Patent Application
20220282248
The present invention relates to a molecular targeted nucleic acid medicine for targeting gastric cancer, particularly peritoneal dissemination of gastric cancer, and more specifically to an antisense oligonucleotide against SYT13 and a pharmaceutical composition comprising the same.
Gastric cancer is common in Asia, including Japan, China, and Korea, as well as in South America. Although the spread of cancer screening has enabled early detection and treatment, and mortality from gastric cancer has decreased, advanced gastric cancer still has a poor prognosis and is an important disease to be overcome.
Peritoneal dissemination is known as one of the recurrence and metastasis forms of gastric cancer. Peritoneal dissemination is most common in cases with stage IV at diagnosis and is also the most common form of recurrence after resection. Further, peritoneal dissemination has a major problem that the efficacy of treatment with resection, radiotherapy, and systemic administration of anticancer drugs is low.
The present inventors' group has previously found that the expression of SYT13 is upregulated specifically in gastric cancer causing peritoneal dissemination, and has reported that the expression can be used as an indicator to forecast peritoneal dissemination after gastric resection and that siRNA against SYT13 can inhibit the proliferative capacity, invasive capacity, and migration capacity of a gastric cancer cell line and can inhibit metastasis through peritoneal dissemination after gastric resection (Patent Literature 1 and Non Patent Literature 1).
SYT13 is a membrane protein belonging to the synaptotagmin (SYT) family. SYT family proteins have been identified as calcium-phospholipid binding molecules on synaptic vesicles and have been suggested to function as a calcium sensor. It has been reported that humans have 17 isoforms distributed mainly in brain tissue. It has also been reported that SYT13, unlike other synaptotagmins, binds to phospholipids regardless of the presence or absence of calcium and is also expressed in various tissues other than the brain (Non Patent Literature 2).
As described above, it has been confirmed that the use of siRNA against SYT13 can inhibit the expression of SYT13 and metastasis through peritoneal dissemination; however, the sequence information on the siRNA actually used is unpublished, and the inhibition of SYT13 expression has not been fully investigated.
Thus, the present inventors have now made an object to provide a nucleic acid medicine having better efficacy for targeting peritoneal dissemination of gastric cancer, by using an antisense oligonucleotide, which is a nucleic acid medicine different from siRNA, to inhibit the expression of SYT13.
In view of the above-mentioned object, the present inventors first focused on the nucleotide sequence of human SYT13 mRNA; as a result of repeated investigations to obtain an antisense oligonucleotide with effectiveness as a medicine and without the possibility of adverse effects, they found that targeting a specific region in the nucleotide sequence of SYT13 mRNA attains particularly high efficacy, leading to the completion of the present invention.
That is, the present invention provides the followings:
1. An antisense oligonucleotide capable of inhibiting expression of human SYT13 mRNA, the antisense oligonucleotide being:
an antisense oligonucleotide consisting of a 11- to 19-base-long nucleotide sequence complementary to a nucleotide sequence at positions 348 to 366, 599 to 627, 997 to 1016, 1069 to 1088, 1419 to 1437, 1612 to 1641, 1775 to 1793, 2629 to 2647, 2810 to 2831, 3244 to 3262, 3315 to 3333, 3423 to 3442, 4266 to 4284, 4328 to 4346, or 4365 to 4400, 4714 to 4751, 4776 to 4795, 4949 to 4968 in a nucleotide sequence set forth in SEQ ID NO: 1; or
an antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases, one to two bases, or one base are substituted, deleted, or inserted with regard to said antisense oligonucleotide.
2. An antisense oligonucleotide consisting of a nucleotide sequence selected from the group consisting of SEQ ID NOs: 3 to 43, or an antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide.
3. An antisense oligonucleotide consisting of a nucleotide sequence selected from the group consisting of SEQ ID NOs: 50 to 59, or an antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide.
4. An antisense oligonucleotide consisting of a nucleotide sequence selected from the group consisting of SEQ ID NOs: 60 to 69, or an antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide.
5. An antisense oligonucleotide consisting of a nucleotide sequence selected from the group consisting of SEQ ID NOs: 70 to 79, or an antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide.
6. An antisense oligonucleotide consisting of a nucleotide sequence selected from the group consisting of SEQ ID NOs: 4, 20, 29, 35, 39, 62, and 79, or an antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide.
7. The antisense oligonucleotide according to any one of 1 to 6 above, wherein the antisense oligonucleotide has an artificial nucleic acid region containing a bicyclic sugar.
8. The antisense oligonucleotide according to any one of 1 to 7 above, wherein at least one internucleoside linkage is a phosphorothioate bond.
9. The antisense oligonucleotide according to any one of 1 to 8 above, wherein the antisense oligonucleotide has an artificial nucleic acid region containing 5-methylcytosine.
10. The antisense oligonucleotide according to any one of 1 to 9 above, wherein the antisense oligonucleotide is 15 to 19 nucleotides in length.
11. The antisense oligonucleotide according to any one of 1 to 10 above, wherein the antisense oligonucleotide is a gapmer.
12. A conjugate comprising: the antisense oligonucleotide according to any one of 1 to 11 above; and a further functional moiety directly or indirectly linked to the antisense oligonucleotide.
13. The conjugate according to 12 above, wherein the further functional moiety is a ligand for target molecule or an agent having antitumor activity.
14. A pharmaceutical composition comprising the antisense oligonucleotide according to any one of 1 to 11 above, or the conjugate according to 12 or 13 above.
15. The pharmaceutical composition according to 14 above, for treatment or prevention of gastric cancer in a human.
16. The pharmaceutical composition according to 15 above, for treatment or prevention of peritoneal dissemination after gastric cancer resection.
The present specification includes the disclosure of Japanese Patent Application No. 2019-154968, which is the basis of the priority of the present application.
The present invention can provide a molecular targeted nucleic acid medicine for gastric cancer that is delivered specifically to a region where SYT13 is highly expressed to inhibit the expression and thus is significantly superior to siRNA.
Hereinafter, the present invention will be described in detail.
The present invention relates to an antisense oligonucleotide. More specifically, the present invention relates to an antisense oligonucleotide having a sequence substantially complementary to a part of the nucleotide sequence of SYT13 mRNA, the antisense oligonucleotide being capable of inhibiting the expression of human SYT13.
The SYT13 gene is present in mammals, such as primates (e.g., cynomolgus monkeys, chimpanzees, and humans) and non-primates (e.g., cattle, pigs, sheep, horses, cats, dogs, guinea pigs, rats, and mice); its nucleotide sequences and amino acid sequences of the SYT13 protein encoded by the nucleotide sequences can be obtained from databases such as a database of the National Center for Biotechnology Information (NCBI). It is also known that there are multiple isoforms for SYT13; examples of human SYT13 mRNA sequence include those set forth in SEQ ID NO: 1 (NM_020826.2) and SEQ ID NO:2 (NM_001247987.1) (shown as DNA sequences in SEQ ID NOs: 1 and 2).
The term “antisense oligonucleotide” as used herein is used synonymously with the term “antisense nucleic acid” commonly used in this field, and refers to a single-stranded oligonucleotide comprising a nucleobase sequence capable of hybridizing to (i.e., complementary to) a part of mRNA of the target gene, SYT13. Although not bound by theory, in the present invention, the antisense oligonucleotide forms a DNA-RNA hybrid with a target RNA, which upon being cleaved by RNaseH degrades the target RNA and thus can inhibit the expression of the target gene. In general, regions in the mRNA of a target gene where an antisense oligonucleotide can hybridize may include 3′UTR, 5′UTR, exons, introns, coding regions, a translation initiation region, a translation termination region, or other nucleic acid regions.
In the present invention, the antisense oligonucleotide can inhibit the expression of human SYT13 mRNA. More specifically, the antisense oligonucleotide of the present invention consists of a nucleotide sequence that is substantially complementary to the nucleotide sequence of a specific region of human SYT13 mRNA. Although not particularly limited, when an animal model transplanted with human cancer cells is used to examine the inhibition of the expression of human SYT13 mRNA, it is preferable to use an antisense oligonucleotide consisting of a nucleotide sequence that is not complementary to the nucleotide sequence of SYT13 mRNA of the animal (e.g., mouse) itself.
