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 .
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.
Withdrawn Objections/Rejections
The objections to the specification are withdrawn in response to the amendments.
The objections to the claims are withdrawn in response to the amendments.
The rejection of claim 23 under 35 U.S.C. 112(a) is withdrawn in response to the amendments.
The rejection of claims 22-23 under 35 U.S.C. 101 is withdrawn in response to the amendments.
The rejection of claim 22 under U.S.C. 103 is withdrawn in response to the amendments. However, new grounds of rejection are set forth below under 112(a).
Priority
Acknowledgment is made of the present application as a proper National Stage (371) entry of PCT Application No. PCT/US20/38244, filed 06/17/2020, which claims benefit under 35 U.S.C. 119(e) to provisional application No. 62/862,587, filed 06/17/2019.
Status of the Claims
Claims 1, 3, 5-6, 10-11, 13-23 and 55-56 are pending; claims 1, 19-20 and 22-23 are amended; claims 2, 4, 7-9, 12 and 24-54 are canceled; claims 55-56 are newly recited; no claims are withdrawn. Claims 1, 3, 5-6, 10-11, 13-23 and 55-56 are examined below.
New Rejection
Claim Rejections - 35 USC § 112
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 22-23 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 enablement requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to use the invention commensurate in scope with these claims. The specification does not reasonably provide enablement for determining whether a subject has sepsis (as recited in claim 22) or for identifying a sepsis condition in a subject (as recited in claim 23).
The specification does not provide sufficient evidence that the claimed methods of measuring the level of resistin (RETN), Interleukin-1 Receptor Type 2 (IL1R2), and clusterin (CLU) in CD14+ monocytes in a blood sample from the subject and comparing the level to a control (claims 22), or of identifying an elevated fraction of CD14+ monocytes characterized by high expression of RETN, IL1R2, and CLU (claim 23), is effective for determining whether a subject has sepsis (as recited in claim 22) or for identifying a sepsis condition in a subject (as recited in claim 23). The evidence provided merely shows that clustering genes of CD45+ PBMCs of subjects with and without sepsis identifies a cluster of high RETN, ALOX5AP and IL1R2 expression in a larger fraction of total cells in intermediate urosepsis (Int-URO), urosepsis (URO), bacteremia and sepsis (Bac-SEP) and sepsis requiring intensive care (ICU-SEP) subjects than in control or leukocytosis urinary-tract infection (Leuk-UTI) patients but not compared to subjects in the ICU for conditions other than sepsis (ICU-NO SEP) (spec. page 46 and page 47 lines 1-5). Notably the gene clustering analysis of PBMCs is not the same as measuring the level of RETN, IL1R2, and CLU in CD14+ monocytes or identifying an elevated fraction of CD14+ monocytes characterized by high expression of RETN, IL1R2, and CLU as claimed. Furthermore, as mentioned above, the specification does not disclose a significant difference between the gene expression profile between ICU-SEP and ICU-NO SEP. Therefore, the specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the invention.
MPEP § 2164.01 states:
The standard for determining whether the specification meets the enablement
requirement was cast in the Supreme Court decision of Minerals Separation Ltd. v. Hyde, 242 U.S.261, 270 (1916) which postured the question: is the experimentation needed to practice the invention undue or unreasonable? That standard is still the one to be applied.
In re Wands, 858F.2d 731, 737, 8 USPQ2d 1400, 1404 (Fed. Cir. 1988). Accordingly, even though the statute does not use the term "undue experimentation," it has been interpreted to require that the claimed invention be enabled so that any person skilled in the art can make and use the invention without undue experimentation.
In re Wands, 858 F.2d at 737, 8 USPQ2d at 1404 (Fed. Cir. 1988).
There are many factors to be considered when determining whether there is sufficient evidence to support a determination that a disclosure does not satisfy the enablement requirement and whether any necessary experimentation is "undue." These factors include, but are not limited to:
(A) The breadth of the claims;
(B) The nature of the invention;
(C) The state of the prior art;
(D) The level of one of ordinary skill;
(E) The level of predictability in the art;
(F) The amount of direction provided by the inventor;
(G) The existence of working examples; and
(H) The quantity of experimentation needed to make or use the invention based on the content of the disclosure.
In re Wands, 858 F.2d 731, 737, 8 USPQ2d 1400, 1404 (Fed. Cir. 1988).
In regard to Wands factors (A) and (B), the breadth of the claims needed to enable the invention is determined by whether the scope of enablement provided to one skilled in the art by the disclosure is commensurate with the scope of protection sought in the claims. AK Steel Corp. v. Sollac, 344 F.3d 1234, 1244, 68 USPQ2d 1280, 1287 (Fed. Cir. 2003); In re Moore, 439 F.2d 1232, 1236, 169 USPQ 236, 239 (CCPA 1971). The propriety of a rejection based upon the scope of a claim relative to the scope of the enablement concerns (1) how broad the claim is with respect to the disclosure and (2) whether one skilled in the art could make and use the entire scope of the claimed invention without undue experimentation.
