WO2018161000A1 - Régulation de protéine modulable dhfr - Google Patents

Régulation de protéine modulable dhfr Download PDF

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WO2018161000A1
WO2018161000A1 PCT/US2018/020718 US2018020718W WO2018161000A1 WO 2018161000 A1 WO2018161000 A1 WO 2018161000A1 US 2018020718 W US2018020718 W US 2018020718W WO 2018161000 A1 WO2018161000 A1 WO 2018161000A1
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Prior art keywords
amino acid
hdhfr
seq
acid sequence
protein
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PCT/US2018/020718
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Vipin Suri
Dan Jun LI
Dexue Sun
Byron Delabarre
Vijaya BALAKRISHNAN
Brian DOLINSKI
Mara Christine INNISS
Grace Y. OLINGER
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Obsidian Therapeutics, Inc.
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Publication of WO2018161000A1 publication Critical patent/WO2018161000A1/fr
Priority to US16/558,224 priority Critical patent/US11629340B2/en
Priority to US17/646,212 priority patent/US20220213449A1/en

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    • C12N9/0004—Oxidoreductases (1.)
    • C12N9/0012—Oxidoreductases (1.) acting on nitrogen containing compounds as donors (1.4, 1.5, 1.6, 1.7)
    • C12N9/0026—Oxidoreductases (1.) acting on nitrogen containing compounds as donors (1.4, 1.5, 1.6, 1.7) acting on CH-NH groups of donors (1.5)
    • C12N9/0028—Oxidoreductases (1.) acting on nitrogen containing compounds as donors (1.4, 1.5, 1.6, 1.7) acting on CH-NH groups of donors (1.5) with NAD or NADP as acceptor (1.5.1)
    • C12N9/003—Dihydrofolate reductase [DHFR] (1.5.1.3)
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    • C07K14/52—Cytokines; Lymphokines; Interferons
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    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C07K14/715—Receptors; Cell surface antigens; Cell surface determinants for cytokines; for lymphokines; for interferons
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    • C12N9/14—Hydrolases (3)
    • C12N9/48—Hydrolases (3) acting on peptide bonds (3.4)
    • C12N9/50—Proteinases, e.g. Endopeptidases (3.4.21-3.4.25)
    • C12N9/64—Proteinases, e.g. Endopeptidases (3.4.21-3.4.25) derived from animal tissue
    • C12N9/6421—Proteinases, e.g. Endopeptidases (3.4.21-3.4.25) derived from animal tissue from mammals
    • C12N9/6472—Cysteine endopeptidases (3.4.22)
    • C12N9/6475—Interleukin 1-beta convertase-like enzymes (3.4.22.10; 3.4.22.36; 3.4.22.63)
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    • C12Y105/01—Oxidoreductases acting on the CH-NH group of donors (1.5) with NAD+ or NADP+ as acceptor (1.5.1)
    • C12Y105/01003—Dihydrofolate reductase (1.5.1.3)
    • A—HUMAN NECESSITIES
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    • C07K2319/00—Fusion polypeptide
    • C07K2319/01—Fusion polypeptide containing a localisation/targetting motif
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    • C12N2740/10011—Retroviridae
    • C12N2740/16011—Human Immunodeficiency Virus, HIV
    • C12N2740/16041—Use of virus, viral particle or viral elements as a vector
    • C12N2740/16043—Use of virus, viral particle or viral elements as a vector viral genome or elements thereof as genetic vector
    • G—PHYSICS
    • G01—MEASURING; TESTING
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    • G01N2333/90—Enzymes; Proenzymes
    • G01N2333/902—Oxidoreductases (1.)

Definitions

  • the present invention relates to regulatable tunable biocircuit systems for the development of controlled and/or regulated therapeutic systems.
  • regulatable biocircuits containing destabilizing domains (DD) derived from human dihydrofolate reductase protein (hDHFR) are disclosed.
  • DDs Destabilizing Domains
  • Destabilizing domains are small protein domains that can be appended to a target protein of interest. DDs render the attached protein of interest unstable in the absence of a DD-binding ligand such that the protein is rapidly degraded by the ubiquitin-proteasome system of the cell (Stankunas, K., et al., (2003). Mo/. Cell 12, 1615-1624; Banaszynski. L.A., et al., (2006) Cell; 126(5): 995-1004; reviewed in Banaszynski, L.A., and Wandless, T.J. (2006) Chem. Biol.
  • biocircuits including those containing DDs can form the basis of a new class of cell and gene therapies that employ tunable and temporal control of gene expression and function.
  • novel moieties are described by the present inventors as stimulus response elements (SREs) which act in the context of an effector module to complete a biocircuit arising from a stimulus and ultimately producing a signal or outcome.
  • SREs stimulus response elements
  • biocircuit systems can be used to regulate transgene and/or protein levels either up or down by perpetuating a stabilizing signal or destabilizing signal. This approach has many advantages over existing methods of regulating protein function and/or expression, which are currently focused on top level transcriptional regulation via inducible promoters.
  • the present invention provides novel protein domains, in particular destabilizing domains (DDs) derived from human dihydrofolate reductase (hDHFR) that display small molecule dependent stability, and the biocircuit systems and effector modules comprising such DDs. Methods fortuning transgene functions using the same are also provided.
  • DDs destabilizing domains
  • hDHFR human dihydrofolate reductase
  • the present invention provides novel protein domains displaying small molecule dependent stability.
  • Such protein domains are called destabilizing domains (DDs).
  • the DD is destabilizing and causes degradation of a payload fused to the DD (e.g., a protein of interest (POI), while in the presence of its binding ligand, the fused DD and payload can be stabilized, and its stability is dose dependent.
  • POI protein of interest
  • the present invention provides biocircuit systems, effector modules and compositions comprising the DDs of the present invention.
  • the biocircuit system is a DD biocircuit system.
  • the present invention provides biocircuit systems which may comprise an effector module.
  • the effector module may comprise a stimulus response element (SRE) and at least one payload.
  • the payload of the effector module may comprise a protein of interest which is attached, appended or associated with the SRE.
  • the SRE comprises a destabilizing domain.
  • the destabilizing domain may comprise in whole or in part, a protein such as, but not limited to human dihydrofolate reductase (hDHFR), a hDHFR mutant and a DHFR variant.
  • the DD may comprise, in whole or in part, a hDHFR mutant.
  • the effector module of the biocircuit may be responsive to one or more stimuli.
  • the DHFR mutant may comprise one, two or three mutations relative to SEQ ID NO. 1.
  • the DHFR mutant may have mutations such as, but not limited to, Mldel, V2A, C7R, I8V, V9A, A10T, A10V, Q13R, N14S, G16S, I17N, I17V, K19E, N20D, G21T, G21E, D22S, L23S, P24S, L28P, N30D, N30H, N30S, E31G, E31D, F32M, R33G, R33S, F35L, Q36R, Q36S, Q36K, Q36F, R37G, M38V, M38T, T40A, V44A, K47R, N49S, N49D, M53T, G54R, K56E, K56R, T57A, F59S, I61T, K64R, N65A, N65S, N65D
  • the DHFR mutant may comprise one or more mutations in an amino acid at the mutation site being identical to one or more vicinal amino acids.
  • the vicinal amino acid may be selected from, but not limited to one, two, three, four, and five amino acids, upstream or downstream from the mutation.
  • the DHFR mutant may be selected from, but not limited to hDHFR (A107V), comprising the amino acid sequence of SEQ ID NO. 48; hDHFR (F59S), comprising the amino acid sequence of SEQ ID NO. 44; hDHFR (117V), comprising the amino acid sequence of SEQ ID NO. 45; hDHFR (K185E), comprising the amino acid sequence of SEQ ID NO. 51; hDHFR (K81R), comprising the amino acid sequence of SEQ ID NO. 42; hDHFR (M140I), comprising the amino acid sequence of SEQ ID NO. 62; hDHFR (N127Y), comprising the amino acid sequence of SEQ ID NO.
  • hDHFR N 186D
  • hDHFR N65D
  • hDHFR N65D
  • hDHFR Y122I
  • Y122I amino acid sequence of SEQ ID NO. 16
  • hDHFR A10V, H88Y
  • hDHFR Amino acid 2-187 of WT
  • Y122I comprising the amino acid sequence of SEQ ID NO. 112
  • hDHFR C7R, Y163C
  • hDHFR E162G, I176F
  • hDHFR (G21T, Y122I), comprising the amino acid sequence of SEQ ID NO. 22; hDHFR (H131R, E144G), comprising the amino acid sequence of SEQ ID NO. 63; hDHFR (117V, Y122I), comprising the amino acid sequence of SEQ ID NO. 398; hDHFR (L74N, Y122I), comprising the amino acid sequence of SEQ ID NO. 20; hDHFR (L94A, T147A), comprising the amino acid sequence of SEQ ID NO. 21; hDHFR (M53T, R1381), comprising the amino acid sequence of SEQ ID NO.
  • hDHFR N127Y, Y122I
  • hDHFR Q36K, Y122I
  • hDHFR T137R, F143L
  • hDHFR T57A, 172A
  • hDHFR V 121 A, Y122I
  • hDHFR V75F, Y122I
  • hDHFR (Y 1221, A125F), comprising the amino acid sequence of SEQ ID NO. 19; hDHFR (Y122I, M140I), comprising the amino acid sequence of SEQ ID NO. 400; hDHFR (Y178H, E181G), comprising the amino acid sequence of SEQ ID NO. 60; hDHFR (Y183H, K185E), comprising the amino acid sequence of SEQ ID NO. 65; hDHFR (Amino acid 2-187 of WT) (G21T, Y122I), comprising the amino acid sequence of SEQ ID NO. 392; hDHFR (Amino acid 2-187 of WT) (I17V, Y122I), comprising the amino acid sequence of SEQ ID NO.
  • hDHFR (Amino acid 2-187 of WT) (L74N, Y122I), comprising the amino acid sequence of SEQ ID NO. 155; hDHFR (Amino acid 2-187 of WT) (L94A, T147A), comprising the amino acid sequence of SEQ ID NO. 158; hDHFR (Amino acid 2-187 of WT) (M53T, R138I), comprising the amino acid sequence of SEQ ID NO. 151; hDHFR (Amino acid 2-187 of WT) (N127Y, Y122I), comprising the amino acid sequence of SEQ ID NO.
  • hDHFR (Amino acid 2-187 of WT) (Q36K, Y122I), comprising the amino acid sequence of SEQ ID NO. 114; hDHFR (Amino acid 2-187 of WT) (V121A, Y122I), comprising the amino acid sequence of SEQ ID NO. 394; hDHFR (Amino acid 2-187 of WT) (V75F, Y122I), comprising the amino acid sequence of SEQ ID NO. 153; hDHFR (Amino acid 2-187 of WT) (Y122I, A125F), comprising the amino acid sequence of SEQ ID NO.
  • hDHFR Amino acid 2-187 of WT
  • Y122I, M140I comprising the amino acid sequence of SEQ ID NO. 333
  • hDHFR E31D, F32M, VI 161
  • hDHFR G21E, I72V, I176T
  • hDHFR I8V, K133E, Y163C
  • hDHFR K19E, F89L, E181G
  • hDHFR L23S, V121A, Y157C
  • hDHFR N49D, F59S, D153G
  • hDHFR Q36F, N65F, Y122I
  • hDHFR Q36F, Y122I, A125F
  • hDHFR VI 10A, V136M, K177R
  • hDHFR (V9A, S93R, P150L), comprising the amino acid sequence of SEQ ID NO. 43; hDHFR (Yl 221, H131R, E144G), comprising the amino acid sequence of SEQ ID NO. 404; hDHFR (G54R, II 15L, M140V, S168C), comprising the amino acid sequence of SEQ ID NO. 56; hDHFR (Amino acid 2-187 of WT) (E31D, F32M, V116I), comprising the amino acid sequence of SEQ ID NO. 341; hDHFR (Amino acid 2-187 of WT) (Q36F, N65F, Y122I), comprising the amino acid sequence of SEQ ID NO.
  • hDHFR (Amino acid 2-187 of WT) (Q36F, Y122I, A125F), comprising the amino acid sequence of SEQ ID NO. 26; hDHFR (Amino acid 2-187 of WT) (Y122I, H131R, E144G), comprising the amino acid sequence of SEQ ID NO. 337; hDHFR (V2A, R33G, Q36R, L100P, K185R), comprising the amino acid sequence of SEQ ID NO. 285; hDHFR(D22S, F32M, R33S, Q36S, N65S), comprising the amino acid sequence of SEQ ID NO.
  • hDHFR Amino acid 2- 187 of WT
  • D22S, F32M, R33S, Q36S, N65S comprising the amino acid sequence of SEQ ID NO. 339
  • hDHFR I17N, L98S, K99R, Ml 12T, E151G, E162G, E172G
  • hDHFR G16S, I17V, F89L, D96G, K123E, M140V, D146G, K156R
  • hDHFR K81R, K99R, LI OOP, E102G, N108D, K123R, H128R, D142G, F180L, K185E), comprising the amino acid sequence of SEQ ID NO. 290; hDHFR (R138G, D142G, F143S, K156R, K158E, E162G, V166A, K177E, Y178C, K185E, N186S), comprising the amino acid sequence of SEQ ID NO.
  • hDHFR (NHS, P24S, F35L, M53T, K56E, R92G, S93G, N127S, H128Y, F135L, F143S, L159P, L160P, E173A, F180L), comprising the amino acid sequence of SEQ ID NO. 291;
  • hDHFR (F35L, R37G, N65A, L68S, 69E, R71G, L80P, K99G, Gl 17D, L132P, I139V, M140I, D142G, D146G, E173G, D187G), comprising the amino acid sequence of SEQ ID NO. 287; hDHFR (L28P, N30H, M38V, V44A, L68S, N73G, R78G, A97T, K99R, A107T, K109R, Dl 1 IN, L134P, F135V, T147A, I152V, K158R, E172G, V182A, E184R), comprising the amino acid sequence of SEQ ID NO.
  • hDHFR (V2A, I17V, N30D, E31G, Q36R, F59S, K69E, I72T, H88Y, F89L, N108D, K109E, V110A, II 15V, Y122D, L132P, F135S, M140V, E144G, T147A, Y157C, V170A, K174R, N186S), comprising the amino acid sequence of SEQ ID NO.
  • hDHFR L100P, E102G, Q103R, P104S, E105G, N108D, V113A, W114R, Y122C, M126I, N127R, H128Y, L132P, F135P, I139T, F148S, F149L, I152V, D153A, D169G, V170A, I176A, K177R, V182A, K185R, N186S), comprising the amino acid sequence of SEQ ID NO.
  • hDHFR (A10T, Q13R, N14S, N20D, P24S, N30S, M38T, T40A, K47R, N49S, K56R, I61T, K64R, K69R, I72A, R78G, E82G, F89L, D96G, N108D, Ml 12V, Wl 14R, Yl 22D, K123E, I139V, Q141R, D142G, F148L, E151G, E155G, Y157R, Q171R, Y183C, E184G, K185del, D187N), comprising the amino acid sequence of SEQ ID NO. 294.
  • the hDHFR mutant may be encoded by a nucleic acid sequence independently selected from, but not limited to, SEQ ID NOs. 27-41, 152, 154, 157, 295-330, 332, 334, 336, 338, 340, 342, 391, 393, 395, 397, 399, 401, 403, 405, 407, or 409.
  • the stimulus of biocircuit system may be Trimethoprim or Methotrexate.
  • the hDHFR mutant may comprise one or more mutations in a region that interacts directly with the stimulus.
  • the effector module may comprise a hDHFR-derived SRE operably linked to a payload.
  • the hDHFR- derived SRE may be a hDHFR mutant that may comprise one, two, three or more mutations selected from, but not limited to, Mldel, V2A, C7R, I8V, V9A, A10T, A10V, Q13R, NHS, G16S, I17N, I17V, K19E, N20D, G21T, G21E, D22S, L23S, P24S, L28P, N30D, N30H, N30S, E31G, E31D, F32M, R33G, R33S, F35L, Q36R, Q36S, Q36K, Q36F, R37G, M38V, M38T, T40A, V44A, K47R, N49S, N49D, M53T, G54R, K56E, K56R
  • the effector module may comprise a hDHFR-derived SRE selected from, but not limited to hDHFR (A 107V), comprising the amino acid sequence of SEQ ID NO. 48; hDHFR (F59S), comprising the amino acid sequence of SEQ ID NO. 44; hDHFR (I17V), comprising the amino acid sequence of SEQ ID NO. 45; hDHFR (K185E), comprising the amino acid sequence of SEQ ID NO. 51; hDHFR (K81R), comprising the amino acid sequence of SEQ ID NO. 42; hDHFR (M140I), comprising the amino acid sequence of SEQ ID NO. 62; hDHFR (N127Y), comprising the amino acid sequence of SEQ ID NO.
  • a 107V comprising the amino acid sequence of SEQ ID NO. 48
  • hDHFR (F59S) comprising the amino acid sequence of SEQ ID NO. 44
  • hDHFR (I17V) comprising the amino acid sequence of SEQ ID NO. 45
  • hDHFR (N186D), comprising the amino acid sequence of SEQ ID NO. 55; hDHFR (N65D), comprising the amino acid sequence of SEQ ID NO. 46; hDHFR (Y122I), comprising the amino acid sequence of SEQ ID NO. 16; hDHFR (A10V, H88Y), comprising the amino acid sequence of SEQ ID NO. 47;
  • hDHFR (Amino acid 2-187 of WT) (Y122I), comprising the amino acid sequence of SEQ ID NO. 112; hDHFR (C7R, Y163C), comprising the amino acid sequence of SEQ ID NO. 49; hDHFR (E162G, I176F), comprising the amino acid sequence of SEQ ID NO. 59; hDHFR (G21T, Y122I), comprising the amino acid sequence of SEQ ID NO. 22; hDHFR (H131R, E144G), comprising the amino acid sequence of SEQ ID NO. 63; hDHFR (I17V, Y122I), comprising the amino acid sequence of SEQ ID NO.
  • hDHFR (L74N, Y122I), comprising the amino acid sequence of SEQ ID NO. 20; hDHFR (L94A, T147A), comprising the amino acid sequence of SEQ ID NO. 21; hDHFR (M53T, R138I), comprising the amino acid sequence of SEQ ID NO. 17; hDHFR (N127Y, Y122I), comprising the amino acid sequence of SEQ ID NO. 402; hDHFR (Q36K, Y122I), comprising the amino acid sequence of SEQ ID NO. 24; hDHFR (T137R, F143L), comprising the amino acid sequence of SEQ ID NO.
  • hDHFR T57A, I72A
  • hDHFR T57A, I72A
  • hDHFR V121A, Y122I
  • hDHFR V75F, Y122I
  • hDHFR Y122I, A125F
  • hDHFR Y 1221, M 1401
  • hDHFR Yl 78H, E181G
  • hDHFR (Y183H, K185E), comprising the amino acid sequence of SEQ ID NO. 65; hDHFR (Amino acid 2-187 of WT) (G21T, Y122I), comprising the amino acid sequence of SEQ ID NO. 392; hDHFR (Amino acid 2-187 of WT) (I17V, Y122I), comprising the amino acid sequence of SEQ ID NO. 331; hDHFR (Amino acid 2-187 of WT) (L74N, Y122I), comprising the amino acid sequence of SEQ ID NO. 155; hDHFR (Amino acid 2-187 of WT) (L94A, T147A), comprising the amino acid sequence of SEQ ID NO.
  • hDHFR (Amino acid 2-187 of WT) (M53T, R138I), comprising the amino acid sequence of SEQ ID NO. 151; hDHFR (Amino acid 2-187 of WT) (N127Y, Y122I), comprising the amino acid sequence of SEQ ID NO. 335; hDHFR (Amino acid 2-187 of WT) (Q36K, Y122I), comprising the amino acid sequence of SEQ ID NO. 114; hDHFR (Amino acid 2-187 of WT) (V121A, Y122I), comprising the amino acid sequence of SEQ ID NO.
  • hDHFR (Amino acid 2-187 of WT) (V75F, Y122I), comprising the amino acid sequence of SEQ ID NO. 153; hDHFR (Amino acid 2-187 of WT) (Y122I, A125F), comprising the amino acid sequence of SEQ ID NO. 113; hDHFR (Amino acid 2-187 of WT) (Y122I, M140I), comprising the amino acid sequence of SEQ ID NO. 333; hDHFR (E3 ID, F32M, VI 161), comprising the amino acid sequence of SEQ ID NO. 408;
  • hDHFR (G21E, I72V, I176T), comprising the amino acid sequence of SEQ ID NO. 66; hDHFR (I8V, K133E, Y163C), comprising the amino acid sequence of SEQ ID NO. 53; hDHFR (K19E, F89L, E181G), comprising the amino acid sequence of SEQ ID NO. 54; hDHFR (L23S, V121A, Y157C), comprising the amino acid sequence of SEQ ID NO. 57; hDHFR (N49D, F59S, D153G), comprising the amino acid sequence of SEQ ID NO.
  • hDHFR (Q36F, N65F, Y122I), comprising the amino acid sequence of SEQ ID NO. 25; hDHFR (Q36F, Y122I, A125F), comprising the amino acid sequence of SEQ ID NO. 396; hDHFR (VI 10A, V136M, K177R), comprising the amino acid sequence of SEQ ID NO. 58; hDHFR (V9A, S93R, P150L), comprising the amino acid sequence of SEQ ID NO. 43; hDHFR (Y122I, H131R, E144G), comprising the amino acid sequence of SEQ ID NO.
  • hDHFR (G54R, II 15L, M140V, S168C), comprising the amino acid sequence of SEQ ID NO. 56; hDHFR (Amino acid 2-187 of WT) (E31D, F32M, VI 161), comprising the amino acid sequence of SEQ ID NO. 341; hDHFR (Amino acid 2-187 of WT) (Q36F, N65F, Y122I), comprising the amino acid sequence of SEQ ID NO. 115; hDHFR (Amino acid 2-187 of WT) (Q36F, Y1221, A125F), comprising the amino acid sequence of SEQ ID NO.
  • hDHFR (Amino acid 2-187 of WT) (Y122I, H131R, E144G), comprising the amino acid sequence of SEQ ID NO. 337; hDHFR (V2A, R33G, Q36R, L100P, K185R), comprising the amino acid sequence of SEQ ID NO. 285; hDHFR(D22S, F32M, R33S, Q36S, N65S), comprising the amino acid sequence of SEQ ID NO. 406; hDHFR (Amino acid 2- 187 of WT) (D22S, F32M, R33S, Q36S, N65S), comprising the amino acid sequence of SEQ ID NO.
  • hDHFR (I17N, L98S, K99R, M112T, E151G, E162G, E172G), comprising the amino acid sequence of SEQ ID NO. 288; hDHFR (G16S, I17V, F89L, D96G, K123E, M140V, D146G, K156R), comprising the amino acid sequence of SEQ ID NO. 286; hDHFR (K81R, K99R, L100P, E102G, N108D, K123R, H128R, D142G, F180L, K185E), comprising the amino acid sequence of SEQ ID NO.
  • hDHFR (R138G, D142G, F143S, K156R, K158E, E162G, V166A, K177E, Y178C, K185E, N186S), comprising the amino acid sequence of SEQ ID NO. 289; hDHFR (NHS, P24S, F35L, M53T, K56E, R92G, S93G, N127S, H128Y, F135L, F143S, L159P, L160P, E173A, F180L), comprising the amino acid sequence of SEQ ID NO. 291;
  • hDHFR (F35L, R37G, N65A, L68S, K69E, R71G, L80P, K99G, Gl 17D, L132P, I139V, M140I, D142G, D146G, E173G, D187G), comprising the amino acid sequence of SEQ ID NO. 287; hDHFR (L28P, N30H, M38V, V44A, L68S, N73G, R78G, A97T, K99R, A107T, K109R, Dl 1 IN, L134P, F135V, T147A, I152V, K158R, E172G, V182A, E184R), comprising the amino acid sequence of SEQ ID NO.