The term “inhibition” with respect to the expression of a gene as used herein refers to reduction of the amount (abundance) of mRNA created through transcription of the gene. The inhibition involves inhibiting the amount of mRNA by 20% or more, 30% or more, or 40% or more, preferably 50% or more, more preferably 80% or more, 90% or more, or 95% or more as compared to a control. The inhibition of gene expression may be determined by any method known in this technical field, but in particular, it may be determined by PCR-based methods such as real-time PCR using cells such as human or mouse cells.
The term “nucleobase” or “base” as used herein refers to a base component of a nucleic acid, which is the heterocycle moiety that can be paired with a base of another nucleic acid. The term “nucleobase sequence” as used herein may refer to a consecutive sequence of nucleobases, not taking into account the sugar, internucleoside linkage, or nucleobase modification that constitutes the nucleic acid.
In one embodiment, the antisense oligonucleotide may comprise a 11- to 19-base-long consecutive nucleobase sequence that are substantially complementary to human SYT13 mRNA, e.g., the nucleotide sequence set forth in SEQ ID NO:1 and/or SEQ ID NO:2. The consecutive nucleobase sequence may be 11 or more, 12 or more, 13 or more, 14 or more, 15 or more, 16 or more, 17 or more, 18 or more, or 19 bases long, e.g., 13, 15, 17, or 19 bases long. The antisense oligonucleotide may consist of a 11- to 19-base-long consecutive nucleobase sequence that are substantially complementary to human SYT13 mRNA, e.g., the nucleotide sequence set forth in SEQ ID NO:1 and/or SEQ ID NO:2.
The term “substantially complementary” refers to a nucleotide sequence that is completely complementary to a nucleotide sequence of interest as well as a nucleotide sequence that has one to several mismatches to a nucleotide sequence of interest but can form complementary base pairs therewith. That is, the antisense oligonucleotide may include a nucleobase sequence complementary to a nucleotide sequence of interest, e.g., a 11- to 19-base-long consecutive nucleotide sequence in which one to several nucleobases, e.g., one, two, or three nucleobases, are substituted, deleted, or inserted (in particular, substituted).
In the present invention, the nucleobase sequence of the antisense oligonucleotide may have no mismatch or 1 to 3, 1 to 2, or 1 mismatch to a part of human SYT13 mRNA. The term “a part” of mRNA refers to a target region in the mRNA where the antisense oligonucleotide can hybridize through base pairing, and the target region can have the same base length as the antisense oligonucleotide. The term “mismatch” refers to inability for a nucleobase of a first nucleic acid to form a base pair with (be complementary to) its corresponding nucleobase of a second nucleic acid.
In a preferred embodiment, the antisense oligonucleotide has a nucleotide sequence that is completely complementary to the nucleotide sequence set forth in SEQ ID NO:1 and/or SEQ ID NO:2.
More specifically, the present invention provides an antisense oligonucleotide capable of inhibiting the expression of human SYT13 mRNA, the antisense oligonucleotide being: an antisense oligonucleotide consisting of a 11- to 19-base-long nucleotide sequence complementary to a nucleotide sequence at positions 348 to 366, 599 to 627, 997 to 1016, 1069 to 1088, 1419 to 1437, 1612 to 1641, 1775 to 1793, 2629 to 2647, 2810 to 2831, 3244 to 3262, 3315 to 3333, 3423 to 3442, 4266 to 4284, 4328 to 4346, 4365 to 4400, 4714 to 4751, 4776 to 4795, 4949 to 4968 in the nucleotide sequence set forth in SEQ ID NO: 1; or an antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases, one to two bases, or one base are substituted, deleted, or inserted with regard to said antisense oligonucleotide.
Examples of the antisense oligonucleotide consisting of a 11- to 19-base-long nucleotide sequence complementary to the nucleotide sequence at positions 348 to 366 in the nucleotide sequence set forth in SEQ ID NO: 1, or the antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide include: an antisense oligonucleotide consisting of a nucleotide sequence set forth in SEQ ID NO: 3, or an antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide. More specific examples include an antisense oligonucleotide depicted as hSYT13-350-AmNA (15) in Examples.
Examples of the antisense oligonucleotide consisting of a 11- to 19-base-long nucleotide sequence complementary to the nucleotide sequence at positions 599 to 627 in the nucleotide sequence set forth in SEQ ID NO: 1, or the antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide include: an antisense oligonucleotide consisting of a nucleotide sequence set forth in any one of SEQ ID NOs: 4 and 50 to 59, or an antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide. More specific examples include an antisense oligonucleotide depicted as hSYT13-605-AmNA(15), hSYT13-607-AmNA(13), hSYT13-609-AmNA(13), hSYT13-603-AmNA(15), hSYT13-607-AmNA(15), hSYT13-609-AmNA(15), hSYT13-601-AmNA(17), hSYT13-603-AmNA(17), hSYT13-605-AmNA(17), hSYT13-607-AmNA(17), or hSYT13-609-AmNA(17) in Examples.
Examples of the antisense oligonucleotide consisting of a 11- to 19-base-long nucleotide sequence complementary to the nucleotide sequence at positions 997 to 1016 in the nucleotide sequence set forth in SEQ ID NO: 1, or the antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide include: an antisense oligonucleotide consisting of a nucleotide sequence set forth in SEQ ID NO: 5 or 6, or an antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide. More specific examples include an antisense oligonucleotide depicted as hSYT13-999-AmNA (15) or hSYT13-1000-AmNA (15) in Examples.
Examples of the antisense oligonucleotide consisting of a 11- to 19-base-long nucleotide sequence complementary to the nucleotide sequence at positions 1069 to 1088 in the nucleotide sequence set forth in SEQ ID NO: 1, or the antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide include: an antisense oligonucleotide consisting of a nucleotide sequence set forth in SEQ ID NO: 7 or 8, or an antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide. More specific examples include an antisense oligonucleotide depicted as hSYT13-1071-AmNA (15) or hSYT13-1072-AmNA (15) in Examples.
Examples of the antisense oligonucleotide consisting of a 11- to 19-base-long nucleotide sequence complementary to the nucleotide sequence at positions 1419 to 1437 in the nucleotide sequence set forth in SEQ ID NO: 1, or the antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide include: an antisense oligonucleotide consisting of a nucleotide sequence set forth in SEQ ID NO: 9, or an antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide. More specific examples include an antisense oligonucleotide depicted as hSYT13-1421-AmNA (15) in Examples.
Examples of the antisense oligonucleotide consisting of a 11- to 19-base-long nucleotide sequence complementary to the nucleotide sequence at positions 1612 to 1641 in the nucleotide sequence set forth in SEQ ID NO: 1, or the antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide include: an antisense oligonucleotide consisting of a nucleotide sequence set forth in any one of SEQ ID NOS: 10 to 16, or an antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide. More specific examples include an antisense oligonucleotide depicted as hSYT13-1614-AmNA (15), hSYT13-1617-AmNA (15), hSYT13-1618-AmNA (15), hSYT13-1619-AmNA (15), hSYT13-1622-AmNA (15), hSYT13-1623-AmNA (15), or hSYT13-1625-AmNA (15) in Examples.
Examples of the antisense oligonucleotide consisting of a 11- to 19-base-long nucleotide sequence complementary to the nucleotide sequence at positions 1775 to 1793 in the nucleotide sequence set forth in SEQ ID NO: 1, or the antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide include: an antisense oligonucleotide consisting of a nucleotide sequence set forth in SEQ ID NO: 17, or an antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide. More specific examples include an antisense oligonucleotide depicted as hSYT13-1777-AmNA (15) in Examples.
Examples of the antisense oligonucleotide consisting of a 11- to 19-base-long nucleotide sequence complementary to the nucleotide sequence at positions 2629 to 2647 in the nucleotide sequence set forth in SEQ ID NO: 1, or the antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide include: an antisense oligonucleotide consisting of a nucleotide sequence set forth in SEQ ID NO: 18, or an antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide. More specific examples include an antisense oligonucleotide depicted as hSYT13-2631-AmNA (15) in Examples.
Examples of the antisense oligonucleotide consisting of a 11- to 19-base-long nucleotide sequence complementary to the nucleotide sequence at positions 2810 to 2831 in the nucleotide sequence set forth in SEQ ID NO: 1, or the antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide include: an antisense oligonucleotide consisting of a nucleotide sequence set forth in any one of SEQ ID NOs: 19 to 22, or an antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide. More specific examples include an antisense oligonucleotide depicted as hSYT13-2812-AmNA (15), hSYT13-2813-AmNA (15), hSYT13-2814-AmNA (15), or hSYT13-2815-AmNA (15) in Examples.
