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 .
Applicant’s amendment to the claims and arguments filed on 01-21-2026 has been entered. Claims 1, 7 have been amended. Claims 2-3, 5-6 are canceled. Claims 1, 4, 7-11 are pending and under consideration.
Priority
The filing date of this application is 12/06/2021. There is no US Provisional application or Foreign application for priority claim.
Withdrawn -Claim Rejections - 35 USC § 112
Claims 1, 4-5, 7-11 were rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention. In view of Applicants' amendment of base claims 1 and 7, the previous rejections of claims are hereby withdrawn. Applicants' arguments with respect to the withdrawn rejections are thereby rendered moot. The claims are however subject to new rejections directed to new limitation.
Withdrawn -Claim Rejections - 35 USC § 103- necessitated by amendments
Claims 7-8 were rejected under 35 U.S.C. 103 as being unpatentable over Barrett (Pub. No.: US 2017/0296700 Al, Pub. Date: Oct. 19, 2017.) in view of Patel et al (Connective Tissue Research, 59(5), 447–457. https://doi.org/10.1080/03008207.2018.1470168, 10 May 2018). In view of Applicants' amendment of base claims 1 and 7, introducing the limitation “selecting and purifying explant cells using droplet digital polymerase chain reaction (ddPCR) guided sorting to obtain a purified population wherein at least 90% of the explant cells express more than 100 copies of the gene tenomodulin (TNMD) and more than 1,000 copies of the gene scleraxis (Scx) per µg of cDNA”. The previous rejections of claims 7-8 (method) are hereby withdrawn. Applicants' arguments with respect to the withdrawn rejections are thereby rendered moot. The product claims 1, 4, 9-11 are however subject to new rejections over the prior art of record as set forth below since the newly added limitations are interpreted as product by process. Note: the support for the limitation can be found in the instant disclosure example 2, page 23.
New-Claim Rejections - 35 USC § 112- necessitated by amendments
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.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1, 4, 7-11 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claims 1 and 7 recite the phrase “the intercellular adhesion bonds between the expanded and suspended isolated tendon explant cells are broken.” Which is vague and renders the claims indefinite. It is unclear what “intercellular adhesion bonds” are referring to bonds from direct cell-cell contact or indirect contact via extracellular matrix bond. It is noted that tendon cells, primarily tenocytes, are connected and organized within a hierarchical network of extracellular matrix (ECM), which is mainly composed of type I collagen fibers.
The instant disclosure only stated that “The term "enzymatic dissociation step" is to be understood as any step, involving an enzyme or a solution (digestion solution) comprising an enzyme, which results in complete or partial disconnection of cells normally present within a geometrically arranged two-dimensional or three-dimensional structure, e.g. a tendon sample. As a final result, a tendon cell solution is eventually obtained, preferably mainly consisting of single tendon cells and/or tendon cell clusters. Dissociation occurs preferably by breaking of the intercellular adhesion bonds of tendon cells.” (Page 6, last para to page 7). However, it is unclear what kind of “intercellular adhesion bonds” can be included or excluded. Furthermore, it is unclear if all or a portion of entire “intercellular adhesion bonds” are broken, and it is unclear if the cells are fully or partially dissociated because the specification also contemplate the embodiments with “tendon cell clusters”. Thus, the claim does not specify the degree to which cell-to-cell and cell-to-extracellular matrix interactions are disrupted by the enzymatic dissociation step, such that the claim can be encompassing embodiments where no meaningful disruption of such cell-cell and cell-extracellular matrix interactions has occurred (e.g., disruption of 1 bond, 2 bonds or how many bonds).
Claim 1 also recites “as determined on a per-cell basis by droplet digital polymerase chain reaction (ddPCR) express more than 100 copies of the gene tenomodulin (TNMD) and more than 1,000 copies of the gene scleraxis (Sex) per µg of cDNA”. Thus, claim 1 requires using droplet digital polymerase chain reaction (ddPCR) on a per-cell basis but also require copies per µg of cDNA not copies per cell. It is unclear how using ddPCR on a per-cell basis with the unit of copies per microliter.
Claims 4, 8-11 are included in the rejection because they directly or indirectly depend from base claim. Appropriate correction is required.
New-Claim Rejections - 35 USC § 112- necessitated by amendments (New matter)
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.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
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 of carrying out his invention.
Claims 1, 4, 9-11 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention. This is a new matter rejection.
In the instant case, the recitation of “as determined on a per-cell basis by droplet digital polymerase chain reaction (ddPCR)” in claim 1 is considered new matter. Applicants do not explicitly point for the specific support of the claimed amendment. Upon further review of the instant specification, examiner could not find support for the recited limitations. There is no explicit or implicit support for “as determined on a per-cell basis”. The guidance provided in the instant specification is limited to, for example, “determining the absolute concentration of the target of interest in terms of the number of copies per microliter (cp/µL) in the ddPCR reaction” (see page 17, 1st para.), “Gene copy numbers (copies/l00µg RNA) were found to be stably expressed under the culture conditions described herein” (page 24, 2nd para.), “Analysis of the data with respect to copies/µg cDNA is consistent with the full array of analyses used to determine the cellular characteristics of the cellular products including assessment of morphology and growth characteristics” ” (page 26, last para.). Thus, there is no guidance for “as determined on a per-cell basis”. Note: The unit determined on a per-cell basis by droplet digital PCR (ddPCR) for quantifying genetic material (such as transgene copies, virus genomes, or gene copy number variations) is typically expressed as copies per cell. Thus, before the effective filing date of claimed invention, an Artisan of skill in the art would not recognize from the disclosure that Applicant was in possession of “as determined on a per-cell basis by droplet digital polymerase chain reaction (ddPCR)”. In case if applicants have evidence to support otherwise, applicants are invited to indicate page and line number for the written support specifically for said limitations. MPEP 2163 .06 notes "If new matter is added to the claims, the examiner should reject the claims under 35 U.S.C. 112, first paragraph-written description requirement". In re Rasmussen, 650 F.2d 1212, 211 USPQ 323 (CCPA 1981)". Claims 4, 9-11 are directly or indirectly depends from the rejected base claim. This is a new matter rejection.
Maintained in modified form - Claim Rejections - 35 USC § 101 - necessitated by amendments
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1, 4, 9-11 remain rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception without significantly more.