  • hDHFR V2A, I17V, N30D, E31G, Q36R, F59S, K69E, I72T, H88Y, F89L, N108D, K109E, VI 10A, I115V, II 15L, Y122D, L132P, F135S, M140V, E144G, T147A, Y157C, V170A, K174R, N186S), comprising the amino acid sequence of SEQ ID NO.
  • hDHFR L100P, E102G, Q103R, P104S, E105G, N108D, VI 13A, W114R, Y122C, M126I, N127R, H128Y, L132P, F135P, I139T, F148S, F149L, I152V, D153A, D169G, V170A, I176A, K177R, V182A, K185R, N186S), comprising the amino acid sequence of SEQ ID NO.
  • hDHFR (A10T, Q13R, NHS, N20D, P24S, N30S, M38T, T40A, K47R, N49S, K56R, I61T, K64R, K69R, I72A, R78G, E82G, F89L, D96G, N108D, Ml 12V, Wl 14R, Y122D, K123E, I139V, Q141R, D142G, F148L, E151G, E155G, Y157R, Q171R, Y183C, E184G, K18Sdel, D187N), comprising the amino acid sequence of SEQ ID NO. 294.
  • the payload of the effector module may be selected from, but not limited to, a natural protein, a variant thereof, a fusion polypeptide, an antibody or a fragment thereof, a therapeutic agent or a gene therapy agent.
  • the effector module may further comprise a protein cleavage site.
  • the protein cleavage site may be a furin cleavage site or a modified furin cleavage site.
  • the hDHFR-derived SRE of the effector module may exhibit both a destabilization ratio between 0 and 0.09 and a destabilizing mutation co-efficient between 0.09.
  • the destabilization ratio may comprise the ratio of expression, function or level of the payload in the absence of the stimulus specific to the hDHFR-derived SRE to the expression, function or level of the payload that is expressed constitutively in the absence of the same stimulus.
  • the destabilizing mutation co-efficient may comprise the ratio of expression, function or level of the payload when operably linked to the hDHFR-derived SRE, in the absence of the stimulus specific to the hDHFR-derived SRE; to the expression, function or level of the payload when operably linked to the wildtype protein from which the hDHFR-derived SRE is derived and in the absence of the same stimulus.
  • the hDHFR-derived SRE of the effector module may stabilize the payload by a stabilization ratio of 1 or more.
  • the stabilization ratio may be the ratio of expression, function or level of the payload in the presence of the stimulus to the expression, function or level of the payload in the absence of the stimulus.
  • the payload of the effector module may be a protein of interest.
  • the present invention also provides vectors which may comprise a nucleic acid independently selected from, but not limited to any of the sequences selected from SEQ ID NOs. 13-15, 87-106, 159-162, 178-180, 226, 227, 273, 275, 346, 347, 354-356, 383-386, 388, or 419- 424.
  • the vector may be a viral vector.
  • the viral vector may be retroviral vector, a lentiviral vector, a rAAV vector, or an oncolytic viral vector.
  • the present invention also provides methods of tuning the expression level and/ or activity of a protein of interest.
  • the method of tuning described herein may comprise appending or attaching a protein of interest to a hDHFR mutant.
  • the hDHFR mutant may comprise one, two, three or more mutations selected from Mldel, V2A, C7R, 18V, V9A, A10T, A10V, Q13R, NHS, G16S, I17N, I17V, K19E, N20D, G21T, G21E, D22S, L23S, P24S, L28P, N30D, N30H, N30S, E31G, E31D, F32M, R33G, R33S, F35L, Q36R, Q36S, Q36K, Q36F, R37G, M38V, M38T, T40A, V44A, K47R, N49S, N49D, M53T, G54R, K56E, K56
  • the DDs of the present invention may be stabilized by ligands such as Trimethoprim and Methotrexate.
  • the effector module of the present invention is a fusion construct comprising a DD of the invention operably linked to a payload.
  • the payload may be any natural protein of interest (POT) or variants thereof, an antibody or fragments thereof, a therapeutic agent, or any artificial peptide or polypeptide.
  • the biocircuit system of the present invention comprising a stimulus and an effector module of the invention.
  • the DD of the effector module binds to the stimulus and regulates the stability of the linked payload.
  • the DD may destabilize the protein of interest by a destabilization ratio between 0, and 0.09, wherein the destabilization ratio comprises the ratio of expression, function or level of a protein of interest in the absence of the stimulus specific to the DD to the expression, function or level of the protein of interest that is expressed constitutively, and in the absence of the stimulus specific to the DD.
  • the DD may stabilize the protein of interest by a stabilization ratio of 1 or more, wherein the stabilization ratio comprises the ratio of expression, function or level of a protein of interest in the presence of the stimulus to the expression, function or level of the protein of interest in the absence of the stimulus.
  • the biocircuit system of the present invention comprising a stimulus and an effector module of the invention.
  • the DD of the effector module binds to the stimulus and regulates the stability of the linked payload.
  • polynucleotides encoding destabilizing domains, effector modules and biocircuit systems are provided.
  • the polynucleotides of the invention may be codon optimized.
  • Vectors comprising polynucleotides of the invention are also provided.
  • the vector may be a non-viral vector, or a viral vector.
  • FIG. 1 shows an overview diagram of a biocircuit system of the invention.
  • the biocircuit comprises a stimulus and at least one effector module responsive to a stimulus, where the response to the stimulus produces a signal or outcome.
  • the effector module comprises at least one stimulus response element (SRE) and one payload.
  • SRE stimulus response element
  • Figure 2 shows representative effector modules carrying one payload.
  • the signal sequence (SS), SRE and payload may be located or positioned in various arrangements without (A to F) or with (G to Z, and AA to DD) a cleavage site.
  • An optional linker may be inserted between each component of the effector module.
  • Figure 3 shows representative effector modules carrying two payloads without a cleavage site.
  • the two payloads may be either directly linked to each other or separated.
  • Figure 4 shows representative effector modules carrying two payloads with a cleavage site.
  • an SS is positioned at the N-terminus of the construct, while other components: SRE, two payloads and the cleavage site may be located at different positions (A to L).
  • the cleavage site is positioned at the N-terminus of the construct (M to X).
  • An optional linker may be inserted between each component of the effector module.
  • Figure 5 shows effector modules of the invention carrying two payloads, where an SRE is positioned at the N-terminus of the construct (A to L), while SS, two payloads and the cleavage site can be in any configuration.
  • An optional linker may be inserted between each component of the effector module.
  • Figure 6 shows effector modules of the invention carrying two payloads, where either the two payloads (A to F) or one of the two payloads (G to X) is positioned at the N-temiinus of the construct (A to L), while SS, SRE and the cleavage site can be in any configuration.
  • An optional linker may be inserted between each component of the effector module.
  • Figure 7A, Figure 7B, and Figure 7C show hDHFR mutants' expression in a western blot using Anti-AcGFP antibody.
  • Figure 7D, Figure 7E, and Figure 7F show hDHFR mutants' expression in a western blot using anti-human DHFR antibody.
  • Figure 8A shows GFP intensity of hDHFR mutants in the absence of ligand as measured by FACS.
  • Figure 8B shows GFP intensity' of hDHFR mutants in the presence of ligand as measured by FACS.
  • Figure 9A shows MTX titration with hDHFR mutant as measured by FACS.
  • Figure 9B shows T P titration with hDHFR mutant as measured by FACS.
  • Figure 10 shows responsiveness of hDHFR mutants to ligand withdrawal as measured by FACS.
  • Figure 11 shows hDHFR-IL15/IL15Ra fusion protein expression in a western blot using anti IL15 and anti hDHFR antibodies.
  • Figure 12A and Figure 12B show the sequence alignment of wildtype DHFR (SEQ ID NO. 432) with hDHFR mutants (SEQ ID NO. 433).
  • Figure 13 shows the expression of ILl 5 IL15Ra fusion protein expression in a western blot using anti IL15 Ra antibody.
  • Figure 14A shows the expression of CD19 chimeric antigen receptors in a western blot using CD3 Zeta antibody.
  • Figure 14B shows the expression of CD19 chimeric antigen receptors in a western blot using 4- IBB antibody.
  • Figure 15A shows the expression of DHFR mutants with increasing concentrations Trimethoprim in a western blot using GFP antibody.
  • Figure 15B shows the expression of DHFR mutants with increasing concentrations Methotrexate in a western blot using GFP antibody.
  • the ability to conditionally control protein levels is a powerful tool in gene and cell therapy. Techniques to control protein expression on a genetic level have been widely studied.
  • the Cre-Lox technology provides a useful approach to activate or inactivate genes. Tissue or cell specific promoters can be used to control spatial and temporal expression of genes of interest. However, this system is limited in application due to the irreversible nature of the perturbation.
  • the transcription of the gene of interest can be conditionally regulated using tools such as Doxycycline (Dox)-inducible system.
  • Dox Doxycycline
  • the stability of mRNA can be regulated using RNA interference techniques. However, methods targeting DNA or RNA are slow acting, irreversible and have low efficiency.
  • rapamycin derivative for the regulation of GSK-3 kinase fused to an unstable triple-mutant of the FRB domain (FRB*) were developed.
  • the rapamycin derivative induces dimerization of the FRB*-GSK-3p and endogenous FKBP12 and stabilizes the FRB* fusion thus restoring the function of the fused kinase.
  • Banaszynski, et al. developed a cell-permeable ligand system using mutants of FKBP12 protein which were engineered to be unstable in the absence of a high-affinity ligand, Shield-1. (Banaszynski et al., Cell. 2006; 126:995-1004). They termed these unstable domains, destabilizing domains (DDs).
  • DDs destabilizing domains
  • the FKBP DD-shield system has been used in cell lines, transgenic mice, protozoan Entamoeba histolytica, the flatworm Caenorhabditis elegans, the medaka, and transgenic xenografts to investigate the activity of a protein of interest (Maynard-Smrth et al, J Biol Chem. 2007, 282(34): 24866-24872; Liu et al, Int J Parasitol. 2014, 44(10):729-735; Cho et al, PLoS One. 2013, 8(8): e72393); Banaszynski et al. Nat Med.
  • the destabilizing domain has been used for the conditional knock down/ knock out of the target gene fused with the destabilizing domain.
  • Park et al achieved this genomic engineering by CRISPR/Cas9-mediated homologous recombination and a donor template coding for a resistance cassette and the DD-tagged TCOF1 sequence (Park et al, PLoS One. 2014, 9(4): e95101).
  • Shield- 1 is a novel drug whose
  • DD ligand pairs include estrogen receptor domains which can be regulated by several estrogen receptor antagonists (Miyazaki et al, J Am Chem. Soc, 2012, 134(9): 3942- 3945), and fluorescent destabilizing domain (FDD) derived from bilirubin-inducible fluorescent protein, UnaG.
  • FDD fluorescent destabilizing domain
  • a FDD and its cognate ligand bilirubin (BR) can induce degradation of a protein fused to the FDD (Navarro et al, ACS Chem Biol, 2016, June 6, Epub).
  • Other known DDs and their applications in protein stability include those described in U.S. Pat. NO. 8,173,792 and U.S. Pat. NO.
  • TMP is commercially available and has desirable pharmacological properties making this protein-ligand pair ideal for development for use as abiocircuit (Iwamoto, et al., Chem Biol. (2010) September 24; 17(9): 981-988).
  • the present invention expands upon the technology of tuning protein stability using novel destabilizing domains derived from hDHFR.
  • the destabilization and stabilization of a protein of interest e.g., a transgene for gene therapy
  • Methotrexate specifically binding to such protein domains.
  • the presence and/or absence of a small molecule ligand can tune the activity of a protein of interest that is genetically fused to the destabilizing domain.
  • DDs destabilizing domains
  • POI protein of interest
  • novel destabilizing domains derived from human DHFR (Dihydrofolate reductase) protein including single mutation: hDHFR (Y122I), hDHFR (K81R), hDHFR (F59S), hDHFR (I17V), hDHFR (N65D), hDHFR (A107V), hDHFR (N127Y), hDHFR (K185E), hDHFR (N186D), and hDHFR (M140I); double mutations: hDHFR (M53T, R138I), hDHFR (V75F, Y122I), hDHFR (A125F, Y122I), hDHFR (L74N, Y122I), hDHFR (L94A, T147A), hDHFR (G21T, Y122I), hDHFR (V121A, Y122I), hDHFR (Q36K, Y122I), hDHFR (C
  • biocircuit systems which comprise, at their core, at least one effector module system.
  • Such effector module systems comprise at least one effector module having associated, or integral therewith, one or more stimulus response elements (SREs).
  • SREs stimulus response elements
  • FIG. 1 The overall architecture of a biocircuit system of the invention is illustrated in Figure 1.
  • biocircuit systems and effector modules comprising the novel destabilizing domains discussed herein are provided.
  • the SRE is hDHFR- derived SRE.
  • the effector module described herein may be a hDHFR- derived SRE operably linked to a payload.
  • a '3 ⁇ 4iocircuit or “biocircuit system” is defined as a circuit within or useful in biologic systems comprising a stimulus and at least one effector module responsive to a stimulus, where the response to the stimulus produces at least one signal or outcome within, between, as an indicator of, or on a biologic system.
  • Biologic systems are generally understood to be any cell, tissue, organ, organ system or organism, whether animal, plant, fungi, bacterial, or viral.
  • biocircuits may be artificial circuits which employ the stimuli or effector modules taught by the present invention and effect signals or outcomes in acellular environments such as with diagnostic, reporter systems, devices, assays or kits.
  • the artificial circuits may be associated with one or more electronic, magnetic, or radioactive components or parts.
  • the biocircuit system is a DD biocircuit system.
  • an "effector module” is a single or multi-component construct or complex comprising at least (a) one or more stimulus response elements (SREs) and (b) one or more payloads (i.e. proteins of interest (POIs).
  • SREs stimulus response elements
  • POIs proteins of interest
  • the SRE is a DD.
  • Payload or “target payload” is defined as any protein or nucleic acid whose function is to be altered. Payloads may include any coding or non-coding gene or any protein or fragment thereof, or fusion constructs, or antibodies.
  • Payloads are often associated with one or more SREs (e.g., DDs) and may be encoded alone or in combination with one or more DD in a polynucleotide of the invention. Payloads themselves may be altered (at the protein or nucleic acid level) thereby providing for an added layer of tenability of the effector module. For example, payloads may be engineered or designed to contain mutations, single or multiple, which affect the stability of the payload or its susceptibility to degradation, cleavage or trafficking.
  • a DD which can have a spectrum of responses to a stimulus with a payload which is altered to exhibit a variety of responses or gradations of output signals, e.g., expression levels, produce biocircuits which are superior to those in the art.
  • mutations or substitutional designs such as those created for IL12 in WO2016048903 (specifically in Example 1 therein), the contents of which are incorporated herein by reference in their entirety, may be used in any protein payload in conjunction with a DD of the present invention to create dual tunable biocircuits.
  • the ability to independently tune both the DD and the payload greatly increases the scope of uses of the effector modules of the present invention.
  • Effector modules may be designed to include one or more payloads, one or more DDs, one or more cleavage sites, one or more signal sequences, one or more tags, one or more targeting peptides, and one or more additional features including the presence or absence of one or more linkers.
  • Representative effector module embodiments of the invention are illustrated in Figures 2-6.
  • the DD can be positioned at the N-terminal end, or the C -terminal end, or internal of the effector module construct.
  • Different components of an effector module such as DDs, payloads and additional features are organized linearly in one construct, or are separately constructed in separate constructs.
  • effector modules of the present invention may further comprise other regulator ⁇ ' moieties such as inducible promoters, enhancer sequences, microRNA sites, and/or microRNA targeting sites that provide flexibility on controlling the activity of the payload.
  • the payloads of the present invention may be any natural proteins and their variants, or fusion polypeptides, antibodies and variants thereof, transgenes and therapeutic agents.
  • the stimulus of the biocircuit system may be, but is not limited to, a ligand, a small molecule, an environmental signal (e.g., pH, temperature, light and subcellular location), a peptide or a metabolite.
  • the stimulus is a DHFR DD binding ligand including methotrexate (MTX) and trimethoprim (TMP).
  • MTX methotrexate
  • TMP trimethoprim
  • the vector may be a plasmid or a viral vector including but not limited to a lentiviral vector, a retroviral vector, a recombinant AAV vector and oncolytic viral vector.
  • biocircuit systems and effector modules of the invention can be used to regulate the expression and activity of a payload in response to the presence or absence of a ligand that specifically binds to the DD integrated within the biocircuit system and effector module.
  • DDs, effector modules and biocircuit systems of the invention may be used to regulate the expression, function and activity of a payload in a cell or a subject.
  • the regulation refers to a lever of change of its expression, function and activity, by at least about 10%, or at least about 20%, or at least about 30%, or at least about 40%, or at least about 50%, or at least about 60%, or at least about 70%, or at least about 80%, or at least about 85%, or at least about 90%, or at least about 95%, or at least about 100%, or at least 20-30%, 20-40%, 20-50%, 20-60%, 20-70%, 20-80%, 20-90%, 20-95%, 20-100%, 30-40%, 30-50%, 30-60%, 30-70%, 30- 80%, 30-90%, 30-95%, 30-100%, 40-50%, 40-60%, 40-70%, 40-80%, 40-90%, 40-95%, 40- 100%, 50-60%, 50-70%, 50-80%, 50-90%
  • the present invention provides methods for modulating protein, expression, function or level by measuring the stabilization ratio, destabilization ratio, and destabilizing mutation co-efficient.
  • the stabilization ratio may be defined as the ratio of expression, function or level of a protein of interest in response to the stimulus to the expression, function or level of the protein of interest in the absence of the stimulus specific to the SRE.
  • the stabilization ratio is at least 1, such as by at least 1-10, 1-20, 1 -30, 1-40, 1-50, 1- 60, 1-70, 1-80, 1- 90, 1-100, 20-30, 20-40, 20-50, 20-60, 20-70, 20-80, 20-90, 20- 95, 20-100, 30-40, 30-50, 30-60, 30-70, 30-80, 30-90, 30-95, 30-100, 40-50, 40-60, 40-70, 40- 80, 40-90, 40-95, 40-100, 50-60, 50-70, 50-80, 50-90, 50-95, 50-100, 60-70, 60-80, 60-90, 60- 95, 60-100, 70-80, 70-90, 70-95, 70-100, 80-90, 80-95, 80-100, 90-95, 90-100 or 95-100.
  • the destabilization ratio may be defined as the ratio of expression, function or level of a protein of interest in the absence of the stimulus specific to the effector module to the expression, function or level of the protein of interest, that is expressed constitutively and in the absence of the stimulus specific to the SRE.
  • constitutively refers to the expression, function or level a protein of interest that is not linked to an SRE or is linked to the wildtype protein from which the SRE is derived, and is therefore expressed both in the presence and absence of the stimulus.
  • the destabilizing mutation co-efficient may be defined as the ratio of expression or level of a protein of interest that is appended to a DD, in the absence of the stimulus specific to the effector module to the expression, function or level of the protein that is appended to the wild type protein from which the DD is derived.
  • the destabilization ratio and the destabilizing mutation co-efficient is at least 0, such as by at least 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, or at least, 0-0.1, 0-0.2, 0 -0.3, 0-0.4, 0-0.5, 0-0.6, 0- 0.7, 0-0.8, 0-0.9, 0.1-0.2, 0.1 -0.3, 0.1-0.4, 0.1-0.5, 0.1-0.6, 0.1-0.7, 0.1-0.8, 0.1-0.9, 0.2 -0.3, 0.2-0.4, 0.2-0.5, 0.2-0.6, 0.2-0.7, 0.2-0.8, 0.2-0.9, 0.3-0.4, 0.3-0.5, 0.3-0.6, 0.3-0.7, 0.3-0.8, 0.3-0.9, 0.4-0.5, 0.4-0.6, 0.4-0.7, 0.4-0.8, 0.4-0.9, 0.5-0.6, 0.5-0.7, 0.5-0.8, 0.5-0.9, 0.6-0.7, 0.5-0.9
  • the position of the payload with respect to the DD, within the SRE may be varied to achieve optimal DD regulation.
  • the payload may be fused to the N terminus of the DD.
  • the payload may be fused to the C terminus of the DDs.
  • An optional start codon nucleotide sequence encoding for methionine may be added to the DD and/or payload.
  • effector modules of the present invention may include one or more degrons to tune expression.
  • a "degron" refers to a minimal sequence within a protein that is sufficient for the recognition and the degradation by the proteolytic system.
  • degrons are transferrable, that is, appending a degron to a sequence confers degradation upon the sequence.
  • the degron may be appended to the destabilizing domains, the payload or both. Incorporation of the degron within the effector module of the invention, confers additional protein instabilityto the effector module and may be used to minimize basal expression.
  • the degron may be an N-degron, a phospho degron, a heat inducible degron, a photosensitive degron, an oxygen dependent degron.
  • the degron may be an Ornithine decarboxylase degron as described by Takeuchi et al.
  • degrons useful in the present invention include degrons described in International patent publication Nos. WO2017004022, WO2016210343, and WO2011062962; the contents of each of which are incorporated by reference in their entirety.
  • more than one biocircuit system may be used in combination to control various protein functions in the same cell or organism, each of which uses different DD and ligand pair and can be regulated separately.
  • biocircuits of the invention may be modified to reduce their immunogenicity.
  • Immunogenicity is the result of a complex series of responses to a substance that is perceived as foreign and may include the production of neutralizing and non-neutralizing antibodies, formation of immune complexes, complement activation, mast cell activation, inflammation, hypersensitivity responses, and anaphylaxis.
  • protein engineering may be used to reduce the immunogenicity of the compositions of the invention.
  • modifications to reduce immunogenicity may include modifications that reduce binding of the processed peptides derived from the parent sequence to MHC proteins.
  • amino acid modifications may be engineered such that there are no or a minimal of number of immune epitopes that are predicted to bind with high affinity, to any prevalent MHC alleles.
  • MHC binding epitopes of known protein sequences are known in the art and may be used to score epitopes in the compositions of the present invention. Such methods are disclosed in US Patent Publication No. US 20020119492, US20040230380, and US
  • Epitope identification and subsequent sequence modification may be applied to reduce immunogenicity.
  • the identification of immunogenic epitopes may be achieved either physically or computationally.
  • Physical methods of epitope identification may include, for example, mass spectrometry and tissue culture/cellular techniques.
  • Computational approaches that utilize information obtained on antigen processing, loading and display, structural and/or proteomic data toward identifying non-self-peptides that may result from antigen processing, and that are likely to have good binding characteristics in the groove of the MHC may also be utilized.
  • One or more mutations may be introduced into the biocircuits of the invention directing the expression of the protein, to maintain its functionality while simultaneously rendering the identified epitope less or non-immunogenic.
  • the endoplasmic reticulum associated degradation (ERAD) pathway may be used to optimize degradation of the payloads described herein e.g. secreted and membrane cargos.
  • the effector modules of the invention may directed to the ER E3 ligases by using adaptor proteins or protein domains.
  • the endoplasmic reticulum is endowed with a specialized machinery to ensure proteins deployed to the distal secretory pathway are correctly folded and assembled into native oligomeric complexes. Proteins failing to meet this conformational standard are degraded by the ERAD pathway, a process through which folding defective proteins are selected and ultimately degraded by the ubiquitin proteasome system.