Examples of the antisense oligonucleotide consisting of a 11- to 19-base-long nucleotide sequence complementary to the nucleotide sequence at positions 3244 to 3262 in the nucleotide sequence set forth in SEQ ID NO: 1, or the antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide include: an antisense oligonucleotide consisting of a nucleotide sequence set forth in SEQ ID NO: 23, or an antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide. More specific examples include an antisense oligonucleotide depicted as hSYT13-3246-AmNA (15) in Examples.
Examples of the antisense oligonucleotide consisting of a 11- to 19-base-long nucleotide sequence complementary to the nucleotide sequence at positions 3315 to 3333 in the nucleotide sequence set forth in SEQ ID NO: 1, or the antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide include: an antisense oligonucleotide consisting of a nucleotide sequence set forth in SEQ ID NO: 24, or an antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide. More specific examples include an antisense oligonucleotide depicted as hSYT13-3317-AmNA (15) in Examples.
Examples of the antisense oligonucleotide consisting of a 11- to 19-base-long nucleotide sequence complementary to the nucleotide sequence at positions 3423 to 3442 in the nucleotide sequence set forth in SEQ ID NO: 1, or the antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide include: an antisense oligonucleotide consisting of a nucleotide sequence set forth in SEQ ID NO: 25 or 26, or an antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide. More specific examples include an antisense oligonucleotide depicted as hSYT13-3425-AmNA (15) or hSYT13-3426-AmNA (15) in Examples.
Examples of the antisense oligonucleotide consisting of a 11- to 19-base-long nucleotide sequence complementary to the nucleotide sequence at positions 4266 to 4284 in the nucleotide sequence set forth in SEQ ID NO: 1, or the antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide include: an antisense oligonucleotide consisting of a nucleotide sequence set forth in SEQ ID NO: 27, or an antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide. More specific examples include an antisense oligonucleotide depicted as hSYT13-4268-AmNA (15) in Examples.
Examples of the antisense oligonucleotide consisting of a 11- to 19-base-long nucleotide sequence complementary to the nucleotide sequence at positions 4328 to 4346 in the nucleotide sequence set forth in SEQ ID NO: 1, or the antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide include: an antisense oligonucleotide consisting of a nucleotide sequence set forth in SEQ ID NO: 28, or an antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide. More specific examples include an antisense oligonucleotide depicted as hSYT13-4330-AmNA (15) in Examples.
Examples of the antisense oligonucleotide consisting of a 11- to 19-base-long nucleotide sequence complementary to the nucleotide sequence at positions 4365 to 4400 in the nucleotide sequence set forth in SEQ ID NO: 1, or the antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide include: an antisense oligonucleotide consisting of a nucleotide sequence set forth in any one of SEQ ID NOs: 29 to 36 and 60 to 69, or an antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide. More specific examples include an antisense oligonucleotide depicted as hSYT13-4367-AmNA(15), hSYT13-4368-AmNA(15), hSYT13-4371-AmNA(15), hSYT13-4373-AmNA(15), hSYT13-4374-AmNA(15), hSYT13-4377-AmNA(15), hSYT13-4378-AmNA(15), hSYT13-4381-AmNA(15), hSYT13-4374-AmNA(13), hSYT13-4376-AmNA(15), hSYT13-4380-AmNA(15), hSYT13-4382-AmNA(15), hSYT13-4374-AmNA(17), hSYT13-4376-AmNA(17), hSYT13-4378-AmNA(17), hSYT13-4380-AmNA(17), hSYT13-4382-AmNA(17), or hSYT13-4374-AmNA(19) in Examples.
Examples of the antisense oligonucleotide consisting of a 11- to 19-base-long nucleotide sequence complementary to the nucleotide sequence at positions 4714 to 4751 in the nucleotide sequence set forth in SEQ ID NO: 1, or the antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide include: an antisense oligonucleotide consisting of a nucleotide sequence set forth in any one of SEQ ID NOs: 37 to 39 and 70 to 79, or an antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide. More specific examples include an antisense oligonucleotide depicted as hSYT13-4716-AmNA(15), hSYT13-4717-AmNA(15), hSYT13-4729-AmNA(15), hSYT13-4725-AmNA(13), hSYT13-4727-AmNA(13), hSYT13-4725-AmNA(15), hSYT13-4727-AmNA(15), hSYT13-4731-AmNA(15), hSYT13-4725-AmNA(17), hSYT13-4727-AmNA(17), hSYT13-4729-AmNA(17), hSYT13-4731-AmNA(17), or hSYT13-4733-AmNA(17) in Examples. Further, an antisense oligonucleotide depicted as 4733-A, 4733-B, 4733-C, 4733-D, 4733-E, 4733-F, 4733-G, 4733-H, 4733-I, 4733-J, 4733-K, 4733-L, 4733-M, or 4733-N in Examples is also included.
Examples of the antisense oligonucleotide consisting of a 11- to 19-base-long nucleotide sequence complementary to the nucleotide sequence at positions 4776 to 4795 in the nucleotide sequence set forth in SEQ ID NO: 1, or the antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide include: an antisense oligonucleotide consisting of a nucleotide sequence set forth in SEQ ID NO: 40 or 41, or an antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide. More specific examples include an antisense oligonucleotide depicted as hSYT13-4778-AmNA (15) or hSYT13-4779-AmNA (15) in Examples.
Examples of the antisense oligonucleotide consisting of a 11- to 19-base-long nucleotide sequence complementary to the nucleotide sequence at positions 4949 to 4968 in the nucleotide sequence set forth in SEQ ID NO: 1, or the antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide include: an antisense oligonucleotide consisting of a nucleotide sequence set forth in SEQ ID NO: 42 or 43, or an antisense oligonucleotide consisting of a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said antisense oligonucleotide. More specific examples include an antisense oligonucleotide depicted as hSYT13-4951-AmNA (15) or hSYT13-4952-AmNA (15) in Examples.
In one preferred embodiment, the nucleotide sequence of the antisense oligonucleotide may be a nucleotide sequence selected from the group consisting of SEQ ID NOs: 3 to 43, or a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said nucleotide sequence. In this embodiment, more specifically, it is preferable that the antisense oligonucleotide be one shown in Table 1 below.
In another preferred embodiment, the nucleotide sequence of the antisense oligonucleotide may be a nucleotide sequence selected from the group consisting of SEQ ID NOs: 50 to 59, or a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said nucleotide sequence. In this embodiment, more specifically, it is preferable that the antisense oligonucleotide be one shown in Table 2 below.
In another preferred embodiment, the nucleotide sequence of the antisense oligonucleotide may be a nucleotide sequence selected from the group consisting of SEQ ID NOs: 60 to 69, or a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said nucleotide sequence. In this embodiment, more specifically, it is preferable that the antisense oligonucleotide be one shown in Table 3 below.
In another preferred embodiment, the nucleotide sequence of the antisense oligonucleotide may be a nucleotide sequence selected from the group consisting of SEQ ID NOs: 70 to 79, or a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said nucleotide sequence. In this embodiment, more specifically, it is preferable that the antisense oligonucleotide be one shown in Table 4 below.
In another preferred embodiment, the nucleotide sequence of the antisense oligonucleotide may be a nucleotide sequence selected from the group consisting of SEQ ID NOs: 4, 20, 29, 35, 39, 62, and 79, or a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said nucleotide sequence.
In another preferred embodiment, the nucleotide sequence of the antisense oligonucleotide may be a nucleotide sequence selected from the group consisting of SEQ ID NOs: 80 to 93, or a nucleotide sequence in which one to three bases are substituted, deleted, or inserted with regard to said nucleotide sequence. In this embodiment, more specifically, it is preferable that the antisense oligonucleotide be one shown in Table 5 below.
Sequence homology can be analyzed using algorithms known in this technical field, for example, by BLAST analysis (see, for example, Altschul, S. F., et al., Basic local alignment search tool. 1990, J. Mol. Biol. 215: 403-410).
The antisense oligonucleotide of the present invention may be in a range of from 11 to 20 bases in length and may be, for example, 12 to 19 bases in length, 14 to 18 bases in length, or 15 to 17 bases in length.
In the present invention, the antisense oligonucleotide may comprise a native (unmodified) nucleotide (deoxyribonucleotide, ribonucleotide, or both) and/or a non-native (modified) nucleotide.
