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 .
Status of the Claims
Claim set received 05 December 2025 has been entered into the application.
Claims 1-16 are pending.
Election/Restrictions
Claims 10-16 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.
Election was made without traverse in the reply filed on 05 December 2025.
Claims 1-9 are currently under examination.
Priority
This application is a 371 of PCT/EP2021/068758 filed 07 July 2021, and claims benefit to EP20185693.7 filed 07/14/2020. It is noted the application filing receipts received 18 May 2023 and 05 June 2023 do not state provide that the application receives foreign priority.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 17 January 2023 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Drawings
The drawings were received on 14 January 2023. These drawings are accepted.
Specification
The specification received 14 January 203 has been entered into the application.
The amendments to the specification received 14 January 203 has been entered into the application.
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
The executable code is located at page 36 line 33 of the specification. It is recommended to amend the specification to “ncbi.nlm.nihdotgov/gds/”.
Claim Objections
Claim 1 is objected to because of the following informalities:
Claim 1 determining differentiation state step recites “…three pathway activities in a reference library, the reference library…”. The claims should be amended to recite “…three pathway activities in a reference library, wherein the reference library…” to address the grammatical correctness.
Claim 1 determining a level step recites “…cellular signaling pathways, the determining being based at least in part on evaluating…”. The claims should be amended to recite “…cellular signaling pathways, wherein the determining being based at least in part on evaluating…” to address the grammatical correctness.
Claim Rejections - 35 USC § 112
35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
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 1-9 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.
Claim 1 recites the limitation "…the differentiation state…" in line 1. There is insufficient antecedent basis for this limitation in the claim. It is recommended to amend the claim to recite “a differentiation state”. Here, “the differentiation state” is indefinite and not clear because stem cells can differentiate into multiple differentiation states (i.e., pluripotent, multipotent, unipotent, or at least partially differentiated). Thus, for clarity of the record, it is recommended to amended the claim to recite “…a differentiation state…”.
Claim 1 recites “An in vitro or ex vivo method…”. The limitation renders the claim indefinite because claim 1 and its associated dependent claims do not recite any physical/clinical/real-world steps for carrying out the “in vitro/ ex vivo” method. For example, claim 1 recites “…in vitro or ex vivo…” but does not set forth using any equipment or steps/protocols (i.e., plates, cells, medium, sequencing devices) for differentiating stem cells into differentiation states. Here, it is known that ex vivo experiments encompass performing biological experiments or procedures on tissues, cells, or organs removed from a living organism that maintain their natural structure.
Furthermore, claim 1 is indefinite because claim 1 recites “…for determining the differentiation of a stem cell…”. The limitation is indefinite because it is an intended use of the claimed step(s) as the claim does not provide or recite any actual steps (i.e., laboratory/clinical techniques) involving stem cells or differentiated stem cells.
Claim 1 calculating step recites “calculating …the at least three cellular signaling pathway activities.” The claim is indefinite because the claimed step does not recite calculating numeric values for the at least three different cellular signaling pathways activities in the stem cell. Therefore, it is not clear if the three signaling pathway activities of the calculating and comparing steps are the same.
Claim 1 comparing step recites "…the at least three cellular signaling pathway activities in the stem cell…” in lines 6-7. There is insufficient antecedent basis for this limitation in the claim. It is recommended to amend the claim to recite “calculating numeric values for at least three cellular signaling pathway activities in the stem cell…".
Claims 2-9 are rejected because they fail to provide limitations to overcome the deficiencies of the base claim(s).
Claim 3 is indefinite because it is not clear how claim 3 is to further limit the method of claim 1. For example, claim 1 does not recite any steps pertaining to stem cells (i.e., physical steps: laboratory or clinical techniques) and the preamble only sets forth an intended use that is not further reflected in the claims.
Claim Rejections - 35 USC § 101
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 1-9 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter.
Claim Analysis
Claim 1 recites an in vitro or ex vivo method for determining the differentiation state of a stem cell. However, under broadest reasonable interpretation (BRI), claims 1 is interpreted as setting forth a method of data analysis using cellular signaling pathway activity and biomarker data and processing said data using mathematical models for determining levels of TGF beta, Jak-Stat3, Hedgehog, Wnt transcription factor data (i.e., levels) for inferring cellular signaling pathway activity. Here, although claim 1 recites a method for in vitro or ex vivo analysis, claim 1 and its subsequent dependent claims do not contain any in vitro or ex vivo limitations/physical (i.e., laboratory/clinical method).
