COMPOSITIONS AND METHODS FOR INHIBITING EXPRESSION OF THE LECT2 GENE

§102 §103

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 . Any rejection or objection not reiterated in this Action is withdrawn. Note this application has been assigned to a different examiner. Claim Rejections - 35 USC § 102 The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action: A person shall be entitled to a patent unless – (a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale or otherwise available to the public before the effective filing date of the claimed invention. Claims 2, 10 and 76 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Naito et al. (US 2008/0113351). Naito et al. disclose siRNA sequences, including one designated as SEQ ID NO: 313644, which is disclosed as an siRNA target sequence for LECT2. Since this is a target sequence it would comprise at least 15 nucleotides of instant SEQ ID NO: 655 and be complementary to at least 15 nucleotides of instant SEQ ID NO: 656, see alignment below. Instant SEQ ID NO: 656 4 AUACUUAAUUGGCUUAAUG 22 |:||::||::|||::||:| Naito SEQ ID NO: 313644 19 ATACTTAATTGGCTTAATG 1 Claims 2, 10 and 76 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Jackson et al. (US 2008/0234941). Jackson et al. disclose siRNA sequences, including one designated as SEQ ID NO: 818 (see table IV) which comprises at least 15 nucleotides of instant SEQ ID NO: 594. The other strand of the siRNA would necessarily comprise at least 15 nucleotides of instant SEQ ID NO: 593, see alignment below. Instant SEQ ID NO: 594 5 AUGAAUACUUCCUAG 19 |:|||:||::||:|| Jackson SEQ ID NO: 818 3 ATGAATACTTCCTAG 17 Claims 2, 10 and 76 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Rossomando et al. (US 2014/0099666). Rossomando et al. disclose siRNA sequences, including one designated as SEQ ID NO: 3160734 which comprises at least 15 nucleotides of instant SEQ ID NO: 597. The other strand of the siRNA would necessarily comprise at least 15 nucleotides of instant SEQ ID NO: 598, see alignment below. Instant SEQ ID NO: 597 1 UGAAGAAUAUUCAAGU 16 :||||||:|::||||: Reference SEQ ID NO: 1360734 17 TGAAGAATATTCAAGT 2 Claims 2, 3, 10, 17, 19, 20, 35, 41, and 76 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Khvorova et al (US 20050255487, of record). Khvorova taught a method for selecting functional hyperfunctional siRNAs. An algorithm was developed for selecting such siRNAs, based on optimized design criteria that take into account characteristics attributed to highly active siRNAs including the identity of specific bases at specific positions, the overall GC content, and melting temperature of potential internal repeats that result in inter- or intra-molecular structures for one strand of the duplex. See paragraphs 144-187. The siRNAs may be used in pools, and each siRNA is preferably 19 base pairs in length (paragraphs 428 and 434) with fully complementary strands. Khvorova also taught a method of gene silencing, comprising introducing into a cell at least one siRNA selected according to the methods of the invention. The siRNAs can be introduced by allowing passive uptake of siRNAs, or through the use of a DNA vector encoding the siRNAs (paragraphs 138 and 188). Khvorova subjected the nucleotide sequence of a LECT2 cDNA (GenBank Accession NM_002302.1) to the algorithm of the invention and generated a pool of siRNA target sequences which can be viewed as 19 nucleotide siRNA sense strands that can be used in siRNAs against LECT2. Khvorova taught that, most preferably, each siRNA will be 19 base pairs in length, and one strand of each of the siRNAs will be identical to a portion of the target mRNA and the other strand will be 100% complementary to a portion of the target mRNA. See paragraph 290. In electronically submitted Tables 12 and 13 (see paragraph 2) Khvorova disclosed the target sequence SEQ ID NOS: 383236 which is aligned below with instant SEQ ID NO: 642. Instant SEQ ID NO: 642 4 AAUUGGCUUAAUGUAGAAC 22 ||::|||::||:|:||||| Khvorova SEQ ID NO: 383236 19 AATTGGCTTAATGTAGAAC 1 Moreover, the Khvorova sequence has 15 contiguous nucleotides of identity to the sense strand corresponding to instant SEQ ID NO: 641. In view of the teaching that the siRNAs of Khvorova preferably comprise 19 base pairs where the antisense strand is 100% complementary to the mRNA target, Khvorova is considered to teach siRNAs comprising the target sequences listed as SEQ ID NO: 383236 a sense strand and its perfect complement as an antisense strand. Thus, Khvorova is considered to have disclosed an siRNA comprising a sense strand and an antisense strand of 19 nucleotides forming 19 base pairs, where the antisense strand comprises a region of at least 15 nucleotides identical to 15 contiguous nucleotides of at least instant SEQ ID NO: 642. Thus, Khvorova anticipated instant claims 2, 10, and 76. With regard to claims 3 and 19-20, Khvorova taught that siRNAs could comprise chemical modifications such 2’-O-methyl, 2’-F, and phosphorothioate groups (paragraph 298), such that one of skill could have immediately envisioned such modifications in the disclosed siRNAs directed to LECT2. With regard to claim 17, Khvorova taught that the siRNAs may have 2-nucleotide 3’-overhangs mimicking natural siRNAs (paragraph 296) such that one of skill could have immediately envisioned this variation to the disclosed LECT2 siRNAs. With regard to claims 35 and 41, the siRNAs of Khvorova could be formulated in physiologically acceptable solutions and lipid carriers (paragraph 445). Thus, Khvorova anticipates the claims. 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 34 is rejected under 35 U.S.C. 103 as being unpatentable over of Khvorova et al (US 20050246794) as applied to claims 2, 3, 10, 17, 19-20, 35, 41, and 76 above, and further in view of Wu et al (Proc. Am. Assoc. Cancer Res. Annual Meeting (2008), of record). As discussed above under 35 USC 102 rejections, Khvorova is considered to have disclosed siRNAs comprising sense strands and antisense strands of 19 nucleotides each forming 19 base pairs, where the antisense strands comprised regions of at least 15 nucleotides that are perfectly identical to at least instant SEQ ID NOS: 642. Thus, Khvorova anticipated instant claims 2, 3, 10, 17, 19-20, 35, 41, and 76. Khvorova taught that siRNAs were useful for the study of gene function (paragraph 378). Wu studied the role of LECT2 in hepatocellular carcinoma invasion and angiogenesis and performed experiments in which Huh7 cells were transfected with siRNA directed against LECT2 mRNA. See abstract and page 12, first paragraph. Wu did not describe the structure of the siRNAs used in the experiments. It would have been obvious to one of ordinary skill in the art at the time of the invention to have used the siRNAs of Khvorova in experiments to study the function of LECT2 in liver cells such as those of Wu. Doing so would have been no more than the simple substitution of one set of siRNAs for another (See MPEP 2143(I)(B). In doing so one would have arrived at the cell of instant claim 34. Thus, the invention as a whole was prima facie obvious. Claims 23, 26, 27, 30, 49, 54, and 56 are rejected under 35 U.S.C. 103 as being unpatentable over of Khvorova et al (US 20050246794) and Wu et al (2008) as applied to claims 2, 3, 10, 17, 19-20, 34, 35, 41, and 76 above, and further in view of Prakash et al (US 20140343123, of record) and Manoharan et al (US 810602, of record). The teachings of Khvorova and Wu are discussed above and can be combined to render obvious methods of studying LECT2 gene function in a liver cell, such as a Huh-7 cell. Khvorova taught that cellular uptake of siRNAs could be facilitated by conjugation of a ligand (paragraph 116, 307, and 316), but did not teach an siRNA sense strand comprising a ligand. Prakash taught that siRNA compounds could be targeted to liver cells by conjugation of N-acetylgalactosamine groups to the 3' end of the sense strand. See abstract and paragraph 7, which refers to US Patent 8106022 (Manoharan) for examples of N-acetylgalactosamine groups for use in conjugating to siRNAs. Manoharan taught many groups comprising N-acetylgalactosamine that were suitable for conjugating to siRNAs, including e.g. PNG media_image1.png 158 364 media_image1.png Greyscale See claim 15. It is noted that this conjugate comprises the structures in instant claims 27 and 30. It would have been obvious to one of ordinary skill in the art at the time of the invention to have modified the duplex RNAs of Khvorova by conjugating an N-acetylgalactosamine targeting ligand to the 3’-end of the sense strand. One would have been motivated to do so in order to facilitate study of LECT2 function in hepatocytes in vivo. The studies of Wu indicated that there was interest in LECT2 function in liver, and it is routine in the art to assess the function of genes in vivo after in vitro studies such as those of Wu. The targeting ligand of Prakash and Manoharan would be expected to allow one of skill to direct the siRNA to liver cells with specificity, and one of skill would have been motivated to take advantage of this effect. Thus claims 23, 26, 27, 30, 49, 54 were prima facie obvious. With regard to claim 56, and the amount of inhibition in the cell, the cited references rendered obvious to structure of the claimed dsRNA as well as a method of using it to inhibit LECT2 expression in a cell. The degree of inhibition is considered to be inherent in the structure of the dsRNA and the amount added to the cells. It would have been obvious to have performed dosage experiments to determine the maximum possible inhibition in the process of characterizing the dsRNA. Allowable Subject Matter Claims 77-79 are objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims. Conclusion Any inquiry concerning this communication or earlier communications from the examiner should be directed to Tracy Vivlemore whose telephone number is (571)272-2914. The examiner can normally be reached Mon-Fri 7:30-4:00. 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For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000. Tracy Vivlemore Supervisory Primary Examiner Art Unit 1638 /Tracy Vivlemore/Supervisory Primary Examiner, Art Unit 1638