In general, a “nucleoside” is a combination of a sugar and a nucleobase. A “nucleotide” further comprises a phosphate group covalently bonded to the sugar moiety of a nucleoside. Phosphate groups typically form internucleoside linkages in oligonucleotides. An oligonucleotide is formed by covalent bonding of nucleosides adjacent to each other, and a linear polymer oligonucleotide is thus formed.
The term “modified nucleoside” as used herein refers to a nucleoside independently having a modified sugar and/or a modified nucleobase. The term “modified nucleotide” as used herein refers to a nucleotide independently having a modified internucleoside linkage, a modified sugar and/or a modified nucleobase. The oligonucleotide comprising a modified nucleotide is preferable to an unmodified form because of desirable properties such as an enhanced affinity for a target nucleic acid and increased resistance to nucleases.
The term “modified internucleoside linkage” as used herein refers to an internucleoside linkage that is a replacement of or has some change from the native internucleoside linkage (i.e., a phosphodiester bond). Examples of the modified internucleoside linkage include, but are not limited to, a phosphorothioate bond, a phosphorodithioate bond, a phosphorodiamidate bond, and a phosphoramidate bond. The phosphorothioate bond refers to an internucleoside linkage in which the non-bridging oxygen atom in the phosphodiester bond is replaced by a sulfur atom. The modified internucleoside linkage is preferably a linkage with higher resistance to nucleases than the native internucleoside linkage.
The term “modified nucleobase” as used herein refers to any nucleobase other than adenine, cytosine, guanine, thymine, or uracil. The term “unmodified nucleobase” or “native nucleobase” refers to the purine bases adenine (A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C), and uracil (U). Examples of the modified nucleobase include, but are not limited to, 5-methylcytosine, 5-fluorocytosine, 5-bromocytosine, or 5-iodocytosine; 5-fluorouracil, 5-bromouracil, 5-iodouracil, or 5-hydroxyuracil; 2-thiothymine; N6-methyladenine or 8-bromoadenine; and N2-methylguanine or 8-bromoguanine.
The term “modified sugar” as used herein refers to a sugar that has a replacement of or has some change from a native sugar moiety (i.e., the sugar moiety found in DNA(2′-H) or RNA(2′-OH)). The modified sugar can provide the oligonucleotide with an enhanced affinity for a target nucleic acid and increased resistance to nucleases. Examples of the modified sugar include bicyclic sugar, 5′-vinyl, 5′-methyl, 4′-S, 2′-F, 2′-OCH3 (2′-methoxy or 2′-O-methyl group), and 2′-O(CH2)2OCH3 substituents.
The term “bicyclic sugar” as used herein refers to a sugar with two rings. A nucleic acid containing a bicyclic sugar moiety is commonly referred to as a bridged nucleic acid (BNA). The bicyclic sugar may be a sugar in which the carbon atom at position 2′ and the carbon atom at position 4′ are bridged by two or more atoms. Examples of the bicyclic sugar include, but are not limited to, sugars having a methyleneoxy (4′-CH2—O-2′) bridge (LNA™, also known as 2′,4′-BNA), sugars having an ethyleneoxy (4′-(CH2)2—O-2′) bridge (also known as ENA), sugars having a 4′-CH(CH3)—O-2′ bridge (cEt, constrained ethyl), sugars having a 4′-CH(CH2OCH3)-0-2′ bridge (cMOE, constrained MOE), and sugars having an amide bridge (AmNA, Amido-bridged nucleic acid).
One example of the sugars having an amide bridge is a sugar having a 4′-C(O)—N(CH3)-2′ bridge. For structures of and preparation methods for the sugars having an amide bridge, see, for example, Yahara, A., et al., Amido-bridged nucleic acids (AmNAs): synthesis, duplex stability, nuclease resistance, and in vitro antisense potency, ChemBioChem, 2012, 13(7): 2513-2516, Yamamoto, T., et al., Amido-bridged nucleic acids with small hydrophobic residues enhance hepatic tropism of antisense oligonucleotides in vivo, Org. Biomol. Chem., 2015, 13:3757-3765, and International Publication No. WO 2011/052436. For sugars having a 4′-CH(CH3)—O-2′ bridge (cEt) and sugars having a 4′-CH(CH2OCH3)—O-2′ bridge (cMOE), see Punit, P. S., et al., Short antisense oligonucleotides with novel 2′-4′ conformationally restricted nucleoside analogues show improved potency without increased toxicity in animals, J. Med. Chem., 2009, 52(1): 10-13.
The antisense oligonucleotide may also comprise a nucleotide mimetic such as peptide nucleic acids and morpholino nucleic acids.
In general, different nucleotides in the same chain can independently undergo different modifications. Also, for example, to enhance the nuclease resistance, the same nucleotide can have a modified internucleoside linkage (e.g., a phosphorothioate bond) and can further have a modified sugar (e.g., a bicyclic sugar). The same nucleotide can also have a modified nucleobase (e.g., 5-methylcytosine) and can further have a modified sugar (e.g., a bicyclic sugar).
In one embodiment, the antisense oligonucleotide may contain at least one modified nucleotide. The modified nucleotide may include a modified internucleoside linkage, a modified sugar moiety, and/or a modified nucleobase.
In one embodiment, at least one of the internucleoside linkages in the antisense oligonucleotide may be a modified internucleoside linkage. At least 70%, at least 80%, at least 90%, or 100% of the internucleoside linkage in the antisense oligonucleotide may be modified internucleoside linkages. The modified internucleoside linkage may be a phosphorothioate bond.
In one embodiment, at least one of the sugar moieties of the antisense oligonucleotide may be a bicyclic sugar. The bicyclic sugar may have a methyleneoxy (4′-CH2—O-2′) bridge or an amide bridge (e.g., 4′-C(O)—N(CH3)-2′ bridge). In the present invention, the antisense oligonucleotide having an amide bridge can be suitably used.
In one embodiment, at least one of the nucleobases of the antisense oligonucleotide may be a modified nucleobase. The modified nucleobase may be 5-methylcytosine.
In a specific embodiment, the antisense oligonucleotide may be a gapmer. The term “gapmer” as used herein refers to an oligonucleotide consisting of a central region containing at least four contiguous deoxyribonucleosides (DNA gap region) and regions containing non-native nucleosides located at the 5′ and 3′ ends of the central region (a 5′ wing region and a 3′ wing region). The DNA gap region may be 4 to 16 bases in length, 5 to 14 bases in length, 6 to 12 bases in length, or 8 to 10 bases in length. The 5′ wing region and the 3′ wing region may be independently 1 to 6 bases in length, 1 to 5 bases in length, or 2 to 4 bases in length. The 5′ wing region and the 3′ wing region contain at least one non-native nucleoside and may contain a native nucleoside. The 5′ wing region and the 3′ wing region may each contain one or more types of non-native nucleosides. All nucleosides in the 5′ wing region and the 3′ wing region may be non-native nucleosides. Alternatively, nucleosides at either or both of the 5′ and 3′ ends (especially at the 3′ end) of the gapmer may be native nucleosides (especially deoxyribonucleosides). A non-native nucleoside contained in the 5′ wing region and the 3′ wing region may be a nucleoside having a bicyclic sugar. The bicyclic sugar may be a sugar having a methyleneoxy (4′-CH2—O-2′) bridge or a sugar having an amide bridge (e.g., 4′-C(O)—N(CH3)-2′ bridge). A non-native nucleoside contained in the 5′ wing region and the 3′ wing region may contain a modified nucleobase (e.g., 5-methylcytosine).
In a suitable embodiment, the antisense oligonucleotide is a gapmer that is used in Examples below.
The antisense oligonucleotide of the present invention can be produced by methods known in the art. For example, the antisense oligonucleotide can be synthesized using a commercially available automated nucleic acid synthesizer, and then purified using a reverse-phase column. Alternatively, the antisense oligonucleotide can be ordered and obtained from a manufacturer (e.g., Gene Design, Inc.) by designating a nucleobase sequence and a modification site and type.
The antisense oligonucleotide of the present invention inhibits the expression of human SYT13 gene, and thus can be used as a medicine that inhibits the peritoneal dissemination in gastric cancer.