Following the flowchart of the MPEP 2106
Step 1 - Process, Machine, Manufacture or Composition
Claims 1-9 are drawn to a method, so a process
Step 2A Prong I - Identification of an Abstract Idea
Claim 1 recites:
calculating numeric values for the at least three cellular signaling pathway activities;
This step can be performed in the human mind by organizing information (i.e.., cellular signaling pathway activities) to calculate numeric values and is therefore an abstract idea. This step encompasses performing mathematical operations for calcualting numeric values which reads on abstract ideas;
comparing the calculated numeric values for the at least three cellular signaling pathway activities in the stem cell with calculated numeric values for at least three reference cellular signaling pathway activities;
This step can be performed in the human mind by observing, judging, and comparing information (i.e., numeric values) between at least three cellular signaling pathway activities and reference cellular signaling pathway activities and is therefore an abstract idea.
determining the differentiation state of the stem cell based on the compared cellular signaling pathway activities, wherein the differentiation state of the stem cell is determined to be pluripotent, multipotent, unipotent, or at least partially differentiated;
This step can be performed in the human mind by observing, judging, and evaluating the information (i.e., compared cellular signaling pathway) to determine the differentiation state of the stem cell (i.e., pluripotent, multipotent, unipotent, or at least partially differentiated) and is therefore an abstract idea.
wherein the comparing step is performed by comparing the at least three cellular signaling pathway activities in the stem cell with the same three pathway activities in a reference library, the reference library comprising the at least three cellular signaling pathway activities determined in at least two reference samples;
This step can be performed in the human mind by observing, evaluated, and comparing information (i.e., cellular signaling pathway activities) of at least three cellular signaling pathway activities with information in a reference library and is therefore an abstract idea.
wherein the numeric values for the at least three cellular signaling pathway activities are calculated based on the expression levels of three or more target genes of the TGFbeta, Notch, JAKSTAT3, Hedgehog, or Wnt cellular signaling pathways measured in the stem cell, wherein the calculating.
This step can be performed in the human mind by organizing information (i.e., expression level of TGFbeta, Notch, JAKSTAT3, Hedgehog, or Wnt) to calculate numeric values for at least target genes and is therefore an abstract idea. This step involves performing mathematical computations to calculate numeric values for the targeted genes which reads on abstract ideas.
determining a level of a TGFbeta, Notch, JAK-STAT3, Hedgehog, or Wnt transcription factor (TF) element in the stem cell, the TGFbeta, Notch, JAK-STAT3, Hedgehog, or Wnt TF element controlling transcription of the three or more target genes of the TGFbeta, Notch, JAK-STAT3, Hedgehog, or Wnt cellular signaling pathways, the determining being based at least in part on evaluating a mathematical model relating expression levels of the three or more target genes of the TGFbeta, Notch, JAK-STAT3, Hedgehog, or Wnt cellular signaling pathways to the level of the TGFbeta, Notch, JAK-STAT3, Hedgehog, or Wnt TF element;
The step can be performed in the human mind by organizing information (i.e., TGFbeta, Notch, JAK-STAT3, Hedgehog, or Wnt transcription factor (TF) elements data) to determine levels of transcription factors in the stem cell and is therefore an abstract idea. This step encompasses performing mathematical operations (i.e., mathematical model relating expression levels) for determining biomarker levels (i.e., TGFbeta, Notch, JAK-STAT3, Hedgehog, or Wnt transcription factor (TF) elements) in a stem cell which reads on abstract ideas. The term “determining” is interpreted as an alternative term for “calculating”. See MPEP 2106.04(a)(2)(I)(C). This step encompasses mathematical models (i.e., Bayesian). This step encompasses the mathematical concepts of using mathematical models for relating expression levels of three or more targeted genes which reads on abstract ideas.
