes the cage and restores affinity biding in defined regions, thereby enabling affinity capture based on the affinity reagent (see pg. 317 Introduction and throughout).
Accordingly, it would have been obvious to one of ordinary skill in the art at the time of filing to bind the photoremovable cage molecule to the affinity reagent of the oligonucleotide constructs of Eberwine, as incorporated into the spatially selective workflow of Oki and Honda, in order to enable light-controlled affinity functionality within the region-specific nucleic acid generation method. Pirrung demonstrate that photoremovable cages bound to affinity reagents function predictably and compatibly with light-directed spatial processing.
Conclusion
No claim is allowed.
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/MATTHEW HAROLD RAYMONDA/Examiner, Art Unit 1684
/AARON A PRIEST/ Primary Examiner, Art Unit 1681