Methods and compositions for engineering synthetic bioswitches for remote control of biological activity
Embodiments of the present disclosure relate generally to compositions and methods for the design of remote controlled biological systems, and more specifically to synthetic bioswitches that provide the ability to non-invasively and remotely control the function and activity of live cells, such as for example and not limitation, the expression of biologically active proteins or biological therapeutics, and the manipulation of physiologic or genetic processes and/or protein expression in live cells, in vivo (including, e.g., at desired anatomical sites) or ex vivo.
1 . A first nucleic acid molecule comprising:
a first synthetic bioswitch; and
a first heterologous nucleic acid;
wherein the first synthetic bioswitch is operably linked to the first heterologous nucleic acid and comprises a first control element that is regulated by a first stimulus; and
wherein the first synthetic bioswitch comprises the sequence of SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, or SEQ ID NO: 50.
2 . The first nucleic acid molecule of claim 1 , wherein the first synthetic bioswitch has no activity to normal basal activity in the absence of the first stimulus.
3 . The first nucleic acid molecule of claim 2 , wherein the first synthetic bioswitch has high activity in the presence of the first stimulus.
4 . The first nucleic acid molecule of claim 3 , wherein the first synthetic bioswitch has a strong induction or activation.
5 . The first nucleic acid molecule of claim 4 , wherein the first synthetic bioswitch has no activity to normal basal activity with a first orthogonal stimulus.
6 . The first nucleic acid molecule of claim 1 , wherein the first synthetic bioswitch further comprises a first spacer region between the first control element and the first heterologous nucleic acid.
7 . The first nucleic acid molecule of claim 6 , wherein the first spacer region comprises a first untranslated region.
8 . The first nucleic acid molecule of claim 7 , wherein the first untranslated region has a length between 1 to 500 nucleotides.
9 . The first nucleic acid molecule of claim 8 , wherein the first untranslated region comprises a first regulatory element.
10 . The first nucleic acid molecule of claim 9 , wherein the first regulatory element comprises a binding site for one or more of E2F, Ik-2, LXRalpha:RXRalpha, TBP, TBX5, AR, ELFI, Nkx3A, SPII, CDX-2, SOX10, Kid3, MAFB, IRF-7, RXR::RAR, UNR, and Mushashi.
11 . The first nucleic acid molecule of claim 6 , wherein the first spacer region comprises one or more of an upstream AUG, an upstream open reading frame (uORFs), and an internal ribosomal entry site (IRES).
12 . The first nucleic acid molecule of claim 1 , wherein the first heterologous nucleic acid comprises a gene that encodes a biologically active protein or biological therapeutic, or a nucleic acid that enables the manipulation of physiologic or genetic processes and/or protein expression in a live cell.
13 . The first nucleic acid molecule of claim 12 , wherein the first heterologous nucleic acid comprises a gene that encodes a genome editing or modifying protein; therapeutic antibody: Bi-specific T-cell engager; chimeric antigen receptor; transgenic T-cell receptor; transferase; differentiating factor; Yamanaka factor for induced pluripotency; transcription factor; structural protein; transposon; non-coding RNA; kinase; or transport protein.
14 . The first nucleic acid molecule of claim 1 , wherein the first heterologous nucleic acid comprises a gene that encodes a first chimeric antigen receptor.
15 . A vector comprising the first nucleic acid molecule of claim 1 .
16 . A cell comprising the first nucleic acid molecule of claim 1 .
17 . A compound synthetic bioswitch system comprising:
the first nucleic acid molecule of claim 1 ; and
a second nucleic acid molecule comprising:
a second synthetic bioswitch; and
a second heterologous nucleic acid;
wherein the second synthetic bioswitch is operably linked to the second heterologous nucleic acid and comprises a second control element that is regulated by a second stimulus.
18 . The compound synthetic bioswitch system of claim 17 , wherein either or both:
the combination of the first and second nucleic acid molecules enable differential regulation of the expression of the first heterologous nucleic acid in response to the first stimulus and the second stimulus; and
the combination of the first and second nucleic acid molecules enable differential regulation of the expression of the first heterologous nucleic acid and the second heterologous nucleic acid in response to the first stimulus and the second stimulus.
19 . The nucleic acid molecule of claim 1 , wherein the first synthetic bioswitch comprises the sequence of SEQ ID NO: 45.
20 . The nucleic acid molecule of claim 1 , wherein the first synthetic bioswitch comprises the sequence of SEQ ID NO: 46.
21 . The nucleic acid molecule of claim 1 , wherein the first synthetic bioswitch comprises the sequence of SEQ ID NO: 47.
22 . The nucleic acid molecule of claim 1 , wherein the first synthetic bioswitch comprises the sequence of SEQ ID NO: 48.
23 . The nucleic acid molecule of claim 1 , wherein the first synthetic bioswitch comprises the sequence of SEQ ID NO: 49.
24 . The nucleic acid molecule of claim 1 , wherein the first synthetic bioswitch comprises the sequence of SEQ ID NO: 50.
25 . The nucleic acid molecule of claim 1 , wherein the first synthetic bioswitch comprises two or more control elements and a first spacer region between the two or more control elements and the heterologous nucleic acid.
26 . The nucleic acid molecule of claim 25 , wherein the first spacer region comprises a 5′ untranslated region.
27 . The nucleic acid molecule of claim 26 , wherein the 5′ untranslated region comprises a regulatory element.
28 . The nucleic acid molecule of claim 27 , wherein the regulatory element comprises a binding site for one or more of E2F, Ik-2, LXRalpha: RXRalpha, TBP, TBX5, AR, ELFI, Nkx3A, SPII, CDX-2, SOXI0, Kid3, MAFB, IRF-7, RXR::RAR, UNR, and Mushashi.
29 . The nucleic acid molecule of claim 25 , wherein the first spacer region comprises one or more of an upstream AUG, an upstream open reading frame (uORF), and an internal ribosomal entry site (IRES).
30 . The nucleic acid molecule of claim 1 , wherein the bioswitch further comprises a TATA box.
31 . The nucleic acid molecule of claim 1 , wherein the first synthetic bioswitch further comprises a TATA box and a first spacer region between the first control element and the first heterologous nucleic acid comprising a first untranslated region, wherein the first synthetic bioswitch comprises the sequence of SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 36, or SEQ ID NO: 37.
32 . The nucleic acid molecule of claim 1 , wherein the heterologous nucleic acid encodes a protein or interfering nucleic acid.
33 . The nucleic acid molecule of claim 32 , wherein the protein is a chimeric antigen receptor, antibody, T cell receptor, cytokine, chemokine, gene editing protein, bispecific T cell engager, transferase, differentiating factor, Yamanaka factor for induced pluripotency, transcription factor, structural protein, kinase, or transport protein.
34 . The nucleic acid of claim 31 , wherein the first synthetic bioswitch further comprises a TATA box and a first spacer region between the first control element and the first heterologous nucleic acid comprising a first untranslated region, wherein the first synthetic bioswitch comprises the sequence of SEQ ID NO: 32.
35 . The nucleic acid of claim 31 , wherein the first synthetic bioswitch further comprises a TATA box and a first spacer region between the first control element and the first heterologous nucleic acid comprising a first untranslated region, wherein the first synthetic bioswitch comprises the sequence of SEQ ID NO: 33.
36 . The nucleic acid of claim 31 , wherein the first synthetic bioswitch further comprises a TATA box and a first spacer region between the first control element and the first heterologous nucleic acid comprising a first untranslated region, wherein the first synthetic bioswitch comprises the sequence of SEQ ID NO: 34.
37 . The nucleic acid of claim 31 , wherein the first synthetic bioswitch further comprises a TATA box and a first spacer region between the first control element and the first heterologous nucleic acid comprising a first untranslated region, wherein the first synthetic bioswitch comprises the sequence of SEQ ID NO: 35.
38 . The nucleic acid of claim 31 , wherein the first synthetic bioswitch further comprises a TATA box and a first spacer region between the first control element and the first heterologous nucleic acid comprising a first untranslated region, wherein the first synthetic bioswitch comprises the sequence of SEQ ID NO: 36.
39 . The nucleic acid of claim 31 , wherein the first synthetic bioswitch further comprises a TATA box and a first spacer region between the first control element and the first heterologous nucleic acid comprising a first untranslated region, wherein the first synthetic bioswitch comprises the sequence of SEQ ID NO: 37.
40 . The nucleic acid of claim 32 , wherein the protein is a CD19 chimeric antigen receptor.