inferring the activity of the TGFbeta, Notch, JAK-STAT3, Hedgehog, or Wnt cellular signaling pathways in the stem cell based on the determined level of the TGFbeta, Notch, JAK-STAT3, Hedgehog, or Wnt TF element in the stem cell, and
This step can be performed in the human mind by organizing information (i.e., determined level of the TGFbeta, Notch, JAK-STAT3, Hedgehog, or Wnt TF element in the stem cell) to infer the activity of the TGFbeta, Notch, JAK-STAT3, Hedgehog, or Wnt cellular signaling pathways and is therefore an abstract idea. This step encompasses performing inferences which are statistical conclusions about a large population based on a smaller sample which reads on abstract ideas.
wherein the three or more TGFbeta target genes are selected from the group consisting of: ANGPTL4, CDC42EP3, CDKNIA, CDKN2B, CTGF, GADD45A, GADD45B, HMGA2, IDl, ILll, SERPINEl, INPP5D, JUNB, MMP2, MMP9, NKX2-5, OVOLl, PDGFB, PTHLH, SGKl, SKIL, SMAD4, SMAD5, SMAD6, SMAD7, SNAil, SNAI2, TIMPl, and VEGFA;
This step can be performed in the human mind by observing, comparing, and evaluating TGF Beta target genes to select at least three genes from a group of genes and is therefore an abstract idea.
wherein the three or more Notch target genes are selected from the group consisting of: CD28, CD44, DLGAP5, DTXl, EPHB3, FABP7, GFAP, GIMAP5, HESl, HES4, HESS, HES7, HEYl, HEY2, HEYL, KLF5, MYC, NFKB2, NOXl, NRARP, PBXl, PINI, PLXNDl, PTCRA, SOX9, and TNC;
This step can be performed in the human mind by observing, comparing, and evaluating Notch target genes to select at least three genes from a group of genes and is therefore an abstract idea.
wherein the three or more JAK-STAT3 target genes are selected from the group consisting of: AKTl, BCL2, BCL2Ll, BIRC5, CCNDl, CD274, CDKNlA, CRP, FGF2, FOS, FSCNl, FSCN2, FSCN3, HIFlA, HSP90AA1, HSP90AB1, HSP90Bl, HSPAlA, HSPAlB, ICAMl, IFNG, ILl0, JunB, MCLI, MMPl, MMP3, MMP9, MUCl, MYC, NOS2, POU2Fl, PTGS2, SAAl, STATl, TIMPl, TNFRSFlB, TWISTl, VIM, and ZEBl;
This step can be performed in the human mind by observing, comparing, and evaluating Jak-Stat3 target genes to select at least three genes from a group of genes and is therefore an abstract idea.
Wherein the three or more Hedgehog target genes are selected from the group consisting of: GLil, PTCHl, PTCH2, IGFBP6, SPPl, CCND2, FST, FOXLl, CFLAR, TSC22D1, RAB34, Sl00A9, Sl00A7, MYCN, FOXMl, GLI3, TCEA2, FYN and CTSLl;
This step can be performed in the human mind by observing, comparing, and evaluating Hedgehog target genes to select at least three genes from a group of genes and is therefore an abstract idea.
wherein the three or more Wnt target genes are selected from the group consisting of: KIAAl 199, AXIN2, RNF43, TBX3, TDGFl, SOX9, ASCL2, IL8, SP5, ZNRF3, KLF6, CCNDl, DEFA6 and FZD7.
This step can be performed in the human mind by observing, comparing, and evaluating Wnt target genes to select at least three genes from a group of genes and is therefore an abstract idea.
Claims 2-9 are further drawn to limitations that describe the abstract ideas of claim 1 and are therefore also abstract ideas.
Step 2A Prong II - Consideration of Practical Application
Here, in the instant case, the claims merely set forth a method of data analysis yielding an inference (i.e., quantitative and/or qualitative generalizations, predictions, or conclusions about a larger population) with respect to the activity of the TGFbeta, Notch, JAK-STAT3, Hedgehog, or Wnt cellular signaling pathways in the stem cells by analyzing genes associated with the signaling pathways. As such, practicing the claims merely results in inferences regarding the activity of the signaling pathways. Such a result only produces information and does not provide for a practical application in the physical-realm of physical things and acts, i.e., the claims do not utilize the data generated by the judicial exception to affect any type of change. See MPEP 2106.04(a)(2)(A)(iv). Therefore, the calculated numeric values, compared numeric values, determined differentiation states, determine signaling pathway levels, and inferred signaling pathway activity, and the abstract ideas to construct a practical application such as treating a subject, transformation of matter, or improving upon an existing technology.