The nature of the invention is a biological/chemical case, where there is natural unpredictability in performance of certain species other than those specifically enumerated; see MPEP § 2163. Accordingly, it is the Office’s position that undue experimentation would be required to practice the claimed method(s), with a reasonable expectation of success, because it would not have been predictable from the disclosure that an elevated level of RETN, IL1R2 and CLU in CD14+ monocytes or an elevated fraction of CD14+ monocytes characterized by high expression of RETN, IL1R2 and CLU, would enable the determining of whether a subject has sepsis or the identifying of a sepsis condition in a subject, respectively (see MPEP § 2164.03).
Although the specification discloses that through non-negative matrix factorization of the genomic data, CLU was identified as highly expressed in ICU-SEP versus ICU-NoSEP (page 47 lines 6-16), there is no sufficient evidence disclosed that the high CLU gene corresponds to a CD+14 monocyte population that is also high in RETN and IL1R2 (“Whereas the MS 1 fraction alone cannot be used as a sepsis classifier in this context, analyzing the co-expression of PLAC8, CLU, and MS 1 marker genes (RETN, CD63, ALOX5AP, SEC61G, TXN, and MTlX) in these datasets performed well in classifying subjects with sepsis against sterile inflammation” page 48 lines 24-31). Furthermore, the specification also discloses that “RETN…correlates negatively with severity” (page 47 lines 24-26) which suggests that high RETN is not a predictable biomarker for determining sepsis or identifying a sepsis condition. Finally, the specification seems to admit that “the performance of MS 1 PLAC8 + CLU may be inflated when applied to a subset of subjects from which MS 1 was derived” (page 48 lines 9-10), which suggests that one skilled in the art would not be able to make and use the entire scope of the claimed invention without undue experimentation.
In regard to Wands factors (C), (D) and (E), the state of the prior art is what one skilled in the art would have known, at the time the application was filed, about the subject matter to which the claimed invention pertains and provides evidence for the degree of predictability in the art; see MPEP § 2164.05(a).
Accordingly, Bloos et al. Virulence 5:1, 154–160; January 1, 2014 (“Bloos”) teaches that “confirming infection as cause of a severe inflammatory response is the main challenge in the diagnosis of sepsis” (page 154 col. 2 para. 1). Bloos further teaches that “[t]here is currently no biochemical technique available which alone allows a rapid and reliable discrimination between sepsis and non-infectious inflammation” (Abstract). Bloos further teaches a list of proposed biomarkers of sepsis (Table 1 page 155) but does not include an elevated level of RETN, IL1R2 and CLU in CD14+ monocytes or an elevated fraction of CD14+ monocytes characterized by high expression of RETN, IL1R2 and CLU. Bloos further teaches that “the currently available biomarkers seem to mainly identify invasive bacterial infections but viruses, fungi, and parasites may also evoke sepsis. Studies about biomarkers and other tools of sepsis diagnosis are also hampered by a poor gold standard as differentiation between colonization and infection is often challenging” (page 157 col. 1 para. 3).
Furthermore, Squair et al. NATURE COMMUNICATIONS | (2021) 12:5692 | https://doi.org/10.1038/s41467-021-25960-2 (“Squair”) teaches that “[w]hile many statistical methods are available to identify differentially expressed genes, the principles that distinguish these methods and their performance remain unclear. Here, we show that the relative performance of these methods is contingent on their ability to account for variation between biological replicates. Methods that ignore this inevitable variation are biased and prone to false discoveries. Indeed, the most widely used methods can discover hundreds of differentially expressed genes in the absence of biological differences” (Abstract). Squair teaches that they “assembled a compendium of 46 scRNA-seq datasets that encompassed disparate species, cell types, technologies, and biological perturbations (Supplementary Fig. 3). We found that single-cell DE methods displayed a systematic preference for highly expressed genes across the entire compendium (Fig. 2f). Together, these experiments suggest that the inferior performance of single-cell methods can be attributed to their bias towards highly expressed genes” (page 3 col. 2 paras. 2-3). Note that one of the scRNA-seq datasets analyzed by Squair appears to be the same data used in the instant disclosure (“Reyes et al.. 2020” page 11 col. 2 para. 14) (Cited on IDS 10/17/2022). Therefore, Squair suggests that the methodology used by the inventors of the instant case is biased.
Given the cited teachings that diagnosing sepsis is difficult, particularly between severely ill patient, and that differential expression analyses are biased, the cited references demonstrate that the use of an elevated level of RETN, IL1R2 and CLU in CD14+ monocytes or an elevated fraction of CD14+ monocytes characterized by high expression of RETN, IL1R2 and CLU for determining/identifying sepsis is unpredictable.
While the level of skill in the art is high, the amount of guidance provided regarding how to use the claimed biomarkers in the claimed methods is scant. Accordingly, the amount of experimentation required to determine how to use the recited biomarkers to determine/identify sepsis in a subject is quite extensive.
Due to the large quantity of experimentation necessary to determine how to use the recited level of RETN, IL1R2 and CLU in CD14+ monocytes or fraction of CD14+ monocytes characterized by high expression of RETN, IL1R2 and CLU for determining/identifying sepsis, the lack of direction/guidance presented in the specification regarding the same, the absence of working examples directed to the same, the complex nature of the invention, the limited state of the prior art, the unpredictability of the effects of complex biological molecules on diseased physiological systems, and the breadth of the claims, undue experimentation would be required of the skilled artisan to make and/or use the claimed invention.