  • ERAD proceeds through four main steps involving substrate selection, dislocation across the ER membrane, covalent conjugation with polyubiquitin, and proteasome degradation. Any of these steps may be modulated to optimize the degradation of the payloads and the effector modules described herein.
  • Protein adaptors within the ER membrane, link substrate recognition to the ERAD machinery (herein referred to as the "dislocon"), which causes the dislocation of the proteins from the ER
  • Non-limiting examples of protein adaptors that may be used to optimize ERAD pathway degradation include, but are not limited to SEL1L (an adaptor that links glycan recognition to the dislocon), Erlins (intermembrane substrate adaptors), Insigs (client specific adaptors), F-Box proteins (act as adaptors for dislocated glycoproteins in the cytoplasm) and viral-encoded adaptors.
  • compositions of the invention may also be useful in the present invention.
  • Compositions of the invention may also be engineered to include non-classical amino acid sidechains to design less immunogenic compositions. Any of the methods discussed in International Patent Publication No. WO2005051975 for reducing immunogenicity may be useful in the present invention (the contents of which are incorporated by reference in their entirety).
  • patients may also be stratified according to the immunogenic peptides presented by their immune cells and may be utilized as a parameter to determine suitable patient cohorts that may therapeutically benefit for the compositions of the invention.
  • reduced immunogenicity may be achieved by limiting immunoproteasome processing.
  • the proteasome is an important cellular protease that is found in two forms: the constitutive proteasome, which is expressed in all cell types and which contains active e.g. catalytic subunits and the immunoproteasome that is expressed in cell of the hematopoietic lineage, and which contains different active subunits termed low molecular weight proteins (LMP) namely LMP-2, LMP- 7 and LMP-10.
  • LMP low molecular weight proteins
  • a well described function of the immunoproteasome is to generate peptides with hydrophobic C terminus that can be processed to fit in the groove of MHC class I molecules.
  • Deol P et al. have shown that immunoproteasomes may lead to a frequent cleavage of specific peptide bonds and thereby to a faster appearance of a certain peptide on the surface of the antigen presenting cells; and enhanced peptide quantities (Deol P et al. (2007) J Immunol 178 (12) 7S57-7562; the contents of which are incorporated herein reference in its entirety). This study indicates that reduced immunoproteasome processing may be accompanied by reduced immunogenicity.
  • immunogenicity of the compositions of the invention may be reduced by modifying the sequence encoding the compositions of the invention to prevent immunoproteasome processing.
  • Biocircuits of the present invention may also be combined with immunoproteasome-selective inhibitors to achieve the same effects.
  • inhibitors useful in the present invention include UK-101 (Bli selective compound), IPSI-001, ONX 0914 (PR-957), and PR-924 (IPSI).
  • DDs Destabilizing Domains
  • DDs destabilizing domains
  • POI target protein of interest
  • a protein domain with destabilizing property e.g.
  • a DD is used in conjunction with a cell-permeable ligand to regulate any protein of interest when it is fused with the destabilizing domain.
  • DDs render the attached protein of interest unstable in the absence of a DD-binding ligand such that the protein is rapidly degraded by the ubiquitin-proteasome system of the cell.
  • a specific small molecule ligand binds its intended DD as a ligand binding partner, the instability is reversed and protein function is restored.
  • the conditional nature of DD stability allows a rapid and non-perturbing switch from stable protein to unstable substrate for degradation. Moreover, its dependency on the
  • concentration of its ligand further provides tunable control of degradation rates.
  • the altered function of the payload may vary, hence providing a Ci tuning'' of the payload function.
  • the post-transcriptional tuning system provides a useful system for gene regulation. Furthermore, the regulation may be dose-dependent, thereby altering the protein-turnover rate to transform a short-lived or no detectable protein into a protein that functions for a precisely controlled period of time (Iwamoto et al., Chem. Biol. 2010, 17: 981-988).
  • the desired characteristics of the DDs may include, but are not limited to, low protein levels in the absence of a ligand of the DD (i.e. low basal stability'), large dynamic range, robust and predictable dose-response behavior, and rapid kinetics of degradation.
  • Candidate DDs that bind to a desired ligand but not endogenous molecules may be preferred.
  • Candidate destabilizing domain sequence identified from protein domains of known wildtype proteins may be mutated to generate libraries of mutants based on the template candidate domain sequence.
  • Mutagenesis strategies used to generate DD libraries may include site-directed mutagenesis e.g. by using structure guided information, or random mutagenesis e.g. using error-prone PCR, or a combination of both.
  • destabilizing domains identified using random mutagenesis may be used to identify structural properties of the candidate DDs that may be required for destabilization, which may then be used to further generate libraries of mutations using site directed mutagenesis.
  • novel DDs may be identified by mutating one or more amino acids in the candidate destabilizing domain to an amino acid that is vicinal to the mutation site.
  • a vicinal amino acid refers to an amino acid that is located 1, 2, 3, 4, 5 or more amino acids upstream or downstream of the mutation site in the linear sequence and/or the crystal structure of the candidate destabilizing domain.
  • the vicinal amino acid may be a conserved amino acid (with similar physicochemical properties as the amino acid at the mutation site), a semi conserved amino acid (e.g. negatively to positively charge amino acid) or a non-conserved amino acid (with different physicochemical properties than the amino acid at the mutation site).
  • DD mutant libraries may be screened for mutations with altered, preferably higher binding affinity to the ligand, as compared to the wild type protein.
  • DD libraries may also be screened using two or more ligands and DD mutations that are stabilized by some ligands but not others may be preferentially selected.
  • DD mutations that bind preferentially to the ligand compared to a naturally occurring protein may also be selected. Such methods may be used to optimize ligand selection and ligand binding affinity of the DD. Additionally, such approaches can be used to minimize deleterious effects caused by off-target ligand binding.
  • suitable DDs may be identified by screening mutant libraries using barcodes. Such methods may be used to detect, identify and quantify individual mutant clones within the heterogeneous mutant library.
  • Each DD mutant within the library may have distinct barcode sequences (with respect to each other).
  • the polynucleotides can also have different barcode sequences with respect to 2,3,4,5,6,7,8,9,10 or more nucleic acid bases.
  • Each DD mutant within the library may also comprise a plurality of barcode sequences. When used in plurality barcodes may be used such that each barcode is unique to any other barcode. Alternatively, each barcode used may not be unique, but the combination of barcodes used may create a unique sequence that can be individually tracked.
  • the barcode sequence may be placed upstream of the SRE, downstream of the SRE, or in some instances may be placed within the SRE.
  • DD mutants may be identified by barcodes using sequencing approaches such as Sanger sequencing, and next generation sequencing, but also by polymerase chain reaction and quantitative polymerase chain reaction.
  • polymerase chain reaction primers that amplify a different size product for each barcode may be used to identify each barcode on an agarose gel.
  • each barcode may have a unique quantitative polymerase chain reaction probe sequence that enables targeted amplification of each barcode.
  • DDs are derived from human DHFR protein (hDHFR).
  • DDs of the invention may be derived from human dihydrofolate reductase (DHFR).
  • DHFR is a small (18 kDa) enzyme that catalyzes the reduction of dihydrofolate and plays a vital role in variety of anabolic pathway.
  • Dihydrofolate reductase (DHFR) is an essential enzyme that converts 7,8-dihydrofolate (DHF) to 5,6,7,8, tetrahydrofolate (THF) in the presence of nicotinamide adenine dihydrogen phosphate (NADPH).
  • DHF 7,8-dihydrofolate
  • THF 5,6,7,8, tetrahydrofolate
  • NADPH nicotinamide adenine dihydrogen phosphate
  • Anti-folate drugs such as methotrexate (MTX), a structural analogue of folic acid, which bind to DHFR more strongly than the natural substrate DHF, interferes with folate metabolism, mainly by inhibition of dihydrofolate reductase, resulting in the suppression of purine and pyrimidine precursor synthesis.
  • MTX is a common cancer therapy.
  • DHFR Dihydrofolate reductase
  • Escherichia coli and various E. coli DHFR (ecDHFR) mutants bind to known DHFR inhibitors: Methotrexate (MTX).
  • MTX Methotrexate
  • DHFR shows conformational changes and changes in thermodynamic stability (Wallace et al., J. Mol. Biol., 2002, 315: 193-211) and such structural changes affect protein stability.
  • Other inhibitors of DHFR folate, TQD, Trimethoprim (TMP), epigallocatechin gallate (EGCG) and ECG (epicatechin gallate) can also bind to ecDHFR mutants and regulates its stability.
  • DDs of the present invention may be identified by utilizing a cocktail of DHFR inhibitors.
  • the suitable DDs may be identified by screening first with one DHFR inhibitor and subsequently screening with a second DHFR inhibitor.
  • the destabilizing domains of the invention may include wildtype nucleotide sequences which may be utilized to reduce the basal expression of the compositions of the invention. Previous studies have shown that dihydrofolate reductase protein molecules can bind to their cognate mRNA and effectively repressing its translation. Alternatively, the nucleic acid sequence of the codons may be selected to alter translation rates. In some embodiments, amino acids identified as critical regulators of DHFR translation repression may be mutated to enhance translation rates. Examples of such mutations include but are not limited to 17 A, R28A and F34S residues of wildtype DHFR protein, described by Tai N et al. (2002), Nucleic Acids Res.
  • the ecDHFR and hDHFR amino acid sequences and nucleotide sequences are provided in Table 1.
  • the linkers are represented in bold and the restriction sites are underlined.
  • the amino acid sequences in Table 1 may comprise a stop codon which is denoted in the table with a "*" at the end of the amino acid sequence.
  • the DHFR derived destabilizing domains may be derived from variants, and or isoforms of DHFR.
  • the three isoforms of DHFR differ in their C and N terminal regions.
  • Isoform 1 is the longest transcript and encodes the longest isoform and is represented by SEQ ID NO. 1, encoded by SEQ ID NO. 8.
  • Isoform 2 lacks an alternate exon in the 5' end compared to isoform 1. This difference causes translation initiation at a downstream AUG and results in an isoform with a shorter N terminus compared to isoform 1.
  • Isoform 2 is represented by SEQ ID NO. 277, encoded by SEQ ID NO. 278.
  • Isoform 3 lacks an alternate exon in the 3' end compared to isoform 1, that causes frameshift. The resulting isoform has a shorter and distinct C terminus compared to isoform 1. Isoform 3 is represented by SEQ ID NO. 279, encoded by SEQ ID NO. 280.
  • the first amino acid from the destabilizing domain may be removed or substituted when fused to the linker region or payload.
  • the first amino acid is methionine (M) and it is removed from the destabilizing domain.
  • DDs of the present invention may also be derived from DHFR variant.
  • Masters JN et al. have described a DHFR variant (SEQ ID NO. 281); which bears 80% identity and 48% query coverage to SEQ ID NO. 1 (Masters JN et al (1983). JMol 5/o/.;167(l):23-36; the contents of which are incorporated by reference in its entirety).
  • the DDs of the present invention may be derived from
  • DHFRL1 is a mitochondrial dihydrofolate reductase with similar enzymatic activity as DHFR
  • the DDs of the invention may be derived from known variants of DHFR such as DHFRP1, DHFRP2, and DHFRP3. Such variants are described in Anagnou NP, et al. (1984) PNAS 81:5170-5174; Anagnou NP et al. (1988) Am J Hum Genet 42:345-352; ShimadaT, (1984). Gene 31:1-8; Maurer BJ et al. (1985) Somatic CellMol Genet 11:79-85; the contents of each of which are incorporated by reference in their entirety.
  • the amino acid sequences of the destabilizing domains encompassed in the invention have at least about 40%, 50% or 60%, 70% identity, preferably at least about 75% or 80% identity, more preferably at least about 85%, 86%, 87%, 88%, 89% or 90% identity, and further preferably at least about 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to the amino acid sequences described therein. Percent identity may be determined, for example, by comparing sequence information using the advanced BLAST computer program, including version Magic-BLAST 1.2.0, available from the National Institutes of Health. The BLAST program is based on the alignment method discussed in Karl and Altschul (1990) Proc. Natl. Acad. Sci USA, 87:2264-68 (the contents of which are incorporated by reference in their entirety).
  • novel DDs of the present invention comprise mutants of human DHFR presented in Table 2.
  • the position of the mutated amino acids listed in Table 2 is relative to the wildtype human DHFR (Uniprot ID: P00374) of SEQ ID NO. 1.
  • mutations are underlined and in bold.
  • the amino acid sequences in Table 2 may comprise a stop codon which is denoted in the table with a "*" at the end of the amino acid sequence.
  • hDHFR destabilizing mutants were discovered by random mutagenesis of the wildtype human DHFR using error prone polymerase chain reaction (PCR). The destabilization of the mutants in the absence of its binding ligand was tested. Binding to DHFR ligands, MTX and TMP to human DHFR was also tested and ligand dependent stabilization was characterized. Several hDHFR destabilizing mutants were discovered. The amino acid sequences of the DDs discovered by random mutagenesis are provided in Table 3. In Table 3, mutations are underlined and in bold. The position of the mutated amino acids listed in Table 3 is relative to the wildtype human DHFR (Uniprot ID: P00374) of SEQ ID NO. 1. Table 3: Human DHFR mutants and new destabilizing domains
  • any of the mutations described in Table 2 may be combined with any of the mutations described in Table 3 to generate destabilizing domains.
  • Exemplary combinations of mutations include, but are not limited to, hDHFR (II TV, Y122I) (SEQ ID NO. 331 (amino acid 2-187 of WT, I17V, Y122I) (encoded by SEQ ID NO. 332) or SEQ ID NO. 398 (117V, Y122I) (encoded by SEQ ID NO. 399)), hDHFR (Y122I, M140I) (SEQ ID NO. 333 (amino acid 2-187 of WT, Y122I, M140I) (encoded by SEQ ID NO. 334) or SEQ ID NO.
  • hDHFR N127Y, Y122I
  • SEQ ID NO. 335 amino acid 2-187 of WT, N127Y, Y122I
  • SEQ ID NO. 402 N127Y, Y122I
  • hDHFR Y122I, H131R, E144G
  • SEQ ID NO. 337 amino acid 2- 187 of WT, Y122I, H131R, E144G
  • the DDs may be derived from hDHFR by mutating one or more amino acids residues between positions 1-10, 10-20, 20-30, 30 ⁇ 0, 40-50, 50-60, 60-70, 70-80, 80-90, 90-100, 100-110, 110-120, 120-130, 130-140, 140-150, 150-160, 160-170, 170-180 or 180-187 of human DHFR wildtype protein (SEQ ID NO. 1).
  • the mutation may be a conserved (with similar physicochemical properties as the amino acid at the mutation site), a semi conserved (e.g.
  • Regions or portions or domains of wild type proteins may be utilized as SREs/DDs in whole or in part. They may be combined or rearranged to create new peptides, proteins, regions or domains of which any may be used as SREs DDs or the starting point for the design of further SREs and/or DDs.
  • the DD mutations identified herein may be mapped to the DHFR sequence to identify mutational hotspots.
  • the DD characteristics may be improved by mutating the amino acids at the hotspot position to any of the known amino acids, including, but not limited to lysine, aspaitic acid, glutamic acid, glutamine, asparagine, histidine, serine, threonine, tyrosine, cysteine, methionine, tryptophan, alanine, isoleucine, leucine, phenylalanine, valine, proline, and glycine.
  • a library of hotspot mutations may be generated by site directed mutagenesis and each of the mutants in the library is fused to a reporter protein e.g. AcGFP or luciferase via a linker.
  • variant libraries may be generated by methods known in the art.
  • VariantFindTM may be used to generate variant library.
  • the VariantFindTM platform is a series of multiplex PCRs that mutates multiple amino acid positions simultaneously. Desired mutations are directly encoded by oligonucleotides, providing high control and specificity during the mutagenesis process. These oligonucleotides are combined in a series of sequential PCRs that result in a ready-to-clone DNA library encoding all desired mutations. In one embodiment, any of the codons in the
  • polynucleotides of the invention may be altered by saturation mutagenesis.
  • a ruleset for amino acid changes may be used to mutate select amino acids of the DDs.
  • the rule may be the mutation of all Arginine residues in the DD to alanine, lysine and/or leucine.
  • all phenyl alanine residues in the DD may be mutated to alanine, leucine and/or threonine.
  • the destabilization domains described herein may also include amino acid and nucleotide substitutions that do not affect stability, including conservative, non-conservative substitutions and or polymorphisms.
  • the PEKN (SEQ ID NO. 427) sequence that spans from 61-65 amino acids from SEQ ID NO. 1 may be deleted or mutated to alternate amino acids.
  • Comparison of human DHFR sequence with folate reductases of other species has revealed that the "PEKN" (SEQ ID NO. 427) insertion found in human DHFR serves as a lid over the substrate Dihydrofolate site and is a major determinant blocking interaction of the human DHFR with DHFR inhibitors with specificity to parasitic and bacterial DHFR
  • GTL glycerol
  • the lack of GOL binding site prevents binding with bacterial DHFR inhibitors.
  • the amino acids equivalent to position tryptophan at position 22, leucine at position 24, aspartic acid at position 27, and glutamine at position 28 of DHFR of M. tuberculosis are inserted into the human DHFR.
  • DD mutations that do not inhibit ligand binding may be preferentially selected.
  • ligand binding may be improved by mutation of residues in DHFR.
  • Amino acid positions selected for mutation include aspartic acid at position 22 of SEQ ID NO. 1, glutamic acid at position 31 of SEQ ID NO. 1; phenyl alanine at position 32 of SEQ ID NO.
  • one or more of the following mutations may be utilized in the DDs of the present invention to improve TMP binding, including but not limited to, D22S, E3 ID, F32M, R33S, Q36S, N65S, and VI 161.
  • Exemplary DDs that may be tested for improved ligand binding properties include but are not limited to hDHFR (D22S, F32M, R33S, Q36S, N65S) (SEQ ID NO.
  • novel DDs derived from human DHFR may include one, two, three, four, five or more mutations including, but not limited to, Mldel, V2A, C7R, I8V, V9A, A10T, A10V, Q13R, N14S, G16S, I17N, I17V, K19E, N20D, G21T, G21E, D22S, L23S, P24S, L28P, N30D, N30H, N30S, E31G, E31D, F32M, R33G, R33S, F35L, Q36R, Q36S, Q36K, Q36F, R37G, M38V, M38T, T40A, V44A, K47R, N49S, N49D, M53T, G54R, K56E, K56R, T57A, F59S, I61T, K64R, N65A, N65S, N65D, N65F,
  • novel DDs derived from human DHFR may comprise amino acids 2-187 of the wild type human DHFR sequence (also referred to as an Mldel mutation), and may include one, two, three, four, five or more mutations including, but not limited to, Mldel, V2A, C7R, I8V, V9A, A10T, A10V, Q13R, N14S, G16S, I17N, I17V, K19E, N20D, G21T, G21E, D22S, L23S, P24S, L28P, N30D, N30H, N30S, E31G, E31D, F32M, R33G, R33S, F35L, Q36R, Q36S, Q36K, Q36F, R37G, M38V, M38T, T40A, V44A, K47R, N49S, N49D, M53T, G54R, K56E, K56R, T57A
  • Newly identified hDHFR mutants are fused to reporter proteins e.g. AcGFP (SEQ ID NO.3) and luciferase (SEQ ID NO. 377, encoded by SEQ ID NO. 378) through a linker sequence GGSGGGSGG (SEQ ID NO. 242), GS, SG or GGSGGG (SEQ ID NO. 4) at either the N- terminal or the C-terminal end of the fusion constructs and cloned into pLVX-IRES-puro vectors.
  • the destabilizing and ligand dependent stabilization properties of the fusion proteins may be evaluated by methods such as western blotting, and FACS.
  • hDHFR mutant fusion constructs are described in Table 4.
  • the amino acid sequences in Table 4 may comprise a stop codon which is denoted in the table with a "*" at the end of the amino acid sequence.
  • the position of the mutated amino acids listed in Table 4 is relative to the wildtype human DHFR (Uniprot ID: P00374) of SEQ ID NO. 1.
  • "del” means that the mutation is the deletion of the amino acid at that position relative to the wild type sequence.
  • DHFR derived DDs described herein and linked to reporter gene e.g. GFP may also be cloned e.g. the protein sequence of SEQ ID NO. 387, encoded by the nucleotide sequence of SEQ ID NO. 388 may be cloned into a pLVX-IRES-mcherry vector to generate OT-hDHFR- 038, or into apLVX-P2A-mcherry vector to generate OT-hDHFR-039.
  • the DHFR derived DD may be truncated and the smallest DHFR based DD may be identified.
  • DHFR DDs described herein may also be fragments of the above destabilizing domains, including fragments containing variant amino acid sequences. Preferred fragments are unstable in the absence of the stimulus and stabilized upon addition of the stimulus. Preferred fragments retain the ability to interact with the stimulus with similar efficiency as the DDs described herein.
  • the hDHFR-derived SRE may be a hDHFR mutant comprising, but not limited to, one, two, three or more mutations selected from Mldel, V2A, C7R, I8V, V9A, A10T, A10V, Q13R, N14S, G16S, I17N, I17V, K19E, N20D, G21T, G21E, D22S, L23S, P24S, L28P, N30D, N30H, N30S, E31G, E31D, F32M, R33G, R33S, F35L, Q36R, Q36S, Q36K, Q36F, R37G, M38V, M38T, T40A, V44A, K47R, N49S, N49D, M53T, G54R, K56E, K56R, T57A, F59S, I61T, K64R, N65A, N65S, N65D,
  • Biocircuits of the invention aie triggered by one or more stimuli.
  • Stimuli may be selected from a ligand, an externally added or endogenous metabolite, the presence or absence of a defined ligand, pH, temperature, light, ionic strength, radioactivity, cellular location, subject site, microenvironment, the presence or the concentration of one or more metal ions.
  • the stimulus is a ligand.
  • Ligands may be nucleic acid-based, protein-based, lipid based, organic, inorganic or any combination of the foregoing.
  • the ligand is selected from the group consisting of a protein, peptide, nucleic acid, lipid, lipid derivative, sterol, steroid, metabolite derivative and a small molecule.
  • the stimulus is a small molecule.
  • the small molecules are cell permeable.
  • Ligands useful in the present invention include without limitation, any of those taught in Table 2 of copending commonly owned US serial number 62/320,864 filed on 4/11/2017 or in US Provisional Application No. 62/466,596 filed March 3, 2017 and the International Publication WO2017/180587, the contents of each of which are incorporated herein by reference in their entirety.
  • the small molecules are FDA-approved, safe and orally administered.
  • the ligand binds to dihydrofolate reductase. In some embodiments, the ligand binds to and inhibits dihydrofolate reductase function and is herein referred to as a dihydrofolate inhibitor. [00118] In some embodiments, the ligand may be a selective inhibitor of human DHFR.
  • Ligands of the invention may also be selective inhibitors of dihydrofolate reductases of bacteria and parasitic organisms such as Pneumocystis spp., Toxoplasma spp.. Trypanosoma spp..
  • DHFR Mycobacterium spp., and Streptococcus spp.
  • Ligands specific to other DHFR may be modified to improve binding to human dihydrofolate reductase.