The antisense oligonucleotide of the present invention can inhibit the proliferation, migration, and/or invasion of cancer cells expressing SYT13 in vitro or in vivo. Delivery of the antisense oligonucleotide into cells can be performed using any method commonly used in this field, such as lipofection, electroporation, microinjection, particle gun, and transduction using viruses or plasmids as vectors. Alternatively, the antisense oligonucleotide can be transfected directly into cells. For example, the antisense oligonucleotide can be suitably delivered into cells in vitro and in vivo using the CEM method (Nucleic Acids Research, 2015, Vol. 43, No. 19, e128; doi: 10.1093/nar/gkv626).
The antisense oligonucleotide of the present invention inhibits the expression of human SYT13 gene and thus can be used as a medicine that inhibits peritoneal dissemination of gastric cancer. The efficacy of the present invention is demonstrated in the Examples below.
The present invention also provides a conjugate comprising the above-described antisense oligonucleotide, and a further functional moiety directly or indirectly linked each other.
The further functional moiety contemplated in the present invention may be a small molecule such as a peptide, sugar, or lipid, and may be, but is not limited to, a ligand for target molecule or an agent with antitumor activity. More specifically, the functional molecule may be, for example, a binding molecule such as an antibody or antigen-binding fragment thereof to a protein that can be highly expressed at a tumor site, GalNAc that can bind to glycoprotein receptors, or a lipid such as cholesterol or a long-chain fatty acid that can enhance cell membrane permeability. In addition, the functional molecule may be, for example, an agent with another antitumor activity.
The antisense oligonucleotide and the further functional moiety may be linked directly or via a linker commonly used in this field. The linkage is preferably, but is not limited to, a covalent bond. Administering the antisense oligonucleotide of the present invention as the conjugate can facilitate the delivery to its target site and/or improve the efficacy of the antisense oligonucleotide of the present invention.
The present invention provides a pharmaceutical composition comprising the antisense oligonucleotide or conjugate of the present invention. The pharmaceutical composition of the present invention can be used, for example, to prevent or treat peritoneal dissemination after gastric cancer resection.
The pharmaceutical composition may further comprise any formulation aids normally used in the field of pharmaceutical formulation. As the formulation aids herein, various carriers or additives such as pharmaceutically acceptable carriers (solid or liquid carriers), excipients, stabilizers, disintegrators, surfactants, binders, lubricants, emulsifiers, suspension agents, antioxidants, odor-masking agents, fillers, solubilizers, coating agents, colorants, taste-masking agents, preservatives, and buffers can be used. Specific examples of the formulation aids include water, physiological saline, other aqueous solvents, pharmaceutically acceptable organic solvents, mannitol, lactose, starch, microcrystalline cellulose, glucose, calcium, polyvinyl alcohol, collagen, polyvinylpyrrolidone, carboxyvinyl polymer, sodium alginate, water-soluble dextran, water-soluble dextrin, sodium carboxymethyl starch, pectin, gum arabic, xanthan gum, casein, gelatin, agar, propylene glycol, polyethylene glycol, vaseline, paraffin, glycerin, stearyl alcohol, stearic acid, and sorbitol. The formulation aid may be selected as appropriate or in combination depending on the dosage form of the pharmaceutical formulation.
The pharmaceutical composition can be administered to a subject orally or parenterally. Examples of parenteral administration include, but are not limited to, intraperitoneal administration. In order to efficiently attain the therapeutic effect, it is preferable that the pharmaceutical composition be administered directly and topically to a damaged site. The pharmaceutical composition can also be continuously administered to the damaged site using a continuous infusion pump. The pharmaceutical composition may be formulated into an injection, a drip, or the like. Those skilled in the art can produce these pharmaceutical formulations in a conventional manner.
The pharmaceutical composition may be administered in a therapeutically effective amount. A specific dosage of the pharmaceutical composition is determined by the physician, for example, based on the disease severity, general health condition, age, sex, body weight, tolerability to the treatment, etc., according to individual subjects. For example, the pharmaceutical composition may be administered such that the dose of the antisense oligonucleotide is 0.000001 mg/kg body weight/day to 1000 mg/kg body weight/day, or 0.001 mg/kg body weight/day to 1 mg/kg body weight/day, or 0.005 mg/kg body weight/day to 0.5 mg/kg body weight/day, or 0.01 mg/kg body weight/day to 0.1 mg/kg body weight/day. The pharmaceutical composition can be administered as a single dose or multiple doses and may be administered to a subject several times or several tens of times, for example, at regular time intervals such as 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 1 week, 2 weeks, 3 weeks, or 1 month. Alternatively, the pharmaceutical composition may be administered continuously using a continuous infusion pump as described above. The dosage (rate), duration, etc. for the continuous administration can be set appropriately by those skilled in the art.
The subject to which the pharmaceutical composition is administered is a mammal such as primates (e.g., cynomolgus monkeys, chimpanzees, and humans) and non-primates (e.g., cattle, pigs, sheep, horses, cats, dogs, guinea pigs, rats, and mice), and is more preferably a human. The subject may be, for example, an animal model for gastric cancer transplanted with human gastric cancer cells.
The present invention also provides a method for preventing or treating peritoneal dissemination after gastric cancer resection, the method comprising administering the antisense oligonucleotide, conjugate, or pharmaceutical composition of the present invention to a subject in need thereof.
The present invention also provides use of the antisense oligonucleotide or conjugate of the present invention in the manufacture of a medicine for preventing or treating peritoneal dissemination after gastric cancer resection.
Hereinafter, the present invention will be described in more detail using Examples. However, the technical scope of the present invention is not limited to these Examples.
As a target region of an antisense oligonucleotide, a region with a sequence commonly included in the mRNA sequences of two variants of SYT13, NM_020826.2 (SEQ ID NO: 1) and NM_001247987.1 (SEQ ID NO: 2) was extracted. At this point, thousands of candidate target sequences were obtained.
Next, after their homology with mouse SYT13 mRNA was examined by BLAST, the conformations of antisense oligonucleotides to be obtained were predicted to exclude sequences that are expected to have a high risk of toxicity manifestation, whereby several hundreds of candidate sequences were selected.
After sequences for antisense strands were obtained from the selected sequences and the candidate sequences were further narrowed down by selection based on their physical properties as antisense oligonucleotides, sequences with a high risk of off-target were excluded to select 41 candidate sequences. Based on these sequences, their respective antisense oligonucleotide molecules were designed and synthesized.
The structure of the antisense oligonucleotide used in this Example is shown in
In the above structure, “Base” means a base, such as adenine, cytosine, guanine, or thymine, but can include a modified base such as 5-methylcytosine in the artificial nucleic acid region.
In
The antisense oligonucleotide used in this Example was prepared to have a phosphorothioate bond instead of a phosphodiester bond found in native nucleic acids to improve its resistance to enzymes.
Table 1 below shows sequence information for antisense oligonucleotides designed based on the candidate sequences selected above and for control antisense oligonucleotides (NEG1 and NEG2) designed not to bind to any of the known genes. For example, “hSYT13-350-AmNA (15)” in Table 1 has a sequence complementary to the consecutive 15 bases from position 350 in SEQ ED NO: 1, which is a nucleotide sequence of human SYT13 mRNA. In Table 1, underlines indicate mismatched bases to mouse SYT13 mRNA.