In view of all of the above, one of skill in the art would be forced into undue experimentation to practice the claimed invention, and thus, the claimed invention does not satisfy the requirements of 35 U.S.C. §112 first paragraph.
Maintained Rejections
Claim Rejections - 35 USC § 103
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, 3, 5-7, 13 and 16-18 are rejected under 35 U.S.C. 103 as being unpatentable over Gainaru et al. Critical Care (2018) 22:56 https://doi.org/10.1186/s13054-018-1977-1 ("Gainaru") and Hu, Wan-Chung Sepsis is a syndrome with hyperactivity of TH17-like innate immunity and hypoactivity of adaptive immunity arXiv.org, e-Print Archive, Quantitative Biology (2013), 1-67 | Language: English, Database: CAplus as evidenced by ClinicalTrials.gov ID NCT01223690 (retrieved online Study Details | Clarithromycin as Immunomodulator for the Management of Sepsis | ClinicalTrials.gov on 6/20/2025) and HealthMatters Absolute CD45 Count (retrieved online https://healthmatters.io/understand-blood-test-results/absolute-cd45-count#:~:text=The%20CD45%20marker%20is%20found,blood%2C%20typically%20measured%20per%20microliter on 6/20/2025).
Regarding claim 1, Gainaru teaches a method for treating a subject for sepsis, comprising: administering an antibiotic to a subject (“[t]his study was approved as a substudy of a randomized clinical study investigating the role of intravenous clarithromycin for the management of patients with proven or suspected Gram-negative sepsis [7]. The study is registered at https://clinicaltrials.gov/ct2/show/NCT01223690 (NCT01223690)” page 2 column 1 paragraph 3) who has been identified as having elevated levels of CD45+ monocytes that are CD14+ relative to a control (“CD14pos/CD16pos/CD45pos monocytes analyzed and reported together as inflammatory monocytes, … The absolute counts of…inflammatory… monocytes were significantly greater among patients than healthy controls (Fig. 3a, b)” page 5 column 1 paragraph 2). Note that as evidence by ClinicalTrials.gov, the administration of antibiotic happened “for four consecutive days” (page 6). Therefore, there was an administration of antibiotic after the elevated level of monocytes was identified (Fig. 3 shows data of day 1 and 3). Gainaru further suggests wherein the CD45+ monocytes are HLA-DRlo (“HLA-DR is expressed on activated CD14 monocytes that are capable of antigen presentation and perpetuation of the inflammatory reaction. In sepsis, the expression of HLA-DR on circulating CD14 monocytes and the number of HLA-DR molecules (mHLA-DR) on the monocyte surface are decreased and this is interpreted as an index of sepsis-induced immunosuppression. To date, decreased mHLA-DR is considered the gold standard for the identification of immunosuppression” page 6 column 1 paragraph 2). Gainaru further teaches that “[i]mmune status in sepsis varies during the course of the disease. The early stages are characterized by a phase of excessive inflammation also known as the “cytokine storm”. In this stage, blood monocytes are overfunctioning for the production of cytokines. As the syndrome progresses, the proinflammation stage is followed by a phase of immune-suppression that is characterized by the inability for cytokine secretion [1]. In this stage monocytes are functionally deactivated, and this is shown by the decreased expression of the human leukocyte antigen (HLA) class II on their cell surface. However, it is also possible that these two phases of proinflammation and anti-inflammation may occur simultaneously.” (page 2 column 1 paragraph 1). Gainaru further teaches that ““classical or inflammatory monocytes” [are] characterized by a bright expression of CD14” (page 2 column 1 paragraph 1).
Gainaru fails to teach wherein the CD45+ monocytes are IL1R2hi+.