  • dihydrofolate inhibitors include, but are not limited to, Trimethoprim (TMP), Methotrexate (MTX), Pralatrexate, Piritrexim Pyrimethamine, Talotrexin,
  • DHFR inhibitors include BAL0030543, BAL0030544 and BAL0030545, developed by Basillea Pharmaceuticals; as well as WR 99210, and P218. Any of the inhibitors described by Zhang Q et al. (2015) Int J Antimicrob Agents. 2015 Aug; 46(2): 174-182 (the contents of which are incorporated herein by reference in their entirety). Some inhibitors contain bulky benzyl groups that dramatically diminish binding to human DHFR. In some embodiments, the inhibitors may be designed without bulky benzyl groups to improve TMP binding.
  • ligands of the present invention may be polyglutamate or non polyglutamylatable.
  • polyglutamatable folates also contain a glutamic acid residue and therefore undergo intracellular polyglutamylation.
  • non- polyglutamatable antifolates are devoid of a glutamate residue and thus are not available for polyglutamylation.
  • polyglutamylatable ligands may be preferred to increase intracellular retention as they can no longer be exported out of the cell. In other embodiments, non polyglutamylatable ligands may be preferred to decrease intracellular retention.
  • ligands of the present invention may include dihydrofolic acid or any of its derivatives that may bind to human DHFR.
  • the ligands of the present invention may be 2,4, diaminohetrocyclic compounds.
  • the 4-oxo group in dihydrofolate may be modified to generate DHFR inhibitors.
  • the 4 -oxo group may be replaced by 4-amino group.
  • Various diamino heterocycles including pteridines, quinazolines, pyridopyrimidines, pyrimidines, and triazines, may also be used as scaffolds to develop DHFR inhibitors and may be used in the present invention.
  • the crystal structure of DHFR in complex with known DHFR inhibitors may be utilized in the rational design of improved DHFR ligands.
  • the ligands used herein include a 2,4-diaminopyrimidine ring with a propargyl group linked to an optionally substituted aryl or heteroaryl ring (as described in US Patent No. US 8,426,432; the contents of which are incorporated herein by reference in their entirety).
  • the ligands of the present invention may be FDA approved ligands capable of binding to the specific DDs or target regions within the DDs.
  • FDA approved ligands may be used to screen potential binders in the human protein.
  • DDs may be designed based on the positive hits from the screen using the portion of the protein that binds to the ligand.
  • proteins that bind to FDA approved ligands as off target interactions may be used to design DDs of the present invention.
  • ligands include TMP- derived ligands containing portions of the ligand known to mediate binding to DHFR. Ligands may also be modified to reduce off-target binding to other folate metabolism enzymes and increase specific binding to DHFR.
  • DHFR inhibitors cover a broad pharmacokinetic space with respect to the approved dose and their duration of action and are described in Table 5.
  • PO stands for per os (i.e. by mouth);
  • QD represents quaque die (i.e. every day);
  • IV represents intravenous;
  • TID represents ter un die (i.e. three times a day); and
  • Cmax represents the peak serum concentration that a drug achieves after its administration.
  • the ligand selection is determined by the magnitude and duration of expression of the effector modules of the invention using the PK parameters described in Table 5.
  • high levels of expression of the payload for a short duration of time may be desired.
  • high levels of expression of the payload may be desired for a long duration.
  • low levels of expression of the payload may be desired for a long duration of time.
  • low levels of expression for a short duration of time may be desired.
  • TMP may be used as the ligand.
  • Ligands may also be selected from the analysis of the dependence of a known DHFR ligand on its molecular/ chemical structure, through Structure Activity Relationships (SAR) study. Any of the methods related to SAR, known in art may be utilized to identify stabilizing ligands of the invention. SAR may be utilized to improve properties of the ligand such as specificity, potency, pharmacokinetics, bioavailability, and safety. SAR analysis of known DHFR inhibitors may also be combined with computational strategies and the high resolution X ray structures of DHFR complexed with ligands may be used to develop compounds that can fit these criteria.
  • SAR Structure Activity Relationships
  • Methotrexate is converted to its polyglutamate form, which is required for the intracellular retention, and represents the most preferred substrate for most folate-dependent enzymes.
  • Analysis of the structure of MTX with human and bacterial DHFR has revealed that the active site of hDHFR is larger than ecDHFR which provides a specific interaction with hDHFR.
  • Human DHFR has a much larger active site for TMP as compared to ecDHFR; thus, hDHFR binds to TMP in a different conformation with fewer hydrogen bonds and is thus a poorer fit for the small inhibitor.
  • the ligands of the invention are designed to be lipophilic to improve cell permeability.
  • payioads can be any natural protein in an organism genome, a fusion polypeptide, an antibody, or variants, mutants and derivatives thereof.
  • payioads of the invention may be a natural protein in an organism genome, or variants, mutants, derivatives thereof.
  • the natural protein may be from, for example, a mammalian organism, a bacterium, and a virus.
  • the payload may be a protein of interest, or a polypeptide from human genome.
  • the payload of the present invention may be cardiac lineage specification factors such as eomesodermin (EOMES), a T-box transcription factor; WNT signaling pathway components such as WNT3 and WNT 3A.
  • EOMES eomesodermin
  • WNT signaling pathway components such as WNT3 and WNT 3A.
  • EOMES is crucially required for the development of the heart.
  • Cairliomyocyte programming by EOMES involves autocrine activation of the canonical WNT signaling pathway and vice versa. Under conditions that are conducive to promoting cardiac lineage, WNT signaling activates EOMES and EOMES in turn promotes WNT signaling creating a self-sustaining loop that promotes the cardiac lineage.
  • An activation loop that is too weak or too strong promotes non-cardiac fates such as endodermal and other mesodermal fates respectively.
  • the DDs of the present invention may be used to tune EOMES and WNT payload levels to generate an activation loop that initiate and/or sustain
  • payloads of the invention may be an antibody or fragments thereof.
  • Antibodies useful in this method include without limitation, any of those taught in copending commonly owned U.S. Provisional Patent Application No. 62/320,864 filed on 4/11/2017 or in US Provisional Application No. 62/466,596 filed March 3, 2017 and the
  • the antibody may be an intact antibody, an antibody light chain, antibody heavy chain, an antibody fragment, an antibody variant, or an antibody derivative.
  • an “antibody” may comprise a heavy and light variable domain as well as an Fc region.
  • the term “native antibody” refers to a usually
  • heterotetrameric glycoprotein of about 150,000 daltons composed of two identical light (L) chains and two identical heavy (H) chains.
  • L light
  • H heavy
  • Genes encoding antibody heavy and light chains are known and segments making up each have been well characterized and described (Matsuda et al., The Journal of Experimental Medicine. 1998, 188(11 ): 2151-62 and Li et al., Blood, 2004, 103(12): 4602-4609; the content of each of which are herein incorporated by reference in their entirety).
  • Each light chain is linked to a heavy chain by one covalent disulfide bond, while the number of disulfide linkages varies among the heavy chains of different immunoglobulin isotypes.
  • Each heavy and light chain also has regularly spaced intrachain disulfide bridges.
  • Each heavy chain has at one end a variable domain (VH) followed by a number of constant domains.
  • Each light chain has a variable domain at one end (VL) and a constant domain at its other end; the constant domain of the light chain is aligned with the first constant domain of the heavy chain, and the light chain variable domain is aligned with the variable domain of the heavy chain.
  • variable domain refers to specific antibody domains found on both the antibody heavy and light chains that differ extensively in sequence among antibodies and are used in the binding and specificity of each particular antibody for its particular antigen. Variable domains comprise hypervariable regions.
  • hypervariable region refers to a region within a variable domain comprising amino acid residues responsible for antigen binding. The amino acids present within the hypervariable regions determine the structure of the complementarity' determining regions (CDRs) that become part of the antigen- binding site of the antibody.
  • CDR refers to a region of an antibody comprising a structure that is complimentary to its target antigen or epitope.
  • the antigen-binding site also known as the antigen combining site or paratope
  • the antigen-binding site comprises the amino acid residues necessary to interact with a particular antigen.
  • the exact residues making up the antigen-binding site are typically elucidated by co-crystallography with bound antigen, however computational assessments can also be used based on comparisons with other antibodies (Strohl, W.R. Therapeutic Antibody Engineering. Woodhead Publishing, Philadelphia PA. 2012. Ch.
  • Determining residues making up CDRs may include the use of numbering schemes including, but not limited to, those taught by Kabat (Wu et al., JEM, 1970, 132(2):211 -250 and Johnson et al., Nucleic Acids Res. 2000, 28(1): 214-218, the contents of each of which are herein incorporated by reference in their entirety), Chothia (Chothia and Lesk, J. Mol. Biol. 1987, 196, 901, Chothia et al. Nature, 1989, 342, 877, and Al-Lazikani et al, J. Mol. Biol.
  • VH and VL domains have three CDRs each.
  • VL CDRs are referred to herein as CDR- Ll, CDR-L2 and CDR-L3, in order of occurrence when moving from N- to C- terminus along the variable domain polypeptide.
  • VH CDRs are referred to herein as CDR-H1, CDR-H2 and CDR-H3, in order of occurrence when moving from N- to C- terminus along the variable domain polypeptide.
  • Each of CDRs have favored canonical structures with the exception of the CDR-H3, which comprises amino acid sequences that may be highly variable in sequence and length between antibodies resulting in a variety of three-dimensional structures in antigen-binding domains (Nikoloudis, et al.
  • CDR-H3s may be analyzed among a panel of related antibodies to assess antibody diversity.
  • Various methods of determining CDR sequences are known in the art and may be applied to known antibody sequences (Strohl, W.R Therapeutic Antibody Engineering. Woodhead Publishing, Philadelphia PA. 2012. Ch. 3, p47-54, the contents of which are herein incorporated by reference in their entirety).
  • the term "light chain” refers to a component of an antibody from any vertebrate species assigned to one of two clearly distinct types, called kappa and lambda based on amino acid sequences of constant domains. Depending on the amino acid sequence of the constant domain of their heavy chains, antibodies can be assigned to different classes. There are five major classes of intact antibodies: IgA, lgD, IgE, IgG, and IgM, and several of these may be further divided into subclasses (isotypes), e.g., IgGl, IgG2, IgG3, IgG4, IgA, and IgA2.
  • the payload maybe a monoclonal antibody.
  • the term "monoclonal antibody” refers to an antibody obtained from a population of substantially homogeneous cells (or clones), i.e., the individual antibodies comprising the population are identical and/or bind the same epitope, except for possible variants that may arise during production of the monoclonal antibodies, such variants generally being present in minor amounts.
  • polyclonal antibody preparations that typically include different antibodies directed against different determinants (epitopes)
  • each monoclonal antibody is directed against a single determinant on the antigen.
  • the modifier "monoclonal” indicates the character of the antibody as being obtained from a substantially homogeneous population of antibodies, and is not to be construed as requiring production of the antibody by any particular method.
  • the monoclonal antibodies herein include "chimeric" antibodies (immunoglobulins) in which a portion of the heavy and/or light chain is identical with or homologous to corresponding sequences in antibodies derived from a particular species or belonging to a particular antibody class or subclass, while the remainder of the chain(s) is identical with or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies.
  • the payload of the present invention may be a humanized antibody.
  • humanized antibody refers to a chimeric antibody comprising a minimal portion from one or more non-human (e.g., murine) antibody source(s) with the remainder derived from one or more human immunoglobulin sources.
  • humanized antibodies are human immunoglobulins (recipient antibody) in which residues from the hypervariable region from an antibody of the recipient are replaced by residues from the hypervariable region from an antibody of a non-human species (donor antibody) such as mouse, rat, rabbit or nonhuman primate having the desired specificity, affinity, and/or capacity.
  • the antibody may be a humanized full-length antibody.
  • the antibody may have been humanized using the methods taught in US Patent Publication NO. US20130303399, the contents of which are herein incorporated by reference in its entirety.
  • the antibody may comprise a modified Fc region.
  • the modified Fc region may be made by the methods or may be any of the regions described in US Patent Publication NO. US20150065690, the contents of which are herein incorporated by reference in its entirety.
  • antibody variant refers to a modified antibody (in relation to a native or starting antibody) or a biomolecule resembling a native or starting antibody in structure and/or function (e.g., an antibody mimetic).
  • Antibody variants may be altered in their amino acid sequence, composition or structure as compared to a native antibody.
  • Antibody variants may include, but are not limited to, antibodies with altered isotypes (e.g., IgA, IgD, IgE, IgGl, IgG2, IgG3, IgG4, or IgM), humanized variants, optimized variants, multispecific antibody variants (e.g., bispecific variants), and antibody fragments.
  • antibody fragments and variants may comprise antigen binding regions from intact antibodies.
  • antibody fragments and variants may include, but are not limited to Fab, Fab', F(ab')2, and Fv fragments; diabodies; linear antibodies; single-chain antibody molecules such as single chain variable fragment (scFv); dimeric single-chain variable fragment (di-scFv), single domain antibody (sdAb) and multispecific antibodies formed from antibody fragments.
  • Papain digestion of antibodies produces two identical antigen-binding fragments, called "Fab” fragments, each with a single antigen-binding site. Also produced is a residual "Fc" fragment, whose name reflects its ability to crystallize readily.
  • Pepsin treatment yields an F(ab')2 fragment that has two antigen-binding sites and is still capable of cross-linking antigen.
  • Pharmaceutical compositions, biocircuits, biocircuit components, effector modules including their SREs or payloads of the present invention may comprise one or more of these fragments.
  • Fv refers to an antibody fragment comprising the minimum fragment on an antibody needed to form a complete antigen-binding site. These regions consist of a dimer of one heavy chain and one light chain variable domain in tight, non-covalent association. Fv fragments can be generated by proteolytic cleavage, but are largely unstable. Recombinant methods are known in the art for generating stable Fv fragments, typically through insertion of a flexible linker between the light chain variable domain and the heavy chain variable domain (to form a single chain Fv (scFv) or through the introduction of a disulfide bridge between heavy and light chain variable domains (Strohl, W.R. Therapeutic Antibody Engineering. Woodhead Publishing, Philadelphia PA. 2012. Ch. 3, p46-47, the contents of which are herein incorporated by reference in their entirety).
  • single chain Fv refers to a fusion protein of VH and VL antibody domains, wherein these domains are linked together into a single polypeptide chain by a flexible peptide linker.
  • the Fv polypeptide linker enables the scFv to form the desired structure for antigen binding.
  • scFvs are utilized in conjunction with phage display, yeast display or other display methods where they may be expressed in association with a surface member (e.g. phage coat protein) and used in the identification of high affinity peptides for a given antigen.
  • tascFv tandem scFv
  • Blinatumomab is an anti-CD19/anti-CD3 bispecific tascFv that potentiates T-cell responses to B-cell non-Hodgkin lymphoma in Phase 2.
  • MT110 is an anti-EP-CAM/anti-CD3 bispecific tascFv that potentiates T-cell responses to solid tumors in Phase 1.
  • Bispecific, tetravalent 'TandAbs are also being researched by Affimed (Nelson, A.
  • maxibodies (bivalent scFv fused to the amino terminus of the Fc (CH2-CH3 domains) of IgG may also be included.
  • bispecific antibody refers to an antibody capable of binding two different antigens. Such antibodies typically comprise regions from at least two different antibodies. Bispecific antibodies may include any of those described in Riethmuller, G. Cancer Immunity. 2012, 12:12-18, Marvin et al., 2005. Acta Pharmacologica Sinica. 2005, 26(6): 649- 658 and Schaefer et al., PNAS. 2011, 108(27): 11187-11192, the contents of each of which are herein incorporated by reference in their entirety. In some aspects, bispecific antibodies may be trifunctional antibodies (3funct) and BiTE (bi-specific T cell engager).
  • diabody refers to a small antibody fragment with two antigen-binding sites. Diabodies are functional bispecific single-chain antibodies (bscAb).
  • Diabodies comprise a heavy chain variable domain VH connected to a light chain variable domain VL in the same polypeptide chain.
  • Diabodies are described more fully in, for example, EP 404,097; WO 93/11161; and HoUinger et al. (HoUinger, P. et al., "Diabodies”: Small bivalent and bispecific antibody fragments. PNAS, 1993. 90: 6444- 6448); the contents of each of which are incorporated herein by reference in their entirety.
  • intrabody refers to a form of antibody that is not secreted from a cell in which it is produced, but instead targets one or more intracellular proteins. Intrabodies may be used to affect a multitude of cellular processes including, but not limited to intracellular trafficking, transcription, translation, metabolic processes, proliferative signaling and cell division.
  • methods of the present invention may include intrabody-based therapies.
  • variable domain sequences and/or CDR sequences disclosed herein may be incorporated into one or more constructs for intrabody-based therapy.
  • antibody variants may be antibody mimetics.
  • antibody mimetic refers to any molecule which mimics the function or effect of an antibody and which binds specifically and with high affinity to their molecular targets.
  • antibody mimetics may be monobodies, designed to incorporate the fibronectin type ffl domain (Fn3) as a protein scaffold (US 6,673,901; US 6,348,584).
  • Fn3 fibronectin type ffl domain
  • antibody mimetics may be those known in the art including, but are not limited to affibody molecules, affilins, affitins, anticalins, avimers, Cent>'rins, DARPINSTM, Fynomers and Kunitz and domain peptides. In other embodiments, antibody mimetics may include one or more non-peptide regions.
  • antibody variants may be multispecific antibodies that bind more than one epitope.
  • the terms “multibody” or “multispecific antibody” refer to an antibody wherein two or more variable regions bind to different epitopes. The epitopes may be on the same or different targets.
  • the multispecific antibody may be generated and optimized by the methods described in International Patent Publication NO.
  • a multi-specific antibody is a "bispecific antibody" which recognizes two different epitopes on the same or different antigens.
  • bispecific antibodies are capable of binding two different antigens.
  • Such antibodies typically comprise antigen-binding regions from at least two different antibodies.
  • a bispecific monoclonal antibody (BsMAb, BsAb) is an artificial protein composed of fragments of two different monoclonal antibodies, thus allowing the BsAb to bind to two different types of antigen.
  • Bispecific antibody frameworks may include any of those described in RiethmuUer, G., 2012. Cancer Immunity, 2012, 12: 12-18; Marvin et al., Acta Pharmacologica Sinica.
  • BsMAb basic bispecific antibodies
  • trifunctional bispecific antibodies consist of two heavy and two light chains, one each from two different antibodies, where the two Fab regions (the arms) are directed against two antigens, and the Fc region (the foot) comprises the two heavy chains and forms the third binding site.
  • antibody variants may be antibodies comprising a single antigen-binding domain. These molecules are extremely small, with molecular weights approximately one-tenth of those observed for full-sized mAbs. Further antibodies may include "nanobodies” derived from the antigen-binding variable heavy chain regions (VHHs) of heavy chain antibodies found in camels and llamas, which lack light chains (Nelson, A. L, MAbs.2010. Jan-Feb; 2(l):77-83). [00154] In some embodiments, the antibody may be ''miniaturized". Among the best examples of mAb miniaturization are the small modular immunopharmaceuticals (SMIPs) from Trubion Pharmaceuticals.
  • SMIPs small modular immunopharmaceuticals
  • TRU-015 an anti-CD20 SMIP developed in collaboration with Wyeth, is the most advanced project, having progressed to Phase 2 for rheumatoid arthritis (RA). Earlier attempts in systemic lupus erythrematosus (SLE) and B cell lymphomas were ultimately discontinued.
  • RA rheumatoid arthritis
  • miniaturized antibodies is called "unibody” in which the hinge region has been removed from IgG4 molecules. While IgG4 molecules are unstable and can exchange light-heavy chain heterodimers with one another, deletion of the hinge region prevents heavy chain-heavy chain pairing entirely, leaving highly specific monovalent light/heavy heterodimers, while retaining the Fc region to ensure stability and half-life in vivo. This configuration may minimize the risk of immune activation or oncogenic growth, as IgG4 interacts poorly with FcRs and monovalent unibodies fail to promote intracellular signaling complex formation (see, e.g., Nelson, A. L., MAbs, 2010. Jan-Feb; 2(l):77-83).
  • antibody variants may include single-domain antibodies (sdAbs, or nanobodies) which are antibody fragment consisting of a single monomelic variable antibody domain. Like a whole antibody, it is able to bind selectively to a specific antigen.
  • a sdAb may be a "Camel Ig or "camelid VHH".
  • camel Ig refers to the smallest known antigen-binding unit of a heavy- chain antibody (Koch-No lte, et al, FASEB J., 2007, 21: 3490- 3498).
  • a “heavy chain antibody” or a “camelid antibody” refers to an antibody that contains two VH domains and no light chains (Riechmann L. et al, J. Immunol. Methods, 1999, 231: 25-38; International patent publication NOs. WO1994/04678 and W01994/025591; and U.S. Patent No. 6,005,079).
  • an sdAb may be a "immunoglobulin new antigen receptor" (IgNAR).
  • immunoglobulin new antigen receptor refers to class of antibodies from the shark immune repertoire that consist of homodimers of one variable new antigen receptor (VNAR) domain and five constant new antigen receptor (CNAR) domains.
  • VNAR variable new antigen receptor
  • CNAR constant new antigen receptor
  • IgNARs represent some of the smallest known immunoglobulin-based protein scaffolds and are highly stable and possess efficient binding characteristics. The inherent stability can be attributed to both (i) the underlying Ig scaffold, which presents a considerable number of charged and hydrophilic surface exposed residues compared to the conventional antibody VH and VL domains found in murine antibodies; and (ii) stabilizing structural features in the complementary determining region (CDR) loops including inter-loop disulphide bridges, and patterns of intra-loop hydrogen bonds.
  • CDR complementary determining region
  • antibody variants may include intrabodies.
  • Intrabodies are a form of antibody that is not secreted from a cell in which it is produced, but instead targets one or more intracellular proteins. Intrabodies are expressed and function intracellularly, and may be used to affect a multitude of cellular processes including, but not limited to intracellular trafficking, transcription, translation, metabolic processes, proliferative signaling and cell division.
  • methods described herein include intrabody-based therapies.
  • variable domain sequences and/or CDR sequences disclosed herein are incorporated into one or more constructs for intrabody-based therapy.
  • intrabodies may target one or more glycated intracellular proteins or may modulate the interaction between one or more glycated intracellular proteins and an alternative protein.
  • intrabodies in different compartments of mammalian cells allows blocking or modulation of the function of endogenous molecules (Biocca, et al., EMBOJ. 1990, 9: 101-108; Colby et al., Proc. Natl. Acad. Sci. U.S.A. 2004, 101: 17616-17621).
  • Intrabodies can alter protein folding, protein-protein, protein-DNA, protein-RNA interactions and protein modification. They can induce a phenotypic knockout and work as neutralizing agents by direct binding to the target antigen, by diverting its intracellular trafficking or by inhibiting its association with binding partners. With high specificity and affinity to target antigens, intrabodies have advantages to block certain binding interactions of a particular target molecule, while sparing others.
  • Intrabodies are often recombinantly expressed as single domain fragments such as isolated VH and VL domains or as a single chain variable fragment (scFv) antibody within the cell.
  • intrabodies are often expressed as a single polypeptide to form a single chain antibody comprising the variable domains of the heavy and light chains joined by a flexible linker polypeptide.
  • Intrabodies typically lack disulfide bonds and are capable of modulating the expression or activity of target genes through their specific binding activity.
  • Single chain intrabodies are often expressed from a recombinant nucleic acid molecule and engineered to be retained intracellularly (e.g., retained in the cytoplasm, endoplasmic reticulum, or periplasm).
  • Intrabodies may be produced using methods known in the art, such as those disclosed and reviewed in: (Marasco et al, PNAS, 1993, 90: 7889-7893; Chen et al. Hum. Gene Ther.
  • antibody variants may include biosynthetic antibodies as described in U.S. Patent No. 5,091,513, the contents of which are herein incorporated by reference in their entirety.
