Use of spliceosome mediated RNA trans-splicing for immunotherapy
Methods and compositions for generating novel nucleic acid molecules through targeted spliceosomal mediated trans-splicing that result in expression of an immunogenic polypeptide. The invention includes pre-trans-splicing molecules (PTMs) designed to interact with a target precursor messenger RNA molecule (target pre-mRNA) and mediate a trans-splicing reaction resulting in the generation of a novel chimeric RNA molecule (chimeric RNA) capable of encoding the immunogenic polypeptide, recombinant vector systems capable of expressing the PTMs of the invention, and cells expressing said PTMs. The target pre-mRNA are those encoding proteins that function in antigen uptake, antigen presentation and chaperoning. The methods of the invention encompass contacting the PTMs of the invention with a target pre-mRNA, under conditions in which a portion of the PTM is trans-spliced to a portion of the target pre-mRNA to form a chimeric mRNA molecule capable of encoding an immunogenic polypeptide.
1 . A cell comprising a nucleic acid molecule wherein said nucleic acid molecule comprises:
a) one or more target binding domains that target binding of the nucleic acid molecule to a target pre-mRNA expressed within the cell, wherein said target pre-mRNA encodes a protein involved in antigen uptake, presentation or chaperoning;
b) a splice region;
c) a spacer region that separates the splice region from the target binding domain; and
d) a nucleotide sequence to be trans-spliced to the target pre-mRNA wherein said nucleotide sequence encodes an antigen of interest;
wherein said nucleic acid molecule is recognized by nuclear splicing components within the cell.
2 . The cell of claim 1 wherein the splice region comprises a 3′ splice region.
3 . The cell of claim 1 wherein the splice region comprises a 5′ splice region.
4 . The cell of claim 2 wherein the 3′ splice region comprises at least one of a branch point and a 3′ splice acceptor site.
5 . The cell of claim 2 wherein the 3′ splice region further comprises a pyrimidine tract.
6 . The cell of claim 2 wherein the nucleic acid molecule further comprises a safety nucleotide sequence comprising one or more complementary sequences that bind to one or more sides of the 3′ splice region
7 . The cell of claim 3 wherein said nucleic acid molecule further comprises a safety sequence comprising one or more complementary sequences that bind to one or both sides of the 5′ splice site.
8 . The cell of claim 3 wherein the nucleic acid molecule further comprises a 5′ donor site.
9 . A method of producing a chimeric RNA molecule in a cell comprising:
contacting a target pre-mRNA expressed in the cell with a nucleic acid molecule recognized by nuclear splicing components wherein said nucleic acid molecule comprises:
a) one or more target binding domains that target binding of the nucleic acid molecule to a target pre-mRNA expressed within the cell, wherein said target pre-mRNA encodes an protein involved in antigen uptake, presentation or chaperoning;
b) a splice region;
c) a spacer region that separates the splice region from the target binding domain; and
d) a nucleotide sequence to be trans-spliced to the target pre-mRNA wherein said nucleotide sequence encodes an antigen of interest;
under conditions in which a portion of the nucleic acid molecule is trans-spliced to a portion of the target pre-mRNA to form a chimeric RNA within the cell.
10 . The method of claim 9 wherein the splice region comprises a 3′ splice region.
11 . The method of claim 9 wherein the splice region comprises a 5′ splice region.
12 . The method of claim 10 wherein the 3′ splice region comprises at least one of a branch point and a 3′ splice acceptor site.
13 . The method of claim 10 wherein the 3′ splice region further comprises a pyrimidine tract.
14 . The method of claim 10 wherein the nucleic acid molecule further comprises a safety nucleotide sequence comprising one or more complementary sequences that bind to one or more sides of the 3′ splice region
15 . The method of claim 11 wherein said nucleic acid molecule further comprises a safety sequence comprising one or more complementary sequences that bind to one or both sides of the 5′ splice site.
16 . The method of claim 11 wherein the nucleic acid molecule further comprises a 5′ donor site.
17 . A nucleic acid molecule comprising:
a) one or more target binding domains that target binding of the nucleic acid molecule to a target pre-mRNA expressed within the cell, wherein said target pre-mRNA encodes an protein involved in antigen uptake, presentation or chaperoning;
b) a splice region;
c) a spacer region that separates the splice region from the target binding domain; and
d) a nucleotide sequence to be trans-spliced to the target pre-mRNA wherein said nucleotide sequence encodes an antigen of interest;
wherein said nucleic acid molecule is recognized by nuclear splicing components within the cell.
18 . The nucleic acid of claim 17 wherein the splice region comprises a 3′ splice region.
19 . The nucleic acid of claim 17 wherein the splice region comprises a 5′ splice region.
20 . The nucleic acid of claim 18 wherein the 3′ splice region comprises at least one of a branch point and a 3′ splice acceptor site.
21 . The nucleic acid of claim 18 wherein the 3′ splice region further comprises a pyrimidine tract.
22 . The nucleic acid of claim 18 wherein the nucleic acid molecule further comprises a safety nucleotide sequence comprising one or more complementary sequences that bind to one or more sides of the 3′ splice region
23 . The nucleic acid of claim 19 wherein said nucleic acid molecule further comprises a safety sequence comprising one or more complementary sequences that bind to one or both sides of the 5′ splice site.
24 . The nucleic acid of claim 19 wherein the nucleic acid molecule further comprises a 5′ donor site.
25 . A nucleic acid molecule comprising:
a) a splice region;
b) a spacer region that separates the splice region from the target binding domain; and
c) a nucleotide sequence to be trans-spliced to the target pre-mRNA wherein said nucleotide sequence encodes an antigen of interest;
wherein the nucleic acid molecule targets a pre-mRNA expressed within the cell, wherein the pre-mRNA encodes a protein involved in antigen uptake, presentation or chaperoning and wherein said nucleic acid molecule is recognized by nuclear splicing components within the cell.
26 . The nucleic acid of claim 25 wherein the splice region comprises a 3′ splice region.
27 . The nucleic acid of claim 25 wherein the splice region comprises a 5′ splice region.
28 . The nucleic acid of claim 26 wherein the 3′ splice region comprises at least one of a branch point and a 3′ splice acceptor site.
29 . The nucleic acid of claim 26 wherein the 3′ splice region further comprises a pyrimidine tract.
30 . The nucleic acid of claim 26 wherein the nucleic acid molecule further comprises a safety nucleotide sequence comprising one or more complementary sequences that bind to one or more sides of the 3′ splice region
31 . The nucleic acid of claim 27 wherein said nucleic acid molecule further comprises a safety sequence comprising one or more complementary sequences that bind to one or both sides of the 5′ splice site.
32 . The nucleic acid of claim 27 wherein the nucleic acid molecule further comprises a 5′ donor site.