Hu teaches that “sepsis is a syndrome with hyperactivity of TH17-like innate immunity and hypoactivity of adaptive immunity” (Title). Hu further teaches that “[d]espite of current antibiotics treatment, sepsis still causes a very high mortality. The pathophysiology of sepsis is still unclear” (page 20 paragraph 2). Hu further teaches “peripheral leukocyte gene expression profiles of sepsis compared to those of healthy controls” (page 5 paragraph 1) using “whole blood RNA” (page 4 paragraph 2). Hu further teaches that “cytokine receptors are differentially regulated in sepsis. On the contrary with cytokine, cytokine in a certain immunological pathway is usually down-regulated… TH22 cytokine receptors… IL1R2, are up-regulated. Thus, TH1, TH2, THαβ, and TH22 are not activated during sepsis” (page 12 paragraph 1). Hu further teaches that “all MHC related genes are down-regulated in leukocytes of septic patients. These down-regulated genes include HLA-DPB, HLA-DQA, HLA-DRB, HLA-DOB, HLA-DRA… Since all the MHC related genes are down-regulated, antigen presentation during sepsis is likely to be impaired” (page 9 paragraph 2). Hu further teaches that “innate immunity related genes are significantly up-regulated. These genes include CD14” (page 22 paragraph 1). Thus, given that Hu teaches that TH22 is not activated (via the differential regulation of cytokine receptor, i.e. IL1R2hi), and teaches that antigen presentation during sepsis is impaired (via HLA-DRlo ), and further teaches that innate immunity related genes are significantly up-regulated (via CD14+), Hu suggests that IL1R2hi, HLA-DRlo, and CD14+ in peripheral leukocytes “demonstrate that sepsis is actually a hyperactivity of innate immunity and hypoactivity of adaptive immunity. Thus, it can well explain the co-existence of hyperimmune and hypoimmune. The hypoimmune adaptive immunity explains why immunocompromised patients tend to suffer from sepsis easily. The hyperimmune innate immunity explains why pro-inflammatory cytokine storm is observed at sepsis.” (page 22 paragraph 2). Note that as evidence by HealthMatters, “→ CD45 is a surface marker expressed on all leukocytes, including…monocytes” (page 1 paragraph 1).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the teachings of Gainaru to include the IL1R2hi taught by Hu in the analysis of CD45+ monocytes taught by Gainaru because Hu suggests that the IL1R2hi marker helps characterize the immune response to sepsis in the subject. A person having ordinary skill in the art would have had a reasonable expectation of success because Hu teaches that IL1R2hi, along with CD14+ and low HLA-DRA and low HLA-DRB (species of HLA-DR), are present in peripheral leukocytes of sepsis patients and Gainaru also teaches that HLA-DRlo and CD14+ are present in peripheral leukocytes of sepsis patients. Furthermore, given that Gainaru teaches that CD14+ is expressed in monocytes, and given that HealthMatters teaches that CD45+ is expressed in all leukocytes, the CD14+ peripheral leukocytes analyzed by Hu would inherently comprise of CD45+ monocytes. Therefore, a person having ordinary skill in the art would reasonably expect success in CD45+ monocytes being IL1R2hi in sepsis.
Regarding claims 3, 6 and 16, Gainaru in view of Hu teach the method of claim 1 as discussed above.
Gainaru in view of Hu further suggests wherein the subject is identified as having elevated levels of CD45+ monocytes that are IL1R2hi, HLA-DRlo, and CD14+ relative to a control by: measuring the fraction of CD45+ monocytes that are IL1R2hi, HLA-DRlo, and CD14+ in a blood sample from the subject; and comparing the fraction of CD45+ monocytes that are IL1R2hi, HLA-DRlo, and CD14+ in the blood sample from the subject to a control, wherein the control is a blood sample from a healthy subject, wherein the blood sample is obtained from a human (“[f]rom each patient and healthy volunteer, 2 ml whole blood were collected” page 2 column 2 paragraph 4 of Gainaru, “Whole blood was incubated with the following combinations of monoclonal antibodies… anti-CD14 at the fluorochrome FITC (clone RMO25, Immunotech), anti-CD16 at the fluorochrome PE (clone 3G8, Immunotech), and anti-CD45 at the fluorochrome PC5 (clone J.33, Immunotech)” page 2 column 2 paragraph 6 of Gainaru and page 5 column 1 paragraph 2 of Gainaru).
Regarding claim 5, Gainaru in view of Hu teach the method of claim 3 as discussed above.
Gainaru in view of Hu further suggest further comprising determining that the subject has sepsis if the fraction of CD45+ monocytes that are IL1R2hi, HLA-DRlo, and CD14+ in the blood sample from the subject is elevated compared to a control (“This study shows that circulating counts of inflammatory and patrolling monocytes are greatly increased in Gram-negative sepsis” page 8 column 1 paragraph 3 of Gainaru, page 5 column 1 paragraph 2 of Gainaru, see Fig. 3a of Gainaru).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the teachings of Gainaru to include the IL1R2hi taught by Hu in the analysis of CD45+ monocytes, for the determination of sepsis in the subject because Hu suggests that IL1R2hi characterizes the pathophysiology of the sepsis. A person having ordinary skill in the art would have had a reasonable expectation of success because both Gainaru and Hu teach methods related to analyzing peripheral leukocytes in blood.
Regarding claim 7, Gainaru in view of Hu teach the method of claim 1 as discussed above.
Gainaru further teaches wherein the control is a predetermined value (page 5 column 1 paragraph 2). Note that the “predetermined value” can be that of a control population according to the specification page 28 lines 1-2. Therefore, the “healthy controls” taught by Gainaru (Fig. 3) addresses the claim.
Regarding claim 13, Gainaru in view of Hu teach the method of claim 3 as discussed above.
Gainaru in view of Hu further teach wherein measuring the fraction of CD45+ monocytes that are IL1R2hi, HLA-DRlo, and CD14+ comprises conducting a flow cytometry assay (“White blood cells were analyzed after running through the Cytomics FC-500 flow cytometer with gating for monocytes based on their characteristic SS/CD45 expression” page 3 column 1 paragraph 1 of Gainaru).
Regarding claims 17-18, Gainaru in view of Hu teach the method of claim 1 as discussed above.
Gainaru further teach wherein the subject is a human patient having, suspected of having, or at risk for a bacterial infection, and wherein the subject is a human patient having, suspected of having, or at risk for sepsis (page 2 column 1 paragraph 3).
Claim 10 is rejected under 35 U.S.C. 103 as being unpatentable over Gainaru and Hu as evidenced by ClinicalTrials.gov and HealthMatters as applied to claim 3 above, and further in view of Kathri and Sweeney (WO 2019168622) ("Kathri").
Regarding claim 10, Gainaru in view of Hu teach the method of claim 3 as discussed above.
Hu suggest conducting an RNA-sequencing assay (“use the healthy control (sample size 21) whole blood RNA from this dataset to compare the septic patients. In this study, I perform further analysis to study peripheral leukocyte gene expression profiles of sepsis compared to those of healthy controls” page 4 paragraph 2 and page 5 paragraph 1).
Gainaru in view of Hu fail to explicitly teach wherein measuring the fraction of CD45+ monocytes that are IL1R2hi, HLA-DRlo, and CD14+ comprises conducting an RNA-sequencing assay.
Kathri teaches “a gene expression-based method for determining whether a subject having sepsis has an Inflammopathic phenotype, an Adaptive phenotype or a Coagulopathic phenotype” (Abstract). Kathri further teaches that “the method may comprise: (a) measuring the amount of RNA transcripts… The measuring step can be done using any suitable method. For example, the amount of the RNA transcripts in the sample may be measured by RNA-seq (see, e.g., Morin et al BioTechniques 2008 45: 81-94; Wang et al 2009 Nature Reviews Genetics 10: 57-63)” (page 7 paragraphs 1-2 and 4). Kathri further teaches that “[t]he sample of RNA obtained from the subject may comprise RNA isolated from whole blood, white blood cells,”(page 8 paragraph 2). Kathri further suggests that the method comprises “monocyte count… and/or whether there are Gram-negative bacteria present” (page 20 lines 4-5). Kathri further teaches that “[t]herapeutic methods are also provided. In some embodiments, these methods may comprise identifying a subject as having a phenotype using the methods described above, and treating a subject based on whether the subject is indicated as having an Inflammopathic phenotype, an Adaptive phenotype or a Coagulopathic phenotype” (page 10 last paragraph).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the teachings of Gainaru in view of Hu to include the conducting an RNA-sequencing assay taught by Kathri because Kathri suggests that this enables the identification of sepsis phenotypes. One would have been motivated to make such a modification because Kathri teaches that identifying the phenotype enables a targeted treatment, i.e. a treatment based on the identified phenotype. A person having ordinary skill in the art would have had a reasonable expectation of success because Kathri uses a blood sample for the RNA-seq assay and further suggests to measure the monocyte count, and Gainaru in view of Hu teach measuring the monocyte count in a blood sample. Furthermore, Kathri provides a reference for information regarding performing the RNA-seq assay.
Claim 11 is rejected under 35 U.S.C. 103 as being unpatentable over Gainaru, Hu and Kathri as evidenced by ClinicalTrials.gov and HealthMatters as applied to claim 10 above, and further in view of Haynes et al. 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Kansas City, MO, USA, 2017, pp. 1446-1450, doi: 10.1109/BIBM.2017.8217875 (“Haynes”).
Regarding claim 11, Gainaru in view of Hu and Kathri teach the method of claim 10 as discussed above,
Gainaru in view of Hu and Kathri fail to teach wherein the RNA-sequencing assay comprises a single cell RNA-sequencing (scRNA-seq) assay.
Haynes teaches [c]omplementing single-cell RNA-seq using bulk transcriptional profiles” (Title). Haynes further teaches that “Villani et al. established transcriptional signatures, referred to as the Villani cell signatures, from single-cell RNA-seq to characterize novel subpopulations of…monocytes” (page 1446 column 1 paragraph 1). Haynes further teaches “that our integrated, multi-cohort analysis framework identifies robust disease signatures that are diagnostic, prognostic, therapeutic, and mechanistic across a broad spectrum of diseases including… infections” (1446 column 1 paragraph 2). Haynes further teaches that “[i]mportantly, this enables rapid understanding of novel cell populations that would otherwise require labor-intensive wet lab experimentation” (page 1447 column 2 paragraph 2).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the teachings of Gainaru, Hu and Kathri to rely on the single cell RNA-sequencing assay taught by Haynes because Haynes teaches that complementing bulk RNA sequencing with single-cell RNA sequencing enables rapid understanding of novel cell populations that would otherwise require labor-intensive wet lab experimentation. A person having ordinary skill in the art would have had a reasonable expectation of success because Haynes teaches single-cell RNA-sequencing in monocytes to characterize signature specific changes in infectious diseases and Gainaru in view of Hu and Kathri also teach RNA-sequencing to characterize monocytes in the context of infectious diseases, i.e. sepsis.
Claims 14 and 19-20 are rejected under 35 U.S.C. 103 as being unpatentable over Gainaru and Hu as evidenced by ClinicalTrials.gov and HealthMatters as applied to claim 13 above, and further in view of Jackson et al. (WO 2006061644 A1) (“Jackson”).
Regarding claim 14, Gainaru in view of Hu teach the method of claim 13 as discussed above.
Gainaru in view of Hu fail to teach wherein the flow cytometry assay comprises a fluorescence activated cell sorting (FACS) assay.
Jackson teaches “a system and method for detecting early signs of infection and, in particular, for identifying individuals most likely to develop sepsis. Measurement of expression levels of particular combinations of cytokines and/or cellular activation markers, optionally combined with the use of predictive algorithms, allows a high degree of accuracy of prediction” (Abstract). Jackson further teaches that “it has been shown that downregulation of monocyte HLA-DR expression is a predictor of a poor outcome in sepsis and may be an indication of monocyte deactivation” (page 5 lines 1-2). Jackson further teaches that “[t]he ability to detect the earliest signs of infection and / or sepsis has clear benefits in terms of allowing treatment as soon as possible” (page 7 lines 28-29). Jackson further teaches that the method comprises measuring total and differential monocyte counts (“set of tests that may be included in the analysis comprise routine clinical data including… total and differential white blood cell count (monocytes” page 8 lines 29-30) and measuring cell surface expression of HLA-DR in CD14+ monocytes in blood samples using flow cytometry and FACS (“the set of informative cell surface biomarkers the expression of which is detected by means of flow cytometry consists of …HLA-DR” page 10 lines 15-17, “Preferably, the labelling is by means of labelled antibodies or antibody fragments and the quantification is by means of fluorescence-activated cell sorting (FACS) or other form of flow cytometry” page 11 lines 19-21, “Example 1…Blood samples were collected daily from these patients throughout their stay in the ICU and in total, twenty-four patients were diagnosed as developing sepsis. Samples… were analysed by …flow cytometry…FACS flow cytometry is very well-known in the art and any standard technique may be used” page 12 lines 29, 34-37, page 13 lines 11-12, “Example 5…Study design an patients See Example 1… The monocyte population was selected by staining for CD14, these cells were probed with …HLA-DR stains” page 20 lines 21-22 and page 21 lines 2-3).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the teachings of Gainaru in view of Hu to rely on the flow cytometry assay comprising a FACS assay taught by Jackson because Jackson suggests that FACS can facilitate the early detection of sepsis which would allow earlier treatment to the patient. Furthermore, relying on FACS would have been obvious because it is a recognized type of flow cytometry used for detecting monocytes and Gainaru teaches using flow cytometry to detect monocytes. A person having ordinary skill in the art would have had a reasonable expectation of success because Jackson teaches that FACS is well known in the art and Gainaru teaches flow cytometry, therefore one would expect success using a specific type of flow cytometry (FACs) for its intended purpose.
Regarding claims 19-20, Gainaru in view of Hu teach the method of claims 17-18 as discussed above.
Gainaru in view of Hu teach wherein the bacterial infection or the sepsis is associated with a Gram negative bacteria (page 2 column 1 paragraph 3 of Gainaru).
Gainaru in view of Hu fail to teach wherein the bacterial infection or the sepsis is associated with a bacteria selected from the group consisting of Bacillus; Bordetella; Borrelia; Campylobacter; Clostridium; Corynebacterium; Enterococcus; Escherichia; Francisella; Haemophilus; Helicobacter; Legionella; Listeria; Mvcobacteriun; Neisseria; Pseudomonas; Salmonella; Shigella; Staphylococcus; Streptococcus; Treponema; Vibrio; and Yersinia..
Jackson suggests wherein the bacterial infection or the sepsis is associated with Escherichia and Pseudomonas (“proportion of cases, an apparently treatable infection leads to the development of sepsis” page 1 lines 8-9, “In Gram-negative bacteraemia due to infections such as…Gram-negative gut organisms such as Escherichia coli, … or Pseudomonas this is largely a response to lipopolysaccharide (LPS) and other components derived from bacterial cell walls” page 1 lines 24-27). Jackson further teaches that “in about 30% of cases [sepsis] leads to death. The incidence of sepsis in the population of North America is about 0.3% of the population annually (about 750,000 cases) with mortality rising to 40% in the elderly and to 50% in cases of the most severe form, septic shock” (page 1 lines 12-14).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention that the Gram negative bacteria taught by Gainaru associated with the sepsis/bacterial infection, is Escherichia or Pseudomonas, taught by Jackson because Escherichia and Pseudomonas are recognized strains of Gram negative bacteria associated with infection/sepsis, as taught by Jackson. One would have been motivated to apply the method taught by Gainaru in view of Hu to treat Escherichia or Pseudomonas because Jackson suggests these bacteria are highly lethal in sepsis patients, particularly the elderly. A person having ordinary skill in the art would have had a reasonable expectation of success because both Gainaru in view of Hu and Jackson teach methods related to treating Gram-negative sepsis comprising measuring monocyte levels.
Claim 15 is rejected under 35 U.S.C. 103 as being unpatentable over Gainaru and Hu as evidenced by ClinicalTrials.gov and HealthMatters as applied to claim 3 above, and further in view of Diao et al. (CN 103869082 A) ("Diao", English Machine Translation attached).
Regarding claim 3, Gainaru in view of Hu teach the method of claim 3 as discussed above.
Gainaru in view of Hu further teach wherein the blood sample comprises total CD45+ monocytes (page 3 column 1 paragraph 1 of Gainaru).
Gainaru in view of Hu fail to teach wherein the sample comprises enriched dendritic cells.
Diao teaches a “method for detecting HLA-DR expression amount evaluating antigen present ability of PBMC” (Title). Diao further teaches that “peripheral blood mononuclear cells, PBMC (peripheral blood mononuclear cell), in the peripheral blood with single core cell comprising lymphocytes, monocytes, dendritic cells, and other small cells (hematopoietic stem cells)” (paragraph 2). Diao further teaches that HLA-DRlo in the blood is a biomarker of sepsis and suggests that diagnosing sepsis helps in the clinical treatment for sepsis (“severe infection such as sepsis HLA-DR in peripheral blood of patients with infection severity is reduced sharply. is the key link of immune activation in the infection and pathogen removal process, antigen-presenting, comprising antigen phagocytosis, processing, presenting and effector cells. Therefore, finding the patient severe infection when antigen-presenting ability relative to the central point, for clinical treatment of severe infection provides help” paragraph 6). Diao teaches measuring HLA-DR in PBMCs from a patient, PBMCs being a blood sample enriched in dendritic cells (“in peripheral blood of the patient from infection-methyl H7N9 separating the peripheral blood mononuclear cells by immunofluorescence detecting expression quantity of HLA-DR” Abstract, “patient peripheral blood from infected type H7N9 in separating out of peripheral blood mononuclear cells PBMC. by immune fluorescence detecting expression quantity of HLA-DR” paragraphs 39 and 41). Note that although Diao fails to use the language “enriched dendritic cells” the teaching of Diao of separating out PBMCs from the blood sample effectively enriches the dendritic cells in the blood sample because the dendritic cells in the PBMCs would make up a larger percentage of the total number of cells in the sample. Diao further teaches how to enrich for dendritic cells, namely using centrifugation (“putting the centrifuge tube into the centrifuge 2000rpm for centrifuging for 20 minutes, taking out, absorbing middle white hair layer into PBS in a centrifuge tube, washing the residual impurities” paragraph 30).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the teachings of Gainaru in view of Hu to rely on the sample that is a PBMC blood sample, namely a sample enriched for cells including dendritic cells, taught by Diao because Diao suggests that this facilitates the diagnosis of sepsis which helps in the clinical treatment of sepsis (a known sample used for screening markers/indicators for sepsis). A person having ordinary skill in the art would have had a reasonable expectation of success because this type of blood sample (PBMC) was recognized suitable for screening for sepsis (Diao). Furthermore, Diao, Gainaru and Hu are all drawn to methods involving measuring HLA-DR in blood samples.
Claim 21 is rejected under 35 U.S.C. 103 as being unpatentable over Gainaru and Hu as evidenced by ClinicalTrials.gov and HealthMatters as applied to claim 1 above, and further in view of Lavoignet, CE., et al. Eur J Clin Microbiol Infect Dis 38, 1523–1532 (2019). https://doi.org/10.1007/s10096-019-03583-2.
Regarding claim 21, Gainaru in view of Hu teach the method of claim 1 as discussed above.
Gainaru in view of Hu fail to teach wherein the subject is a human patient having, suspected of having, or at risk for urinary tract infection (UTI).
Lavoignet teaches “[w]hite blood cell count and eosinopenia as valuable tools for the diagnosis of bacterial infections in the ED” (Title). Lavoignet further suggests wherein the subject is a human patient having a UTI (“This retrospective and observational study was carried out in the ED over a 6-month period from 1 September 2015 to 29 February 2016. It was held in the adult emergency department of the Strasbourg University Hospital that accounts for nearly 70,000 ED visits each year… Urinary tract infection was confirmed by positive urinary culture with relevant clinic and/or imaging” page 1524 column 2 paragraphs 1-2, “In the study group…135 (29.0%) patients presented with sepsis while only 13 (2.8%) patients were in septic shock” page 1525 column 1 paragraph 3). Lavoignet further suggests that the patients had elevated levels of monocytes (“With a cut-off at 1000/mm3, monocytosis presented a sensitivity
of 45.7% and a specificity of 88.4%, for all infection sites combined (Table 2). Positive and negative likelihood ratios were 3.9 and 0.6, respectively. The AUC was 72%. For the diagnosis of male urinary tract infection, the AUC of monocytes was 75.2%” page 1526 column 2 paragraph 3). Lavoignet further teaches that “[a]n early treatment of infections in the ED has led to improved outcomes” (page 1524 column 1 paragraph 1).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the teachings of Gainaru in view of Hu to apply the method for treating sepsis taught by Gainaru in view of Hu on patients having a UTI taught by Lavoignet because Lavoignet suggests that UTI is an early indicator of sepsis and that elevated levels of monocytes are a biomarker of UTIs. One would have been motivated to make such a modification because Lavoignet suggests that identifying sepsis early leads to early treatments and improved outcomes. A person having ordinary skill in the art would have had a reasonable expectation of success because both Gainaru and Lavoignet teach measuring an elevated level of monocytes in sepsis patients.
Claims 55-56 are rejected under 35 U.S.C. 103 as being unpatentable over Gainaru and Hu as evidenced by ClinicalTrials.gov and HealthMatters as applied to claim 1 above, and further in view of Dulhunty et al. Clinical Infectious Diseases, Volume 56, Issue 2, 15 January 2013, Pages 236–244, https://doi.org/10.1093/cid/cis856 ("Dulhunty").
Regarding claims 55-56, Gainaru in view of Hu teach the method of claim 1 as discussed above.
Gainaru in view of Hu fail to teach wherein the antibiotic is selected from the group consisting of: beta-lactam, aminoglycoside, chloramphenicol, glycopeptide, ansamycin, streptogramin, sulfonamide, tetracycline, oxazolidinone, quinolone, and lipopeptide, wherein the antibiotic is not clarithromycin.
Dulhunty teaches a method for treating a subject for sepsis, comprising: administering an antibiotic to a subject (“Beta-lactam antibiotics are a commonly used treatment for severe sepsis” Abstract). Dulhunty further teaches wherein the antibiotic is beta-lactam, i.e. the antibiotic is not clarithromycin (“This was a prospective, double-blind, randomized controlled trial of continuous infusion versus intermittent bolus dosing of piperacillin-tazobactam, meropenem, and ticarcillin-clavulanate conducted in 5 intensive care units across Australia and Hong Kong” Abstract). Dulhunty further teaches that “[c]ontinuous administration of beta-lactam antibiotics achieved higher plasma antibiotic concentrations than intermittent administration with improvement in clinical cure” (Abstract).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the teachings of Gainaru in view of Hu to substitute the clarithromycin antibiotic taught by Gainaru for the beta-lactam antibiotic taught by Dulhunty because Dulhunty suggests that beta-lactam treatment, namely in continuous administration, is an effective treatment for sepsis and Gainaru in view of Hu are concerned with sepsis. A person having ordinary skill in the art would have had a reasonable expectation of success given that Dulhunty teaches that beta-lactam is a commonly used antibiotic for treating sepsis and both Dulhunty and Gainaru in view of Hu teach a method for treating a subject for sepsis comprising administering an antibiotic to the subject.
Response to Arguments
Applicant's arguments filed 10/1/2025 have been fully considered but they are not persuasive.
Regarding the 103 rejections, Applicant argues that “the authors of Gainaru report that there were problems with applying mHLA-DR as a diagnostic tool, suggesting that one or ordinary skill in the art may not have been motivated to select mHLA-DRlo, let alone combine it specifically with IL1R2hi for use as a diagnostic tool” (page 10 para. 3). However, the authors of Gainaru teach that there were problems with applying mHLA-DR as a “universal” diagnostic tool “which are mainly associated with the interlaboratory variability of the assay” (page 6 col. 1 para. 2). Gainaru merely teaches that “recent studies” had different results regarding the HLA-DR expression on survivors and non survivor patients between day one of sampling compared to “upon worsening on days 3 and 7” (page 6 col. 1 para. 3 and col. 2 para. 1). However, Gainaru importantly clarifies that there are interlaboratory differences, namely one study analyzed “percentage of CD14 cells expressing HLA-DR and mHLA-DR”, whereas they analyzed “the absolute count of circulating CD14pos/HLA-DRpos/CD45pos cells” (page 6 col. 2 para. 1). Therefore, Gainaru does not provide a reason to not choose HLA-DRlo as a species of CD45+ monocytes to be used for treating sepsis. On the contrary, the teachings of Gainaru further suggest its combination with other monocyte markers in order to better characterize the disease. Note also, that the claim is not limited to a method of diagnosing sepsis, and the broadest reasonable interpretation is being given to the claim as recited. Applicant further argues that “Hu reports a microarray study that discloses hyperactivity of THI 7-like innate immunity and failure of adaptive immunity are noted in sepsis patients. Hu discloses IL1R2 in table 8, which shows cytokine receptors differentially regulated in sepsis in THI 7-like and Treg cells, and discloses that IL1R2 is upregulated in sepsis (page 12). However, there is no suggestion in Hu to specifically select IL1R2hi as a marker for sepsis, let alone combine it with HLA-DRlo, in particular in view of the disclosure noted above in Gainaru” (page 10 para. 3). However, Hu explicitly discloses that “TH22 cytokine receptors, IL1R1 and IL1R2, are up-regulated. Thus, TH1, TH2, THαβ, and TH22 are not activated during sepsis” (page 12 para. 1). Therefore, Hu suggests that the IL1R2hi marker helps characterize the immune response to sepsis in the subject, which would motivate a person having ordinary skill in the art to include IL1R2hi in the analysis of CD45+ monocytes taught by Gainaru, i.e. to better characterize the disease (see rejection above). Furthermore, there is a reasonable expectation of success in including IL1R2hi taught by Hu in the analysis of CD45+ monocytes taught by Gainaru (see rejection above). Applicant further argues that “Nor do the NCT01223690 and HealthMatters references remedy the deficiencies in Gainaru and Hu” (page 10 para. 3). However, there are no deficiencies in Gainaru and Hu. Applicant further argues that “Kathri… Haynes… Jackson… Diao… Lavoignet does not remedy the deficiencies of Gainaru, Hu, NCT01223690, and HealthMatters” (pages 11-13). However, there are no deficiencies in Gainaru and Hu as evidenced by NCT01223690 and HealthMatters (see rejection above).
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to FERNANDO IVICH whose telephone number is (703)756-5386. The examiner can normally be reached M-F 9:30-6:00 (E.T.).
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, Gregory S. Emch can be reached at (571) 272-8149. 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://patentc