  • Such antibody may include one or more sequences of amino acids constituting a region which behaves as a biosynthetic antibody binding site (BABS).
  • the sites comprise 1) non-covalently associated or disulfide bonded synthetic VH and VL dimers, 2) VH- VL or VL-VH single chains wherein the VH and VL are attached by a polypeptide linker, or 3) individuals VH or VL domains.
  • the binding domains comprise linked CDR and FR regions, which may be derived from separate immunoglobulins.
  • the biosynthetic antibodies may also include other polypeptide sequences which function, e.g., as an enzyme, toxin, binding site, or site of attachment to an immobilization media or radioactive atom. Methods are disclosed for producing the biosynthetic antibodies, for designing BABS having any specificity that can be elicited by in vivo generation of antibody, and for producing analogs thereof.
  • antibody variants may include antibodies with antibody acceptor frameworks taught in U.S. Patent No. 8,399,625. Such antibody acceptor frameworks may be particularly well suited accepting CDRs from an antibody of interest.
  • the antibody may be a conditionally active biologic protein.
  • An antibody may be used to generate a conditionally active biologic protein which are reversibly or irreversibly inactivated at the wild type normal physiological conditions as well as to such conditionally active biologic proteins and uses of such conditional active biologic proteins are provided.
  • Such methods and conditionally active proteins are taught in, for example,
  • the antibodies and fragments and variants thereof as described herein can be produced using recombinant polynucleotides.
  • the polynucleotides have a modular design to encode at least one of the antibodies, fragments or variants thereof.
  • the polynucleotide construct may encode any of the following designs: (1) the heavy chain of an antibody, (2) the light chain of an antibody, (3) the heavy and light chain of the antibody, (4) the heavy chain and light chain separated by a linker, (5) the VH1, CHI, CH2, CH3 domains, a linker and the light chain or (6) the VH1, CHI, CH2, CH3 domains, VL region, and the light chain. Any of these designs may also comprise optional linkers between any domain and region.
  • the polynucleotides of the present invention may be engineered to produce any standard class of immunoglobulins using an antibody described herein or any of its component parts as a starting molecule.
  • antibody payloads of the present invention may be therapeutic antibodies.
  • antibodies and fragments and variants thereof may be specific to tumor associated antigens, or tumor specific antigens, or pathogen antigens.
  • antibodies may be blocking antibodies (also referred to as antagonistic antibodies), for example, blocking antibodies against PD-1, PD-L1, PD-L2, CTLA-4 and other inhibitory molecules.
  • antibodies may be agonist antibodies such as agonistic antibodies specific to stimulatory molecules, e g., 4-1BB (CD137), OX40 (CD134), CD40, GITRand CD27.
  • exemplar ⁇ ' therapeutic antibodies may include, but arc not limited to,
  • Altumomab Amatuximab, Anetumab, Anifrolumab, Apolizumab, Arcitumomab, Ascrinvacumab, Aselizumab, Atezolizumab, Atinumab, Atlizumab, Atorolimumab, Avelumab, Bapineuzumab, Basiliximab, Bavituximab, Bectumomab, Begelomab, Belimumab,
  • Bimagrumab Bimekizumab, Bivatuzumab, Bleselumab, Blinatumomab, Blinatumomab, Blosozumab, Bococizumab, Brentuximab, Briaknumab, Brodalumab, Brolucizumab,
  • Lilotomab Lintuzumab, Lirilumab, Lodelcizumab, Lokivetmab, Lorvotuzumab, Lucatumumab, Lulizumab pegol, Lumiliximab, Lumietuzumab, Mapatumumab, Margetuximab, Maslimomab, Methosimumab, Matuzumab, Mepolizumab, Metelimumab, Milatuzumab, Minrctumomab, Mirvetuximab, Mitumomab, Mogamulizumab, Monalizumab, Morolimumab, Motavizumab, Moxetumomab pasudotox, Muromonab-CD3, nacolomab tafenatox, Namilumab, naptumomab, naratuximab, Narnatumab, Natal
  • Panitumumab Pankomab, Panobacumab, Parsatuzumab, Pascolizumab, Pasotuxizumab, Pateclizumab, Patritumab, Pembrolizumab, Pemtumomab, Perakizumab, Peituzumab,
  • Pexelizumab Pidilizumab, Pinatuzumab, Pintumomab, Placulumab, Plozalizumab, Pogalizumab, Polatuzumab, Ponezumab, Prezalizumab, Priliximab, Pritoxaximab, Pritumumab, PRO 140, Quilizumab, Racotumomab, Radretumab, Rafivirumab, Ralpancizumab, Ramucirumab, Ranibizumab, Raxibacumab, Refanezumab, Regavirumab, Reslizumab, Rilotumumab,
  • Sonepcizumab Sontuzumab, Stamulumab, Sulesomab, Suvizumab, tabalumab, Tacatuzumab, Tadocizumab, Talizumab, Tamtuvetmab, Tanezumab, Taplitumomab, Tarextumab,
  • Tefibazumab Telimomab aritox, Tenatumomab, Teneliximab, Teplizumab, Teprotumumab, Tesidolumab, Tetulomab, Tezepelumab, TGN1412, Ticilimumab, Tildrakizumab, Tigatuzumab, Timolumab, Tisotumab vedotin, TNX-650, Tocilizumab, Toralizumab, Tosatoxumab,
  • Tremelimumab Trevognimab, Tucotuzumab, Tuvirumab, Ublituximab, Ulcocuplumab, Urelumab, Urtoxazumab, Ustekinumab, Vadastuximab taurine, Vandortuzumab vedotin, Vantictumab, Vanucizumab, Vapaliximab, Varlilumab, Vatelizumab, Vedolizumab,
  • a bicistronic payload is a polynucleotide encoding a two-protein chain antibody on a single polynucleotide strand.
  • a pseudo-bicistronic payload is a polynucleotide encoding a single chain antibody ⁇ continuously on a single polynucleotide strand.
  • the encoded two strands or two portions/regions and/or domains are separated by at least one nucleotide not encoding the strands or domains. More often the separation comprises a cleavage signal or site or a non- coding region of nucleotides.
  • Such cleavage sites include, for example, furin cleavage sites encoded as an "RKR" site, or a modified furin cleavage site in the resultant polypeptide or any of those taught herein.
  • a single domain payload comprises one or two polynucleotides encoding a single monomelic variable antibody domain.
  • single domain antibodies comprise one variable domain (VH) of a heavy-chain antibody.
  • a single chain Fv payloads is a polynucleotide encoding at least two coding regions and a linker region.
  • the scFv payload may encode a fusion protein of the variable regions of the heavy (VH) and light chains (VL) of immunoglobulins, connected with a short linker peptide often to about 25 amino acids.
  • the linker is usually rich in glycine for flexibility, as well as serine or threonine for solubility, and can either connect the N- terminus of the VH with the C-terminus of the VL, or vice versa.
  • Other linkers include those known in the art and disclosed herein.
  • a bispecific payload is a polynucleotide encoding portions or regions of two different antibodies.
  • Bispecific payloads encode polypeptides which may bind two different antigens.
  • Polynucleotides of the present invention may also encode trispecific antibodies having an affinity for three antigens.
  • payloads of the present invention may be a therapeutic agent, such as a cancer therapeutic agent, an immune-therapeutic agent, an anti-pathogen agent or a gene therapy agent.
  • the immune-therapeutic agent may be a TCR receptor, a chimeric antigen receptor (CAR), a chimeric switch receptor, an antagonist of a co-inhibitory molecule, an agonist of a co-stimulatory molecule, a cytokine, a cytokine receptor, a chemokine, a chemokine receptor, a metabolic factor, a homing receptor and a safety switch.
  • chimeric antigen receptor refers to a synthetic receptor that mimics TCR on the surface of T cells.
  • a CAR is composed of an extracellular targeting domain, a transmembrane domain/region and an intracellular
  • the extracellular targeting domain comprises a targeting domain/moiety (e.g., a scFv) that recognizes a specific tumor antigen or other tumor cell-surface molecules.
  • a targeting domain/moiety e.g., a scFv
  • the intracellular region may contain a signaling domain of TCR complex (e.g., the signal region of CD3Q, and/or one or more costimulatory signaling domains, such as those from CD28, 4- IBB (CD137) and OX-40 (CD134).
  • a "first-generation CAR" only has the CD3C, signaling domain, whereas in an effort to augment T-cell persistence and proliferation, costimulatory intracellular domains are added, giving rise to second generation CARs having a 0 ⁇ 3 ⁇ £ ⁇ 1 domain plus one costimulatory signaling domain, and third generation CARs having CD3 ⁇ signal domain plus two or more costimulatory signaling domains.
  • a CAR when expressed by a T cell, endows the T cell with antigen specificity determined by the extracellular targeting moiety of the CAR.
  • a CAR may be capable of binding to a tumor specific antigen selected from 5T4, 707- AP, A33, AFP (a-fetoprotein), AKAP-4 (A kinase anchor protein 4), ALK, a5pi-integrin, androgen receptor, annexin II, alpha- actinin-4, ART-4, Bl, B7H3, B7H4, BAGE (B melanoma antigen), BCMA, BCR-ABL fusion protein, beta-catenin, BKT-antigen, BTAA, CA-I (carbonic anhydrase I), CA50 (cancer antigen 50), CA125, CA15-3, CA195, CA242, calretinin, CAIX (carbonic anhydrase), CAMEL (cytotoxic T-lymphocyte recognized antigen on melanoma), CAM43, CAP-1, Caspase-8/m, CD4, CD5, CD7, CD19, CD20, CD22, CD23, CD25, a
  • Exemplary CAR constructs may include a CAR targeting mesothelin (US Pat. NOs. 9,272, 002 and 9, 359,447); EGFRvlll specific CARs in US Pat. NO. 9,266,960; anti-TAG CARs in US Pat. NO. 9,233,125; CD19 CARs in US Patent Publication NO. 2016/014533; CD19 CAR having the amino acid sequence of SEQ ID NO. 24 of US Pat. NO. 9,328,156; CD19 CARs in US Pat NOs. 8,911,993, 8,975,071, 9,101,584, 9,102,760, and 9,102,761; BCMA (CD269) specific CARs disclosed in International Patent Publication NOs.
  • CAR targeting mesothelin US Pat. NOs. 9,272, 002 and 9, 359,447
  • EGFRvlll specific CARs in US Pat. NO. 9,266,960
  • anti-TAG CARs in US Pat. NO. 9,233,125
  • CLL-1 C-type lectin-like molecule 1
  • CARs comprising the amino acid sequences of SEQ ID NOs. 99, 96, 100, 101, 102, 91, 92, 93, 94, 95, 97, 98, 103, and 197 disclosed in International Patent Publication NO. WO2016/014535
  • CD33 specific CARs comprising the amino acid sequences of SEQ ID NOs. 48-56 in International Patent Publication NO. WO2016/014576
  • CD33 specific CARs comprising the amino acid sequences of SEQ ID NOs. 19-22, 27-30 and 35-38 in International Patent Publication NO.
  • WO2016/016344 ROR-1 specific multi-chain CARs in International patent publication NO. WO2016/016343; trophoblast glycoprotein (5T4, TPBG) specific CARs comprising the amino acid sequences of SEQ ID NOs. 21, 27, 33, 39, 23, 29, 34, 41, 19, 25, 31, 37, 20, 26, 32, 38, 22, 28, 34, 40, 24, 30, 36 and 42 in International Patent Publication NO. WO2016/034666;
  • EGFRvIII specific CARs comprising the amino acid sequences of SEQ ID NOs. 15, 17, 24, 25, 26 and 27 in International Patent Publication NO. WO2016016341; a TEM 8 CAR comprising the amino acid sequence of SEQ ID NO. 1 in International Patent Publication NO.
  • WO2014164544 a TEM1 CAR comprising the amino acid sequence of SEQ ID NO. 2 in International Patent Publication NO. WO2014164544; GPC-3 CAR having the amino acid sequences of SEQ ID NOs. 3 and 26 in International Patent Publication NO. WO2016/049459; a chondroitin sulfate proteoglycan-4 (CSPG4) CAR in International Patent Publication NO. WO2015/080981; Kappa/lambda CARs in International Patent Publication NO.
  • CSPG4 chondroitin sulfate proteoglycan-4
  • the CAR constructs may include CAIX (carboxy-anhydrase-IX (CAIX) specific CAR (Lamers et al., Biochem Soc Trans, 2016, 44(3): 951-959), HTV-1 specific CAR (Ah et al., J Virol., 2016, May 25, pii: JVI.00805-16), CD20 specific CAR (Rufener et al., Cancer Immunol.
  • CAIX carboxy-anhydrase-IX
  • the payload of the invention is a CD 19 specific CAR operably linked to human DHFR DD.
  • the amino acid sequences of the CD 19 CAR may comprise the components and sequences listed in Table 6. Nucleic acid sequences encoding the amino acid sequences are also described in Table 6. In the Table, the transmembrane domain is underlined to differentiate it from the adjacent sequence components. In Table 6, the amino acid sequences may comprise a stop codon at the end which is denoted in the table with a "*".
  • constructs OT-CD19N-008 to OT-CD19-011 are driven by a CMV promoter and constructs OT-CD19-014 and 015 are driven by a EFla promoter.
  • the position of the mutated amino acids listed in Table 6 is relative to the wildtype human DHFR (Uniprot ID: P00374) of SEQ ID NO. 1.
  • Constructs disclosed in Table 6, which are transcriptionally controlled by a CMV promoter may be placed under the transcriptional control of a different promoter to test the role of promoters in CD19 CAR expression.
  • the CMV promoter may be replaced by an EFla promoter.
  • the CMV promoter of the CD19 CAR, OT-CD19C-008 construct may be replaced to generate OT-CD19C-024 construct, with a EFla promoter.
  • the CMV promoter of the CD19 CAR, OT-CD19C-009 construct may be replaced to generate OT-CD19C-025 construct, with a EFla promoter.
  • payloads of the invention may be cytokines, and fragments, variants, analogs and derivatives thereof, including but not limited to interleukins, tumor necrosis factors (TNFs), interferons (IFNs), TGF beta and chemokines.
  • TNFs tumor necrosis factors
  • IFNs interferons
  • TGF beta TGF beta
  • chemokines including but not limited to interleukins, tumor necrosis factors (TNFs), interferons (IFNs), TGF beta and chemokines.
  • a cytokine may be an interleukin (IL) selected from IL1, IL1 alpha (also called hematopoietin-1), ILlbeta (catabolin), IL1 delta, ILlepsilon, ILleta, IL1 zeta, interleukin- 1 family member 1 to 11 (IL1F1 to IL1F11), interleukin- 1 homolog 1 to 4 (IL1H1 to 1L1H4), 1L1 related protein 1 to 3 (IL1RP1 to 1L1RP3), 1L2, 1L3, IL4, IL5, IL6, IL7, IL8, IL9, IL10, IL10C, IL10D, IL11, ILl la, ILllb, IL12, IL13, IL14, IL15, IL16, IL17, IL17A, I117B, IL17C, IL17E, IL17F,
  • IL1 alpha also
  • a cytokine may be a type I interferons (IFN) including IFN- alpha subtypes (IFN- ol, IFN- alb, IFN- ale), IFN-beta, IFN-delta subtypes (IFN-delta 1, IFN- delta 2, IFN-delta 8), IFN-gamma, IFN-kappa, and IFN-epsilon, IFN-lambda, IFN -omega, IFN- tau and IFN-zeta.
  • IFN interferons
  • a cytokine may be a member of tumor necrosis factor (TNF) superfamily, including TNF-alpha, TNF-beta (also known as lymphotoxin-alpha (LT-a)), lymphotoxin-beta (LT- ⁇ ), CD40L(CD154), CD27L (CD70), CD30L(CD153), FASL(CD178), 4- 1BBL (CD137L), OX40L, TRAIL (TNF-related apoptosis inducing ligand), APRIL (a proliferation-inducing ligand), TWEAK, TRANCE, TALL-1, GITRL, LIGHT and TNFSF1 to TNFSF20 (TNF ligand superfamily member 1 to 20).
  • TNF tumor necrosis factor
  • a cytokine may be a chemokine selected from SCYAl-28 (CCLl-28), SCYBl-16 (CXCLl-16), SCYCl-2 (XCLl-2), SCYD-l.SCYE-l, XCL1.XCL2, CCL1, CCL2, CCL3, CCL4, CCL5, CCL6, CCL7, CCL8, CCL9, CCL10, CCL11, CCL12, CCL13, CCL14, CCL15, CCL16, CCL17, CCL18, CCL19, CCL20, CCL21, CCL22, CCL23, CCL24, CCL25, CCL26, CCL27, CCL28, CXCL1, CXCL2, CXCL3, CXCL4, CXCL5, CXCL6, CXCL7, CXCL8, CXCL9, CXCL10, CXCL11, CXCL12, CXCL13, CXCL14, CXCL15, CXCL
  • the payload of the present invention may be a cytokine fused to a cytokine receptor.
  • the payload may be IL15 fused to IL15 Receptor alpha subunit.
  • a unique feature of IL15 mediated activation is the mechanism of trans-presentation in which IL15 is presented as a complex with the alpha subunit of IL15 receptor (1L15Ra) that binds to and activates membrane bound IL15 beta/gamma receptor, either on the same cell or a different cell.
  • the lL15/IL15Ra complex is much more effective in activating IL15 signaling, than IL15 by itself.
  • the may be a IL15/IL15Ra fusion polypeptide described in US patent publication NO. US20160158285A1 (the contents of which are incorporated herein by reference in their entirety).
  • the IL15 receptor alpha comprises an extracellular domain called the sushi domain that is considered to contain most of the structural elements necessary for binding to IL15.
  • the payload may be the IL15/IL15Ra sushi domain fusion polypeptide described in US Patent Publication NO. US20090238791A1 (the contents of which are incorporated herein by reference in their entirety).
  • the effector modules containing lL15/IL15Ra, and/or DD-IL15/lL15Ra sushi domain may be designed to be secreted (using e.g. IL2 signal sequence) or membrane bound (using e.g. IgE or CD8a signal sequence).
  • the DD-IL115/IL1 SRa comprises the amino acid sequences described in Table 7. Nucleic acid sequences encoding the amino acid sequences are also described in Table 7. In Table 7, the amino acid sequences may comprise a stop codon at the end which is denoted in the table with a "*". The position of the mutated amino acids listed in Table 7 is relative to the wildtype human DHFR (Uniprot ID: P00374) of SEQ ID NO. 1.
  • the payload of the invention may be IL12 fusion.
  • This regulatable DD- IL12 fusion polypeptide may be directly used as an immune-therapeutic agent or be transduced into an immune effector cell (T cells and TIL cells) to generate modified T cells with greater in vivo expansion and survival capabilities for adoptive cell transfer.
  • the 1L12 may be a Flexi IL12, wherein both p35 and p40 subunits, are encoded by a single cDNA that produces a single chain polypeptide.
  • the human DHFR-IL12 comprises the amino acid sequences described in Table 8. Nucleic acid sequences encoding the amino acid sequences are also described in Table 8.
  • amino acid sequences may comprise a stop codon at the end which is denoted in the table with a "*' ⁇
  • the position of the mutated amino acids listed in Table 8 is relative to the wildtype human DHFR (Uniprot ID: P00374) of SEQ ID NO. 1.
  • payloads fused to the DDs of the invention may be an inhibitor of an immunosuppressive molecule such as TGF-beta and 1DO.
  • payloads of the present invention may comprise SRE regulated safety switches that can eliminate adoptively transferred cells in the case of severe toxicity, thereby mitigating the adverse effects of T cell therapy.
  • Adoptively transferred T cells in immunotherapy may attack normal cells in response to normal tissue expression of TAA. Even on-tumor target activity of adoptively transferred T cells can result in toxicities such as tumor lysis syndrome, cytokine release syndrome and the related macrophage activation syndrome.
  • Safety switches may be utilized to eliminate inappropriately activated adoptively transferred cells by induction of apoptosis or by immunosurveillance.
  • payloads of the present invention may comprise inducible killer/suicide genes that acts as a safety switch.
  • the killer/suicide gene when introduced into adoptively transferred immune cells, could control their alloreactivity.
  • the killer/suicide gene may be an apoptotic gene (e.g., any Caspase gene) which allows conditional apoptosis of the transduced cells by administration of anon-therapeutic ligand of the SRE (e.g., DD).
  • the payloads of the present invention may be Caspase 9.
  • Caspase 9 may be modified to have low basal expression and lacking the Caspase recruitment domain (CARD) (SEQ ID NO. 26 and SEQ ID NO. 28 of US Patent No.
  • the payload of the present invention is a suicide gene system, iCasp9/Chemical induced dimerization (CID) system which consists of a polypeptide derived from the Caspase9 gene fused to a drug binding domain derived from the human FK506 protein.
  • CID iCasp9/Chemical induced dimerization
  • Administration of bioinert, small molecule AP1903 (rimiducid) induces cross linking of the drug binding domains and dimerization of the fusion protein and in turn the dimerization of Caspase 9.
  • the payload of the invention may comprise Caspase 9.
  • the effector module of the invention may be a DD-Caspase9 fusion polypeptide.
  • the DD-Caspase 9 may comprise the amino acid sequences provided in Table 9.
  • the amino acid sequences may comprise a stop codon at the 3' end which is denoted in the table with a "*".
  • the iCasp9/ClD system has been shown to have a basal rate of dimerization even in the absence of rimiducid, resulting in unintended cell death.
  • Regulating the expression levels of iCasp9/CID is critical for maximizing the efficacy of iCasp9/CID system.
  • Biocircuits of the present invention and/or any of their components may be utilized in regulating or tuning the iCasp9/CID system to optimize its utility.
  • proteins used in dimerization-induced apoptosis paradigm may include, but are not limited to Fas receptor, the death effector domain of Fas-associated protein, FADD, Caspase 1, Caspase 3, Caspase 7 and Caspase 8.
  • Fas receptor the death effector domain of Fas-associated protein
  • FADD the death effector domain of Fas-associated protein
  • Caspase 1 the death effector domain of Fas-associated protein
  • Caspase 8 Caspase 8.
  • the safety switch of the present invention may comprise a metabolic enzyme, such as herpes simplex virus thymidine kinase (HSV-TK) and cytosine deaminase (CD).
  • HSV-TK phosphorylates nucleoside analogs, including acyclovir and ganciclovir (GCV) to generate triphosphate form of nucleosides. When incorporated into DNA, it leads to chain termination and cell death.
  • a metabolic enzyme such as herpes simplex virus thymidine kinase (HSV-TK) and cytosine deaminase (CD).
  • HSV-TK phosphorylates nucleoside analogs, including acyclovir and ganciclovir (GCV) to generate triphosphate form of nucleosides. When incorporated into DNA, it leads to chain termination and cell death.
  • GCV ganciclovir
  • Cytosine deaminase can converts 5- fluorocytosine (5-FC) into the cytotoxic 5-fluorouracil (5-FU) (Tiraby et al., FEMSLett., 1998, 167: 41-49).
  • the safety switch of the present invention may comprise a CYP4B1 mutant (as suicide gene), which may be co-expressed in a CAR engineered T cells (Roellecker et al., Gen Ther., 2016, May 19, doi: 10.1038/gt.2016.38.).
  • the payload of the present invention may comprise a fusion construct that can induce cell death, for example, a polypeptide with the formula of St-Rl-Sl-Q- S2-R2, wherein the St is a stalk sequence, Rl/2 and Q are different epitopes; and S 1/2 are optional spacer sequences (See International Patent Publication NO. WO2013153391; the content of which are incorporated herein by reference in their entirety).