A(Y){circumflex over ( )}G(Y){circumflex over ( )}T(Y){circumflex over ( )}a{circumflex over ( )}g{circumflex over ( )}t{circumflex over ( )}g{circumflex over ( )}g{circumflex over ( )}a{circumflex over ( )}g{circumflex over ( )}t{circumflex over ( )}t{circumflex over ( )}T(Y){circumflex over ( )}G(Y){circumflex over ( )}g
5(Y){circumflex over ( )}5(T){circumflex over ( )}A(Y){circumflex over ( )}a{circumflex over ( )}g{circumflex over ( )}a{circumflex over ( )}a{circumflex over ( )}g{circumflex over ( )}g{circumflex over ( )}g{circumflex over ( )}a{circumflex over ( )}g{circumflex over ( )}G(Y){circumflex over ( )}5(Y){circumflex over ( )}a
T(Y){circumflex over ( )}G(Y){circumflex over ( )}T(Y){circumflex over ( )}t{circumflex over ( )}t{circumflex over ( )}t{circumflex over ( )}t{circumflex over ( )}a{circumflex over ( )}g{circumflex over ( )}c{circumflex over ( )}c{circumflex over ( )}a{circumflex over ( )}G(Y){circumflex over ( )}A(Y){circumflex over ( )}g
T(Y){circumflex over ( )}T(Y){circumflex over ( )}G(Y){circumflex over ( )}t{circumflex over ( )}t{circumflex over ( )}t{circumflex over ( )}t{circumflex over ( )}t{circumflex over ( )}a{circumflex over ( )}g{circumflex over ( )}c{circumflex over ( )}c{circumflex over ( )}A(Y){circumflex over ( )}G(Y){circumflex over ( )}a
5(Y){circumflex over ( )}5(Y){circumflex over ( )}A(Y){circumflex over ( )}a{circumflex over ( )}a{circumflex over ( )}g{circumflex over ( )}g{circumflex over ( )}c{circumflex over ( )}a{circumflex over ( )}g{circumflex over ( )}a{circumflex over ( )}a{circumflex over ( )}T(Y){circumflex over ( )}5(Y){circumflex over ( )}c
A(Y){circumflex over ( )}A(Y){circumflex over ( )}T(Y){circumflex over ( )}t{circumflex over ( )}c{circumflex over ( )}t{circumflex over ( )}g{circumflex over ( )}t{circumflex over ( )}c{circumflex over ( )}t{circumflex over ( )}t{circumflex over ( )}a{circumflex over ( )}G(Y){circumflex over ( )}G(Y){circumflex over ( )}g
G(Y){circumflex over ( )}A(Y){circumflex over ( )}A(Y){circumflex over ( )}a{circumflex over ( )}a{circumflex over ( )}a{circumflex over ( )}a{circumflex over ( )}t{circumflex over ( )}a{circumflex over ( )}a{circumflex over ( )}t{circumflex over ( )}g{circumflex over ( )}A(Y){circumflex over ( )}5(Y){circumflex over ( )}c
A(Y){circumflex over ( )}G(Y){circumflex over ( )}A(Y){circumflex over ( )}a{circumflex over ( )}a{circumflex over ( )}a{circumflex over ( )}a{circumflex over ( )}a{circumflex over ( )}t{circumflex over ( )}a{circumflex over ( )}a{circumflex over ( )}t{circumflex over ( )}G(Y){circumflex over ( )}A(Y){circumflex over ( )}c
T(Y){circumflex over ( )}T(Y){circumflex over ( )}T(Y){circumflex over ( )}a{circumflex over ( )}c{circumflex over ( )}c{circumflex over ( )}a{circumflex over ( )}t{circumflex over ( )}t{circumflex over ( )}g{circumflex over ( )}a{circumflex over ( )}g{circumflex over ( )}A(Y){circumflex over ( )}A(Y){circumflex over ( )}c
T(Y){circumflex over ( )}A(Y){circumflex over ( )}G(Y){circumflex over ( )}g{circumflex over ( )}c{circumflex over ( )}a{circumflex over ( )}a{circumflex over ( )}a{circumflex over ( )}t{circumflex over ( )}a{circumflex over ( )}g{circumflex over ( )}t{circumflex over ( )}A(Y){circumflex over ( )}A(Y){circumflex over ( )}t
G(Y){circumflex over ( )}T(Y){circumflex over ( )}T(Y){circumflex over ( )}g{circumflex over ( )}a{circumflex over ( )}t{circumflex over ( )}t{circumflex over ( )}a{circumflex over ( )}c{circumflex over ( )}a{circumflex over ( )}t{circumflex over ( )}t{circumflex over ( )}T(Y){circumflex over ( )}A(Y){circumflex over ( )}c
T(Y){circumflex over ( )}G(Y){circumflex over ( )}T(Y){circumflex over ( )}t{circumflex over ( )}g{circumflex over ( )}a{circumflex over ( )}t{circumflex over ( )}t{circumflex over ( )}a{circumflex over ( )}c{circumflex over ( )}a{circumflex over ( )}t{circumflex over ( )}T(Y){circumflex over ( )}T(Y){circumflex over ( )}a
A(Y){circumflex over ( )}T(Y){circumflex over ( )}5(Y){circumflex over ( )}t{circumflex over ( )}g{circumflex over ( )}t{circumflex over ( )}t{circumflex over ( )}g{circumflex over ( )}a{circumflex over ( )}t{circumflex over ( )}t{circumflex over ( )}a{circumflex over ( )}5(Y){circumflex over ( )}A(Y){circumflex over ( )}t
T(Y){circumflex over ( )}5(Y){circumflex over ( )}A(Y){circumflex over ( )}t{circumflex over ( )}c{circumflex over ( )}t{circumflex over ( )}g{circumflex over ( )}t{circumflex over ( )}t{circumflex over ( )}g{circumflex over ( )}a{circumflex over ( )}t{circumflex over ( )}T(Y){circumflex over ( )}A(Y){circumflex over ( )}c
T(Y){circumflex over ( )}T(Y){circumflex over ( )}5(Y){circumflex over ( )}a{circumflex over ( )}t{circumflex over ( )}c{circumflex over ( )}t{circumflex over ( )}g{circumflex over ( )}t{circumflex over ( )}t{circumflex over ( )}g{circumflex over ( )}a{circumflex over ( )}T(Y){circumflex over ( )}T(Y){circumflex over ( )}a
5(Y){circumflex over ( )}T(Y){circumflex over ( )}5(Y){circumflex over ( )}t{circumflex over ( )}t{circumflex over ( )}c{circumflex over ( )}a{circumflex over ( )}t{circumflex over ( )}c{circumflex over ( )}t{circumflex over ( )}g{circumflex over ( )}t{circumflex over ( )}T(Y){circumflex over ( )}G(Y){circumflex over ( )}a
T(Y){circumflex over ( )}5(Y){circumflex over ( )}T(Y){circumflex over ( )}c{circumflex over ( )}t{circumflex over ( )}t{circumflex over ( )}c{circumflex over ( )}a{circumflex over ( )}t{circumflex over ( )}c{circumflex over ( )}t{circumflex over ( )}g{circumflex over ( )}T(Y){circumflex over ( )}T(Y){circumflex over ( )}g
T(Y){circumflex over ( )}A(Y){circumflex over ( )}T(Y){circumflex over ( )}t{circumflex over ( )}c{circumflex over ( )}t{circumflex over ( )}c{circumflex over ( )}t{circumflex over ( )}t{circumflex over ( )}c{circumflex over ( )}a{circumflex over ( )}t{circumflex over ( )}5(Y){circumflex over ( )}T(Y){circumflex over ( )}g
5(Y){circumflex over ( )}5(Y){circumflex over ( )}5(Y){circumflex over ( )}g{circumflex over ( )}a{circumflex over ( )}t{circumflex over ( )}t{circumflex over ( )}t{circumflex over ( )}t{circumflex over ( )}c{circumflex over ( )}t{circumflex over ( )}a{circumflex over ( )}T(Y){circumflex over ( )}5(Y){circumflex over ( )}c
T(Y){circumflex over ( )}5(Y){circumflex over ( )}5(Y){circumflex over ( )}c{circumflex over ( )}g{circumflex over ( )}a{circumflex over ( )}t{circumflex over ( )}t{circumflex over ( )}t{circumflex over ( )}t{circumflex over ( )}c{circumflex over ( )}t{circumflex over ( )}A(Y){circumflex over ( )}T(Y){circumflex over ( )}c
A(Y){circumflex over ( )}T(Y){circumflex over ( )}G(Y){circumflex over ( )}a{circumflex over ( )}g{circumflex over ( )}g{circumflex over ( )}g{circumflex over ( )}c{circumflex over ( )}a{circumflex over ( )}g{circumflex over ( )}a{circumflex over ( )}c{circumflex over ( )}T(Y){circumflex over ( )}5(Y){circumflex over ( )}c
G(Y){circumflex over ( )}5(Y){circumflex over ( )}T(Y){circumflex over ( )}c{circumflex over ( )}a{circumflex over ( )}a{circumflex over ( )}c{circumflex over ( )}a{circumflex over ( )}a{circumflex over ( )}a{circumflex over ( )}t{circumflex over ( )}a{circumflex over ( )}G(Y){circumflex over ( )}A(Y){circumflex over ( )}t
T(Y){circumflex over ( )}G(Y){circumflex over ( )}5(Y){circumflex over ( )}t{circumflex over ( )}c{circumflex over ( )}a{circumflex over ( )}a{circumflex over ( )}c{circumflex over ( )}a{circumflex over ( )}a{circumflex over ( )}a{circumflex over ( )}t{circumflex over ( )}A(Y){circumflex over ( )}G(Y){circumflex over ( )}a
5(Y){circumflex over ( )}A(Y){circumflex over ( )}5(Y){circumflex over ( )}a{circumflex over ( )}t{circumflex over ( )}t{circumflex over ( )}t{circumflex over ( )}t{circumflex over ( )}a{circumflex over ( )}c{circumflex over ( )}c{circumflex over ( )}c{circumflex over ( )}A(Y){circumflex over ( )}G(Y){circumflex over ( )}g
5(Y){circumflex over ( )}5(Y){circumflex over ( )}A(Y){circumflex over ( )}c{circumflex over ( )}a{circumflex over ( )}t{circumflex over ( )}t{circumflex over ( )}t{circumflex over ( )}t{circumflex over ( )}a{circumflex over ( )}c{circumflex over ( )}c{circumflex over ( )}5(Y){circumflex over ( )}A(Y){circumflex over ( )}g
The antisense oligonucleotides were synthesized according to a method commonly used in this field.