Claim interpretation:
Amended claims 1, 4, 9-11 with recitation in base claim 1 of the phrases “purified”, “wherein the tendon explant cells are selected and purified by droplet digital polymerase chain reaction (ddPCR) to meet said copy-number threshold”, “suspended isolated” are interpreted as product by process limitation as directed to tendon explant cells. MPEP 2113 states that “[E]ven though product-by-process claims are limited by and defined by the process, determination of patentability is based on the product itself. The patentability of a product does not depend on its method of production. If the product in the product-by-process claim is the same as or obvious from a product of the prior art, the claim is unpatentable even though the prior product was made by a different process.” In re Thorpe, 777 F.2d 695, 698, 227 USPQ 964, 966 (Fed. Cir. 1985) (citations omitted). In the instant case, the “the selectively expanded and suspended tendon explant cells undergo at least one enzymatic dissociation step prior to being suspended” appears to be similar to natural occurring tendon cells.
Step 1: Is the claim to a process, machine, manufacture or composition of matter?
The claims recite “expanded and suspended isolated tendon explant cells”. Here, because the cell population is a composition of matter, the claim is to at least one statutory category of invention (Step 1: YES).
Step 2(A), Prong 1: Does the claim recite an abstract idea, law of nature or natural phenomenon?
Under the broadest reasonable interpretation, the terms of the claim are presumed to have their plain meaning consistent with the specification as it would be interpreted by one of ordinary skill in the art (See MPEP 2111). The specification and the claims describe a therapeutic cellular-composition comprising expanded and suspended isolated tendon explant cells which cells express more than 100 copies of the gene tenomodulin (TNMD) and more than 1,000 copies of the gene scleraxis (Scx) per µg of cDNA. The broadest reasonable interpretation covers the naturally occurring composition comprising tendon explant cells expressing different genes.
Claim 1 is directed to a therapeutic cellular composition comprising selectively expanded and suspended isolated tendon explant cells, wherein the selectively expanded and suspended tendon explantcells express more than 100 copies of the gene tenomodulin (TNMD) and more than 1,000 copies of the gene scleraxis (Scx) per µg of cDNA as detected by droplet digital polymerase chain reaction (ddPCR), wherein the composition comprises a therapeutically effective amount of the selectively expanded and suspended isolated tendon explant cells, and wherein the selectively expanded and suspended tendon explant cells undergo at least one enzymatic dissociation step prior to being suspended. Claim 4 is directed to the therapeutic cellular composition of claim 1, wherein said tendon cells further express one or more marker selected from the group consisting of collagen I (CollA1), thrombospondin-4 (TSP-4), tenascin-C (TSC), decorin (DCN), fibronectin (FN1), biglycan (BGN), and fibromodulin (FMOD) or combination thereof. Claim 5 is directed to the therapeutic cellular composition of claim 4, further comprising a pharmaceutically acceptable carrier. Claim 9 is directed to the therapeutic cellular composition of claim 1, wherein the scleraxis gene expression is greater than or equal to 10,000 copies per µg of cDNA. Claim 10 is directed to the therapeutic cellular composition of claim 4, wherein the COLlAl gene expression is greater than or equal to 10,000 copies per µg of cDNA. Claim 11 is directed to the therapeutic cellular composition of claim 1, wherein the tenomodulin (TNMD) gene expression is greater than or equal to 1,000 copies per µg of cDNA.
The markedly different characteristics analysis is performed by comparing the nature-based product limitation in the claim to its naturally occurring counterpart to determine if it has markedly different characteristics from the counterpart. MPEP 2106.04(c) (11). Here, the closest natural counterpart is naturally occurring tendon tissues or tendon cells. When the claimed tendon explant cells are compared to this counterpart, the comparison indicates that there are no differences in structure, function, or other characteristics. The claims recite the tendon explant cells have gene expression of more than 100 copies of the gene tenomodulin (TNMD) and more than 1,000 copies of the gene scleraxis (Scx) per µg of cDNA detected by droplet digital polymerase chain reaction. The expression of these genes is naturally occurring in tendon cells without requirements of any cellular modification as described in the 35 USC§ 103 rejection described below. Briefly, Patel et al (Connective Tissue Research, 59(5), 447–457. DOI: 10.1080/03008207.2018.1470168, 10 May 2018) teach “Total RNA for gene expression analysis was isolated from patellar tendons” (Page 2, right column, last para.) and “ddPCR reactions were prepared in duplex, ……, cDNA (1 ng or 15 ng, Table 2)” (Page 3, left column, 1st para.) and Patel et al teach more than 100 copies of the gene tenomodulin (TNMD) and more than 1,000 copies of the gene scleraxis (Scx) per µg of cDNA (See table 2 below). It is noted that according to table 2: there are about 3520 SCX copies in 15ng (234667 SCX copies in 1 µg) and 2136 copies TNMD in 1 ng (about 2136000 TNMD copies in 1 µg). Since patellar tendons is product of nature and having teach more than 100 copies of the gene tenomodulin (TNMD) and more than 1,000 copies of the gene scleraxis (Scx) per µg of cDNA, the claimed cellular composition is not markedly different from product of nature.
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The newly added limitation of at least 90% cells expressing TNMD and Scx has also been considered. However, Li et al (Front. Cell Dev. Biol. 9:629515. doi: 10.3389/fcell.2021.629515) teach “Tenocytes are tendon-specific fibroblasts and are considered to be made up approximately 95% of tendon tissue…... Tenocytes are laid between collagen fibrils and are in charge of the production of extracellular matrix (ECM) as well as maintenance and restore of tendon tissue” (Page 2, left column, 3rd para.) and Scleraxis (Scx) and Tenomodulin (TNMD) are confirmed to be relatively specific molecular markers of tendons and Tenocytes (Page 2, left to right column). Thus, approximately 95% of tendon tissue is Tenocytes which express both Scleraxis (Scx) and Tenomodulin (TNMD) and the limitation of does not make the claimed cellular composition markedly different from product of nature.
Additionally, gene expression levels in tenocytes/ tendon cells are highly dynamic and subject to variation based on a variety of natural factors that influence tendon metabolism, structure, and function. Key factors including mechanical loading: Tenocytes are mechanosensitive cells that alter gene expression in response to physical forces; Inflammatory and Cytokine Signaling: Inflammatory environments can significantly alter gene expression, shifting the balance from tissue repair to degradation; Growth Factors and Signaling Pathways: Key growth factors such as TGF-β2, TGF-β3, and BMP12 are essential for regulating tenogenic markers, including scleraxis (SCX), tenomodulin (TNMD), and mohawk (MKX); Environmental Cues: The 3D environment, including extracellular matrix (ECM) composition, stiffness, and nutrient availability, influences tenocyte phenotype; Injury Response: Following injury, tenocytes change their expression profile to initiate a healing response, which often involves temporary upregulation of specific markers like Tenascin-C (TNC); Transcriptional Regulation: The expression of tenocyte genes is controlled by key transcription factors, including Scleraxis (SCX), Mohawk (MKX), and Early Growth Response protein-1 (EGR-1). Therefore, there is no evidence in record that expression level of TNMD and Scx as recited in the claims are markedly different from the product of nature which have wide ranges of gene expression levels.