This judicial exception is not integrated into a practical application because the claims do not meet any of the following criteria:
An additional element reflects an improvement in the functioning of a computer, or an improvement to other technology or technical field;
an additional element that applies or uses a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition;
an additional element implements a judicial exception with, or uses a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim;
an additional element effects a transformation or reduction of a particular article to a different state or thing; and
an additional element applies or uses the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception.
Step 2B - Consideration of Additional Elements and Significantly More
The claimed method also recites "additional elements" that are not limitations drawn to an abstract idea.
The recited additional element of using stem cells of claims 1, 3, and 6-8 does not add significantly more than the recited judicial exception because using cells as a source of nucleic acid for analyzing biomarker data (i.e., gene expression levels) that is subsequently analyzed by the abstract idea is deemed well-known and conventional. See MPEP 2106.05(d)(II) (I, iii, v, vii) and 2106.05(g). To provide evidence of conventionality, Ang et al (Ang) discloses a method for differentiating stem cells [tile]. Ang discloses methods for differentiating pluripotent stem cells or pluripotent stem cells of many lineages [page left col para 0002]. Ang discloses using IPSC’s, multipotent stem cells, embryonic stem cells, [page 2 right para 0028-31]. Ang discloses using pancreatic progenitor lineage and hepatocyte progenitor lineage [page 4 left col para 0045] (U.S Patent Pub: US 2015/0329821, Patent Pub Date: 19 November 2015) (Cited in the IDS received 17 January 2023; US Patent Pub Cite No.: 1).
In conclusion, and when viewed as a whole, these additional claim element(s) do not provide meaningful limitation(s) to transform the abstract idea recited in the instantly presented claims into a patent eligible application of the abstract idea such that the claim(s) amounts to significantly more than the abstract idea itself. Therefore, the claim(s) are rejected under 35 U.S.C. 101 as being directed to non-statutory subject matter.
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.
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.
Claim(s) 1-5 are rejected under 35 U.S.C. 103 as being unpatentable over Ooijen (U.S Patent Pub: US 2016/0117439, Patent Pub Date: 28 April 2016) in view of Sun et al. (PloS one, 2008-10, Vol.3 (10), p.e3406)
Claim 1 recites calculating numeric values for the at least three cellular signaling pathway activities.
Claim 1 recites comparing the calculated numeric values for the at least three cellular signaling pathway activities in the stem cell with calculated numeric values for at least three reference cellular signaling pathway activities.
Claim 1 recites determining the differentiation state of the stem cell based on the compared cellular signaling pathway activities, wherein the differentiation state of the stem cell is determined to be pluripotent, multipotent, unipotent, or at least partially differentiated.
Claim 1 recites wherein the comparing step is performed by comparing the at least three cellular signaling pathway activities in the stem cell with the same three pathway activities in a reference library, the reference library comprising the at least three cellular signaling pathway activities determined in at least two reference samples.
Claim 1 recites wherein the numeric values for the at least three cellular signaling pathway activities are calculated based on the expression levels of three or more target genes of the TGFbeta, Notch, JAKSTAT3, Hedgehog, or Wnt cellular signaling pathways measured in the stem cell, wherein the calculating comprises:
Claim 1 recites determining a level of a TGFbeta, Notch, JAK-STAT3, Hedgehog, or Wnt transcription factor (TF) element in the stem cell, the TGFbeta, Notch, JAK-STAT3, Hedgehog, or Wnt TF element controlling transcription of the three or more target genes of the TGFbeta, Notch, JAK-STAT3, Hedgehog, or Wnt cellular signaling pathways, wherein the determining being based at least in part on evaluating a mathematical model relating expression levels of the three or more target genes of the TGFbeta, Notch, JAK-STAT3, Hedgehog, or Wnt cellular signaling pathways to the level of the TGFbeta, Notch, JAK-STAT3, Hedgehog, or Wnt TF element.
Claim 1 recites inferring the activity of the TGFbeta, Notch, JAK-STAT3, Hedgehog, or Wnt cellular signaling pathways in the stem cell based on the determined level of the TGFbeta, Notch, JAK-STAT3, Hedgehog, or Wnt TF element in the stem cell, and
Claim 1 recites wherein the three or more TGFbeta target genes are selected from the group consisting of: ANGPTL4, CDC42EP3, CDKNIA, CDKN2B, CTGF, GADD45A, GADD45B, HMGA2, IDl, ILll, SERPINEl, INPP5D, JUNB, MMP2, MMP9, NKX2-5, OVOLl, PDGFB, PTHLH, SGKl, SKIL, SMAD4, SMAD5, SMAD6, SMAD7, SNAil, SNAI2, TIMPl, and VEGFA.