  • safety' switch may be mediated by therapeutic antibodies which specifically bind to an antigen that is expressed in the plasma membrane of adoptively transferred cells.
  • the antigen-antibody interaction allows cell removal after administration of a specific monoclonal antibody against the antigen.
  • payloads of the present invention may comprise the antigen and antibody pair used to mediate safety switch such as CD20 and anti-CD20 antibody (Griffioen et al., Haematologica, 2009, 94: 1316-1320), a protein tag and anti-tag antibody (Kieback et al., Natl. Acad. Sci.
  • payloads of the present invention may be components of gene editing systems including a CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats), CRISPR enzyme (Cas9), CRISPR-Cas9 or CRISPR system and CRISPR-CAS9 complex. It may also be other genomic editing systems, such as Zinc finger nucleases, TALEN (Transcription activator-like effector-based nucleases) and meganucleases.
  • CRISPR Clustered Regularly Interspaced Short Palindromic Repeats
  • Cas9 CRISPR enzyme
  • CRISPR-Cas9 CRISPR system and CRISPR-CAS9 complex
  • It may also be other genomic editing systems, such as Zinc finger nucleases, TALEN (Transcription activator-like effector-based nucleases) and meganucleases.
  • the effector module of the present invention may further comprise a signal sequence which regulates the distribution of the payload, a cleavage and/or processing feature which facilitate cleavage of the payload from the effector module construct, a targeting and/or penetrating signal which can regulate the cellular localization of the effector module, and/or one or more linker sequences which link different components (e.g. a DD and a payload) of the effector module.
  • a signal sequence which regulates the distribution of the payload
  • a cleavage and/or processing feature which facilitate cleavage of the payload from the effector module construct
  • a targeting and/or penetrating signal which can regulate the cellular localization of the effector module
  • one or more linker sequences which link different components (e.g. a DD and a payload) of the effector module.
  • effector modules of the invention may further comprise one or more signal sequences.
  • Signal sequences (sometimes referred to as signal peptides, targeting signals, target peptides, localization sequences, transit peptides, leader sequences or leader peptides) direct proteins (e.g., the effector module of the present invention) to their designated cellular and/or extracellular locations. Protein signal sequences play a central role in the targeting and translocation of nearly all secreted proteins and many integral membrane proteins.
  • a signal sequence is a short (5-30 amino acids long) peptide present at the N-terminus of the majority of newly synthesized proteins that are destined towards a particular location.
  • Signal sequences can be recognized by signal recognition particles (SRPs) and cleaved using type I and type II signal peptide peptidases.
  • SRPs signal recognition particles
  • Signal sequences derived from human proteins can be incorporated as a regulatory module of the effector module to direct the effector module to a particular cellular and/or extracellular location. These signal sequences are experimentally verified and can be cleaved (Zhang et al., Protein Sci. 2004, 13:2819-2824).
  • a signal sequence may be, although not necessarily, located at the N-terminus or C-terminus of the effector module, and may be, although not necessarily, cleaved off the desired effector module to yield a "mature" payload, i.e., an immunotherapeutic agent as discussed herein.
  • a signal sequence may be a secreted signal sequence derived from a naturally secreted protein, and its variant thereof.
  • the secreted signal sequences may be cytokine signal sequences such as, but not limited to, IL2 signal sequence comprising amino acid of SEQ ID NO. 228, encoded by the nucleotide of SEQ ID NOs. 229-232 and/or p40 signal sequence comprising the amino acid sequence of SEQ ID NO. 181, encoded by the nucleotide of SEQ YD NOs. 181-196 or a GMCSF leader sequence comprising the amino acid sequence of SEQ ID NOs. 357-359.
  • IL2 signal sequence comprising amino acid of SEQ ID NO. 228, encoded by the nucleotide of SEQ ID NOs. 229-232 and/or p40 signal sequence comprising the amino acid sequence of SEQ ID NO. 181, encoded by the nucleotide of SEQ YD NOs. 181-196 or a GMCSF leader sequence compris
  • signal sequences directing the payload to the surface membrane of the target cell may be used.
  • Expression of the payload on the surface of the target cell may be useful to limit the diffusion of the payload to non-target in vivo environments, thereby potentially improving the safety profile of the payloads.
  • the membrane presentation of the payload may allow for physiologically and qualitative signaling as well as stabilization and recycling of the payload for a longer half-life.
  • Membrane sequences may be the endogenous signal sequence of the N terminal component of the payload.
  • Signal sequences may be selected based on their compatibility with the secretory pathway of the cell type of interest so that the payload is presented on the surface of the T cell.
  • the signal sequence may be IgE signal sequence comprising amino acid SEQ ID NO. 163 and nucleotide sequence of SEQ ID NO. 170, a CD8a signal sequence comprising amino acid SEQ ID NO. Ill and nucleotide sequence of SEQ ID NOs. 141-145, 343-345 or an IL15Ra signal sequence, comprising amino acid SEQ ID NO. 425, encoded by SEQ ID NO. 426.
  • signal sequences include, a variant may be a modified signal sequence discussed in U.S. Patent Nos. 8,148,494, 8,258,102, 9,133,265, 9,279,007, and U.S. Patent Application Publication NO. 2007/0141666; and International Patent Publication NO. WO1993/018181; the contents of each of which are incorporated herein by reference in their entirety.
  • a signal sequence may be a heterogeneous signal sequence from other organisms such as virus, yeast and bacteria, which can direct an effector module to a particular cellular site, such as a nucleus (e.g., EP 1209450).
  • NSP24 Aspartic Protease (NSP24) signal sequences from Trichoderma that can increase secretion of fused protein
  • enzymes e.g., U. S. Patent NO. 8,093,016 to Cervin and Kim
  • bacterial lipoprotein signal sequences e.g., International Patent Publication NO. WO 1991/09952 to Lau and Rioux
  • Kcoli enterotoxin ⁇ signal peptides e.g., U.S. Patent NO. 6,605,697 to Kwon et al.
  • Kcoli secretion signal sequence e.g., U.S. Patent Publication NO.
  • a lipase signal sequence from a methylotrophic yeast e.g., U.S. Patent NO. 8,975,041
  • signal peptides for DNases derived from Coryneform bacteria e.g., U.S. Patent NO.
  • Signal sequences may also include nuclear localization signals (NLSs), nuclear export signals (NESs), polarized cell tubulo-vesicular structure localization signals (See, e.g., U.S. Patent NO. 8, 993,742; Cour et al., Nucleic Acids Res. 2003, 31(1): 393-396; the contents of each of which are incorporated herein by reference in their entirety),extracellular localization signals, signals to subcellular locations (e.g. lysosome, endoplasmic reticulum, golgi, mitochondria, plasma membrane and peroxisomes, etc.) (See, e.g., U.S. Patent NO. 7,396,811; and Negi et al., Database, 2015, 1-7; the contents of each of which are incorporated herein by reference in their entirety).
  • NLSs nuclear localization signals
  • NESs nuclear export signals
  • polarized cell tubulo-vesicular structure localization signals See, e.g., U.S. Patent NO
  • signal sequences of the present invention include without limitation, any of those taught in Table 6 of copending commonly owned U.S. Provisional Patent Application No. 62/320,864 filed on 4/11/2017 or in US Provisional Application No. 62/466,596 filed March 3, 2017 and the International Publication WO2017/180587, the contents of each of which are incorporated herein by reference in their entirety.
  • the effector module comprises a cleavage and/or processing feature.
  • the effector module of the present invention may include at least one protein cleavage signal/site.
  • the protein cleavage signal/site may be located at the N-terminus, the C -terminus, at any space between the N- and the C- termini such as, but not limited to, half-way between the N- and C-termini, between the N-terminus and the half-way point, between the half-way point and the C-terminus, and combinations thereof.
  • the effector module may include one or more cleavage signal(s)/site(s) of any proteinases.
  • the proteinases may be a serine proteinase, a cysteine proteinase, an endopeptidase, a dipeptidase, a metalloproteinase, a glutamic proteinase, a threonine proteinase and an aspartic proteinase.
  • the cleavage site may be a signal sequence of furin, actinidain, calpain-1, carboxypeptidase A, carboxypeptidase P, carboxypeptidase Y, caspase-1, caspase-2, caspase-3, caspase-4, caspase-5, caspase-6, caspase-7, caspase-8, caspase-9, caspase-10, cathepsin B, cathepsin C, cathepsin G, cathepsin H, cathepsin K, cathepsin L, cathepsin S, cathepsin V, clostripain, chymase, chymotrypsin, elastase, endoproteinase, enterokinase, factor Xa, formic acid, granzyme B, Matrix metallopeptidase-2, Matrix metallopeptidase-3, pepsin, proteinase K,
  • the cleavage site is a furin cleavage site comprising the amino acid sequence SARNRQKRS (SEQ ID NO. 233), encoded by nucleotide sequence of SEQ ID NO. 234), or a revised furin cleavage site comprising the amino acid sequence ARNRQKRS (SEQ ID NO. 235), encoded by nucleotide sequence of SEQ ID NO. 236); or a modified furin site comprising the amino acid sequence ESRRVRRNKRSK (SEQ ID NO. 183), encoded by nucleotide sequence of SEQ ID NO. 203-205); or a SGESRRVRRNKRSK (SEQ ID NO.
  • the cleavage site is a P2A cleavage site, ATNFSLLKQAGDVEENPGP (SEQ ID NO. 360), encoded by SEQ ID NO. 361, wherein NPGP (SEQ ID NO. 429) is the P2A site.
  • cleavage sites of the present invention include without limitation, any of those taught in Table 7 of copending commonly owned U.S. Provisional Patent Application No. 62/320,864 filed on 4/11/2017 or in US Provisional Application No. 62/466,596 filed March 3, 2017 and the International Publication WO2017/180587, the contents of each of which are incorporated herein by reference in their entirety.
  • the effector module of the invention may comprise a protein tag.
  • the protein tag may be used for detecting and monitoring the process of the effector module.
  • the effector module may include one or more tags such as an epitope tag (e.g., a FLAG or hemagglutinin (HA) tag). A large number of protein tags may be used for the present effector modules.
  • haloalkane dehalogenase halotag2 or halotag7
  • ACP tag e.g., haloalkane dehalogenase (halotag2 or halotag7)
  • ACP tag e.g., haloalkane dehalogenase (halotag2 or halotag7)
  • ACP tag e.g., haloalkane dehalogenase (halotag2 or halotag7)
  • ACP tag e.g., haloalkane dehalogenase (halotag2 or halotag7)
  • ACP tag e.g., haloalkane dehalogenase (halotag2 or halotag7)
  • ACP tag e.g., haloalkane dehalogenase (halotag2 or halotag7)
  • ACP tag e.g., haloalkane dehalogenase (halotag
  • affinity tags e.g., maltose-binding protein (MBP) tag, glutathione-S-transferase (GST) tag
  • immunogenic affinity tags e.g., protein A/G, IRS, AU1, AU5, glu-glu, KT3, S-tag, HSV, VSV-G, Xpress and V5
  • other tags e.g., biotin (small molecule), StrepTag (Strepll), SBP, biotin carboxyl carrier protein (BCCP), eXact, CBP, CYD, HPC, CBD intein-chitin binding domain, Trx, NorpA, and NusA.
  • a tag may also be selected from those disclosed in U.S. Patent Nos. 8,999,897, 8,357,511, 7,094,568, 5,011,912, 4,851,341, and 4,703,004; U.S Patent Application Publication NOs. 2013/115635 and 2013/012687; and International Patent
  • a multiplicity of protein tags may be used; each of the tags may be located at the same N- or C-terminus, whereas in other cases these tags may be located at each terminus.
  • protein tags of the present invention include without limitation, any of those taught in Table 8 of copending commonly owned U.S. Provisional Patent
  • the effector module of the invention may further comprise a targeting and/or penetrating peptide.
  • Small targeting and/or penetrating peptides that selectively recognize cell surface markers e.g. receptors, trans-membrane proteins, and extra-cellular matrix molecules
  • cell surface markers e.g. receptors, trans-membrane proteins, and extra-cellular matrix molecules
  • Short peptides (5-50 amino acid residues) synthesized in vitro and naturally occurring peptides, or analogs, variants, derivatives thereof, may be incorporated into the effector module for homing the effector module to the desired organs, tissues and cells, and/or subcellular locations inside the cells.
  • a targeting sequence and/or penetrating peptide may be included in the effector module to drive the effector module to a target organ, or a tissue, or a cell (e.g., a cancer cell).
  • a targeting and/or penetrating peptide may direct the effector module to a specific subcellular location inside a cell.
  • a targeting peptide has any number of amino acids from about 6 to about 30 inclusive.
  • the peptide may have 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 amino acids.
  • a targeting peptide may have 25 or fewer amino acids, for example, 20 or fewer, for example 15 or fewer.
  • Exemplar ⁇ ' targeting peptides may include, but are not limited to, those disclosed in the art, e.g., U.S. Patent NOs. 9,206,231, 9,110,059, 8,706,219, and 8,772,449; and U.S. Patent Application Publication NOs. 2016/089447, 2016/060296, 2016/060314, 2016/060312, 2016/060311, 2016/009772, 2016/002613, 2015/314011 and 2015/166621; and International Patent Publication NOs. WO2015/179691 and WO2015/183044; the contents of each of which are incorporated herein by reference in their entirety.
  • targeting peptides of the present invention include without limitation, any of those taught in Table 9 of copending commonly owned U.S. Provisional Patent Application No. 62/320,864 filed on 4/11/2017 or in US Provisional Application No. 62/466,596 filed March 3, 2017 and the International
  • the effector module of the invention may further comprise a linker sequence.
  • the linker region serves primarily as a spacer between two or more
  • linker refers to a molecule or group of molecules that connects two molecules, or two parts of a molecule such as two domains of a recombinant protein.
  • Linker refers to an oligo- or polypeptide region of from about 1 to 100 amino acids in length, which links together any of the domains/regions of the effector module (also called peptide linker).
  • the peptide linker may be 1-40 amino acids in length, or 2-30 amino acids in length, or 20-80 amino acids in length, or 50-100 amino acids in length.
  • Linker length may also be optimized depending on the type of payload utilized and based on the crystal structure of the payload. In some instances, a shorter linker length may be preferably selected.
  • the peptide linker is made up of amino acids linked together by peptide bonds, preferably from 1 to 20 amino acids linked by peptide bonds, wherein the amino acids are selected from the 20 naturally occurring amino acids: Glycine (G), Alanine (A), Valine (V), Leucine (L), Isoleucine (I), Serine (S), Cysteine (C), Threonine (T), Methionine (M), Proline (P), Phenylalanine (F), Tyrosine (Y), Tryptophan (W), Histidine (H), Lysine (K), Arginine (R), Aspartate (D), Glutamic acid (£), Asparagine (N), and Glutamine (Q).
  • amino acids of a peptide linker may be selected from Alanine (A), Glycine (G), Proline (P), Asparagine (R), Serine (S), Glutamine (Q) and Lysine (K).
  • an artificially designed peptide linker may preferably be composed of a polymer of flexible residues like Glycine (G) and Serine (S) so that the adjacent protein domains are free to move relative to one another.
  • Longer linkers may be used when it is desirable to ensure that two adjacent domains do not interfere with one another.
  • the choice of a particular linker sequence may concern if it affects biological activity, stability, folding, targeting and/or pharmacokinetic features of the fusion construct.
  • Examples of peptide linkers include, but are not limited to. SG, MH, GGSG (SEQ ID NO. 237; encoded by the nucleotide sequence SEQ ID NO 238), GGSGG (SEQ ID NO.
  • GGSTSGSGKSSEGKG (SEQ ID NO. 263), GSTSGSGKSSSEGSGSTKG (SEQ ID NO. 264), GSTSGSGKPGSGEGSTKG (SEQ ID NO. 265), VDYPYDVPDYALD (SEQ ID NO. 266; encoded by nucleotide sequence SEQ ID NO. 267), EGKSSGSGSESKEF (SEQ ID NO. 268), SG3-(SG4)3-SG3-SLQ- YPYDVPDYA (SEQ ID NO. 364), encoded by the nucleotide sequence of SEQ ID NO. 365; DYKDDDDK (SEQ ID NO. 366), encoded by the nucleotide sequence of SEQ ID NO. 367; SG3-(SG4)5-SG3-S (SEQ ID NO. 368), encoded by SEQ ID NO. 369;
  • GGGGSGGGGSGGGGS (SEQ ID NO. 182), encoded by SEQ ID NO. 197-202;
  • SGGGSGGGGSGGGGSGGGGSYPYDVPDYASGGGS (SEQ ID NO. 370), encoded by SEQ ID NO. 371; GSGATNFSLLKQAGDVEENPGP (SEQ ID NO. 372), encoded by SEQ ID NO. 373; or SGGGGSGGGGSGGGGSGGGSLQ (SEQ ID NO. 428).
  • a peptide linker may be made up of a majority of amino acids that are stericaUy unhindered, such as Glycine (G) and Alanine (A).
  • exemplary linkers are polyglycines (such as (G) 4 (SEQ ID NO. 430), (G)s (SEQ ID NO. 244), (G)s (SEQ ID NO. 431)), poly(GA), and polyalanines.
  • the linkers described herein are exemplary, and linkers that are much longer and which include other residues are contemplated by the present invention.
  • a linker sequence may be a natural linker derived from a multi-domain protein.
  • a natural linker is a short peptide sequence that separates two different domains or motifs within a protein.
  • linkers may be flexible or rigid. In other aspects, linkers may be cleavable or non- cleavable. As used herein, the terms "cleavable linker domain or region” or “cleavable peptide linker” are used interchangeably. In some embodiments, the linker sequence may be cleaved enzymatically and/or chemically. Examples of enzymes (e.g.,
  • proteinase/peptidase useful for cleaving the peptide linker include, but are not limited, to Arg-C proteinase, Asp-N endopeptidase, chymotrypsin, clostripain, enterokinase, Factor Xa, glutamyl endopeptidase, Granzyme B, Achromobacter proteinase I, pepsin, proline endopeptidase, proteinase K, Staphylococcal peptidase I, thermolysin, thrombin, trypsin, and members of the Caspase family of proteolytic enzymes (e.g. Caspases 1-10).
  • Chemical sensitive cleavage sites may also be included in a linker sequence.
  • Examples of chemical cleavage reagents include, but are not limited to, cyanogen bromide, which cleaves methionine residues; N-chloro succinimide, iodobenzoic acid or BNPS-skatole [2-(2-nitrophenylsulfenyl)-3-methylindole], which cleaves tryptophan residues; dilute acids, which cleave at aspartyl-prolyl bonds; and e aspartic acid- proline acid cleavable recognition sites (i.e., a cleavable peptide linker comprising one or more D-P dipeptide moieties).
  • the fusion module may include multiple regions encoding peptides of interest separated by one or more cleavable peptide linkers.
  • a cleavable linker may be a "self-cleaving" linker peptide, such as 2A linker (for example T2A), 2A-like linkers or functional equivalents thereof and combinations thereof.
  • the linkers include the picornaviral 2A-like linker, CHYSEL sequences of porcine teschovirus (P2A), Thosea asigna virus (T2A) or combinations. variants and functional equivalents thereof.
  • the biocircuits of the present invention may include 2A peptides.
  • the 2A peptide is a sequence of about 20 amino acid residues from a virus that is recognized by a protease (2A peptidases) endogenous to the cell.
  • the 2A peptide was identified among picornaviruses, a typical example of which is the Foot-and Mouth disease virus (Robertson BH, et. al., J Virol 1985, 54:651-660). 2A-like sequences have also been found in Picornaviridae like equine rhinitis A virus, as well as unrelated viruses such as porcine teschovirus-1 and the insect Thosea asigna virus (TaV). In such viruses, multiple proteins are derived from a large polyprotein encoded by an open reading frame. The 2A peptide mediates the co-translational cleavage of this polyprotein at a single site that forms the junction between the virus capsid and replication polyprotein domains.
  • the 2A sequences contain the consensus motif D-V/I-E-X-N-P-G-P (SEQ ID NO. 374 (where the second amino acid is V) or SEQ ID NO. 375 (where the second amino acid is I)). These sequences are thought to act co- translationally, preventing the formation of a normal peptide bond between the glycine and last proline, resulting in the ribosome skipping of the next codon (Donnelly ML et al. (2001). J Gen Virol, 82: 1013-1025).
  • the short peptide After cleavage, the short peptide remains fused to the C -terminus of the protein upstream of the cleavage site, while the proline is added to the N -terminus of the protein downstream of the cleavage site.
  • FMDV 2A abbreviated herein as F2A
  • E2A equine minitis A virus
  • P2A porcine teschovirus-1 2A
  • T2A Those aasigna virus 2A
  • the 2A peptide sequences useful in the present invention are selected from SEQ ID NO. 8-11 of International Patent Publication WO2010042490, the contents of which are incorporated by reference in its entirety.
  • the linkers of the present invention may also be non-peptide linkers.
  • alkyl linkers may further be substituted by any non-sterically hindering group such as lower alkyl (e.g., Ci-Ce) lower acyl, halogen (e.g., CI, Br), CN, NHb, phenyl, etc.
  • the linker may be an artificial linker from U.S. Patent Nos. 4,946,778, 5,525,491, 5,856,456; and International Patent Publication NO. WO2012/083424; the contents of each of which are incorporated herein by reference in their entirety.
  • linkers of the present invention include without limitation, any of those taught in Table 11 of copending commonly owned U.S. Provisional Patent Application No. 62/320,864 filed on 4/11/2017 or in US Provisional Application No. 62/466,596 filed March 3, 2017 and the International Publication WO2017/180587, the contents of each of which are incorporated herein by reference in their entirety.
  • micro RNAs are 19-25 nucleotide long noncoding RNAs that bind to the 3'UTR of nucleic acid molecules and down-regulate gene expression either by reducing nucleic acid molecule stability or by inhibiting translation.
  • the polynucleotides of the invention may comprise one or more microRNA target sequences, microRNA sequences, or microRNA seeds. Such sequences may correspond to any known microRNA such as those taught in US
  • a microRNA sequence comprises a "seed" region, i.e., a sequence in the region of positions 2-8 of the mature microRNA, which sequence has perfect Watson-Crick
  • a microRNA seed may comprise positions 2-8 or 2-7 of the mature microRNA.
  • a microRNA seed may comprise 7 nucleotides (e.g., nucleotides 2-8 of the mature microRNA), wherein the seed-complementary site in the corresponding miRNA target is flanked by an adenine (A) opposed to microRNA position 1.
  • a microRNA seed may comprise 6 nucleotides (e.g., nucleotides 2-7 of the mature microRNA), wherein the seed-complementary site in the corresponding miRNA target is flanked by an adenine (A) opposed to microRNA position 1.
  • microRNA target sequences into the polynucleotides encoding the biocircuit components, effector modules, SREs or payloads of the invention one can target the molecule for degradation or reduced translation, provided the microRNA in question is available. This process will reduce the hazard of off target effects upon nucleic acid molecule delivery.
  • miR-122 a microRNA abundant in liver, can inhibit the expression of the polynucleotide if one or multiple target sites of miR-122 are engineered into the polynucleotide.
  • Introduction of one or multiple binding sites for different microRNA can be engineered to further decrease the longevity, stability, and protein translation of a polynucleotide hence providing an additional layer of tenability beyond the stimulus selection, SRE design and payload variation.
  • microRNA site refers to a microRNA target site or a microRNA recognition site, or any nucleotide sequence to which a microRNA binds or associates. It should be understood that “binding” may follow traditional Watson-Crick hybridization rules or may reflect any stable association of the microRNA with the target sequence at or adjacent to the microRNA site.
  • microRNA binding sites can be engineered out of (i.e. removed from) sequences in which they naturally occur in order to increase protein expression in specific tissues.
  • miR-122 binding sites may be removed to improve protein expression in the liver.
  • Regulation of expression in multiple tissues can be accomplished through introduction or removal or one or several microRNA binding sites.
  • microRNAs are known to be differentially expressed in immune cells (also called hematopoietic cells), such as antigen presenting cells (APCs) (e.g. dendritic cells and macrophages), macrophages, monocytes, B lymphocytes, T lymphocytes, granulocytes, natural killer cells, etc.
  • APCs antigen presenting cells
  • microRNAs are involved in immunogenicity
  • Immune cells specific microRNAs also regulate many aspects of development, proliferation, differentiation and apoptosis of hematopoietic cells (immune cells).
  • miR-142 and miR-146 are exclusively expressed in the immune cells, particularly abundant in myeloid dendritic cells.
  • Introducing the miR-142 binding site into the 3'-UTR of a polypeptide of the present invention can selectively suppress the gene expression in the antigen presenting cells through miR-142 mediated mRNA degradation, limiting antigen presentation in professional APCs (e.g. dendritic cells) and thereby preventing antigen-mediated immune response after gene delivery (see, Annoni A et al., blood, 2009, 114, 5152-5161, the content of which is herein incorporated by reference in its entirety.)
  • microRNAs binding sites that are known to be expressed in immune cells in particular, the antigen presenting cells, can be engineered into the
  • polynucleotides to suppress the expression of the polynucleotide in APCs through microRNA mediated RNA degradation, subduing the antigen-mediated immune response, while the expression of the polynucleotide is maintained in non-immune cells where the immune cell specific microRNAs are not expressed.
  • microRNA expression studies have been conducted, and are described in the art, to profile the differential expression of microRNAs in various cancer cells /tissues and other diseases. Some microRNAs are abnormally over-expressed in certain cancer cells and others are under-expressed. For example, microRNAs are differentially expressed in cancer cells
  • WO2008/054828, US8252538 lung cancer cells (WO2011/076143, WO2013/033640, WO2009/070653, US2010/0323357); cutaneous T cell lymphoma (WO2013/011378); colorectal cancer cells (WO2011/0281756, WO2011/076142); cancer positive lymph nodes
  • microRNA may be used as described herein in support of the creation of tunable biocircuits.
  • effector modules may be designed to encode (as a DNA or RNA or mRNA) one or more payloads, SREs and/or regulatory sequence such as a microRNA or microRNA binding site.
  • any of the encoded payloads or SREs may be stabilized or de-stabilized by mutation and then combined with one or more regulatory sequences to generate a dual or multi-tuned effector module or biocircuit system.
  • Each aspect or tuned modality may bring to the effector module or biocircuit a differentially tuned feature.
  • an SRE may represent a destabilizing domain
  • mutations in the protein payload may alter its cleavage sites or dimerization properties or half- life and the inclusion of one or more microRNA or microRNA binding site may impart cellular detargeting or trafficking features. Consequently, the present invention embraces biocircuits which are multifactorial in their tenability.
  • compositions of the invention may include optional proteasome adaptors.
  • proteasome adaptor refers to any nucleotide/ amino acid sequence that targets the appended payload for degradation.
  • the adaptors target the payload for degradation directly thereby circumventing the need for ubiquitination reactions.
  • Proteasome adaptors may be used in conjunction with destabilizing domains to reduce the basal expression of the payload.
  • Exemplary proteasome adaptors include the UbL domain of Rad23 or hHR23b, HPV E7 which binds to both the target protein Rb and the S4 subunit of the proteasome with high affinity, which allows direct proteasome targeting, bypassing the ubiquitination machinery; the protein gankyrin which binds to Rb and the proteasome subunit S6.
  • Such biocircuits may be engineered to contain one, two, three, four or more tuned features.
  • microRNA sequences of the present invention include without limitation, any of those taught in Table 13 of copending commonly owned U.S. Provisional Patent Application No. 62/320,864 filed on 4/11/2017 or in US Provisional Application No. 62/466,596 filed March 3, 2017 and the International Publication WO2017/180587, the contents of each of which are incorporated herein by reference in their entirety.
  • the present invention provides polynucleotides encoding novel hDHFR DDs, effector modules comprising payloads and associated DDs, biocircuit systems comprising DDs and effector modules, and other components of the present invention.
  • polynucleotide or "nucleic acid molecule” in its broadest sense, includes any compound and/or substance that comprise a polymer of nucleotides, e.g., linked nucleosides. These polymers are often referred to as polynucleotides.
  • nucleic acids or polynucleotides of the invention include, but are not limited to, ribonucleic acids (RNAs), deoxyribonucleic acids (DNAs), threose nucleic acids (TNAs), glycol nucleic acids (GNAs), peptide nucleic acids (PNAs), locked nucleic acids (LNAs, including LNA having a ⁇ - D-ribo configuration, a-LNA having an a-L-ribo configuration (a diastereomer of LNA), 2'-amino-LNA having a 2'-amino functionalization, and 2'-amino- a-LNA having a 2'-amino functionalization) or hybrids thereof.
  • RNAs ribonucleic acids
  • DNAs deoxyribonucleic acids
  • TAAs threose nucleic acids
  • GNAs glycol nucleic acids
  • PNAs peptide nucleic acids
  • LNAs locked
  • polynucleotides of the invention may be a messenger RNA (mRNA) or any nucleic acid molecule and may or may not be chemically modified.
  • the nucleic acid molecule is a mRNA.
  • messenger RNA messenger RNA
  • mRNA refers to any polynucleotide which encodes a polypeptide of interest and which is capable of being translated to produce the encoded polypeptide of interest in vitro, in vivo, in situ or ex vivo.
  • the basic components of an mRNA molecule include at least a coding region, a 5'UTR, a 3'UTR, a 5' cap and a poly-A tail.
  • the present invention expands the scope of functionality of traditional mRNA molecules by providing payload constructs which maintain a modular organization, but which comprise one or more structural and/or chemical modifications or alterations which impart useful properties to the polynucleotide, for example tenability of function.
  • a payload constructs which maintain a modular organization, but which comprise one or more structural and/or chemical modifications or alterations which impart useful properties to the polynucleotide, for example tenability of function.
  • structural feature or modification is one in which two or more linked nucleosides are inserted, deleted, duplicated, inverted or randomized in a polynucleotide without significant chemical modification to the nucleosides themselves. Because chemical bonds will necessarily be broken and reformed to effect a structural modification, structural modifications are of a chemical nature and hence are chemical modifications. However, structural modifications will result in a different sequence of nucleotides. For example, the polynucleotide "ATCG” may be chemically modified to "AT-5meC-G". The same polynucleotide may be structurally modified from “ATCG” to "ATCCCG". Here, the dinucleotide "CC" has been inserted, resulting in a structural
  • polynucleotides of the present invention may harbor 5'UTR sequences which play a role in translation initiation.
  • 5'UTR sequences may include features such as Kozak sequences which are commonly known to be involved in the process by which the ribosome initiates translation of genes, Kozak sequences have the consensus XCCR(A/G)CC- start codon (AUG), where R is a purine (adenine or guanine) three bases upstream of the start codon (AUG) and X is any nucleotide.
  • the Kozak sequence is ACCGCC.
  • polynucleotides which may contain an internal ribosome entry site (IRES) which play an important role in initiating protein synthesis in the absence of 5' cap structure in the polynucleotide.
  • IRES may act as the sole ribosome binding site, or may serve as one of the multiple binding sites.
  • Polynucleotides of the invention containing more than one functional ribosome binding site may encode several peptides or polypeptides that are translated independently by the ribosomcs giving rise to bicistronic and/or multicistronic nucleic acid molecules.
  • polynucleotides encoding biocircuits, effector modules, DDs and payloads may include from about 30 to about 100,000 nucleotides (e.g., from 30 to 50, from 30 to 100, from 30 to 250, from 30 to 500, from 30 to 1,000, from 30 to 1,500, from 30 to 3,000, from 30 to 5,000, from 30 to 7,000, from 30 to 10,000, from 30 to 25,000, from 30 to 50,000, from 30 to 70,000, from 100 to 250, from 100 to 500, from 100 to 1,000, from 100 to 1,500, from 100 to 3,000, from 100 to 5,000, from 100 to 7,000, from 100 to 10,000, from 100 to 25,000, from 100 to 50,000, from 100 to 70,000, from 100 to 100,000, from 500 to 1,000, from 500 to 1,500, from 500 to 2,000, from 500 to 3,000, from 500 to 5,000, from 500 to 7,000, from 500 to 10,000, from 500 to 25,000, from 500 to 50,000, from 500 to 70,000, from 500 to
  • Regions of the polynucleotides which encode certain features such as cleavage sites, linkers, trafficking signals, tags or other features may range independently from 10-1,000 nucleotides in length (e.g., greater than 20, 30, 40, 45, 50, 55, 60, 70, 80, 90, 100, 120, 140, 160, 180, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, and 900 nucleotides or at least 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 70, 80, 90, 100, 120, 140, 160, 180, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, and 1,000 nucleotides).
  • polynucleotides of the present invention may further comprise embedded regulatory moieties such as microRNA binding sites within the 3'UTR of nucleic acid molecules which when bind to microRNA molecules, down-regulate gene expression either by reducing nucleic acid molecule stability or by inhibiting translation.
  • microRNA binding sites can be engineered out of (i.e. removed from) sequences in which they naturally occur in order to increase protein expression in specific tissues.
  • miR-142 and miR-146 binding sites may be removed to improve protein expression in the immune cells.
  • any of the encoded payloads may be may be regulated by an SRE and then combined with one or more regulatory sequences to generate a dual or multi-tuned effector module or biocircuit system.
  • polynucleotides of the present invention may encode fragments, variants, derivatives of polypeptides of the inventions.
  • the variant sequence may keep the same or a similar activity.
  • the variant may have an altered activity (e.g., increased or decreased) relative to the start sequence.
  • variants of a particular polynucleotide or polypeptide of the invention will have at least about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% but less than 100% sequence identity to that particular reference polynucleotide or polypeptide as determined by sequence alignment programs and parameters described herein and known to those skilled in the art.
  • Such tools for alignment include those of the BLAST suite (Stephen et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res., 1997, 25:3389-3402.)
  • polynucleotides of the present invention may be modified.
  • nucleoside is defined as a compound containing a sugar molecule (e.g., a pentose or ribose) or a derivative thereof in combination with an organic base (e.g., a purine or pyrimidine) or a derivative thereof (also referred to herein as “nucleobase”).
  • organic base e.g., a purine or pyrimidine
  • nucleotide is defined as a nucleoside including a phosphate group.
  • the modification may be on the internucleoside linkage (e.g., phosphate backbone).
  • phosphate backbone e.g., phosphate backbone
  • backbone phosphate groups can be modified by replacing one or more of the oxygen atoms with a different substituent.
  • the modified nucleosides and nucleotides can include the wholesale replacement of an unmodified phosphate moiety with another internucleoside linkage.
  • modified phosphate groups include, but are not limited to, phosphorothioate, phosphoroselenates, boranophosphates, boranophosphate esters, hydrogen phosphonates, phosphoramidates, phosphorodiamidates, alkyl or aryl phosphonates, and phosphotriesters.
  • Phosphorodithioates have both non-linking oxygens replaced by sulfur.
  • the phosphate linker can also be modified by the replacement of a linking oxygen with nitrogen (bridged phosphoramidates), sulfur (bridged phosphorothioates), and carbon (bridged methylene-phosphonates).
  • Other modifications which may be used are taught in, for example, Internationa] Application NO. WO2013/052523, the contents of which are incorporated herein by reference in their entirety.
  • nucleotides or nucleobases of the polynucleotides of the invention which are useful in the present invention include any modified substitutes known in the art, for example, ( ⁇ )l-(2-Hydroxypropyl)pseudouridine TP, (2R)-l-(2- Hydroxypropyl)pseudouridine TP, 1 ⁇ -Memoxy-phenylJpseudo-UTT ⁇ '-O-dimethyladenosine, l,2'-0-dimethylguanosine, l,2'-0-dimethylinosine, 1-Hexyl-pseudo-UTP, 1- Homoallylpseudouridine TP, l-Hydroxymethylpseudouridine TP, 1-iso-propyl-pseudo-UTP, 1- Me-2-thio-pseudo-UT
  • Xanthosine-5'-TP xylo-adenosine, zebularine, a-thio-adenosine, a-tWo-cytidine, a-thio- guanosine, and/or a-thio-uridine.
  • Polynucleotides of the present invention may comprise one or more of the
  • nucleotide analogs or other modification(s) may be located at any position(s) of a polynucleotide such that the function of the polynucleotide is not substantially decreased.
  • a modification may also be a 5' or 3' terminal modification.
  • the polynucleotide may contain from about 1% to about 100% modified nucleotides (either in relation to overall nucleotide content, or in relation to one or more types of nucleotide, i.e.
  • any one or more of A, G, U or C) or any intervening percentage e.g., from 1% to 20%, from 1% to 25%, from 1% to 50%, from 1% to 60%, from l%to 70%, from l%to 80%, from l%to 90%, from l%to 95%, from 10% to 20%, from 10% to 25%, from 10% to 50%, from 10% to 60%, from 10% to 70%, from 10% to 80%, from 10% to 90%, from 10% to 95%, from 10% to 100%, from 20% to 25%, from 20% to 50%, from 20% to 60%, from 20% to 70%, from 20% to 80%, from 20% to 90%, from 20% to 95%, from 20% to 100%, from 50% to 60%, from 50% to 70%, from 50% to 80%, from 50% to 90%, from 50% to 95%, fiom 50% to 100%, fiom 70% to 80%, from 70% to 90%, from 70% to 95%, from 70% to 100%, from 80% to 90%, from 80% to 95%, from 90% to 100%,
  • one or more codons of the polynucleotides of the present invention may be replaced with other codons encoding the native amino acid sequence to tune the expression of the SREs, through a process referred to as codon selection. Since mRNA codon, and tRNA anticodon pools tend to vary among organisms, cell types, sub cellular locations and over time, the codon selection described herein is a spatiotemporal (ST) codon selection.
  • ST spatiotemporal
  • certain polynucleotide features may be codon optimized.
  • Codon optimization refers to a process of modifying a nucleic acid sequence for enhanced expression in the host cell by replacing at least 1, 2, 3, 4, 5, 10, 15, 20, 25, 50 or more codons of the native sequence with codons that are most frequently used in the genes of that host cell while maintaining the native amino acid sequence.
  • Codon usage may be measured using the Codon Adaptation Index (CAI) which measures the deviation of a coding polynucleotide sequence from a reference gene set.
  • CAI Codon Adaptation Index
  • Codon usage tables are available at the Codon Usage Database (http://www.kazusa.or.jp/codon/) and the CAI can be calculated by EMBOSS CAI program (http://emboss.sourceforge.net/). Codon optimization methods are known in the art and may be useful in efforts to achieve one or more of several goals. These goals include to match codon frequencies in target and host organisms to ensure proper folding, bias nucleotide content to alter stability or reduce secondary structures, minimize tandem repeat codons or base runs that may impair gene construction or expression, customize transcriptional and translational control regions, insert or remove protein signaling sequences, remove/add post translation modification sites in encoded protein (e.g.
  • Codon optimization tools, algorithms and services are known in the art, and non-limiting examples include services from GeneArt (Life Technologies), DNA2.0 (Menlo Park CA), OptimumGene (GenScript,
  • a polynucleotide sequence or portion thereof is codon optimized using optimization algorithms. Codon options for each amino acid are well-known in the art as are various species table for optimizing for expression in that particular species.
  • certain polynucleotide features may be codon optimized. For example, a preferred region for codon optimization may be upstream (5 " ) or downstream (3') to a region which encodes a polypeptide. These regions may be incorporated into the polynucleotide before and/or after codon optimization of the payload encoding region or open reading frame (ORF).
  • the polynucleotide components are reconstituted and transformed into a vector such as, but not limited to, plasmids, viruses, cosmids, and artificial chromosomes.
  • Spatiotemporal codon selection may impact the expression of the polynucleotides of the invention, since codon composition determines the rate of translation of the mRNA species and its stability. For example, tRNA anticodons to optimized codons are abundant, and thus translation may be enhanced. In contrast, tRNA anticodons to less common codons are fewer and thus translation may proceed at a slower rate. Presnyak et al. have shown that the stability of an mRNA species is dependent on the codon content, and higher stability and thus higher protein expression may be achieved by utilizing optimized codons (Presnyak et al. (2015) Cell 160, 1111-1124; the contents of which are incorporated herein by reference in their entirety).
  • ST codon selection may include the selection of optimized codons to enhance the expression of the SRES, effector modules and biocircuits of the invention.
  • spatiotemporal codon selection may involve the selection of codons that are less commonly used in the genes of the host cell to decrease the expression of the compositions of the invention.
  • the ratio of optimized codons to codons less commonly used in the genes of the host cell may also be varied to tune expression.
  • certain regions of the polynucleotide may be preferred for codon selection.
  • a preferred region for codon selection may be upstream (5') or downstream (3') to a region which encodes a polypeptide. These regions may be incorporated into the polynucleotide before and/or after codon selection of the payload encoding region or open reading frame (ORF).
  • the stop codon of the polynucleotides of the present invention may be modified to include sequences and motifs to alter the expression levels of the SREs, payloads and effector modules of the present invention. Such sequences may be incorporated to induce stop codon readthrough, wherein the stop codon may specify amino acids e.g. selenocysteine or pyrrolysine. In other instances, stop codons may be skipped altogether to resume translation through an alternate open reading frame. Stop codon read through may be utilized to tune the expression of components of the effector modules at a specific ratio (e.g.as dictated by the stop codon context). Examples of preferred stop codon motifs include UGAN, UAAN, and UAGN, where N is either C or U.
  • Polynucleotide modifications and manipulations can be accomplished by methods known in the art such as, but not limited to, site directed mutagenesis and recombinant technology.
  • the resulting modified molecules may then be tested for activity using in vitro or in vivo assays such as those described herein or any other suitable screening assay known in the art.
  • polynucleotides of the invention may comprise two or more effector module sequences, or two or more payload sequences, which are in a pattern such as ABABAB or AABBAABBAABB or ABCABCABC or variants thereof repeated once, twice, or more than three times.
  • a pattern such as ABABAB or AABBAABBAABB or ABCABCABC or variants thereof repeated once, twice, or more than three times.
  • each letter, A, B, or C represent a different effector module component.
  • polynucleotides of the invention may comprise two or more effector module component sequences with each component having one or more SRE sequences (DD sequences), or two or more payload sequences.
  • the sequences may be in a pattern such as ABABAB or AABBAABBAABB or ABCABCABC or variants thereof repeated once, twice, or more than three times in each of the regions.
  • the sequences may be in a pattern such as ABABAB or
  • each letter, A, B, or C represent a different sequence or component.
  • polynucleotides encoding distinct biocircuits, effector modules, SREs and payload constructs may be linked together through the 3'-end using nucleotides which are modified at the 3'-terminus. Chemical conjugation may be used to control the stoichiometry of delivery into cells. Polynucleotides can be designed to be conjugated to other polynucleotides, dyes, intercalating agents (e.g. acridines), cross-linkers (e.g.
  • psoralene mitomycin C
  • porphyrins TPPC4, texaphyrin, Sapphyrin
  • polycyclic aromatic hydrocarbons e.g., phenazine, dihydrophenazine
  • artificial endonucleases e.g. EDTA
  • alkylating agents phosphate, amino, mercapto, PEG (e.g., PEG-40K), MPEG, [MPEG]2, polyamino, alkyl, substituted alkyl, radiolabeled markers, enzymes, haptens (e.g.
  • biotin e.g., aspirin, vitamin E, folic acid
  • transport/absorption facilitators e.g., aspirin, vitamin E, folic acid
  • synthetic ribonucleases proteins, e.g., glycoproteins, or peptides, e.g., molecules having a specific affinity for a co-ligand, or antibodies e.g., an antibody, that binds to a specified cell type such as a cancer cell, endothelial cell, or bone cell, hormones and hormone receptors, non-peptidic species, such as lipids, lectins, carbohydrates, vitamins, cofactors, or a drug. As non-limiting examples, they may be conjugates with other immune conjugates.
  • the compositions of the polynucleotides of the invention may generated by combining the various components of the effector modules using the Gibson assembly method.
  • the Gibson assembly reaction consists of three isothermal reactions, each relying on a different enzymatic activity including a 5' exonuclease which generates long overhangs, a polymerase which fills in the gaps of the annealed single strand regions and a DNA ligase which seals the nicks of the annealed and filled-in gaps.
  • Polymerase chain reactions are performed prior to Gibson assembly which may be used to generate PCR products with overlapping sequence. These methods can be repeated sequentially, to assemble larger and larger molecules.
  • the method can comprise repeating a method as above to join a second set of two or more DNA molecules of interest to one another, and then repeating the method again to join the first and second set DNA molecules of interest, and so on.
  • the assembled DNA can be amplified by transforming it into a suitable microorganism, or it can be amplified in vitro (e.g., with PCR).
  • polynucleotides of the invention may encode a fusion polypeptide comprising a destabilizing domain (DD) and at least one immune-therapeutic agent taught herein.
  • the DD domain may be a hDHFR mutant derived by site directed mutagenesis and may be selected from the single mutation hDHFR (Y122I) (e.g., the nucleic acid sequence of SEQ ID NO . 27 (starting from amino acid 2- 187 of the wild type hDHFR sequence) or the codon optimized nucleic acid sequence of SEQ ID NO. 28), double mutations hDHFR (M53T, R138I) (e.g., the nucleic acid sequence of SEQ ID NO.
  • hDHFR V75F, Y122I
  • hDHFR A125F, Y122I
  • hDHFR A125F, Y122I
  • hDHFR L74N, Y122I
  • hDHFR L94A, T147A
  • hDHFR G21T, Y122I
  • hDHFR V121A, Y122I
  • hDHFR Q36K, Y122I
  • triple mutations hDHFR Q36F, N65F, Y122I
  • the DHFR mutant may be derived by random mutagenesis and may include hDHFR mutant comprising the nucleic acid sequence of SEQ ID NO. 295-330.
  • the polynucleotides of the invention may encode effector modules comprising the hDHFR DD-CD19CAR fusion polypeptide comprising the nucleotide sequence of SEQ ID NO. 159-162, 273, 275, or 346-347 or hDHFR DD-IL15/IL15Ra fusion polypeptide comprising the nucleotide sequence of SEQ ID NO. 178-180, or hDHFR DD-IL 12 fusion polypeptide comprising the nucleotide sequence of SEQ ID NO. 226-227; or a hDHFR DD- Caspase 9 fusion polypeptide comprising the nucleotide sequence of SEQ ID NO. 354-356.
  • the present invention further provides pharmaceutical compositions comprising the DDs of the invention, one or more stimuli, effector modules and biocircuit systems comprising the same, and optionally at least one pharmaceutically acceptable excipient or inert ingredient.
  • the term "pharmaceutical composition” refers to a preparation of activate agents (e.g., DDs, ligands of the DDs, effector modules and biocircuits), other components, vectors, cells and described herein, or pharmaceutically acceptable salts thereof, optionally with other chemical components such as physiologically suitable carriers and excipients.
  • the pharmaceutical compositions of the invention comprise an effective amount of one or more active compositions of the invention.
  • the preparation of a pharmaceutical composition that contains at least one composition of the present invention and/or an additional active ingredient will be known to those skilled in the art in light of the present disclosure, as exemplified by Remington's Pharmaceutical Sciences, 18th Ed. Mack Printing Company, 1990, incorporated herein by reference.
  • excipient or “inert ingredient” refers to an inactive substance added to a pharmaceutical composition and formulation to further facilitate administration of an active ingredient.
  • active ingredient generally refers to any one or more biocircuits, effector modules, DDs, stimuli and payloads (i.e., immunotherapeutic agents), other components, vectors, and cells to be delivered as described herein.
  • pharmaceutically acceptable refers to molecular entities and compositions that do not produce an adverse, allergic or other untoward reaction when administered to an animal, such as, for example, a human, as appropriate.
  • compositions and formulations are administered to humans, human patients or subjects.
  • pharmaceutical compositions are principally directed to pharmaceutical compositions which are suitable for administration to humans, it will be understood by the skilled artisan that such compositions are generally suitable for administration to any other animal, e.g., to non-human animals, e.g. non-human mammals.
  • Subjects to which administration of the pharmaceutical compositions is contemplated include, but are not limited to, non-human mammals, including agricultural animals such as cattle, horses, chickens and pigs, domestic animals such as cats, dogs, or research animals such as mice, rats, rabbits, dogs and non-human primates. It will be understood that, for human administration, preparations should meet sterility, pyrogenicity, general safety and purity standards as required by FDA Office of Biological Standards.
  • a pharmaceutical composition and formulation in accordance with the invention may be prepared, packaged, and/or sold in bulk, as a single unit dose, and/or as a plurality of single unit doses.
  • a "unit dose" is discrete amount of the pharmaceutical composition comprising a predetermined amount of the active ingredient.
  • the amount of the active ingredient is generally equal to the dosage of the active ingredient which would be administered to a subject and/or a convenient fraction of such a dosage such as, for example, one-half or one-third of such a dosage.
  • compositions of the present invention may be formulated in any manner suitable for delivery.
  • the formulation may be, but is not limited to, nanoparticles, poly (lactic-co- glycolic acid) (PLGA) microspheres, lipidoids, lipoplex, liposome, polymers, carbohydrates (including simple sugars), canonic lipids and combinations thereof.
  • PLGA poly (lactic-co- glycolic acid)
  • the formulation is a nanoparticle which may comprise at least one lipid.
  • the lipid may be selected from, but is not limited to, DLin-DMA, DLin-K-DMA, 98N12- 5, C12-200, DLin-MC3-DMA, DLin-KC2-DMA, DODMA, PLGA, PEG, PEG-DMG and PEGylated lipids.
  • the lipid may be a cationic lipid such as, but not limited to, DLin-DMA, DLin-D-DMA, DLin-MC3-DMA, DLin-KC2-DMA and DODMA.
  • the formulation may be selected from any of those taught, for example, in International Application PCT/US2012/069610, the contents of which are incorporated herein by reference in its entirety.
  • compositions in accordance with the invention will vary, depending upon the identity, size, and/or condition of the subject treated and further depending upon the route by which the composition is to be administered.
  • the composition may comprise between 0.1% and 100%, e.g., between 0.5 and 50%, between 1-30%, between 5-80%, at least 80% (w/w) active ingredient.
  • Efficacy of treatment or amelioration of disease can be assessed, for example by measuring disease progression, disease remission, symptom severity, reduction in pain, quality of life, dose of a medication required to sustain a treatment effect, level of a disease marker or any other measurable parameter appropriate for a given disease being treated or targeted for prevention. It is well within the ability of one skilled in the art to monitor efficacy of treatment or prevention by measuring any one of such parameters, or any combination of parameters.
  • compositions of the present invention "effective against” for example a cancer, indicates that administration in a clinically appropriate manner results in a beneficial effect for at least a statistically significant fraction of patients, such as an improvement of symptoms, a cure, a reduction in disease load, reduction in tumor mass or cell numbers, extension of life, improvement in quality of life, or other effect generally recognized as positive by medical doctors familiar with treating the particular type of cancer.
  • a treatment or preventive effect is evident when there is a statistically significant improvement in one or more parameters of disease status, or by a failure to worsen or to develop symptoms where they would otherwise be anticipated.
  • a favorable change of at least 10% in a measurable parameter of disease, and preferably at least 20%, 30%, 40%, 50% or more can be indicative of effective treatment.
  • Efficacy for a given composition or formulation of the present invention can also be judged using an experimental animal model for the given disease as known in the art. When using an experimental animal model, efficacy of treatment is evidenced when a statistically significant change is observed.
  • the polypeptides of the invention may be delivered to the cell directly.
  • the polypeptides of the invention may be delivered using synthetic peptides comprising an endosomal leakage domain (ELD) fused to a cell penetration domain (CLD).
  • ELD endosomal leakage domain
  • CLD cell penetration domain
  • the polypeptides of the invention are co introduced into the cell with the ELD-CLD- synthetic peptide.
  • ELDs facilitate the escape of proteins that are trapped in the endosome, into the cytosol.
  • Such domains are derived proteins of microbial and viral origin and have been described in the art.
  • CPDs allow the transport of proteins across the plasma membrane and have also been described in the art.
  • the ELD-CLD fusion proteins synergistically increase the transduction efficiency when compared to the co-transduction with either domain alone.
  • a histidine rich domain may optionally be added to the shuttle construct as an additional method of allowing the escape of the cargo from the endosome into the cytosol.
  • the shuttle may also include a cysteine residue at the N or C terminus to generate muhimers of the fusion peptide. Multimers of the ELD-CLD fusion peptides generated by the addition of cysteine residue to the terminus of the peptide show even greater transduction efficiency when compared to the single fusion peptide constructs.
  • polypeptides of the invention may also be appended to appropriate localization signals to direct the cargo to the appropriate sub-cellular location e.g. nucleus.
  • appropriate localization signals e.g. nucleus.
  • WO2017175072 may be useful in the present invention (the contents of each of which are herein incorporated by reference in their entirety).
  • cancers may be treated with pharmaceutical compositions, biocircuits, biocircuit components, effector modules including their SREs or payloads of the present invention.
  • cancer refers to any of various malignant neoplasms characterized by the proliferation of anaplastic cells that tend to invade surrounding tissue and metastasize to new body sites and also refers to the pathological condition characterized by such malignant neoplastic growths.
  • Cancers may be tumors or hematological malignancies, and include but are not limited to, all types of lymphomas/leukemias, carcinomas and sarcomas, such as those cancers or tumors found in the anus, bladder, bile duct, bone, brain, breast, cervix, colon/rectum, endometrium, esophagus, eye, gallbladder, head and neck, liver, kidney, larynx, lung, mediastinum (chest), mouth, ovaries, pancreas, penis, prostate, skin, small intestine, stomach, spinal marrow, tailbone, testicles, thyroid and uterus.
  • lymphomas/leukemias such as those cancers or tumors found in the anus, bladder, bile duct, bone, brain, breast, cervix, colon/rectum, endometrium, esophagus, eye, gallbladder, head and neck, liver, kidney, larynx, lung, mediastinum (ches
  • Types of carcinomas which may be treated with the compositions of the present invention include, but are not limited to, papilloma/carcinoma, choriocarcinoma, endodermal sinus tumor, teratoma, adenoma/adenocarcinoma, melanoma, fibroma, lipoma, leiomyoma, rhabdomyoma, mesothelioma, angioma, osteoma, chondroma, glioma, lymphoma/leukemia, squamous cell carcinoma, small cell carcinoma, large cell undifferentiated carcinomas, basal cell carcinoma and sinonasal undifferentiated carcinoma.
  • Types of carcinomas which may be treated with the compositions of the present invention include, but are not limited to, soft tissue sarcoma such as alveolar soft part sarcoma, angiosarcoma, derrnatofibrosarcoma, desmoid tumor, desmoplastic small round cell tumor, extraskeletal chondrosarcoma, extraskeletal osteosarcoma, fibrosarcoma, hemangiopericytoma, hemangiosarcoma, Kaposi's sarcoma, leiomyosarcoma, liposarcoma, lymphangiosarcoma, lymphosarcoma, malignant fibrous histiocytoma, neurofibrosarcoma, rhabdomyosarcoma, synovial sarcoma, and Askin's tumor, Ewing's sarcoma (primitive neuroectodermal tumor), malignant hemangioendothelioma, malignant schwannoma,
  • Cholangiocarcinoma Chondrosarcoma, Chronic lymphocytic leukemia, Chronic myelogenous leukemia, Colon cancer, Colorectal cancer, Craniopharyngioma, Cutaneous lymphoma,
  • Cutaneous melanoma Diffuse astrocytoma, Ductal carcinoma in situ, Endometrial cancer, Ependymoma, Epithelioid sarcoma, Esophageal cancer, Ewing sarcoma, Extrahepatic bile duct cancer, Eye cancer, Fallopian tube cancer, Fibrosarcoma, Gallbladder cancer, Gastric cancer, Gastrointestinal cancer, Gastrointestinal carcinoid cancer, Gastrointestinal stromal tumors, General, Germ cell tumor, Glioblastoma multiforme, Glioma, Hairy cell leukemia, Head and neck cancer, Hemangioendothelioma, Hodgkin lymphoma, Hodgkin's disease, Hodgkin's lymphoma, Hypopharyngeal cancer, Infiltrating ductal carcinoma, Infiltrating lobular carcinoma, Inflammatory breast cancer, Intestinal Cancer, Intrahepatic bile duct cancer
  • Laryngeal cancer Leiomyosarcoma, Leptomeningeal metastases, Leukemia, Lip cancer, Lipo sarcoma.
  • Liver cancer Lobular carcinoma in situ, Low-grade astrocytoma, Lung cancer, Lymph node cancer, Lymphoma, Male breast cancer, Medullary carcinoma, Medulloblastoma, Melanoma, Meningioma, Merkel cell carcinoma, Mesenchymal chondrosarcoma,
  • Oligodendroglioma Oral cancer, Oral cavity cancer.
  • Oropharyngeal cancer Osteogenic sarcoma, Osteosarcoma, Ovarian cancer, Ovarian epithelial cancer, Ovarian germ cell tumor, Ovarian primary peritoneal carcinoma, Ovarian sex cord stromal tumor, Paget's disease, Pancreatic cancer, Papillary carcinoma, Paranasal sinus cancer, Parathyroid cancer, Pelvic cancer.
  • Penile cancer Peripheral nerve cancer, Peritoneal cancer, Pharyngeal cancer, Pheochromocytoma, Pilocytic astrocytoma, Pineal region tumor, Pineoblastoma, Pituitary gland cancer, Primary central nervous system lymphoma, Prostate cancer. Rectal cancer, Renal cell cancer.
  • Renal pelvis cancer Rhabdomyosarcoma, Salivary gland cancer, Sarcoma, Sarcoma, bone, Sarcoma, soft tissue, Sarcoma, uterine, Sinus cancer, Skin cancer, Small cell lung cancer, Small intestine cancer, Soft tissue sarcoma, Spinal cancer, Spinal column cancer, Spinal cord cancer, Spinal tumor, Squamous cell carcinoma, Stomach cancer, Synovial sarcoma, T-cell lymphoma ), Testicular cancer, Throat cancer, Thymoma / thymic carcinoma, Thyroid cancer, Tongue cancer, Tonsil cancer, Transitional cell cancer, Transitional cell cancer, Transitional cell cancer, Triple- negative breast cancer, Tubal cancer, Tubular carcinoma, Ureteral cancer, Ureteral cancer, Urethral cancer, Uterine adenocarcinoma, Uterine cancer, Uterine sarcoma, Vaginal cancer, and Vulvar cancer.
  • the invention further relates to the use of pharmaceutical compositions, biocircuits, biocircuit components, effector modules including their SREs or payloads of the present invention for treating one or more forms of cancer, in combination with other pharmaceuticals and/or other therapeutic methods, e.g., with known pharmaceuticals and/or known therapeutic methods, such as, for example, those which are currently employed for treating these disorders.
  • the pharmaceutical compositions, biocircuits, biocircuit components, effector modules including their SREs or payloads of the present invention can also be administered in conjunction with one or more additional anti-cancer treatments, such as biological,
  • a treatment can include, for example, imatinib (Gleevac), all-trans-retinoic acid, a monoclonal antibody treatment (gemtuzumab, ozogamicin), chemotherapy (for example, chlorambucil, prednisone, prednisolone, vincristine, cytarabine, clofarabine, farnesyl transferase inhibitors, decitabine, inhibitors of MDR1), rituximab, interferon- ⁇ anthracycline drugs (such as daunorubicin or idarubicin), L-asparaginase, doxorubicin, cyclophosphamide, doxorubicin, bleomycin, fludarabine, etoposide, pentostatin, or cladribine), bone marrow transplant, stem cell transplant, radiation therapy, anti-metabolite drugs (methotrexate and 6-mercaptopurine), or
  • Radiation therapy is the use of ionizing radiation to kill cancer cells and shrink tumors. Radiation therapy can be administered externally via external beam radiotherapy (EBRT) or internally via brachytherapy. The effects of radiation therapy are localized and confined to the region being treated. Radiation therapy may be used to treat almost every type of solid tumor, including cancers of the brain, breast, cervix, larynx, lung, pancreas, prostate, skin, stomach, uterus, or soft tissue sarcomas. Radiation is also used to treat leukemia and lymphoma.
  • Chemotherapy is the treatment of cancer with drugs that can destroy cancer cells.
  • chemotherapy usually refers to cytotoxic drugs which affect rapidly dividing cells in general, in contrast with targeted therapy.
  • Chemotherapy drugs interfere with cell division in various possible ways, e.g. with the duplication of DNA or the separation of newly formed chromosomes.
  • Most forms of chemotherapy target all rapidly dividing cells and are not specific to cancer cells, although some degree of specificity may come from the inability of many cancer cells to repair DNA damage, while normal cells generally can.
  • chemotherapeutic agents include, but are not limited to, 5-FU Enhancer, 9-AC, AG2037, AG3340, Aggrecanase Inhibitor, Aminoglutethimide, Amsacrine (m-AMSA), Asparaginase, Azacitidine, Batimastat (BB94), BAY 12-9566, BCH-4556, Bis-Naphtalimide, Busulfan, Capecitabine, Carboplatin, Carmustaine+Polifepr Osan, cdk4/cdk2 inhibitors, Chlorambucil, CI-994, Cisplatin, Cladribine, CS-682, Cytarabine HC1, D2163, Dactinomycin, Daunorubicin HC1, DepoCyt, Dexifosamide, Docetaxel, Dolastain, Doxifluridine, Doxorubicin, DX8951f, E
  • compositions, biocircuits, biocircuit components, effector modules including their SREs or payloads of the present invention may be used in the modulation or alteration or exploitation of the immune system to target one or more cancers.
  • This approach may also be considered with other such biological approaches, e.g., immune response modifying therapies such as the administration of interferons, interleukins, colony-stimulating factors, other monoclonal antibodies, vaccines, gene therapy, and nonspecific immunomodulating agents are also envisioned as anti-cancer therapies to be combined with the pharmaceutical compositions, biocircuits, biocircuit components, effector modules including their SREs or payloads of the present invention.
  • Cancer immunotherapy refers to a diverse set of therapeutic strategies designed to induce the patient's own immune system to fight the cancer.
  • therapeutic strategies designed to induce the patient's own immune system to fight the cancer.
  • compositions, biocircuits, biocircuit components, effector modules including their SREs or payloads of the present invention are designed as immune-oncology therapeutics. 6.
  • Cell therapies are designed as immune-oncology therapeutics. 6.
  • TIL tumor infiltrating lymphocyte
  • CARs genetically engineered T cells bearing chimeric antigen receptors
  • the biocircuits and systems may be used in the development and implementation of cell therapies such as adoptive cell therapy.
  • the biocircuits, their components, effector modules and their SREs and payloads may be used in cell therapies to effect TCR removal -TCR gene disruption, TCR engineering, to regulate epitope tagged receptors, in A PC platforms for stimulating T cells, as a tool to enhance ex vivo APC stimulation, to improve methods of T cell expansion, in ex vivo stimulation with antigen, in TCR/CAR combinations, in the manipulation or regulation of TILs, in allogeneic cell therapy, in combination T cell therapy with other treatment lines (e.g.
  • cytokines to encode engineered TCRs, or modified TCRs, or to enhance T cells other than TCRs (e.g by introducing cytokine genes, genes for the checkpoint inhibitors PD1, CTLA4).
  • improved response rates are obtained in support of cell therapies.
  • Expansion and persistence of cell populations may be achieved through regulation or fine tuning of the payloads, e.g., the receptors or pathway components in T cells, NK cells or other immune-related cells.
  • biocircuits, their components, SREs or effector modules are designed to spatially and/or temporally control the expression of proteins which enhance T-cell or NK cell response.
  • biocircuits, their components, SREs or effector modules are designed to spatially and/or temporally control the expression of proteins which inhibit T-cell or NK cell response.
  • biocircuits, their components, SREs or effector modules are designed to reshape the tumor microenvironment in order to extend utility of the biocircuit or a pharmaceutical composition beyond direct cell killing.
  • biocircuits, their components, SREs or effector modules are designed to reduce, mitigate or eliminate the CAR cytokine storm. In some embodiments such reduction, mitigation and/or elimination occurs in solid tumors or tumor microenvironments.
  • the effector modules may encode one or more cytokines.
  • the cytokine is IL15.
  • Effector modules encoding IL15 may be designed to induce proliferation in cytotoxic populations and avoid stimulation of T regs. In other cases, the effector modules which induce proliferation in cytotoxic populations may also stimulate NK and NKT cells.
  • effector modules may encode, or be tuned or induced to produce, one or more cytokines for expansion of cells in the biocircuits of the invention.
  • the cells may be tested for actual expansion. Expansion may be at least 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or more.
  • the tumor microenvironment may be remodeled using a biocircuit containing an effector module encoding IL17.
  • biocircuits, their components, SREs or effector modules are designed to modulate Tregs to attenuate autoimmune disorders.
  • IL2 may be regulated using a singly tuned module or one having multiple tuned features as described herein.
  • biocircuits, their components, SREs or effector modules are designed to be significantly less immunogenic than other biocircuits or switches in the art.
  • the term refers to a detectable decrease in immunogenicity.
  • the term refers to a fold decrease in immunogenicity.
  • the term refers to a decrease such that an effective amount of the biocircuits, their components, SREs or effector modules which can be administered without triggering a detectable immune response.
  • the term refers to a decrease such that the biocircuits, their components, SREs or effector modules can be repeatedly administered without eliciting an immune response.
  • the decrease is such that the biocircuits, their components, SREs or effector modules can be repeatedly administered without eliciting an immune response.
  • the biocircuits, their components, SREs or effector modules is 2-fold less immunogenic than its unmodified counterpart or reference compound.
  • immunogenicity is reduced by a 3-fold factor.
  • immunogenicity is reduced by a S-fold factor.
  • immunogenicity is reduced by a 7-fold factor.
  • immunogenicity is reduced by a 10-fold factor.
  • immunogenicity is reduced by a 15-fold factor.
  • immunogenicity is reduced by a fold factor.
  • immunogenicity is reduced by a 50-fold factor. In another embodiment, immunogenicity is reduced by a 100-fold factor. In another embodiment, immunogenicity is reduced by a 200-fold factor. In another embodiment, immunogenicity is reduced by a 500-fold factor. In another embodiment, immunogenicity is reduced by a 1000-fold factor. In another embodiment, immunogenicity is reduced by a 2000-fold factor. In another embodiment, immunogenicity is reduced by another fold difference.
  • Methods of determining immunogenicity include, e.g. measuring secretion of cytokines (e.g. IL12, IFNalpha, TNF-alpha, RANTES, MlP-lalphaor beta, IL6, IFN-beta, or IL8), measuring expression of DC activation markers (e.g. CD83, HLA- DR, CD80 and CD86), or measuring ability to act as an adjuvant for an adaptive immune response.
  • cytokines e.g. IL12, IFNalpha, TNF-alpha, RANTES, MlP-lalphaor beta, IL6, IFN-beta, or IL8
  • DC activation markers e.g. CD83, HLA- DR, CD80 and CD86
  • the chimeric antigen receptor (CAR) of the present invention may be a conditionally active CAR.
  • a wild type protein or domain thereof, such as those described herein may be used to generate a conditionally active biologic protein which are reversibly or irreversibly inactivated at the wild type normal physiological conditions as well as to such conditionally active biologic proteins and domains and uses of such conditional active biologic proteins and domains are provided.
  • Such methods and conditionally active proteins are taught in, for example, International Publication No. WO2016033331, the contents of which are incorporated herein by reference in their entirety.
  • the CAR comprises at least one antigen specific targeting region evolved from a wild type protein or a domain thereof and one or more of a decrease in activity in the assay at the normal physiological condition compared to the antigen specific targeting region of the wild-type protein or a domain thereof, and an increase in activity in the assay under the aberrant condition compared to the antigen specific targeting region of the wild-type protein or a domain thereof.
  • infectious diseases may be treated with pharmaceutical compositions, biocircuits, biocircuit components, effector modules including their SREs or payloads of the present invention.
  • infectious disease refers to any disorders caused by organisms such as bacteria, viruses, fungi or parasites.
  • infectious disease may be Acute bacterial rhinosinusitis, 14-day measles.
  • ACA Acrodermatitis chronica atrophicans
  • ATLL American T-cell Leukemia- Lymphoma
  • AIDS Acquired Immunodeficiency
  • Amebiasis Amebic meningoencephalitis, Anaplasmosis, Anthrax, Arboviral or parainfectious, Ascariasis -(Roundworm infections ), Aseptic meningitis, Athlete's foot (Tinea pedis ), Australian tick typhus, Avian Influenza, Babesiosis, Bacillary angiomatosis. Bacterial meningitis, Bacterial vaginosis, Balanitis, Balantidiasis, Bang's disease.
  • Barman Forest virus infection Bartonellosis (Verruga peruana; Carrion's disease; Oroya fever ), Bat Lyssavirus Infection, Bay sore (Chiclero's ulcer ), Baylisascaris infection (Racoon roundworm infection), Beaver fever, Beef tapeworm, Bejel (endemic syphilis ), Biphasic meningoencephalitis, Black Bane, Black death, Black piedra, Blackwater Fever, Blastomycosis, Blennorrhea of the newborn, Blepharitis, Boils, Bornholm disease (pleurodynia), Borrelia miyamotoi Disease, Botulism, Boutonneuse fever, Brazilian purpuric fever, Break Bone fever, Brill, Bronchiolitis, Bronchitis, Brucellosis (Bang's disease ), Bubonic plague, Bullous impetigo, Burkholderia mallei
  • Campylobacteriosis Candidiasis, Canefield fever (Canicola fever; 7-day fever; Weil's disease; leptospirosis; canefield fever), Canicola fever, Capillariasis, Carate, Carbapenem-resistant Enterobacteriaceae (CRE), Carbuncle, Carrion's disease, Cat Scratch fever, Cave disease, Central Asian hemorrhagic fever, Central European tick, Cervical cancer, Chagas disease, Chancroid (Soft chancre ), Chicago disease, Chickenpox (Varicella), Chiclero's ulcer, Chikungunya fever, Chlamydial infection.
  • Cryptococcosis Cryptosporidiosis (Crypto), Cutaneous Larval Migrans, Cyclosporiasis, Cystic hydatid, Cysticercosis, Cystitis, Czechoslovak tick, D68 (EV-D68), Dacryocytitis, Dandy fever, Darling's Disease, Deer fly fever, Dengue fever (1, 2, 3 and 4), Desert rheumatism, Devil's grip, