DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
Application Status
This action is written in response to applicant’s correspondence received on 8/12/2025. Claims 1-2, 4-9, 11-18, 20, and 23-24 are pending. Claims 1 and 20 have been amended. Claims 3, 10, 19, and 21-22 have been cancelled. All pending claims are currently under examination.
Any rejection or objection not reiterated herein has been overcome by amendment. Applicant’s amendments and arguments have been thoroughly reviewed, but are not persuasive to place the claims in condition for allowance for the reasons that follow. This Office Action is Final.
112(a) Rejection – Withdrawn
The Applicant’s arguments received 8/12/2025 with regards to the 112(a) rejection have been reviewed and are persuasive. The Applicant argues that the claims are drawn to a method, where knowledge of the outcome and products are not required. This is persuasive. Furthermore, the Applicant points out that, within the context of the present application, the Applicant has defined “therapeutic target” to mean an activity-dependent gene pairing. The Applicant appears to have shown possession of such an assay which can be used to identify such “therapeutic targets.”
Claim Rejections - 35 USC § 103 – Updated in Response to Amendment
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
This application currently names joint inventors. In considering patentability of the claims under pre-AIA 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of pre-AIA 35 U.S.C. 103(c) and potential pre-AIA 35 U.S.C. 102(e), (f) or (g) prior art under pre-AIA 35 U.S.C. 103(a).
Claims 1, 2, and 23 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Rakhade (Rakhade SN et al. Epilepsia. 2007;48 Suppl 5:86-95) in view of Qureshi 2 (Qureshi et al. Trends Mol Med. 2011 June ;17(6):337-346), and Bennett (WO 2012/012467 A2, published 1/26/2012). The rejection is further evidenced by Mercer (Mercer TR et al. Proc Natl Acad Sci U S A. 2008 Jan 15;105(2):716-21).
Regarding claim 1, Rakhade is a research article which examines activity-dependent gene expression and its correlation with interictal spiking in epilepsy patients (Title, Summary, and throughout). Rakhade teaches that:
“we explore this further by comparing the expression of these genes within human epileptic neocortex to both ictal and specific electrical parameters of interictal spiking from subdural recordings prior to surgical resection in order to determine the electrical properties of the human neocortex that correlate best to the expression of these genes,”(Summary).
Rakhade therefore teaches that their methods are performed with neocortex tissue samples (Summary).
Rakhade also teaches that:
“together with deafferented regions of nearby control tissue, seizure onset zones were removed along with deafferented seizure-spread tissue in an enbloc resection” ( see Methods, e.g., second paragraph).
Rakhade therefore teaches a method of obtaining pair samples from the neocortex from a human brain, where the human is a patient with epilepsy, where each sample has a different level of brain electrical brain activity (i.e., control tissue versus seizure onset zones”). Furthermore, Rakhade teaches and focuses on the correlation of gene expression profiles with human epilepsy, and teaches that:
“we have recently identified a common group of genes induced in human epileptic foci, including EGR1, EGR2, c-fos, and MKP-3. We found that the expression levels of these genes correlate precisely with the frequency of interictal activity and can thus serve as markers of epileptic activity,” (Summary).
Rakhade further teaches that:
“In this study we have further refined the link between the expression of these genes and quantitative measures of interictal epileptiform activity in human neocortex by showing that the expression of 3 of these genes (c-fos, EGR1, EGR2) is highly correlated with a number of interictal spike parameters including spike amplitude, frequency, and area,” (page 92, left column, first paragraph).
Therefore Rakhade teaches not only sampling paired brain tissue with different electrical properties in epilepsy patients, but also teaches that gene expression profiling is critical to elucidating differentially expressed genes in epileptic brain tissue, where the differential expression was evaluated in paired brain sample tissues from the neocortex in epileptic patients by measuring interictal epileptiform spike parameters (Summary, Methods second paragraph, and page 92, left column, first paragraph).
Additionally, Rakhade teaches that “electricocography (ECoG) using subdural grids of electrodes are often used to delineate…epileptic activity at each electrode,” (page 86, left column, first paragraph). Furthermore, Rakhade teaches the use of ECoG in their methods, where electrodes are surgically implanted in the epilepsy patient brain to monitor electrical activity of the brain to monitor interictal epileptiform spikes, and also teaches excising pairs of tissue samples displaying different interictal spiking patterns (see Methods, page 87, right column, and also page 88, left column final paragraph into the right column, first paragraph).
Furthermore, Rakhade also teaches the use of microarrays to measure differential gene expression profiles designed to identify differentially expressed genes in epileptically active versus inactive neocortex, and therefore teaches transcriptome wide profiling using a microarray (page 91, right column, first paragraph).
Rakhade also teaches that:
“Understanding the potential roles of interictal spike activity and the genes that are induced together with that spiking should offer us further clues on both the causes of focal neocortical epilepsy as well as potential therapeutic treatments for the future,” (page 94, left column, first paragraph).
Rakhade therefore teaches that elucidating genes which are upregulated and coupled to spiking is important to understanding causes of epilepsy and to identify therapeutic targets (page 94, left column, first paragraph). Rakhade therefore teaches a motivation to further explore differentially expressed genes in the context of epilepsy, specifically within the neocortex by using paired tissue sample microarray profiling.
Rakhade, while teaching a method of comparing expression profiles of neocortical tissue to elucidate molecular mechanisms of epilepsy based on interictal spiking, does not tech lncRNAs, or the identification of paired lncRNA/mRNA differentially expressed gene pairs.
Qureshi 2 is a research article that focuses on non-coding RNAs and their association with cognitive disorders (Title, Abstract, and throughout). Qureshi 2 teaches the non-coding RNA (ncRNA) HAR1, that this ncRNA is coexpressed with the glycoprotein reelin, a critical developmental factor implicated in cognitive function and the pathogenesis of diverse cognitive disorders including epilepsy (page 2 final paragraph into page 3, first paragraph). Furthermore, Qureshi 2 teaches that:
“additional lncRNAs are associated with epilepsy and stroke,” (page 8, final two lines). Thus, Qureshi 2 teaches that lncRNAs are associated with epilepsy, and therefore teaches a motivation to include lncRNAs in expression profiling of epilepsy tissues. Furthermore, Qureshi 2 and Rakhade directly overlap in subject matter because both focus on underlying mechanisms of epilepsy (Title, Abstract, and see both documents).
Bennett discloses a method for identifying putative therapeutic targets (page 38, lines 20-24) comprising: identifying long non-protein-coding RNA (IncRNA) molecules (page 27, lines 6-10) and protein-coding messenger RNA (mRNA) molecules (mRNAs) (page 38, lines 20-24) that are differentially expressed in association with a disease or disorder (page 27, lines 6-10); linking a first differentially expressed IncRNA with a differentially expressed mRNA and/or a second differentially expressed IncRNA (linking an expressed IncRNA with an expressed mRNA or second RNA, such as an RNAi (page 23, lines 8-18; page 24, line 26 to page 25, line 2) when the gene encoding the first differentially expressed IncRNA overlaps with, or is adjacent to, the gene encoding the differentially expressed mRNA and/or the gene encoding the differentially expressed second IncRNA along the human genome the IncRNA overlaps with, or is adjacent to (i.e., “cis”) the gene encoding the paired mRNA (“Non-coding RNA” section, pages 23-28), thereby identifying an IncRNA/ mRNA gene pair and/or an IncRNA/IncRNA gene pair (an IncRNA/mRNA gene pair and/or an IncRNA/IncRNA gene pair; page 27, lines 6-10) as putative therapeutic targets (page 24, lines 5-6) (page 38, lines 20-24); Bennett therefore teaches differentially expressed lncRNAs and mRNAs to elucidate lncRNA/mRNA gene pairs in the context of disease, and that it was known that lncRNA and mRNA expression are coupled (above). Bennett further teaches that lncRNA are known to be implicated in various diseases of the brain (page 27, second paragraph). Bennett teaches large-scale transcriptomic analysis to characterize ncRNAs (page 24, lines 1-5, and furthermore the references taught on page 24, first paragraph).
Furthermore, Bennett teaches that lncRNA and their target mRNAs can occur in cis or trans (page 24, first paragraph). By teaching cis-acting lncRNA/mRNA pairings, Bennett teaches the known association of lncRNAs with mRNAs, where lncRNAs are known to act on target mRNAs (page 24, first paragraph). Bennett lists known lncRNA and mRNA pairings, including reference to Mercer. Mercer teaches that specific lncRNAs are expressed in the mouse brain (Title, Abstract, and throughout). Mercer further teaches that lncRNAs are known to be associated with and paired with mRNAs, as lncRNAs are known to regulate the expression of protein coding genes via mechanisms such as cis-antisense, bidirectional, and intronic (page 717 final paragraph to page 718, Figure 2). Thus, as Bennett teaches cis ncRNA, and offers Mercer as a reference and example of such lncRNA/mRNA (protein coding gene), where furthermore Bennett teaches cis-acting lncRNA operating on protein coding genes (mRNA), Bennett teaches cis-acting lncRNA pairings on page 24, first paragraph, as referenced by Mercer. In other words, Bennett clearly teaches that lncRNAs are functionally paired with nearby mRNA/protein coding genes (acting in “cis”). Thus, it was known in the art that lncRNAs are paired with mRNAs, where the investigation of lncRNAs is paired with the mRNAs that they affect (Bennett page 24, as evidenced by Mercer page 717 final paragraph to page 718, Figure 2). Bennett therefore provides motivation to explore lncRNA and mRNA pairings, as well as their expression profiles, as taught by Bennett and evidenced by Mercer (page 24).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the presently claimed invention to modify the paired sampling method of Rakhade to include lncRNAs as taught by both Qureshi 2 and Bennett because lncRNAs, as taught by Qureshi 2, are associated with epilepsy, the stated focus of the method of Rakhade. A practitioner would therefore be motivated to include lncRNAs as part of the investigatory method of Rakhade because Qureshi 2 directly teaches that lncRNAs are associated with epilepsy. Furthermore, Bennett teaches that lncRNA/mRNA pairs can be targeted as therapeutics, and that such gene pairs can be coupled/overlap/are “cis.” This is further evidenced by Mercer; it was thus clear in the art that it was known that ncRNAs influence mRNA in cis-acting mechanisms, where furthermore transcriptomic analysis is a known method of exploring such RNA expression levels (e.g., Bennett, page 24, first paragraph). Thus, a practitioner would be motivated to include lncRNAs with the microarray profiling method of Rakhade, as it was already known that such molecules are associated with epilepsy and can be targeted as therapeutics, and furthermore, it was known that lncRNAs and paired with mRNAs in cis fashion.
Regarding claim 2, Rakhade teaches interictal spike detection wherein amplitude is a component in measuring the interictal spike in Figure 2. Figure 2 also depicts seizure spikes compared with control spikes, and therefore teaches the classification of high (“seizure onset”) and low (“control”) electrical brain activity (Figure 2).
Regarding claim 23, Rakhade teaches correlation of gene expression patterns of activity-dependent genes in their methods (Title, Abstract), and teaches expression patterns of known activity-dependent coding genes (Abstract, e.g., c-fos, EGR1, and EGR2). Furthermore, as discussed above, Rakhade in combination with Qureshi 2 and Bennett render obvious determining differentially expressed lncRNA, where such lncRNA would be activity-dependent as taught by Rakhade (Abstract). Additionally, Rakhade teaches microarray profiling, which, in combination with lncRNA profiling rendered obvious by Qurshi 2 and Bennett, would yield correlation data between lncRNAs and activity-dependent coding gene expression (see rejection of claim 1). Furthermore, Bennett also teaches that it is known that ncRNAs correlate with gene expression profiles (e.g., page 24, first paragraph, and section entitled “Non-coding RNA,” pages 23-31). It would therefore be obvious to correlate lncRNA expression with the expression patterns of genes (Bennet, page 24 first paragraph and “Non-coding RNA,” pages 23-31).
Claim 4 is rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Rakhade (Rakhade SN et al. Epilepsia. 2007;48 Suppl 5:86-95) in view of Qureshi 2 (Qureshi et al. Trends Mol Med. 2011 June ;17(6):337-346), and Bennett (WO 2012/012467 A2, published 1/26/2012) as evidenced by Mercer (Mercer TR et al. Proc Natl Acad Sci U S A. 2008 Jan 15;105(2):716-21) and Zhang (Zhang X et al. Neurobiol Dis. 2012 Oct;48(1):1-8, published online 6/16/2012), as applied to claims 1, 2, and 23 and further in view of Lippa (Lippa KA et al. BMC Res Notes. 2010 Dec 28;3:349).
The teachings of Rakhade, Qureshi 2, and Bennett are discussed above with regards to independent claim 1.
Regarding claim 4, as discussed above, the combination of Rakhade, Qureshi 2, Bennett, and Zhang renders obvious the invention of claim 1. Furthermore, Zhang teaches the use of microarrays for the profiling of lncRNAs and mRNAs (“Data sets characteristics” section” and “LncRNA expression profiles on Affymetrix HG-U133 Plus 2.0 arrays”, section, and Discussion).
The above prior art does not teach the use of correlating the fold-change of a protein-coding control gene that is common to both arrays.
Lippa is a research article focused on the use of internal and external controls when using microarrays (Title and throughout). Lippa teaches that:
“whole-array metrics and information from a standard mixture of external spike-in and endogenous internal controls. Spike-in controls were found to carry the same information about technical performance as whole-array metrics and endogenous "housekeeping" genes. These results support the use of spike-in controls as general tools for performance assessment across time, experimenters and array batches, suggesting that they have potential for comparison of microarray data generated across species using different technologies,” (Background, first paragraph).
Thus, Lippa teaches that, when comparing data from multiple microarrays, positive controls to control for consistency of data can be used to generate comparable datasets across microarrays, including endogenous protein-coding genes common to the arrays (“housekeeping” genes, Background, first paragraph).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Rakhade, Qureshi 2, Bennett, Zhang and Lippa, to include a protein-coding gene control common to both the lncRNA and mRNA arrays, because, as taught by Lippa, this is simply the use of a known technique to improve a similar method in the same way. In the present case, the use of an endogenous control when comparing microarray data is a known technique taught by Lippa which would be applied to the known method of microarray analysis of lncRNA and mRNA taught by Zhang. A practitioner would be motivated to include a positive control across the data to ensure that the results of the data are consistent.
Claims 5, and 9 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Rakhade (Rakhade SN et al. Epilepsia. 2007;48 Suppl 5:86-95) in view of Qureshi 2 (Qureshi et al. Trends Mol Med. 2011 June ;17(6):337-346), and Bennett (WO 2012/012467 A2, published 1/26/2012) as evidenced by Mercer (Mercer TR et al. Proc Natl Acad Sci U S A. 2008 Jan 15;105(2):716-21), as applied to claims 1, 2, and 23 above, and further in view of Zhang (Zhang X et al. Neurobiol Dis. 2012 Oct;48(1):1-8, published online 6/16/2012, previously supplied). Claims 5 and 9 are further evidenced by Thermo (Product insert for Affymetrix HG-U133 Plus 2.0 arrays, published 2007, previously supplied).
The teachings of Rakhade, Qureshi 2, and Bennett are discussed above with regards to independent claim 1.
Regarding claim 5, Rakhade teaches a method to identify differentially expressed genes between two paired brain tissue samples (Summary, and throughout, see rejection of claim 1,above). Rakhade also teaches the use of microarray profiling/probes to identify differentially expressed genes (page 91, right column, first paragraph). Qureshi 2 teaches a motivation to identify differential expression of lncRNAs in diseased versus control tissue in epilepsy patients (page 8, final two lines).
Rakhade, Qureshi 2, and Bennett do not teach that measuring the expression of lncRNAs and mRNAs comprises contacting the sample with at least 1000 lncRNA probes and at least 4000 mRNA probes.
Zhang is a research article focused on lncRNA expression profiles, and how these expression profiles can predict glioma phenotypes (Title, Abstract, and throughout). Zhang teaches obtaining brain tissue samples and also performing lncRNA expression profiling using Affymetrix microarrays to determine lncRNA expression levels (“Data sets characteristics” section” and “LncRNA expression profiles on Affymetrix HG-U133 Plus 2.0 arrays”, section). Zhang also teaches that:
“in this study, we re-annotated the HG-U133 Plus 2.0 probe sets and developed a lncRNA classification pipeline to identify the lncRNAs represented on this array. This method is feasible and attractive in its accuracy and low cost. It also allows the analysis of mRNA and lncRNA expressions at the same time and is easier to follow than transcript sequencing analysis,” (Discussion, second paragraph).
Thus, Zhang teaches lncRNA expression profiling of human brain tissue, that such a method can be coupled with mRNA expression profiling, and that such a method is attractive because of its low cost and accuracy (Discussion, second paragraph). Zhang overlaps with the research scope of Qureshi 2 and Rakhade because these research efforts concern expression profiling of human brain tissue. Zhang teaches that “2448 lncRNA probe sets” were analyzed (page 3, left column, third paragraph). Furthermore, Zhang teaches the use of Affymetrix HG-U133 Plus 2.0 arrays (Results, second paragraph). As evidenced by Thermo, the Affymetrix HG-U133 Plus 2.0 arrays target up to 14,500 genes/mRNAs (page 2, middle column, first paragraph). Furthermore, the fact that Thermo, a commercial supplier of molecular biology reagents and supplies, has a product insert concerning array chip probes is evidence in the industry that such tests are routine.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the presently claimed invention to modify the microarray/lncRNA expression methods rendered obvious by Rakhade, Qureshi 2, and Bennett to include at probes for at least 1000 lncRNAs and at least 4000 mRNAs because such a combination is the simple combination of known prior art elements to yield predictable results. Furthermore, Zhang teaches that such testing is cost effective and simple. Additionally, as evidenced by Thermo, such probe arrays are commercially available and therefore routine and predictable in the art.
Regarding claim 9, Zhang teaches the use of Affymetrix HG-U133 Plus 2.0 arrays and, as evidenced by Thermo, these arrays comprise 11 probe pairs per sequence (Zhang, “Data sets characteristics” section” and “LncRNA expression profiles on Affymetrix HG-U133 Plus 2.0 arrays”, section, Thermo page 4, top table).
Claim 6 is rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Rakhade (Rakhade SN et al. Epilepsia. 2007;48 Suppl 5:86-95) in view of Qureshi 2 (Qureshi et al. Trends Mol Med. 2011 June ;17(6):337-346), and Bennett (WO 2012/012467 A2, published 1/26/2012) as evidenced by Mercer (Mercer TR et al. Proc Natl Acad Sci U S A. 2008 Jan 15;105(2):716-21), as applied to claims 1, 2, and 23 above, and further in view of Lu (Lu R et al. BMC Bioinformatics. 2008 Jul 19;9:314).
Regarding claim 6, the limitations of claims 1 and 5 are addressed above. The above prior art does not teach contacting the pair of samples with dyes before contacting the samples with probes, wherein each member of the paired samples is contacted with a different dye than the other member.
Lu is a research article which focuses on probe-specific dyes and slide biases in two-color microarrays (Title and throughout). Lu teaches that:
“a primary reason for using two-color microarrays is that the use of two samples labeled with different dyes on the same slide, that bind to probes on the same spot, is supposed to adjust for many factors that introduce noise and errors into the analysis,” (Abstract).
It would have been obvious to a person of ordinary skill in the art, before the time of the effective filing date, to combine the teachings of Rakhade, Qureshi 2, and Bennett with the teachings of Lu because such a combination is the simple combination of known prior art elements to yield predictable results. As discussed above, Rakhade teaches the use of microarrays, and Lu teaches that it is a known method to use different dyes for different samples to adjust for background noise and errors in the analysis. Thus, a practitioner would be motivated to use different dyes for the different samples to yield more accurate data and to differentiate the samples.
Claim 7 is rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Rakhade (Rakhade SN et al. Epilepsia. 2007;48 Suppl 5:86-95) in view of Qureshi 2 (Qureshi et al. Trends Mol Med. 2011 June ;17(6):337-346), and Bennett (WO 2012/012467 A2, published 1/26/2012) as evidenced by Mercer (Mercer TR et al. Proc Natl Acad Sci U S A. 2008 Jan 15;105(2):716-21), as applied to claims 1, 2, and 23 above, and further in view of Yuan (Yuan DS et al. Nucleic Acids Res. 2005 Jul 1;33(12):e103).
Regarding claim 7, as discussed above the limitations of claim 1 are rendered obvious by the combination of Rakahde, Qureshi 2, and Bennett. Rakhade teaches the use of microarrays (see above rejection of claim 1). These prior art references do not teach the use of a dye flip microarray.
Yuan is a research article focused on the improvement of microarray methods (Title and throughout). Yuan teaches that:
“microarrays are fundamentally an assay methodology for detecting specific nucleic acids. A foremost concern of any assay is to determine its sensitivity and specificity. This is a potentially complex problem in the case of microarrays, not only because of the multiplexed nature of the assay but also because of the diverse range of experimental variables that come into play during the assay procedure. As a control for these variables, we performed a ‘dye-flip’ experiment in which matched samples were hybridized on consecutive days by the same person to the same slides using the same reagents, but with labels that were in reversed order on the second day,” (section entitled “A dye-flip experiment for microarray diagnostics”, first paragraph).
Thus, Yuan teaches that performing dye flip experiments when using microarrays offers better control of experimental variables (section entitled “A dye-flip experiment for microarray diagnostics”, first paragraph).
It would have been obvious to a person of ordinary skill in the art, before the time of the effective filing date, to combine the teachings of Rakhade, Qureshi 2, and Bennett with the dye flip microarray teachings of Yuan because performing a dye flip microarray confers better control of experimental variables, as taught by Yuan. Thus, a practitioner using the microarrays taught by Rakhade would be motivated to do a dye flip microarray taught by Yuan, for better experimental results.
Claim 8 is rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Rakhade (Rakhade SN et al. Epilepsia. 2007;48 Suppl 5:86-95) in view of Qureshi 2 (Qureshi et al. Trends Mol Med. 2011 June ;17(6):337-346), and Bennett (WO 2012/012467 A2, published 1/26/2012) as evidenced by Mercer (Mercer TR et al. Proc Natl Acad Sci U S A. 2008 Jan 15;105(2):716-21), as applied to claims 1, 2, and 23 above, and further in view of Kaposi-Novak (Kaposi-Novak P et al. Biotechniques. 2004 Oct;37(4):580, 582-6, 588).
As discussed above, the combination of Rakhade, Qureshi 2, and Bennett, render obvious to claim limitations recited in claim 1. These prior art references do not teach generating aminoally-aRNA from RNA in the samples before measuring expression.
Kaposi-Novak is a research article focused on microarray analysis of aminoally-labeled oligonucleotides from RNA amplification (Title and throughout). Kaposi-Novak teaches aRNA synthesis during microarray analysis, and also that their methods yielded highly reproducible results (Abstract).
It would have been obvious to a person of ordinary skill in the art, before the time of the effective filing date of the claimed invention, to combine the teachings of Rakhade, Qureshi 2, Bennett, and Kaposi-Novak to arrive at the invention claimed in claim 8 because such a combination is the simple combination of known prior art elements to yield predictable results. The results are predictable because the methods taught by Rakhade use microarrays, and Kaposi-Novak’s methods also use microarrays in combination with aRNA, wherein Kaposi-Novak teaches that their method is “highly reproducible” (Abstract) The combination of the teachings would therefore produce predictable results, where a practitioner would be motivated to combine the teachings of Kaposi-Novak because such methods are highly reproducible.
Claims 20 and 24 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Rakhade (Rakhade SN et al. Epilepsia. 2007;48 Suppl 5:86-95) in view of Qureshi 2 (Qureshi et al. Trends Mol Med. 2011 June ;17(6):337-346), and Bennett (WO 2012/012467 A2, published 1/26/2012) as evidenced by Mercer (Mercer TR et al. Proc Natl Acad Sci U S A. 2008 Jan 15;105(2):716-21), as applied to claims 1, 2, and 23 above, and further in view of Jia (Jia H et al. RNA. 2010 Aug;16(8):1478-87, provided in the IDS filed 4/28/2020).
Regarding 20, as discussed above, the combination of Rakhade, Qureshi 2, and Bennett, render obvious to claim limitations recited in claim 1. Rakhade teaches the use of microarrays/probes (see above rejection of claim 1). Qureshi 2 teaches that lncRNAs are associated with epilepsy and therefore teaches a motivation to target and measure lncRNAs to determine their mechanistic role in epilepsy (see rejection of claim 1).
The prior art references cited do not teach that the plurality of lncRNA genes are 6736 lncRNA genes.
Jia is a research article that teaches genome-wide identification and annotation of lncRNA genes (Title, Abstract, and throughout). Jia teaches that they have identified 5446 lncRNA genes, and that they combined this dataset with other published work to derive 6736 lncRNA genes (Abstract). Thus, Jia teaches known pools of lncRNAs of 6736 genes which have been manually annotated/curated and verified (Abstract and Title). Jia further teaches that lncRNAs are widely unexplored, and may have great biological relevance (page 1478, right column, first paragraph).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to combine the microarray methods of Rakhade to measure lncRNAs and associated lncRNA/mRNA pairs in the context of epilepsy as taught by Qureshi 2 and Bennett with the lncRNA pools taught by Jia, and to measure 6736 lncRNAs because Jia has already taught a manually curated set of 6736 lncRNAs which are useful for exploring lncRNAs using microarrays. A practitioner would be motivated to use Jia’s dataset of 6736 lncRNAs because they have been manually curated for accuracy.
Regarding claim 24, the method claim of 24 appears to be identical to the method of claim 1, the rejection of which is incorporated herein, with the exception that claim 24 recites specific probes for lncRNAs. For instance, claim 24 recites a probe for lncRNA AF086035 (SEQ ID NO: 3). It is further important to note that the high density microarray as claimed is not limited to one or more of the lncRNAs recited, but that such one or more probes are simply a part of the microarray.
As discussed above, Jia teaches lncRNA panel. Furthermore, the supplemental data of Jia teaches that AF086035 is one of the lncRNAs used in microarray profiling (see the supplemental data set attached at the end of Jia, where the supplemental data was pulled from the online publication and lists each of the lncRNAs). As seen in the supplemental data, AF086035 is one of the lncRNAs identified as part of the annotated set of Jia (see the 16th page of the listed lncRNAs, line 30, “AF086035”). As Jia teaches this lncRNA, they furthermore inherently teach its sequence (i.e., SEQ ID NO: 3). Therefore, a practitioner using the lncRNA set taught by Jia would be using a probe for microarray analysis for AF086035. Thus, the combination of Rakhade/Quereshi 2/Bennett/Jia renders obvious the limitations of claim 24.
Claims 11-13 and 17-18 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Rakhade (Rakhade SN et al. Epilepsia. 2007;48 Suppl 5:86-95) in view of Qureshi 2 (Qureshi et al. Trends Mol Med. 2011 June ;17(6):337-346), and Bennett (WO 2012/012467 A2, published 1/26/2012).
Regarding claim 11, all of these claim limitations are addressed in the rejection of claim 1 (see rejection of claim 1, above). The combination of Rakhade, Qureshi 2, and Bennett renders obvious the recited method of identifying putative therapeutic targets by obtaining at least a pair of brain tissue samples from a human brain, wherein each sample has a different level of electrical activity from the other, and measuring the expression of lncRNAs and mRNAs in the samples to determine differentially expressed lncRNAs and mRNAs in the samples (see claim 1 rejection, above). Furthermore, the rejection of claim 1 addresses the broadest reasonable interpretation of claim 11, which includes linking a differentially expressed lncRNA with a differentially expressed mRNA when the gene encoding the differentially expressed lncRNA overlaps with or is adjacent to the gene encoding the differentially expressed mRNA and identifying the pair as a cis-encoded target because Bennett teaches that lncRNA can act on “cis” encoded targets (page 24, line 5).
Regarding claim 12, Rakhade teaches observed gene expression in more than one brain sample pair (page 91, column 2 paragraph 1; page 92, column 1, paragraph 1). Additionally, Rakahde teaches the collection of multiple brain tissue samples/pairs per patient (page 87, right column, final paragraph). Thus, Rakhade teaches the collection of multiple brain tissue pairs (page 87, right column, final paragraph). Rakhade also teaches each pair having a low electrical brain member and a high electrical brain activity member (page 92, column 2, and Figure 5).
Regarding claim 13, Rakhade teaches interictal spike detection wherein amplitude is a component in measuring the interictal spike in Figure 2. Figure 2 also depicts seizure spikes compared with control spikes, and therefore teaches the classification of high (“seizure onset”) and low (“control”) electrical brain activity (Figure 2).
Regarding claim 17, Rakhade teaches that:
“understanding the potential roles of interictal spike activity and the genes that are induced together with that spiking should offer us further clues on both the causes of focal neocortical epilepsy as well as potential therapeutic treatments for the future,” (page 94, left column, first paragraph).
Thus, Rakahde teaches that their method can be used to identify potential therapeutic treatments. It is inherently obvious that a therapeutic target would be a site of effective intervention because if the site were not a site of effective intervention it would offer no benefit to target as a therapy.
Regarding claim 18, the methods of Rakhade, Qureshi 2, and Bennett are directed to identifying lncRNAs and/or mRNAs which could be used as putative therapeutic targets (see the rejection of claim 1).
Claims 14, and 15 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Rakhade (Rakhade SN et al. Epilepsia. 2007;48 Suppl 5:86-95) in view of Qureshi 2 (Qureshi et al. Trends Mol Med. 2011 June ;17(6):337-346), and Bennett (WO 2012/012467 A2, published 1/26/2012) as applied to claims 11, 12, 13, 17, 18, above, and further in view of Zhang (Zhang X et al. Neurobiol Dis. 2012 Oct;48(1):1-8, published online 6/16/2012, previously supplied).
The teachings of Rakhade, Qureshi 2, and Bennett are discussed above with regards to independent claim 11.
Regarding claims 14 and 15, Zhang is a research article focused on lncRNA expression profiles, and how these expression profiles can predict glioma phenotypes (Title, Abstract, and throughout). Zhang teaches obtaining brain tissue samples and also performing lncRNA expression profiling using Affymetrix microarrays to determine lncRNA expression levels (“Data sets characteristics” section” and “LncRNA expression profiles on Affymetrix HG-U133 Plus 2.0 arrays”, section). Zhang also teaches that:
“in this study, we re-annotated the HG-U133 Plus 2.0 probe sets and developed a lncRNA classification pipeline to identify the lncRNAs represented on this array. This method is feasible and attractive in its accuracy and low cost. It also allows the analysis of mRNA and lncRNA expressions at the same time and is easier to follow than transcript sequencing analysis,” (Discussion, second paragraph).
Thus, Zhang teaches lncRNA expression profiling of human brain tissue, that such a method can be coupled with mRNA expression profiling, and that such a method is attractive because of its low cost and accuracy (Discussion, second paragraph). Zhang overlaps with the research scope of Qureshi 2 and Rakhade because these research efforts concern expression profiling of human brain tissue. Zhang teaches that “2448 lncRNA probe sets” were analyzed (page 3, left column, third paragraph). Furthermore, Zhang teaches the use of Affymetrix HG-U133 Plus 2.0 arrays (Results, second paragraph). As evidenced by Thermo, the Affymetrix HG-U133 Plus 2.0 arrays target up to 14,500 genes/mRNAs (page 2, middle column, first paragraph). Furthermore, the fact that Thermo, a commercial supplier of molecular biology reagents and supplies, has a product insert concerning array chip probes is evidence in the industry that such tests are routine. Regarding claims 14 and 15, Zhang teaches the use of Affymetrix microarrays to detect lncRNAs and mRNAs, and therefore teaches quantifying lncRNA and mRNA and a microarray capable of quantifying lncRNA and mRNA (“Data sets characteristics” section and “LncRNA expression profiles on Affymetrix HG-U133 Plus 2.0 arrays”, section, and Discussion).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Rakhade, Quereshi 2 and Bennett with those of Zhang to arrive at a microarray capable of quantifying lncRNA and mRNA, as such a combination is the simple combination of known prior art elements to arrive at predictable results. In the present case, Zhang teaches that such microarrays can quantify lncRNA and mRNA; as such a practitioner would be motivated lncRNA and mRNA simply because of such a requirement to quantify and measure target variables/RNAs rendered obvious by Rakhade, Qureshi 2, and Bennett.
Claim 16 is rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Rakhade (Rakhade SN et al. Epilepsia. 2007;48 Suppl 5:86-95) in view of Qureshi 2 (Qureshi et al. Trends Mol Med. 2011 June ;17(6):337-346), and Bennett (WO 2012/012467 A2, published 1/26/2012) and Zhang (Zhang X et al. Neurobiol Dis. 2012 Oct;48(1):1-8, published online 6/16/2012), as applied to claims 11, 14, and 15 and further in view of Lippa (Lippa KA et al. BMC Res Notes. 2010 Dec 28;3:349).
The teachings of Rakhade, Qureshi 2, and Bennett are discussed above with regards to independent claim 11.
Regarding claim 16, as discussed above, the combination of Rakhade, Qureshi 2, Bennett, and Zhang renders obvious the invention of claim 11. Furthermore, Zhang teaches the use of microarrays for the profiling of lncRNAs and mRNAs (“Data sets characteristics” section” and “LncRNA expression profiles on Affymetrix HG-U133 Plus 2.0 arrays”, section, and Discussion).
The above prior art does not teach the use of correlating the fold-change of a protein-coding control gene that is common to both arrays.
Lippa is a research article focused on the use of internal and external controls when using microarrays (Title and throughout). Lippa teaches that:
“whole-array metrics and information from a standard mixture of external spike-in and endogenous internal controls. Spike-in controls were found to carry the same information about technical performance as whole-array metrics and endogenous "housekeeping" genes. These results support the use of spike-in controls as general tools for performance assessment across time, experimenters and array batches, suggesting that they have potential for comparison of microarray data generated across species using different technologies,” (Background, first paragraph).
Thus, Lippa teaches that, when comparing data from multiple microarrays, positive controls to control for consistency of data can be used to generate comparable datasets across microarrays, including endogenous protein-coding genes common to the arrays (“housekeeping” genes, Background, first paragraph).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Rakhade, Qureshi 2, Bennett, Zhang and Lippa, to include a protein-coding gene control common to both the lncRNA and mRNA arrays, because, as taught by Lippa, this is simply the use of a known technique to improve a similar method in the same way. In the present case, the use of an endogenous control when comparing microarray data is a known technique taught by Lippa which would be applied to the known method of microarray analysis of lncRNA and mRNA taught by Zhang. A practitioner would be motivated to include a positive control across the data to ensure that the results of the data are consistent.
Response to Arguments
The Applicant’s arguments received 8/12/2025 have been considered but are not persuasive to place the claims in condition for allowance.
The Applicant argues that a practitioner, when considering Rakhade, would not look at all differentially expressed genes, but would only look at transcription factors. However, the Applicant’s arguments appear to rely only on piecemeal analysis of the rejection as a whole, where the combination of references and their teachings are not addressed. In response to applicant's arguments against the references individually, 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). In the present case, Qureshi 2 teaches that lncRNAs are associated with epilepsy; thus, Qureshi 2 teaches the motivation to look at lncRNAs using the method of Rakhade. Furthermore, Rakhade’s conclusion of their paper is:
“Understanding the potential roles of interictal spike activity and the genes that are induced together with that spiking should offer us further clues on both the causes of focal neocortical epilepsy as well as potential therapeutic treatments for the future,” (page 94, left column, first paragraph).
Thus, Rakhade teaches that understanding genes induced in spiking are important for identifying therapeutic targets. Given the teachings of Qureshi 2, that lncRNAs are associated with epilepsy, a practitioner would be motivated to include expression analysis of lncRNAs in the context of epilepsy, so that potential therapeutic avenues could be identified.
The Applicant appears to argue that Rakhade and Qureshi 2 may be non-analogous art, as Qureshi 2 only mentions epilepsy twice. In response to applicant's argument that Qureshi is nonanalogous art, it has been held that a prior art reference must either be in the field of the inventor' s endeavor or, if not, then be reasonably pertinent to the particular problem with which the inventor was concerned, in order to be relied upon as a basis for rejection of the claimed invention. See In re Oetiker, 977 F.2d 1443, 24 USPQ2d 1443 (Fed. Cir. 1992). In this case, Qureshi 2 is analogous art to Rakhade because Qureshi 2 teaches mechanisms of cognitive disorders such as epilepsy (top of page 3). Furthermore, Qureshi 2 teaches that lncRNAs are associated with epilepsy; thus, Qureshi 2 is analogous art with Rakhade and the present invention because it teaches and addresses an underlying mechanism of epilepsy, which was the focus and endeavor of Rakhade and the present application. Qureshi 2 teaches the same disease as Rakhade and the present application, as well as underlying mechanisms of the disease. Qureshi 2 is therefore reasonably pertinent to the particular problem of the inventor.
The Applicant argues that Qureshi 2 only offers a passing mention of epilepsy and lncRNA. However, the Applicant’s response does not weigh the full substance of what Qureshi 2 has taught: namely, that it was already known in the art that lncRNAs were known to be associated with epilepsy, as Qureshi 2 references a paper in the final line of page 8 which is specifically dedicated to epilepsy (“Epigenetic mechanisms underlying human epileptic disorders and the process of epileptogenesis.”). Thus, Qureshi 2 is summarizing the results of a paper specifically focused on epilepsy, where a practitioner would reasonably be motivated to quantify lncRNAs in the context of an epileptic patient giving the guidance of Qureshi 2.
The Applicant argues that Bennett does not teach epilepsy, which is again a piecemeal analysis, where each reference is attacked individually as opposed the combined teaching of the references. In response to applicant's arguments against the references individually, 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).
The combination of Qureshi 2 and Rakhade is sufficient to motivate a practitioner to measure lncRNAs in the context of epilepsy to identify therapeutic targets. Given that lncRNA analysis is rendered obvious in the disease context of epilepsy, the teachings of Bennett are used in the rejection to show that it was known in the art that lncRNA and mRNA act in tandem, and it would therefore be obvious to determine lncRNAs which are paired with mRNA, and the relationship between their expression, because Bennett teaches that lncRNAs directly influence mRNA expression levels (see page 24, first paragraph). Bennett teaches that ncRNAs are known act in “cis” with their targets (page 24, first paragraph). Furthermore, Bennett offers numerous examples of ncRNA, including the work of Mercer (page 24, first paragraph). As evidenced by Mercer, “cis-acting” lncRNAs were known to affect their mechanism of action on protein-coding genes, where furthermore it was known that cis-acting lncRNA act adjacently or within a given protein coding gene (i.e., intronically or adjacent with an mRNA, per Mercer Figure 2 and page 718). Thus, it was known in the art that lncRNAs are actively paired with mRNAs within 10kb of their genomic loci, as presently recited. Furthermore, contrary to the Applicant’s assertion, Bennett does teach lncRNA and mRNA gene pairing in the list of ncRNA and their targets on page 24, first paragraph, for instance, the teachings of Mercer. Thus, lncRNA/mRNA gene pairs are taught by Bennett, as previously discussed above and in the office action mailed 3/12/2025 (page 14 of the 3/12/2025 action, first paragraph: “lncRNA overlaps with, or is adjacent to (i.e., “cis”) the gene encoding the paired mRNA…pages 23-28 [Bennett])”).
In response to applicant's argument that the examiner's conclusion of obviousness is based upon improper hindsight reasoning, it must be recognized that any judgment on obviousness is in a sense necessarily a reconstruction based upon hindsight reasoning. But so long as it takes into account only knowledge which was within the level of ordinary skill at the time the claimed invention was made, and does not include knowledge gleaned only from the applicant's disclosure, such a reconstruction is proper. See In re McLaughlin, 443 F.2d 1392, 170 USPQ 209 (CCPA 1971).
In the present case, the tissue sampling method to determine activity-dependent gene expression and differentially expressed genes dependent upon paired samples in the disease context of epilepsy is known as taught by Rakhade (above). Further, it was known that lncRNAs are associated with epilepsy (per Qureshi 2, above). Thus, a practitioner would be motivated to measure differentially expressed lncRNAs in the context of epileptic disease. Furthermore, it is known that lncRNAs have paired, “cis” mRNA targets, per Bennett, and further evidenced by Mercer. Thus, it would further be obvious to determine lncRNA/mRNA cis-gene pairs as presently recited. Thus, knowledge of the art at the time of filing is sufficient to render the invention obvious regardless of the Applicant’s disclosure.
Conclusion
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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/D.C.R./Examiner, Art Unit 1635
/KIMBERLY CHONG/Primary Examiner, Art Unit 1636