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 .
Claims 1-10 are pending.
Claim Objections
Claims 4 and 10 are objected to because of the following informalities: Claims recite limitations in the form of abbreviations such as “ALS” and “CRISPR” which needs to be recited in full form for the first time they occur in the claim.
Appropriate correction is required.
Nucleotide and/or Amino Acid Sequence Disclosures
Specific deficiency – Nucleotide and/or amino acid sequences appearing in the drawings are not identified by sequence identifiers in accordance with 37 CFR 1.821(d). Sequence identifiers for nucleotide and/or amino acid sequences must appear either in the drawings or in the Brief Description of the Drawings.
Required response – Applicant must provide:
Replacement and annotated drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers into the Brief Description of the Drawings, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
In instant case, applicants have not provided SEQ ID NOs for amino acid sequences appearing in Figures 1, 3 and 11. For example, figure 1 shows “SYGQ-rich LC” in FUS LC domain where SYGQ is amino acid sequence.
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 1-10 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention. This is a written description rejection.
Claims 1-10 recite:
A method of preventing aggregation of RNA-binding protein by altering the amino acid structure of the RNA-binding protein as compared to wild type and expressing the protein in a subject, identifying the aggregation prone regions, increasing the proline content in those aggregation prone regions and treating ALS/FTD and cancer by using this composition.
The broad claims encompass the large genus: any RNA binding proteins, any amino acid alteration to any RNA binding protein that prevents their aggregation including identifying regions of RNA binding protein responsible for aggregation.
An original claim may lack written description support when a broad genus is presented but the specification or disclosure discloses a narrow species with no evidence that the genus is contemplated. For example, the specification discloses five different types of RNA binding proteins that are related and homologues including Fused in Sarcoma (FUS), Ewing's sarcoma breakpoint region 1, TAF15, hnRNPA2, and TDP-43 (see paragraph 0007 of specification). However, the specification does not provide representative species or common structural characteristics sufficient to support the broad genus encompassed by the claimed invention. Furthermore, the specification does not describe the regions of the RNA binding proteins responsible for aggregation.
The state of the prior art teaches that the RNA-binding proteins comprise a large and structurally diverse class of proteins. For example, the art of Gerstberger et al. 2014 (A census of human RNA-binding proteins, Nature Genetics Review, 15:829-845, “Gerstberger”) identified a census of 1,542 RNA binding proteins, representing approximately 600 structurally distinct RNA-binding proteins. Gerstberger further teaches that RNA-binding proteins are among the most abundant proteins in cells and participate in numerous distinct cellular processes.
The art of Lunde et al. 2007 (RNA-binding proteins: modular design for efficient function, Molecular cell biology, 8:479-490, “Lunde”) also teaches that RNA-binding proteins have a modular structure and are composed of multiple repeats of small domains, enabling them to perform diverse biological roles. Lunde provides Figure 1 showing that many RNA-binding proteins have different modular structure.
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The state of the art further teaches that RNA-binding proteins and their aggregation mechanism are highly complex and heterogenous. Harrison and Shorter, 2017 (RNA-binding proteins with prion-like domains in health and disease, Biochemical Journal, 474:1417-1438, “Harrison”) teaches 70 human RNA-binding proteins containing prion-like domain that promote phase separation and aggregation; however, the molecular mechanism determining the aggregation remain incompletely understood. Harrison further teaches that aggregation of RNA binding proteins is influence by many factors including amino acid sequence, domain organization, intermolecular interactions, and cellular conditions, thereby making the development of therapeutic strategies targeting RNA-binding proteins challenging.
Together these arts teach that RNA-binding proteins comprise a structurally and functionally diverse class of proteins containing numerous distinct domains. Because RNA-binding proteins very substantially in both structure and biological function, disclosure of only a limited number of RNA-binding proteins (e.g., Fused in Sarcoma (FUS), Ewing's sarcoma breakpoint region 1, TAF15, hnRNPA2, and TDP-43) is not reasonably representative of the full scope of the claimed genus. Furthermore, prior art does not teach the region that is common to various RNA binding protein what is responsible for the aggregation. The specification does not identify any common structural features shared across the claimed genus that would allow and artisan to recognize that the inventors and/or applicant were in possession of the entire claimed genus at the time of filing.
Furthermore, the specification does not provide any other identifying characteristics of claimed genus of RNA binding protein beyond the shared functional property of aggregation.
Claims 1-10 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. This is a scope of enablement rejection.
There are many factors to assess when determining there is sufficient evidence to support a determination that a disclosure does not satisfy the enablement requirement and whether any necessary experimentation is “reasonable” or “undue” (see MPEP 2164.01). These factors are: (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.
The breadth of the claims: the claims as currently drafted are broad and they encompass any RNA binding proteins, any amino acid alteration to any RNA binding protein that prevents their aggregation including identifying regions of RNA binding protein responsible for aggregation, expressing in any subject, methods of treating ALS/FTD and cancer, increasing proline content by 5-80%, and use of any method to deliver protein in a subject and treat claimed diseases (e.g., gene therapy, mRNA delivery, or CRISPR).
The nature of the invention: the claimed invention pertains to a method of preventing aggregation of RNA-binding proteins and then expressing the proteins in a subject to treat ALS/FTD and cancer diseases. The effect of amino acid substitutions on protein function and structure, stability, aggregation, and therapeutic efficiency are complex and unpredictable. Successful implementation of claimed method and disease treatment requires balance between aggregation and effective expression of proteins. Therefore, to make such a claimed method perform as described, prevent aggregation of any RNA-binding proteins and use to treat disease, will be undue burden as it will require undue experimentation.
The state of the prior art: It is unpredictable to change the amino acid structure of any RNA-binding proteins in a subject because each amino acid has very important role in the structure and function of protein and if we just alter them to reduce the aggregation of RNA-binding protein, then the cellular mechanism may be affected. For example, Gebauer et al. 2021 (RNA binding proteins in human genetic disease, Nature Review Genetics, 22:185-198, “Gebauer”) teaches that mutations in RNA binding proteins change the amino acid composition altering the protein function. Furthermore, Gebauer teaches that amino acid substitution can affect RNA binding, protein-protein interaction, cellular localization, phase separation, aggregation, and disease phenotype.
Proline residue and proline rich domain contributes to the structure and function of many RNA-binding proteins. For example, Li et al. 2006 (Effect of proline rich domain of an RNA-binding protein Sam68 in cell growth process, death and B cell signal transduction, Chinese Medical Journal, 119:1536-1542, “Li”) teaches that deletion of proline rich domain of RNA-binding protein Sam68 resulted in slower cell growth, increased number of cell death, reduced B-cell receptor signaling etc. Although the role of proline content in RNA-binding protein is important, the effect of altering proline content of RNA binding protein by 5-80%, as recited in instant application, is largely unknown.
Furthermore, the state of the art demonstrates that preventing aggregation of RNA-binding proteins and treating ALS remained highly challenging and unpredictable. The prior art recognizes that although numerous therapeutic strategies are under active investigation, no broadly effective treatment capable of preventing ALS has been established. Gene therapy has been considered as a promising approach to treat diseases including ALS and cancer; however, the effectiveness of gene therapy in treating ALS and cancer still presents significant challenges.
Rummens and Cruz, 2025 (RNA-binding proteins in ALS and FTD: from pathogenic mechanisms to therapeutic insights, Molecular Neurodegenerations, 20:64) teaches that although several novel therapies are currently under investigation for ALS/FTD treatment, current efforts to cure or effective treatment of ALS/FTD have been unsuccessful (see “therapeutic strategies to encounter RBP pathology” section).
Priyadarshini and Airoud-Driss, 2023 (Update on ALS treatment. Current Treatment Options in Neurology, 25:199-212) teaches that ALS treatment requires multiple therapeutic approaches, reflecting the complexity of the disease.
Fang et al. 2022 (Gene Therapy in Amyotrophic Lateral Sclerosis, Cells, 11:2066) teaches that several gene therapy have been investigated to suppress the toxic effects of gene related to ALS, and some of them were found effective. However, only 10% of the cause of ALS is related to genetics, effectiveness of gene therapy is still unclear.
Mittal et al. 2024 (Challenges and Opportunities of Gene Therapy in Cancer, OBM Genetics, 8:1-501) teaches that although there has been a lot of progress made on treating cancer by using gene therapy, there are still a lot of problem that needs to be addressed including non-specific expression, low-efficiency, and biosafety.
FDA currently approved three medications for the treatment of ALS, but those medications are directed towards reducing the decline of daily functioning rather than treatment of the disease (Amyotrophic lateral sclerosis (ALS) - Diagnosis and treatment - Mayo Clinic).
The cause of ALS is still largely unknown. A genetic cause of ALS is found in about 10% of people (Amyotrophic lateral sclerosis (ALS) - Symptoms and causes - Mayo Clinic)
Therefore, the state of the art demonstrates that the claimed method of preventing aggregation of RNA binding protein by amino acid substitution and use of altered protein in limiting ALS/FTD and cancer is unpredictable and practicing the full scope of the claimed invention would require undue experimentation.
The level of one of ordinary skill: due to the unpredictable nature of the claimed method and the broad scope of the claims, an artisan would still be required to perform experimentations to screen and optimize amino acid substitution that prevents aggregation while maintaining protein function and achieving therapeutic efficiency.
The level of predictability in the art: in view of state of the art and the level of skill in the art, the claimed method of preventing aggregation of RNA-binding protein and limiting ALS/FTD and cancer by preventing aggregation of RNA-binding proteins is unpredictable.
The amount of direction provided by the inventor, the existence of working examples, and the quantity of experimentation needed to make or use the invention based on the content of the disclosure: the applicant has not provided sufficient direction to practice the full scope of the claimed invention. The applicant has not provided working examples to show how the amino acid structure of the RNA-binding protein is altered as compared to wild type, how the aggregation prone region in the protein is identified, and the efficiency of disclosed method for the treatment of ALS/FTD and cancer. Examples 2-5 in specification discloses that by using a composition disclosed herein halted progression of the diseases and decreased the symptoms but did not provide in details how the experimentation was performed. The standard of an enabling disclosure is not the ability to make and test if the invention works but one of the abilities to make and use with a reasonable expectation of success. The instant specification is not enabling because one cannot follow the guidance presented herein or within the art at the time of filing.
In conclusion, the specification provides enablement for an in vitro method of reducing aggregation of RNA-binding protein fused in sarcoma (FUS) by altering the proline content. However, the specification does not provide any working examples, animal studies, or other experimental evidences demonstrating that altering any RNA-binding proteins can be successfully expressed in any subject (in vivo) for limiting ALS/FTD or cancer. The state of art teaches that in vitro experiments are not fully predictive of in vivo. For example, Hill et al. 2016 (Overcoming Gene-Delivery Hurdles: Physiological Considerations for Nonviral Vectors, Trends in Biotechnology, 34:91-105, “Hill”) teaches that results obtained from in vitro experiment do not guarantee success in animal models. Hill also teaches that in vitro studies overestimate gene delivery efficiency, producing false positive results and is not predictive of in vivo conditions.
MPEP 2164.01(a) states that “a conclusion of lack of enablement means that, based on the evidence regarding each of the above factors, the specification, at the time the application was filed, would not have taught one skilled in the art how to make and/or use the full scope of the claimed invention without undue experimentation. In re Wright, 999 F.2d 1557, 1562, 27 USPQ2d 1510, 1513 (Fed. Cir. 1993)”. That conclusion is justified by our analysis presented above. The Wands Factors have been analyzed which also supported undue experimentations would be required to practice the invention as claimed due to the amount of experimentation necessary, state of the prior arts and its predictability, the high level of skill required to practice the alleged invention, and the limited amount of guidance provided by the applicant in the form of varied working examples in the specification.
Relevant prior arts
These arts are cited because they are relevant to the claimed invention.
Morimoto et al. 2002 (Biochemical and biophysical research communications, 295:306-311, “Morimoto”, cited in IDS)
Morimoto teaches Amyloid β peptide (Aβ1-42), which plays a critical role in pathogenesis of Alzheimer’s disease. To identify amino acid residues that are important for the b-sheet formation, Morimoto synthesized a series of proline-substituted mutants of Aβ1-42 peptides at positions 19–26, and their aggregation ability and neurotoxicity on PC12 cells were investigated (abstract). Morimoto teaches that Proline substituted mutants showed that they were hard to aggregate and weaker cytotoxicity than the wild type (abstract, and under “aggregation studies” of result section). Morimoto teaches about Amyloid β peptide, which is an RNA binding protein. However, Morimoto does not teach expressing the protein in a subject.
US Pre-Grant Publication NO. US2022/0283180 (published 8 September 2022, “Wong”).
Wong teaches a chimeric TDP-43 protein comprising N-terminal domain of TDP-43 fused to a heterologous C-terminal splicing repressor domain. The chimeric protein is administered to a subject by using viral vector to treat or prevent disease manifesting TDP-43 proteinopathy including amyotrophic lateral sclerosis (ALS) or frontotemporal dementia (FTD) (see abstract and paragraph 0011).
US Patent Application Publication No. US 9922164 B2 (published 20 March 2018, “Chennamsetty”).
Chennamsetty teaches identification of aggregation prone region in proteins computationally and then making substitutions in those regions to reduce the aggregations (see abstract).
Although these prior arts teach the RNA-binding proteins, method of preventing aggregation of RNA binding proteins by proline substitution, and expressing the engineered proteins in a subject, none of them teaches in-vivo method of preventing aggregation of RNA binding proteins by altering the amino acid structure and expressing the protein.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to SURAJ SAPKOTA whose telephone number is (571)270-0842. The examiner can normally be reached Monday-Thursday 7am-5pm.
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Suraj Sapkota
Patent Examiner
AU 1635
/RAM R SHUKLA/Supervisory Patent Examiner, Art Unit 1635
Prosecution Insights