Human signet ring cell carcinoma-derived gastric cancer cell line KATOIII (obtained from American Type Culture Collection, ATCC) cultured at 37° C. under 5% CO2 in a medium prepared by mixing RPMI1640 (Nacalai Tesque Inc.) and DMEM (Nacalai Tesque Inc., Low-Glucose) at 1:1 and adding thereto 10% fetal bovine serum (FBS, biowest) and 1% penicillin-streptomycin mixed solution (Nacalai Tesque Inc., Stabilized) was seeded at a concentration of 10,000 cells/100_4 per well in DMEM containing 10% FBS in a 96-well plate, and cultured at 37° C. under 5% CO2 for 24 hours.
Cell transfection was performed by the CEM method. Specifically, 900 mM calcium chloride was added to the DMEM containing 10% FBS to prepare a 100-fold dilution, and then the antisense oligonucleotide synthesized in Example 1 was added to obtain a final concentration of 6.25 nM, 25 nM, or 100 nM, and cells were further cultured at 37° C. under 5% CO2 for 24 hours.
RNA was extracted from the transfected cells and reverse-transcribed into cDNA using Cell Lysis & RT Kit (TOYOBO SuperPrep™Cell Lysis & RT Kit for qPCR).
The obtained cDNA was subjected to real-time PCR (RT-PCR) using ABI PowerUp™ SYBR□ Green Master Mix and the following primers (200 nM each). PCR was performed using a thermal cycler (ABI StepOnePlus™ Real-Time PCR System) under the following conditions: 95° C. for 30 seconds, followed by 45 cycles of 95° C. for 3 seconds and 60° C. for 30 seconds.
A relative expression level of SYT13 mRNA was calculated from the measured expression levels of SYT13 mRNA and GAPDH mRNA (a comparative control). Some of the results are shown in
As shown in
Human gastric cancer cell lines MKN1, MKN45, and OCUM-1 (obtained from the JCRB cell bank of the National Institutes of Biomedical Innovation, Health and Nutrition, Japan) were used to examine the efficacy of the antisense oligonucleotides synthesized in Example 1. For operational procedure for the cell culture and the like, those suitable for each cell line were used as appropriate but were substantially the same as in Example 2.
For MKN1 cells, MKN1 cells that were cultured in RPMI 1640 (Nacalai Tesque Inc.) supplemented with 10% FBS (biowest) and 1% penicillin-streptomycin mixed solution (Nacalai Tesque Inc., Stabilized) at 37° C. under 5% CO2 were seeded at a concentration of 8,000 cells/100 μL per well in DMEM containing 10% FBS in a 96-well plate, and cultured at 37° C. under 5% CO2 for 24 hours; subsequently, the antisense oligonucleotide synthesized in Example 1 was added to prepare a final concentration of 6.25 nM, 25 nM, or 100 nM, and cells were further cultured at 37° C. under 5% CO2 for 24 hours. For extraction of RNA from the transfected cells, RNA was extracted and reverse-transcribed into cDNA using Cell Lysis & RT Kit (TOYOBO SuperPrep™Cell Lysis & RT Kit for qPCR).
For MKN45 cells, MKN45 cells that were cultured in RPMI 1640 (Nacalai Tesque Inc.) supplemented with 10% FBS (biowest) and 1% penicillin-streptomycin mixed solution (Nacalai Tesque Inc., Stabilized) at 37° C. under 5% CO2 were seeded at a concentration of 30,000 cells/500_4 per well in DMEM containing 10% FBS in a 24-well plate, and cultured at 37° C. under 5% CO2 for 24 hours; subsequently, the antisense oligonucleotide synthesized in Example 1 was added to prepare a final concentration of 50 nM or 200 nM, and cells were further cultured at 37° C. under 5% CO2 for 24 hours. Extraction of RNA from the transfected cells was performed using QIAGEN Rneasy□ Mini Kit)(QIAGEN□) and reverse-transcribed into cDNA using a high-capacity cDNA reverse transcription kit (ABI High-Capacity cDNA Reverse Transcription Kit).
For OCUM-1 cells, OCUM-1 cells that were cultured in DMEM (Nacalai Tesque Inc., Low-Glucose) supplemented with 10% FBS (biowest), 1% penicillin-streptomycin mixed solution (Nacalai Tesque Inc., Stabilized), and 0.5 mM sodium pyruvate at 37° C. under 5% CO2 were seeded at a concentration of 7,500 cells/100_4 per well in DMEM containing 10% FBS in a 96-well plate, and cultured at 37° C. under 5% CO2 for 24 hours; subsequently, the antisense oligonucleotide synthesized in Example 1 was added to prepare a final concentration of 50 nM, 100 nM, or 200 nM, and cells were further cultured at 37° C. under 5% CO2 for 24 hours. For extraction of RNA from the transfected cells, RNA was extracted and reverse-transcribed into cDNA using Cell Lysis & RT Kit (TOYOBO SuperPrep™Cell Lysis & RT Kit for qPCR).
As a result, as shown in
For each of the three antisense oligonucleotides, hSYT13-605-AmNA (15), hSYT113-4378-AmNA (15), and hSYT13-4729-AmNA (15), which were confirmed to have particularly good efficacy in the screening test of Example 2, ten antisense oligonucleotides were designed and synthesized by varying the length and position of the native nucleic acid region with the number of introduced artificial nucleic acids fixed. Table 2 below shows sequence information for antisense oligonucleotides designed for the optimization examination using hSYT13-605-AmNA (15) as a parent sequence, Table 3 shows sequence information for antisense oligonucleotides designed for the optimization examination using hSYT113-4378-AmNA (15) as a parent sequence, and Table 4 shows sequence information for antisense oligonucleotides designed for the optimization examination using hSYT13-4729-AmNA (15) as a parent sequence.
Each of the antisense oligonucleotides synthesized in Example 4 was examined for the inhibitory effect on the expression of SYT13 in OCUM-1, MKN1, and NUGC-4 cells in the same manner as in Example 3. In this Example, the final concentration of antisense oligonucleotides was set to 100 nM or 400 nM.
The operational procedures for the OCUM-1 and MKN1 cells were the same as in Example 3.
For NUGC-4 cells, NUGC-4 cells that were cultured in RPMI 1640 (Nacalai Tesque Inc.) supplemented with 10% FBS (biowest) and 1% penicillin-streptomycin mixed solution (Nacalai Tesque Inc., Stabilized) at 37° C. under 5% CO2 were seeded at a concentration of 8,000 cells/100_4 per well in DMEM containing 10% FBS in a 96-well plate, and cultured at 37° C. under 5% CO2 for 24 hours. For extraction of RNA from the transfected cells, RNA was extracted and reverse-transcribed into cDNA using Cell Lysis & RT Kit (TOYOBO SuperPrep™Cell Lysis & RT Kit for qPCR).
As a result, as shown in
hSYT13-605-AmNA (15), hSYT13-2813-AmNA (15), hSYT13-4367-AmNA (15), hSYT13-4378-AmNA (15), and hSYT13-4729-AmNA (15), the sequence information of which was shown in Table 1, and which were shown to have high inhibitory effect on the expression of SYT13 mRNA as confirmed in Example 2, were examined for an inhibitory effect on the proliferative capacity of cancer cells in vitro.
MKN1/Luc, NUGC4, AGS, N87, and GSU cells were seeded at a concentration of 3000 cells/well and KATO3 and OCUM1 cells were seeded at a concentration of 5000 cells/well in a 96-well plate, transfected with the antisense oligonucleotide at a final concentration of 400 nM (MKN1/Luc, NUGC4) or 100 nM (AGS, N87, GSU, KATO3, OCUM1) by the CEM method and then cultured; the number of cells was determined using Cell Counting Kit-8 (Dojindo Molecular Technologies, Inc.) on days 0, 1, 3, and 5, and a fold change relative to the number of cells at the initial stage of culture was calculated. The fold changes in eight wells were determined for each sample, and their mean value and standard deviation were calculated.
As a result, as shown in
Accell SYT13 siRNA (manufactured by Dharmacon Inc.) was used as siRNA that can target human SYT13 mRNA, and 400 nM of the siRNA was transfected into 50,000 cells/mL of MKN1 and NUGC4 cell lines by the CEM method in the same manner as in Example 6, and then, the effect on the proliferative capacity of these cell lines was examined. As a control, siRNA designed not to bind to any of the known genes (Accell Green Non-targeting, manufactured by Dharmacon Inc.) was used for comparison.
As a result, as shown in
An ibidi Culture-Insert (ibidi GmbH, Martinsried, Germany) was used to examine the inhibitory effect of the antisense oligonucleotide of the present invention on the migration capacity of gastric cancer cell lines in vitro.
Using MKN1/Luc (3×104 cells/well), N87 (30×104 cells/well), and NUGC4 (3.5×104 cells/well) as the cells as well as any one of antisense oligonucleotides hSYT13-605-AmNA (15), hSYT13-2813-AmNA (15), hSYT13-4367-AmNA (15), hSYT13-4378-AmNA (15), and hSYT13-4729-AmNA (15) of the present invention, or a control antisense oligonucleotide (NEG1), the inhibitory effect on the cell migration into a cell-free gap was examined.
As a result, as shown in
BioCoat Matrigel Invasion Chamber (BD Biosciences, Bedford, Mass., USA) was used to examine the inhibitory effect of the antisense oligonucleotide of the present invention on the invasive capacity of gastric cancer cell lines in vitro.
Using MKN1/Luc (2.5×104 cells/well), AGS (5×104 cells/well), GSU (5×104 cells/well) as the cells as well as any one of antisense oligonucleotides hSYT13-605-AmNA (15), hSYT13-2813-AmNA (15), hSYT13-4367-AmNA (15), hSYT13-4378-AmNA (15), and hSYT13-4729-AmNA (15) of the present invention, or a control antisense oligonucleotide (NEG1), the numbers of invasive cells in the chamber were compared.
As a result, as shown in
Using the same method as that described in WO2016/143697, immunodeficient mice (10-week-old male BALBc-nu/nu) were intraperitoneally administered with 1 ml of luciferase-gene-introduced MKN1-luc cells or NUGC4 cells at a dose of 1×106 cells/ml to prepare a peritoneal dissemination model, and the in vivo efficacy of the antisense oligonucleotide of the present invention was examined.
After the transplantation of the cancer cells, 0.2 mg per dose (equivalent to 10 mg/kg with a mouse body weight of 20 g) of hSYT13-4729 (15) or hSYT13-4378 (15) (both with a molecular weight of about 5000) added to 500 μL of 5% glucose solution was administered twice a week for 6 weeks (
The mice transplanted with MKN1-luc cells were subjected to in vivo imaging using an In Vivo Imaging System (IVIS□) Lumina (Xenogen Corporation, Alameda, Calif., USA). Specifically, 2, 4, or 6 weeks after the cell transplantation, the mice were intraperitoneally administered with D-luciferin (150 mg/kg) (Summit Pharmaceuticals International, Tokyo, Japan), and 15 minutes later, photographed with IVIS□ to measure a signal intensity with Living Image□ Version 2.6 Software (Xenogen Corporation). As a result, in the mice to which the antisense oligonucleotide was not administered and the mice to which the control antisense oligonucleotide or siRNA was administered, luminescence indicating the survival of peritoneal dissemination-like cells was observed, whereas in the mice to which the antisense oligonucleotide of the present invention was administered, luminescence could not be detected, or even if it could, the amount of luminescence was significantly small (data not shown).
Six weeks after the cancer cell transplantation, some mice were sacrificed to compare total weights of peritoneal dissemination lesions of the mice for each group. The results are shown in
Four antisense oligonucleotides, hSYT13-4380 (17) and hSYT13-4733 (17) (for which sequence information is shown in Table 3 and Table 4, respectively), which showed suitable activity in Example 5, in addition to hSYT13-4378 (15) and hSYT13-4729 (15) were used to examine the inhibitory effect on the proliferative capacity of MKN1 cells or NUGC4 cells in vitro in the same manner as in Example 6.
As a result, as shown in
Four antisense oligonucleotides, hSYT13-4378 (15), hSYT13-4729 (15), hSYT13-4380 (17), and hSYT13-4733 (17) were used to examine the inhibitory effect on the migration capacity of MKN1 cells or NUGC4 cells in vitro in the same manner as in Example 7.
As a result, as shown in
Four antisense oligonucleotides, hSYT13-4378 (15), hSYT13-4729 (15), hSYT13-4380 (17), and hSYT13-4733 (17) were used to examine the inhibitory effect on the invasive capacity of MKN1 cells or NUGC4 cells in vitro in the same manner as in Example 8.
As a result, as shown in
As shown in
An in vivo test was performed using a mouse model of peritoneal dissemination prepared in the same manner as in Example 9.
A mouse model of peritoneal dissemination was prepared by intraperitoneal implantation of 1 ml of NUGC4 cell line at 2×106 cells/ml, and thereafter, 0.2 mg per dose (equivalent to 10 mg/kg with a mouse body weight of 20 g) of antisense oligonucleotides hSYT13-4378 (15) and hSYT13-4733 (17), and a control antisense oligonucleotide (NEG1, SEQ ID NO: 44) added to 5004 of 5% glucose solution were administered twice a week for 12 weeks (
Eight weeks after the transplantation of the cancer cells, some mice were sacrificed for macroscopic examination on tumor proliferation. As a result, the mice with no antisense oligonucleotide administration (Control) and the mice with the control antisense oligonucleotide administration (NEG1) showed a significant growth of peritoneal dissemination-like tumor, whereas the mice with hSYT13-4378 (15) administration and the mice with hSYT13-4733 (17) administration had almost no peritoneal dissemination confirmed (data not shown).
The number of days of survival after cancer cell transplantation (seeding) was determined for mice with and without the antisense oligonucleotide administration for 12 weeks (8 mice per group) in Example 13.
As a result, as shown in
Based on hSYT13-4733-AmNA (17) (SEQ ID NO: 79), which was shown to have high inhibitory activity on the expression of SYT13 mRNA in Example 5, fourteen antisense oligonucleotides (4733-A to 4733-N), with its modification patterns of sugar, nucleobase and/or internucleoside linkage changed, were designed and synthesized. The sequence information for these antisense oligonucleotides is shown in Table 5.
As understood from Table 5 and the accompanying sequence listing, hSYT13-4733-AmNA (17) and 4733-A to 4733-N are gapmers that are 17 bases in length.
hSYT13-4733-AmNA (17) comprises non-native nucleosides (depicted as “AmNA” in the table) with a sugar having an amide bridge, three on the 5′ end and two on the 3′ end, and all the internucleoside linkages are phosphorothioate bonds.
In contrast, in six antisense oligonucleotides 4733-A to 4733-F, part of their internucleoside linkages in either or both of the wing regions at the 5′ and 3′ ends (5′ wing region and 3′ wing region) as well as at the boundary between the wing region and the DNA gap region are phosphodiester bonds.
In addition, in eight antisense oligonucleotides 4733-G to 4733-N, the number and/or position of non-native nucleosides (AmNAs) with a sugar having an amide bridge is changed in either or both of the 5′ wing region and the 3′ wing region, and 4733-H, 4733-K, and 4733-M include 5-methylcytosine in the 3′ wing region.
hSYT13-4733-AmNA (17) (SEQ ID NO: 79) and the above fourteen antisense oligonucleotides (4733-A to 4733-N) were examined for the inhibitory effect on the expression of SYT13 in NUGC-4 cells in the same manner as in Example 5.
As a result, as shown in
All publications, patents, and patent applications cited herein are hereby incorporated by reference in their entirety.
| Number | Date | Country | Kind |
|---|---|---|---|
| 2019-154968 | Aug 2019 | JP | national |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/JP2020/032270 | 8/27/2020 | WO |