Next, there are no modification in the cells for the expression of the group of markers consisting of Col1A1, TSP-4, TSC, DCN, FN1, BGN, and FMOD. The claims recite “expanded and suspended isolated tendon explant cells”; however, there is no difference in the claims to distinguish the “expanded and suspended isolated tendon explant cells” with the naturally occurring tendon explant cells. Further, the limitation “the expanded and suspended tendon explant cells undergo at least one enzymatic dissociation step prior to being suspended” is interpreted as a product by process limitation that does not necessarily distinguish structurally or functionally the claimed tendon explant cells from naturally occurring tendon cells. For example, this phrase does not specify the degree to which cell-to-cell and cell-to-extracellular matrix interactions are disrupted by the enzymatic dissociation step, such that it is reasonable to interpret this limitation as encompassing embodiments where no meaningful disruption of such cell-cell and cell-extracellular matrix interactions has occurred. In other words, this phrase does not necessarily mean that a change to the enzymatically-treated cell population is significant enough to make the treated cell population markedly different from their natural counterparts in this regard. Similarly, the limitation “wherein the intercellular adhesion bonds between the expanded and suspended isolated tendon explant cells are broken” does not make the claimed product structurally or functionally markedly different from product of nature as explained above.
Furthermore, intercellular adhesion bonds between tenocytes (specifically cadherins and gap junctions) can be broken and remodeled naturally in vivo. These dynamic changes occur as part of the tendon's response to mechanical loading, injury repair, and remodeling:
Sakai et al (J. Biol. Chem. (2025) 301(4) 108353, Doi: 10.1016/j.jbc.2025.108353) teach “Tendon is a dense fibrous connective tissue with an abundant extracellular matrix (ECM)” (page 1, left column) and “In the intrinsic cellular process, cells derived from both the tendon parenchyma (residential tenocytes) and the peritenon migrate to the wound site and synthesize new ECM which is primarily composed of collagens” (page 1, right column, last para.).
Leong et al (J Orthop Res. 2020 January ; 38(1): 7–12. doi:10.1002/jor.24475) teach “other studies on tendon and ligament healing have also observed migration of cells from the epitenon into the injury site. Recent studies using murine genetic lineage tracing have identified several distinct populations of resident tendon stem/progenitor cells that are involved in tendon healing. These include cells from tendon fascicles with markers Sca-1, CD90, CD44, Scx, and Tnmd, cells from epitendon with markers Sca-1, Laminin, αSMA and PDGFα 40,41, and perivascular cells from epitendon with markers αSMA, Nes, and CD133” (Page 4, 2nd para.).
The bond between tendon cells (tenocytes) and the extracellular matrix (ECM) can be broken naturally by natural enzymes as part of normal tissue remodeling, repair, and adaptation to mechanical stress:
Buono et al (Muscles, Ligaments and Tendons Journal 2013; 3 (1): 51-57) teach that “Matrix metalloproteinases (MMP) are involved in the development of tendinopathy. These potent enzymes completely degrade all components of the connective tissue, modify the extracellular matrix (ECM), and mediate the development of painful tendinopathy. To control the local activity of activated proteinases, the same cells produce tissue inhibitors of metalloproteinases (TIMP). These latter bind to the enzyme and prevent degradation. The balance between the activities of MMPs and TIMPs regulates tendon remodeling, whereas an imbalance produces a collagen dis-regulation and disturbances in tendons. ADAMs (a disintegrin and metalloproteinase) are cell membrane-linked enzymes with proteolytic and cell signaling functions. ADAMTSs (ADAM with thrombospondin motifs) are secreted into the circulation and constitute a heterogenous family of proteases with both anabolic and catabolic functions. Further studies are needed to better define the mechanism of action, and whether these new strategies are safe and effective in larger models.” (Abstract)
The claims do not specify the difference between the claimed tendon explant cells and naturally occurring tendon cells. Thus, it appears that the claimed “expanded and suspended isolated tendon explant cells” are not markedly different to what exists in nature (e.g., same genotype and phenotype), regardless of how they were prepared or its intended use for therapeutic purposes in a therapeutically effective amount or not. There is nothing in the claim that is markedly different phenotypically or functionally from what exists in nature or any difference that arose due to applicant's efforts. The claim thus encompasses cells that are not markedly different to naturally occurring cells. Because there is no difference between the claimed and naturally occurring cells for at least some of the embodiments encompassed by the claim, the claimed cells do not have markedly different characteristics, and thus are a "product of nature" exception. In re Roslin Institute (Edinburgh), 750 F.3d 1333, 1338-39 (Fed. Cir. 2014).
Therefore, it is reasonable to conclude that the claimed tendon explant cells are not markedly different from its closest naturally-occurring counterpart (Step 2A, Prong I: YES).
Step 2(A), Prong 2: Do the claims recite additional elements that integrate the judicial exception into a practical application?
In view of foregoing analysis, it is apparent that the claims recite judicial exceptions that are product of nature. While the claims would still be patent-eligible if “the claims as a whole integrate the recited judicial exceptions (product of nature) into a practical application of the exception”, the additional limitations recited in the instant claims do not integrate the judicial exceptions into a practical application of the recited judicial exceptions. Here, there is no additional element that integrates the recited naturally occurring product (naturally occurring tendon cells) into a practical application of the judicial exception. For example, claim 1 is directed to a therapeutic cellular composition comprising expanded and suspended isolated tendon explant cells, wherein the selectively expanded and suspended tendon explant cells express more than 100 copies of the gene tenomodulin (TNMD) and more than 1,000 copies of the gene scleraxis (Scx) per µg of cDNA as detected by droplet digital polymerase chain reaction (ddPCR). The phrases “selectively expanded and suspended”, “detection by ddPCR”, “at least one enzymatic dissociation step prior to being suspended ”, and “the tendon explant cells are selected and purified by droplet digital polymerase chain reaction (ddPCR) to meet said copy-number threshold” are the product-by-process steps recited/implied by the claim. These limitations are all directed to obtaining the particular cells of the claimed composition, but are not directed to an application of the judicial exception of the claimed explant cells).
The phrase “for tendon-repair therapy” is also considered as intended use; however, the recitation of intended use “for tendon-repair therapy” does not indicate any structural or manipulative difference in the invention recited in the body of the claim. It should be noted that a recitation of the intended use of the claimed invention must result in a structural difference between the claimed invention and the prior art in order to patentably distinguish the claimed invention from the prior art. However, there is no modifications structurally or functionally by applicants’ efforts for this intended use to be practical application.
Claim 4 specifies said tendon cells further express one or more marker selected from the group consisting of collagen I (CollAl), thrombospondin-4 (TSP-4), tenascin-C (TSC), decorin (DCN), fibronectin (FNl), biglycan (BGN), and fibromodulin (FMOD) or combination thereof. Claim 9 specifies the scleraxis gene expression is greater than or equal to 10,000 copies per µg of cDNA. Claim 10 specifies the COLlAl gene expression is greater than or equal to 10,000 copies per µg of cDNA. Claim 11 specifies the tenomodulin (TNMD) gene expression is greater than or equal to 1,000 copies per µg of cDNA. Thus, measuring gene expression with ddPCR and combining the claimed composition with pharmaceutically-acceptable carrier do not integrate the judicial exceptions into a practical application of the recited judicial exceptions.
In summary, there are no additional elements recited in the claims, considered individually or in combination, that integrate the judicial exception of product of nature into a practical application of the judicial exception and the claims are therefore considered to be directed to the judicial exceptions recited in claims 1 (Step 2A, Prong II: NO).
Step 2(B): Does the claim recite additional elements that amount to significantly more than the judicial exception?
There are no elements recited in the claims, other than the naturally occurring cells, that add an inventive concept beyond routine, conventional, or well-understood activities. Thus, the claims recite a naturally occurring tendon cells. The only elements recited in the claims, other than the naturally occurring cells, includes a pharmaceutically acceptable carrier as recited in claim 1. However, it is apparent that the pharmaceutically acceptable carrier does not react with the active composition and do not make modification to the cellular composition. The specification of the claimed invention teaches that “Any suitable pharmaceutical acceptable carrier maybe used as long as it is suitable for use in vivo i.e. inert” (Page 20, 2nd para)
The claims as a whole does not amount to significantly more than the “product of nature” itself. Thus, the claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception and does not qualify as patent eligible subject matter. Therefore, the answer to step 2B of the 101 Subject Matter Eligibility Test is “No” (Step 2B: NO).
Conclusion: Given the analysis above, it is reasonable to conclude that claims 1, 4-5, 9-11 encompass embodiments that are not directed to patent-eligible subject matter.
Response to Arguments
Applicant's arguments filed 01-21-2026 have been fully considered but they are not persuasive.
Applicants argue that recited "expanded and suspended isolated tendon explant cells" of the claimed "therapeutic cellular composition" are now defined in a manner such that they have been altered from their natural state and thus are "markedly different" from any naturally occurring counterpart cell population. Accordingly, the claimed subject matter constitutes a human-made invention rather than a mere discovery of a natural product, and thus satisfies the requirements of § 101.
Even if, arguendo, the tendon cells of the claims are not markedly different from its closest naturally-occurring counterpart, which Applicant is not conceding, additional claim limitations integrate the judicial exception into a practical application under Step 2A Prong 2 of the§ 101 analysis. For example, the amended claims recite a specific treatment: a cellular composition "compris[ing] a therapeutically effective amount" expressly intended "for tendon-repair therapy", thereby converting a natural substance into a man-made therapeutic. As a second example, the amended claims are directed to a technological improvement: the ddPCR-based per-cell selection protocol improves upon prior tendon-cell preparations by delivering >90 % purity and defined gene-expression thresholds, thereby solving the prior art problem of heterogeneity and insufficient potency (see, for example paragraphs [0129]-[0139]).
Furthermore, in view of the claim amendments, which add recitations "a purified population of' and "at least 90% of the therapeutic cellular composition comprises" Applicant submits the claimed therapeutic composition is new and improved because using ddPCR-based cell selection, produces a tangible and useful result (e.g., a purified population of tendon cells with a specific genotype) and thus falls outside inventions that are directed to patent ineligible concepts.
The amended claims are not drawn to a law of nature or natural phenomenon because naturally occurring tendon cells are structurally and functionally distinct from any tendon cells in their natural state and the claimed composition does not occur in nature. (Remarks, page 5-6).
Response to Arguments:
The claimed cells are not markedly different structurally and functionally from tendon cells in their natural state:
The closest natural counterpart is naturally occurring tendon tissues or tendon cells. The claims recite the tendon explant cells have gene expression of more than 100 copies of the gene tenomodulin (TNMD) and more than 1,000 copies of the gene scleraxis (Scx) per µg of cDNA detected by droplet digital polymerase chain reaction. The expression of these genes is naturally occurring in tendon cells without requirements of any cellular modification : Patel et al teach “Total RNA for gene expression analysis was isolated from patellar tendons” (Page 2, right column, last para.) and more than 100 copies of the gene tenomodulin (TNMD) and more than 1,000 copies of the gene scleraxis (Scx) per µg of cDNA (See explanation in the 101 rejection above or 103 rejection below). Since patellar tendons is product of nature and having teach more than 100 copies of the gene tenomodulin (TNMD) and more than 1,000 copies of the gene scleraxis (Scx) per µg of cDNA, the claimed cellular composition is not markedly different from product of nature.
Next, there are no modification in the cells for the expression of the group of markers consisting of Col1A1, TSP-4, TSC, DCN, FN1, BGN, and FMOD. The claims recite “expanded and suspended isolated tendon explant cells”; however, there is no difference in the claims to distinguish the “expanded and suspended isolated tendon explant cells” with the naturally occurring tendon explant cells. Further, the limitation “the expanded and suspended tendon explant cells undergo at least one enzymatic dissociation step prior to being suspended” is interpreted as a product by process limitation that does not necessarily distinguish structurally or functionally the claimed tendon explant cells from naturally occurring tendon cells. For example, this phrase does not specify the degree to which cell-to-cell and cell-to-extracellular matrix interactions are disrupted by the enzymatic dissociation step, such that it is reasonable to interpret this limitation as encompassing embodiments where no meaningful disruption of such cell-cell and cell-extracellular matrix interactions has occurred. In other words, this phrase does not necessarily mean that a change to the enzymatically-treated cell population is significant enough to make the treated cell population markedly different from their natural counterparts in this regard.
The limitation “wherein the intercellular adhesion bonds between the expanded and suspended isolated tendon explant cells are broken” does not make the claimed product structurally or functionally markedly different from product of nature. Furthermore, intercellular adhesion bonds between tenocytes (specifically cadherins and gap junctions) can be broken and remodeled naturally in vivo. These dynamic changes occur as part of the tendon's response to mechanical loading, injury repair, and remodeling (see above).The bond between tendon cells (tenocytes) and the extracellular matrix (ECM) can be broken naturally by natural enzymes as part of normal tissue remodeling, repair, and adaptation to mechanical stress (see above).
There is no additional element that integrates the recited naturally occurring product (naturally occurring tendon cells) into a practical application of the judicial exception.
The phrases “selectively expanded and suspended”, “detection by ddPCR”, “at least one enzymatic dissociation step prior to being suspended ”, and “the tendon explant cells are selected and purified by droplet digital polymerase chain reaction (ddPCR) to meet said copy-number threshold” are the product-by-process steps recited/implied by the claim. These limitations are all directed to obtaining the particular cells of the claimed composition, but are not directed to an application of the judicial exception of the claimed explant cells).
The phrase “for tendon-repair therapy” is also considered as intended use; however, the recitation of intended use “for tendon-repair therapy” does not indicate any structural or manipulative difference in the invention recited in the body of the claim. It should be noted that a recitation of the intended use of the claimed invention must result in a structural difference between the claimed invention and the prior art in order to patentably distinguish the claimed invention from the prior art. However, there is no modifications structurally or functionally by applicants’ efforts for this intended use to be practical application.
There are no elements recited in the claims, other than the naturally occurring cells, that add an inventive concept beyond routine, conventional, or well-understood activities.
The only elements recited in the claims, other than the naturally occurring cells, includes a pharmaceutically acceptable carrier as recited in claim 1. However, it is apparent that the pharmaceutically acceptable carrier does not react with the active composition and do not make modification to the cellular composition. The specification of the claimed invention teaches that “Any suitable pharmaceutical acceptable carrier maybe used as long as it is suitable for use in vivo i.e. inert” (Page 20, 2nd para).
Maintained in modified form and New -Claim Rejections - 35 USC § 103- necessitated by amendments
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.
Claims 1, 4, 9-11 remain rejected under 35 U.S.C. 103 as being unpatentable over Barrett (Pub. No.: US 2017/0296700 Al, Pub. Date: Oct. 19, 2017.) in view of Patel et al (Connective Tissue Research, 59(5), 447–457. https://doi.org/10.1080/03008207.2018.1470168, 10 May 2018) as evidenced by Li et al (Front. Cell Dev. Biol. 9:629515. doi: 10.3389/fcell.2021.629515).
Claim interpretation:
Claims 1, 4, 9-11 with the limitations “as determined on a per-cell basis by droplet digital polymerase chain reaction (ddPCR)”, “the selectively expanded and suspended tendon explant cells undergo at least one enzymatic dissociation step prior to being suspended” ; “the tendon explant cells are selected and purified by droplet digital polymerase chain reaction (ddPCR) to meet said copy-number threshold” are interpreted as product by process limitation. MPEP 2113 states that “[E]ven though product-by-process claims are limited by and defined by the process, determination of patentability is based on the product itself. The patentability of a product does not depend on its method of production. If the product in the product-by-process claim is the same as or obvious from a product of the prior art, the claim is unpatentable even though the prior product was made by a different process.” In re Thorpe, 777 F.2d 695, 698, 227 USPQ 964, 966 (Fed. Cir. 1985) (citations omitted).
The specification of the claimed invention teaches that “Gene copy numbers (copies/l00µg RNA) were found to be stably expressed under the culture conditions described herein” (Page 24, Example 2) and “The total amount of cDNA per ddPCR reaction (in final volume of 20µL) (per Table 1) was used to calculate the copies target gene per µg cDNA” (Page 24, Example 2, also see Table 1). Therefore: (i) “Copies of the gene” in claim 1 is interpreted as encompassing the use of RNA to make cDNA for counting copies number in ddPCR; (ii) the gene expression in claims 9, 10, 11 is interpreted as encompassing being measured by copies of the gene by ddPCR.
The phrase “for tendon-repair therapy” is interpreted as intended use. It should be noted that a recitation of the intended use of the claimed invention must result in a structural difference between the claimed invention and the prior art in order to patentably distinguish the claimed invention from the prior art.
Regarding to claims 1, 4, 9-11, Barrett teaches formulations that can contain an amount a therapeutically effective amount of a cell population ([0173], page 9), and populations of tendon progenitor cells (TPCs) composition can be made by isolating a piece of tendon tissue ([0153], page 8). Barrett teaches isolation of tendon cells: Tendon tissue (e.g., about a 2cm x 2cm x 6cm piece) was dissected from the outer covering of the tendon (e.g., superficial digital flexor tendon) and kept in warm media until processing and about 10 mL collagenase containing solution was used per about 1 g of tendon tissue. ([0338], page 21). Barrett teaches expanded and suspended tendon explant cells undergo at least one enzymatic dissociation step : The resulting pellet was resuspended in 15 mL of a solution containing 2% dispase (enzymatic dissociation) ([0339], page 21). The resulting pellet was resuspended in Tendon Medium, and collected cells were plated on tissue/cell culture plates (e.g., T75 culture flasks) ([0340], page 21). Plated cells were feed every two days after having had about 4 days to attach to the cell culture plate. When cells were about 80% confluent, cells were passaged ([0341], page 21). Barrett teaches suitable pharmaceutically acceptable carriers include, but are not limited to, water, salt solutions, alcohols, gum Arabic, vegetable oils, benzyl alcohols, polyethylene glycols, gelatin, carbohydrates such as lactose ([0176], Page 9).
It is also noted that Barrett teaches expanded and suspended tendon explant cells undergo at least one enzymatic dissociation step : “About 10 mL collagenase containing solution was used per about 1g of tendon tissue” ([0338], page 21), and “the resulting pellet was resuspended in 15 mL of a solution containing 2% dispase” (enzymatic dissociation) ([0339], page 21), and the specification of the claimed invention teaches “Suitable enzymatic solutions (digestion solution) that can be used for this enzymatic dissociation step may comprise Collagenase type I, Collagenase type II, Collagenase type III, papain and Dispase” (page 7, 3rd para). Thus, applicant’s disclosure provide evidence for using Collagenase and dispase in dissociation step so that it is inherent that the intercellular adhesion bonds between the expanded and suspended, isolated tendon explant cells are broken by using collagenase and/or dispase.
Barrett teaches mRNA profiles of tenocytic marker genes scleraxis (SCX) (FIG. 49A), collagen types-I/III (COL-I (FIG. 49B) and COL-III (FIG. 49C)), decorin (DCN) (FIG. 49D), and biglycan (BGN) (FIG. 49E) ([0053], page 2) (For claim 1 and 4).
Barrett does not specifically teach cells express more than 100 copies of the gene tenomodulin (TNMD) and more than 1,000 copies of the gene scleraxis (Scx) per µg of cDNA as detected by droplet digital polymerase chain reaction (PCR) (Claim 1). Barrett does not specifically teach scleraxis (Scx) gene expression is greater than or equal to 10,000 copies per µg of cDNA (Claims 9), the COLlA1 gene expression is greater than or equal to 10,000 copies per µg of cDNA (Claims 10), the tenomodulin (TNMD) gene expression is greater than or equal to 1,000 copies per µg of cDNA (Claims 11). However, Patel et al cures the deficiency.
Patel et al teach RNA was isolated from the patellar tendon for determination of mRNA transcripts using droplet digital PCR (ddPCR) (Abstract). Patel et al teach “Tendon gene expression” (Page 2 right column), and ddPCR reactions were prepared in duplex, in a final volume of 20 µl with 2x ddPCR Supermix for Probes (No dUTP) (BioRad), 20x reference probe FAM, 20x reference probe HEX, cDNA (1 ng or 15 ng, Table 2) (Page 3, left column).
Patel et al teaches transcripts counts for Col1a1, Scx, Tnmd (Page 4, table 2). Note: control group is non-diabetic sample.
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Patel et al also teaches copy numbers of Tnmd, Scx, and Col1a1 in 20ul in Figures 2 and 4 (page 5 and 6, respectively).
According to Tendon gene expression in the Materials and methods (Page 3, left column) and the above table 2 and Figure 2 and 4:
Copy number of Tnmd is 2136 per 1ng of cDNA. Therefore, 1000 ng (1µg) should have at least 2136 x 1000 = 2136000 copies (For claims 1, 11).
Copy number of Scx is 3520 per 15 ng of cDNA. Therefore, 1000 ng (1µg) should have at least (3520 x 1000) /15 = 234666.666 copies (For claims 1, 9).
Copy number of Col1a1 is 43683 per 1ng of cDNA. Therefore, 1000 ng (1µg) should have at least 43683 x 1000 = 43683000 copies (For claims 10).
Since total 20ul final volume of the reaction in ddPCR contains 1ng – 15ng of cDNA input, the copy number of Scx, TNMD, and Col1a1 can be calculated as above for 1µg of cDNA and the expression of these genes is more than 10,000 copies per µg of cDNA. This information can be used as references to isolate different tendon samples with high expression of TNMD, Scx, and Col1a1.
Therefore, it would have been prima facie obvious for a person of ordinary skill in the art before the effective filing date of the rejected claims to combine the teachings of prior art to modify the method of obtaining a cellular composition comprising tendon cells isolated from tendon tissue with mRNA profiles of tenocytic marker genes as taught by Barrett by determining gene expression of tendon marker (Scx, TNMD, and Col1a1) from the patellar tendon using droplet digital PCR (ddPCR) as taught by Patel et al as instantly claimed, with a reasonable expectation of success. Said modification amounting to combining prior art elements according to known methods to yield predictable results. One of ordinary skill in the art would have been motivated to do so because Patel et al stated that utilizing ddPCR offers many advantages over traditional qRT-PCR including increased target sensitivity (sensitive to one transcript), absolute quantification of gene targets without the need of standard curves, and the ability to report data without the need of an endogenous control gene (Page 3, left column) and showing rapid and large changes in the expression of several genes that are key to ECM remodeling, maintenance, and maturation (Abstract). One of ordinary skill in the art would have had a reasonable expectation of success in doing so because Barrett and Patel et al both provide detailed instruction for culturing tendon cells and measuring gene expression of marker of tendon cell.
As mentioned above, Barrett teaches mRNA profiles of tenocytic marker genes scleraxis (SCX) (FIG. 49A), collagen types-I/III (COL-I (FIG. 49B) and COL-III (FIG. 49C)), decorin (DCN) (FIG. 49D), and biglycan (BGN) (FIG. 49E) ([0053], page 2), and gene expression profiles during bioreactor-induced tenogenesis ([0388], page 27) and relative gene expression data is shown in FIGS. 62A-62J ([0389], page 27) and “highly purified bovine: tendon, porcine: dermis, and rat: tendon” ([0320], page 19). Thus, Barrett recognized measuring relative gene expression of TNMD and SCX is result effective variable to measure tendon genes expression for bioreactor-induced tenogenesis, and Barrett concerned about highly purified tendon. Additionally, Patel et al teach “RNA was isolated from the patellar tendon for determination of mRNA transcripts using droplet digital PCR (ddPCR)”. Thus, a person of ordinary skill in the art to combine the teachings of prior art references to use droplet digital PCR for measuring tendon genes expression. (For the claimed: as determined on a per-cell basis by droplet digital polymerase chain reaction (ddPCR)).
As evidenced by Li et al teaches “Tenocytes are tendon-specific fibroblasts and are considered to be made up approximately 95% of tendon tissue…... Tenocytes are laid between collagen fibrils and are in charge of the production of extracellular matrix (ECM) as well as maintenance and restore of tendon tissue” (Page 2, left column, 3rd para.) and Scleraxis (Scx) and Tenomodulin (TNMD) are confirmed to be relatively specific molecular markers of tendons and Tenocytes (Page 2, left to right column). Thus, approximately 95% of tendon tissue as taught by Patel et al is Tenocytes which express both Scleraxis (Scx) and Tenomodulin (TNMD). It is noted that:
Copy number of Tnmd is 2136 copies per 1ng of cDNA. Therefore, 95% is 2029.2 copies per 1ng of cDNA, and 1000 ng (1µg) should have at least 2029.2 x 1000 = 2029200 copies.
Copy number of Scx is 3520 copies per 15 ng of cDNA. Therefore, 95% is 3344 copies per 15 ng of cDNA. 1000 ng (1µg) should have at least (3344 x 1000) /15 = 222,933.33 copies.
Also, Barrett teaches “compositions that can be used to treat soft tissue injuries, including tendon and ligament injuries” (Abstract), and Barrett described formulations that can contain an amount, including a therapeutically effective amount of cell population or composition as described herein ([0173], page 9) and Barrett teaches “effective amount is an amount sufficient to effect beneficial or desired biological, emotional, medical, or clinical response of a cell, tissue, system, animal, or human” ([0096], page 4). Thus, a person of ordinary skill in the art would recognize the amount of cells population in a pharmaceutical composition as result effective variable, and would be motivated to use various amount of cells percentage such as 90% or more in the formulations with measuring relative gene expression of TNMD and SCX also being result effective variable to measure tendon genes expression for bioreactor-induced tenogenesis. (For the claimed: at least 90% of the explant cells express more than 100 copies of the gene tenomodulin (TNMD) and more than 1,000 copies of the gene scleraxis (Scx) per µg of cDNA as detected by droplet digital polymerase chain reaction (ddPCR)).
Response to Arguments
Applicant's arguments filed 01-21-2026 have been fully considered but they are not persuasive.
1. Applicants argue that “Barrett does not teach or suggest measuring specific copy numbers of genes per µg cDNA. Whilst Barrett shows relative gene expression data in the form of fold-change measurements and mRNA profiles, Barrett does not teach measuring absolute copy numbers per µg cDNA. Furthermore, Barrett does not mention droplet digital PCR anywhere in the disclosure, nor teaches selection criteria based on specific gene expression thresholds, such as selecting or purifying cells based on whether they express more than 100 copies of TNMD or more than 1,000 copies of Scx per µg cDNA.”
“Patel does not cure the deficiencies of Barrett. Patel is a review article that discusses the use of tendon explant models as research tools for studying tendon homeostasis and pathophysiology. Patel describes using ddPCR to measure gene expression in tendon tissue samples from diabetic rats…..”
“Importantly, Patel uses ddPCR in a fundamentally different context than the claimed invention. Patel describes tendon explant models as "a valuable tool for the discovery and study of mechanisms associated with tendon homeostasis and pathophysiology" as stated in the Abstract, making clear that the article is about research models rather than therapeutic cell compositions. Patel also measures gene expression in whole patellar tendon tissue samples from rats, not in isolated, expanded, and purified cell populations.” (Remarks, Page 7-9)
Response to Arguments:
In response to applicant's arguments against the references individually pertaining to Barrett and Patel et al, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). Also, it appears that Applicant is arguing that the cited references do not expressly suggest the claimed invention. However, it is well established in case law that a reference must be considered not only for what it expressly teaches, but also for what it fairly suggests. In re Burkel, 201 USPQ 67 (CCPA 1979). Furthermore, in the determination of obviousness, the state of the art as well as the level of skill of those in the art are important factors to be considered. The teaching of the cited references must be viewed in light of these factors. The Barrett reference is cited to show that Barrett teaches isolation of tendon cells: Tendon tissue was dissected from the outer covering of the tendon and kept in warm media until processing and about 10 mL collagenase containing solution was used per about 1 g of tendon tissue ([0338], page 21). Barrett teaches expanded and suspended tendon explant cells undergo at least one enzymatic dissociation step : The resulting pellet was resuspended in 15 mL of a solution containing 2% dispase (enzymatic dissociation) ([0339], page 21). The resulting pellet was resuspended in Tendon Medium, and collected cells were plated on tissue/cell culture plates (e.g., T75 culture flasks) ([0340], page 21). Plated cells were feed every two days after having had about 4 days to attach to the cell culture plate. When cells were about 80% confluent, cells were passaged ([0341], page 21). Barrett teaches suitable pharmaceutically acceptable carriers include, but are not limited to, water, salt solutions, alcohols, gum Arabic, vegetable oils, benzyl alcohols, polyethylene glycols, gelatin, carbohydrates such as lactose ([0176], Page 9).
Patel et al teaches RNA was isolated from the patellar tendon for determination of mRNA transcripts using droplet digital PCR (ddPCR) (Abstract). Patel et al teaches “Tendon gene expression” (Page 2 right column), and ddPCR reactions were prepared in duplex, in a final volume of 20 µl with 2x ddPCR Supermix for Probes (No dUTP) (BioRad), 20x reference probe FAM, 20x reference probe HEX, cDNA (1 ng or 15 ng, Table 2) (Page 3, left column).
Patel et al teaches transcripts counts for Col1a1, Scx, Tnmd (Page 4, table 2). Note: control group is non-diabetic sample.
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One of ordinary skill in the art would have been motivated combine the references because Patel et al stated that utilizing ddPCR offers many advantages over traditional qRT-PCR including increased target sensitivity (sensitive to one transcript), absolute quantification of gene targets without the need of standard curves, and the ability to report data without the need of an endogenous control gene (Page 3, left column) and showing rapid and large changes in the expression of several genes that are key to ECM remodeling, maintenance, and maturation (Abstract).
2. Applicants further argue that Patel cannot cure Barrett's deficiencies because of
(1) Different Biological Materials: “Patel and Barrett work with fundamentally different biological materials. Patel measures gene expression in intact tendon tissue explants that retain native tissue architecture, multiple cell types, cell-cell and cell-matrix connections, and extracellular matrix components. Patel explicitly emphasizes that "tendon explants retain native cell-cell and cell-matrix connections" as a key feature of the explant model (Abstract). In contrast, Barrett works with isolated individual cells that have been enzymatically dissociated from tendon tissue, disrupting cell-cell and cell-matrix connections, and then expanded in culture on plastic surfaces…..”
(2) Tissue-Level vs. Cellular-Level Measurements “Barrett works with isolated cell populations. In contrast, Patel performs bulk tissue measurements where RNA is isolated from whole tendon tissue samples and ddPCR provides a total transcript count representing aggregate expression from all cells and components in the tissue. A bulk measurement from tissue containing, for example, 1,000 cells that shows 3,520 copies of Scx per 15 ng cDNA does not reveal how many individual cells express Scx, what the expression level is in each cell, or what percentage of cells meet any particular threshold. Patel provides no teaching for how to measure gene expression on a per-cell basis using ddPCR, how to determine what percentage of cells in a population meet specific expression criteria, or how to sort or select cells based on such measurements.”
(3) No Teaching of Selection or Purification Methods: “Patel uses ddPCR purely as an analytical technique to characterise tissue samples. The article does not teach or suggest using ddPCR measurements to select cells, sorting cells based on gene expression levels, purifying cell populations to achieve specific purity thresholds, or any method for isolating cells that meet specific expression criteria.”
(Remarks, page 10).
Response to Arguments:
Patel et al and Barrett both work with in intact tendon tissue and isolated individual cells that have been enzymatically dissociated from tendon tissue: Barrett teaches tendon tissue (e.g. about a 2 cmx2 cmx6 cm piece) was dissected from the outer covering of the tendon and dissociated with collagenase and dispase ([0338]-[0339], page 21). Patel et al teach “total RNA for gene expression analysis was isolated from patellar tendons” (Page 2, right column) and mechanically disrupted the tissue and treated with proteinase K to dissociate cells (Page 3, left column). Note: Proteinase K is a powerful, broad-spectrum serine protease used to dissociate cells and tissues by digesting cell membrane proteins and extracellular matrix components.
Applicant also argue that “A bulk measurement from tissue containing, for example, 1,000 cells that shows 3,520 copies of Scx per 15 ng cDNA does not reveal how many individual cells express Scx, what the expression level is in each cell, or what percentage of cells meet any particular threshold. Patel provides no teaching for how to measure gene expression on a per-cell basis using ddPCR, how to determine what percentage of cells in a population meet specific expression criteria, or how to sort or select cells based on such measurements”. It is noted that the claims 1, 4, 9-11 are directed to product by process, and the claims require copies per µg of cDNA not copies per cell. The instant specification teaches “determining the absolute concentration of the target of interest in terms of the number of copies per microliter (cp/µL) in the ddPCR reaction” (see page 17, 1st para.), “Gene copy numbers (copies/l00µg RNA) were found to be stably expressed under the culture conditions described herein” (page 24, 2nd para.), In the instant case, Patel et al teach RNA was isolated from the patellar tendon for determination of mRNA transcripts using droplet digital PCR (ddPCR) (Abstract). Patel et al teach ddPCR reactions were prepared in duplex, in a final volume of 20 µl with cDNA (1 ng or 15 ng, Table 2) (Page 3, left column). Since the claimed product specifically require copies of the gene per µg of cDNA not copies per cell, and the prior art reference Patel et al teach ddPCR with copies per µg of cDNA, the prior art reference’s teachings meet the requirement of the claims.
Regarding applicants’ arguments for “no teaching of selection or purification methods”, as mentioned above, the claims 1, 4, 9-11 are directed to product-by-process. MPEP 2113 states that “[E]ven though product-by-process claims are limited by and defined by the process, determination of patentability is based on the product itself. The patentability of a product does not depend on its method of production. If the product in the product-by-process claim is the same as or obvious from a product of the prior art, the claim is unpatentable even though the prior product was made by a different process.” In re Thorpe, 777 F.2d 695, 698, 227 USPQ 964, 966 (Fed. Cir. 1985) (citations omitted).
3. Applicants further argue that the Office Action states that "Copy number of Tnmd is 2136 per 1 ng of cDNA. Therefore, 1000 ng (1 µg) should have at least 2136 x 1000 =2,136,000 copies." This calculation is fundamentally flawed for several reasons. First, Patel measures expression in 1 ng of cDNA derived from whole tissue whilst the claimed invention measures expression per µg of cDNA from purified cell populations, and these are not equivalent measurements. Second, the calculation assumes a linear relationship between cDNA input and measured copy numbers across three orders of magnitude from 1 ng to 1000 ng - this assumption is not supported by Patel or general knowledge in the art. Third, even if the extrapolation were valid for bulk measurements, Patel provides no teaching for how to determine expression "on a per-cell basis" or how to achieve a population wherein "at least 90%" of cells meet the thresholds. Finally, the expression levels in intact tissue as measured by Patel would not be expected to be the same as in isolated, expanded, suspended cells as required by the claimed invention. The specification acknowledges that "a degree of down-regulation is expected in association with transition from in vivo to in vitro proliferation" as stated in paragraph [0128]. (Remarks, page 10-11).
Response to Arguments:
First, the claims require population of any cells expressing TNMD and Scx in tendon explant, and the claims also recite the term “comprising”. As per MPEP 2111.03 (I), The transitional term "comprising", which is synonymous with "including," "containing," or "characterized by," is inclusive or open-ended and does not exclude additional, unrecited elements or method steps. See, e.g., Mars Inc. v. H.J. Heinz Co., 377 F.3d 1369, 1376, 71 USPQ2d 1837, 1843 (Fed. Cir. 2004). Applicants have not explained and provided evidences for why and how it is not equivalent measurements.
Second, even without the calculation, Patel et al provided raw data: copy number of Tnmd is 2136 per 1ng of cDNA, and copy number of Scx is 3520 per 15 ng of cDNA. These numbers are well above 100 and 1000 copies per µg for Tnmd and Scx, respectively (see Page 4, table 2). Applicants have not explained how these numbers 2136 per 1ng of cDNA and 3520 per 15 ng of cDNA would be lower in 1000ng (1µg) of cDNA.
Third, the claims require copies per µg of cDNA not copies per cell.
Fourth, it is noted that the tendon cells as taught Patel et al are isolated from frozen patellar tendons which are not freshly isolated from in vivo condition: “Total RNA for gene expression analysis was isolated from patellar tendons. ….. frozen tendon tissue was pulverized…..” (Page 2, right column, last para). Also, even the Tnmd and Scx genes in tendon cells will be down regulated over time from in vivo to in vitro proliferation, the cited reference Patel et al clearly provide evidence for the Tnmd and Scx genes in tendon cells at that time point satisfy the requirement of the claims. These are product-by-process claims.
4. Applicants further argue No Motivation to Modify Barrett: Patel's focus is on maintaining tendon explants in culture to study tissue biology under controlled conditions. The article discusses challenges in 'maintaining tendon homeostasis in explants' and states that 'very little is known about the healthy tendon environment' as disclosed on page 10. Patel teaches maintaining intact tissue architecture and cell-cell and cell-matrix connections, stating that "tendon explants retain native cell-cell and cell-matrix connections" and presenting this as a key advantage of explant models in the Abstract. Because Patel is focused on intact tissue explants for research purposes whilst Barrett is focused on isolated therapeutic cells, one of ordinary skill would have no motivation to apply Patel's analytical techniques to Barrett's cell populations, particularly not for the purpose of selecting and purifying cells to achieve specific population characteristics (Remarks, page 11).
Response to Arguments:
In response to applicant’s argument that there is no teaching, suggestion, or motivation to combine the references, the examiner recognizes that obviousness may be established by combining or modifying the teachings of the prior art to produce the claimed invention where there is some teaching, suggestion, or motivation to do so found either in the references themselves or in the knowledge generally available to one of ordinary skill in the art. See In re Fine, 837 F.2d 1071, 5 USPQ2d 1596 (Fed. Cir. 1988), In re Jones, 958 F.2d 347, 21 USPQ2d 1941 (Fed. Cir. 1992), and KSR International Co. v. Teleflex, Inc., 550 U.S. 398, 82 USPQ2d 1385 (2007). In this case, Barrett teaches mRNA expression of tenocytic marker genes such as SCX and TNMD (e.g., [0066], page 3). Patel et al teach determination of mRNA transcripts using droplet digital PCR (ddPCR) (Abstract). Patel et al teach “Tendon gene expression” (Page 2 right column), and ddPCR reactions were prepared in with cDNA (1 ng or 15 ng, Table 2) (Page 3, left column). One of ordinary skill in the art would have been motivated combine the references because Patel et al stated that utilizing ddPCR offers many advantages over traditional qRT-PCR including increased target sensitivity (sensitive to one transcript), absolute quantification of gene targets without the need of standard curves, and the ability to report data without the need of an endogenous control gene (Page 3, left column) and showing rapid and large changes in the expression of several genes that are key to ECM remodeling, maintenance, and maturation (Abstract).
Conclusion
No claim is allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/KHOA NHAT TRAN/Examiner, Art Unit 1632
/PETER PARAS JR/Supervisory Patent Examiner, Art Unit 1632
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