Claim 1 recites wherein the three or more Notch target genes are selected from the group consisting of: CD28, CD44, DLGAP5, DTXl, EPHB3, FABP7, GFAP, GIMAP5, HESl, HES4, HESS, HES7, HEYl, HEY2, HEYL, KLF5, MYC, NFKB2, NOXl, NRARP, PBXl, PINI, PLXNDl, PTCRA, SOX9, and TNC.
Claim 1 recites wherein the three or more JAK-STAT3 target genes are selected from the group consisting of: AKTl, BCL2, BCL2Ll, BIRC5, CCNDl, CD274, CDKNlA, CRP, FGF2, FOS, FSCNl, FSCN2, FSCN3, HIFlA, HSP90AA1, HSP90AB1, HSP90Bl, HSPAlA, HSPAlB, ICAMl, IFNG, ILl0, JunB, MCLI, MMPl, MMP3, MMP9, MUCl, MYC, NOS2, POU2Fl, PTGS2, SAAl, STATl, TIMPl, TNFRSFlB, TWISTl, VIM, and ZEBl.
Claim 1 recites wherein the three or more Hedgehog target genes are selected from the group consisting of: GLil, PTCHl, PTCH2, IGFBP6, SPPl, CCND2, FST, FOXLl, CFLAR, TSC22D1, RAB34, Sl00A9, Sl00A7, MYCN, FOXMl, GLI3, TCEA2, FYN and CTSLl,
Claim 1 recites wherein the three or more Wnt target genes are selected from the group consisting of: KIAAl 199, AXIN2, RNF43, TBX3, TDGFl, SOX9, ASCL2, IL8, SP5, ZNRF3, KLF6, CCNDl, DEFA6 and FZD7.
Ooijen et al. (Ooijen) discloses the results of the risk score based on a Multi-Pathway Score includes the sum of terms to denote the inferred activity of TGF-beta, PI3K, Wnt, ER, and HH pathways [Ooijen, disclosure page 51 right col para 0571 tables 23-24], claim 1 step 2 (c-d)], as in claim 1 calculating numeric values step.
Ooijen discloses calcualting the activity levels of TGF-β using a calibrated model pathway model with the calibrated pathway model (i.e., references) compares the expression level of at least three TGF-β genes in the calibrated pathway model which define an activity level of the transcription TGF-β factor element [Ooijen, disclosure page 5 left col 0039]. Ooijen discloses calcualting the transcription factor elements of the additional cellular signaling pathway (i.e., Wnt, HH) in a sample using a calibrated model pathway with the calibrated pathway model comparing the expression levels of the at least three target genes from the additional cellular signaling pathway in the sample with expression levels of the at least three target genes from the additional cellular signaling pathway in the calibrated pathway model which define an activity level of the transcription factor element of the additional cellular signaling pathway. [Ooijen, disclosure page 5 left col para 0041-044]. Here, the calibrated expression levels of the at least three TGF-β target and additional genes in the calibrated pathway model which define an activity level of the TGF-β and additional cellular signaling pathway transcription factor elements reads on comparing genes and pathway to reference cellular pathways (i.e., calibrated) and reads on comparing more than one samples as the calibrated pathways model is comparing the TGF-β target genes and pathways and additional genes and pathways (i.e., Wnt and HH). Ooijen discloses numeric values (i.e., MPS risk scores) for the reference breast cancer patients from E-MTAB365, GSE20685, AND GSE21653 [page 51 table 23]. Ooijen discloses the MPS for 20, 12, and 7 gene shortlists related to TGF-β pathway activity and comparing different numeric values of the levels [page 51 right col para 0571 tables 23-24]. Ooijen discloses assessing the pathway activities for ER, AR, Wnt, HH, TGF-β and the PI3K using the reference data of Affymetrix HG-UL33 Plus 2.0, microarray data from 1,294 breast cancer tissue samples from public data sets GSE6532, GSE9195, GSE20685, GSE21653 and E-MTAB-365 [Ooijen, disclosure page 55 right col para 0598]. Ooijen discloses a subject suffering from embryonal cell carcinoma (i.e., cancerous embryonic stem cells/pluripotent malignant stem cells) [Ooijen, page 30 left col top of col para 0369], as in instant claim 1 comparing the calculated numeric values step.
Ooijen discloses using sets of curated genes [pages 36-37 table 1-4]. Ooijen discloses using three test sets E-MTAB-365, GSE20685 and GSE21653 (i.e., at least two reference samples) and comparing results (i.e., numeric values) of the test sets (i.e., MPE score, HR, Cox) to the results of the list of 20, 12, and 7 gene short-lists for TGFβ pathways [tables 2-8], Wnt pathway [tables 13-16], and Hedgehog (HH) [tables 19-21]. Ooijen discloses the MPS for 20, 12, and 7 gene shortlists related to TGF-β pathway activity and comparing different numeric values of the levels [page 51 right col para 0571 tables 23-24]. Ooijen discloses calcualting the activity levels of TGF-β using a calibrated model pathway model with the calibrated pathway model (i.e., references) compares the expression level of at least three TGF-β genes in the calibrated pathway model which define an activity level of the transcription TGF-β factor element [Ooijen, disclosure page 5 left col 0039], as in instant claim 1 wherein the comparing step. It is noted the specification discloses the reference library refers to “…a set of numerical values representing the pathways activities of three or more cellular signaling pathways as obtained in one or more stem cells.” [Spec page 30 lines 23-27], as in instant claim 1 wherein the comparing step
OoijOoijen discloses the TGF-β, HH, and Wnt pathways are based on expression levels or one or more target genes of the cellular signaling pathways [Ooijen, page 54, left col 0583]. Ooijen discloses determining MPS and calculating activities for the TGFβ, HH, and Wnt pathways [Ooijen, claims 15-16]. Ooijen discloses numeric values (i.e., MPS risk scores) for the reference breast cancer patients from E-MTAB365, GSE20685, AND GSE21653 [page 51 table 23]. Ooijen discloses calcualting the activity levels of TGF-β using a calibrated model pathway model with the calibrated pathway model (i.e., references/references libraries) compares the expression level of at least three TGF-β genes in the calibrated pathway model which define an activity level of the transcription TGF-β factor element [Ooijen, disclosure page 5 left col 0039]. Ooijen discloses the MPS for 20, 12, and 7 gene shortlists (i.e., additional references libraries) related to TGF-β pathway activity and comparing different numeric values of the levels [page 51 right col para 0571 tables 23-24]. Ooijen discloses different numeric values related target genes of TGFβ, HH, and Wnt [Ooijen, disclosure page 51 para 0571 tables 23-24], as in instant claim 1 wherein the numeric values step.
Ooijen also discloses methods using physical steps (i.e., in vitro methods) for processing genetic data related to cellular signaling pathways [Ooijen, claim 51]. Ooijen discloses a method for analyzing two or more cellular signaling pathways (i.e., TGF Beta, Wnt, Hedgehog) by calculating activity level of transcription factor elements of three or more genes (i.e., TGF Beta, Wnt, Hedgehog) and using a calibrated mathematical model relating to the gene expression of one or more genes for determining said activity levels [Ooijen, claims 1 step 2 and claim 2 step c]. Ooijen also disclose methods using physical steps (i.e., in vitro methods) for processing genetic data related to cellular signaling pathways [Ooijen, claim 51], as in instant claim 1 determining levels of a TGFbeta, Hedgehog, or Wnt transcription factor (TF) element step.
Ooijen discloses calculating the activity of each of two or more cellular signaling pathways (i.e., TGF beta, Wnt, and Hedgehog) in the subject based on expression levels of three or more target genes of the respective cellular signaling pathway measured in a sample of the subject [Ooijen, claim 1], as in instant claim 1 inferring the activity step.
Ooijen discloses using at least three TGF Beta target genes ANGPTL4, CDC42EP3, CDKNlA, CTGF, GADD45A, GADD45B, HMGA2, IDl, ILll, JUNB, PDGFB, PTHLH, SERPINEl, SGKl, SKIL, SMAD4, SMAD5, SMAD6, SMAD7, SNAI2, and VEGF A for inferring TGF beta activity [Ooijen, claims 10 and 48], as in claim 1 the three or more TGF beta target genes.
Ooijen discloses using at three or more Wnt target genes: AXIN2, RNF43, TBX3, SOX9, ZNFR3, CCND1, SP5, KLF6, DEFA6, FZD7 for inferring Wnt activity [Ooijen, disclosure page 4 right col para 0032], as in claim 1 three or more Wnt target genes.
Ooijen discloses using three or more hedgehog (HH) targeted genes: GLil, PTCHl, PTCH2, IGFBP6, SPPl, CCND2, FST, FOXLl, CFLAR, TSC22D1, RAB34, SIO0A9, SIO0A7, MYCN, FOXMl, GLI3, TCEA2, FYN, and CTSLl for inferring HH activity [Ooijen, disclosure page 5 right col para 0034], as in claim 1 three or more hedgehog targeted genes.
Dependent claim(s): 2-5
Ooijen discloses analyzing the FOXO gene in the PI3K pathway [page 41 right col para 0523]. Ooijen discloses ER, PR, AR, and NFkB [Ooijen, page 1 right col para 0007], as in instant claim 2.
Ooijen discloses a subject suffering from embryonal cell carcinoma (i.e., cancerous embryonic stem cells/pluripotent malignant stem cells) [Ooijen, page 30 left col top of col para 0369], as in instant claim 3. Here, because the Ooijen is using “cancerous embryonic cells” the cells read on stem cells.
Ooijen discloses methods for calculating the activity of TGFβ [Ooijen, claim 1 step 2] and Wnt and HH [Ooijen, claim 1 steps b-2], as in instant claim 4.
Ooijen discloses determining expression levels for three or more target genes associating with TGFβ, Wnt, and HH signaling pathways [Ooijen, claim 16], as in claim 5.
Ooijen does not teach claim 1 determining the differentiation state of the stem cell based on the compared cellular signaling pathway activities, wherein the differentiation state of the stem cell is determined to be pluripotent, multipotent, unipotent, or at least partially differentiated. Ooijen does not teach claim 6.
Sun et al. (Sun) teaches conducting transcriptional interventions in silico of every gene combination to model dynamic pathway behavior of pathways (i.e., JAK-STAT [page 5], Wnt [page5], TGF-β [page 11]) in transition to embryonic stem cells (ESC) to embryoid bodies (EB) [page 4 right col section 3]. Sun teaches dynamic behavior of pathways was examined to demonstrate how much and in which specific ways each gene or gene combination effects the behavior transition of a pathway in response to ESC differentiation or pluripotency induction [abstract]. Sun teaches the modeling pathway dynamic behavior allows the identification of genes that contribute to the network transition in response to ESC differentiation or pluripotency induction Sun, page 4 right col section 3], as in claim 1 stems cells and determining the differentiation state of the stem cell based on the compared cellular signaling pathway activities, wherein the differentiation state of the stem cell is determined to be pluripotent, multipotent, unipotent, or at least partially differentiated.
It would be obvious to one of ordinary skill in the art by the effective filing date of the claimed invention to modify Ooijen in view of Sun because Sun teaches analyzing TGFβ, Wnt, and JAK/STAT activities pathways with respect to embryonic stem cells (ESC) and embryoid bodies (EB) differentiation or pluripotency induction. One of ordinary skill in the art would recognize that Ooijen and Sun are in similar fields of endeavor of analyzing targeted genes that can influence cellular pathway activities of cells (i.e., cancer cells and stem cells). Additionally, one of ordinary in the art would further recognize that while Ooijen does not disclose determining differentiation states of stem cells, Ooijen discloses that a subject can suffer from embryonal cell carcinoma which applies the method to disease state but does not apply the method for differentiating the state of a stem cell. Here, the embryonal cell carcinoma cells of Ooijen could be combined with Sun’s signaling pathway differentiation state analysis (i.e., pluripotency induction) for determining the differentiation state of metastatic said embryonal cell carcinoma cells. Thus, one of ordinary skill in the art would be motivated to combine Ooijen in view of Sun because Sun teaches analyzing TGFβ, Wnt, and JAK/STAT pathway activities in stem cells for determining ESC differentiation and/or pluripotency induction (i.e., differentiation state). Thus, one of ordinary skill in the art would have a reasonable expectation of success combining the embryonal cell carcinoma pathway analysis of Ooijen with the stem cell pathway analysis of Sun because Sun teaches species specific modulation of gene expression controlling ESC pluripotency with respect to evaluating TGFβ, Wnt, and JAK/STAT pathway activities. Therefore, combining the pathway analysis methods of Ooijen with the stem cell pathway analysis of Sun would construct a predictable method for analyzing biological activity pathways (i.e., TGFβ, Wnt, JAK/STAT, HH, and Notch) using gene expression levels of targeted genes for making in vitro or ex vivo determinations regarding the differentiation states of stem cells.
Claim(s) 9 are rejected under 35 U.S.C. 103 as being unpatentable over Ooijen (U.S Patent Pub: US 2016/0117439, Patent Pub Date: 28 April 2016) in view of Sun et al. (PloS one, 2008-10, Vol.3 (10), p.e3406), as applied to claims 1-5, and in further view of Ang et al. ((U.S Patent Pub: US 2015/0329821, Patent Pub Date: 19 November 2015).
Ooijen in view of Sun teaches claims 1-5.
Ooijen in view of Sun teaches an in vitro/ex vivo method determining the differentiation states of a stem cell using gene expression levels of cellular signaling pathways genes and associated transcription factors.
Ooijen in view of Sun does not teach claim 9.
Ang discloses using induced pluripotent stem cells [Ang, page 2 right col para 0029]. Ang discloses cell lineages can be endoderm, mesoderm, or ectoderm [Ang, 4 left col para 0045]. Ang discloses the pluripotent stem cells may be differentiated into cell lineages of the endoderm that may include but are not limited to the anterior primitive streak (APS) lineage, definitive endoderm (DE) lineage, anterior foregut (AFG) lineage, posterior foregut (PFG) lineage, midgut hind (MHG) lineage, pancreatic progenitor lineage, or hepatocytic progenitor lineage [Ang, page 4 para 0045]. Sun teaches demonstrating specific ways genes or gene combination effects the behavior transition of a pathway response to ESC differentiation or pluripotency [abstract], as in claim 9.
It would be obvious to one of ordinary skill in the art by the effective filing date of the claimed invention to modify Ooijen in view of Sun and in further view of Ang because Ang discloses methods for differentiating stem cells using different lineages [Ang, title]. One of ordinary skill in the art would recognize that Ooijen, Sun, and Ang are in similar field of endeavor of analyzing signaling pathways of cells of embryonic cells (i.e., embryonal cell carcinoma, ESC, EB) associated with gene expression levels. One of ordinary skill in the be motivated to combine Ooijen in view of Sun and in further view of Ang because Ang also discloses pathway analysis using TGFβ, Wnt, and HH gene of multiple stem types for differentiating cells into different lineages [Ang, page 11 paras 0180 and 0189]. Furthermore, while Ang discloses determining lineages of stem cell (i.e., ancestry and developmental history), one of ordinary skill would recognize that the lineage analysis could be combined with the differentiations states of Sun for determining the differentiation states of induced pluripotent cells (i.e., IPsc’s) using cell lineages in combination with cellular signaling pathway data. Thus, one of ordinary in the would be motivated to combine the signaling pathway analysis of using TGFβ, Wnt, and HH gene and pathways of Ooijen in view of the cell differentiations states of Sun with the differentiating stem cell lineages of Ang to construct a method step using the expression levels of cellular signaling pathways (i.e., TGFβ, Wnt, HH) and differentiation states of stems cells (i.e., pluripotent stem cells) and stem cell lineage for determining differentiation states. Therefore, combining Ooijen in view of Sun and in further view of Ang would construct a predictable method step using cellular signaling pathway gene expression levels for determining the differentiation state and the lineage of stem cells.
Conclusion
Claims 1-9 are rejected.
No claims are allowed.
Finality
This Office action is a Non-Final action. A shortened statutory period for reply to this action is set to expire THREE MONTHS from the mailing date of this action.
Inquiries
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JOSEPH C PULLIAM whose telephone number is (571)272-8696. The examiner can normally be reached 0730-1700 M-F.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Karlheinz Skowronek can be reached at (571) 272-9047. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/J.C.P./Examiner, Art Unit 1687
/Anna Skibinsky/
Primary Examiner, AU 1635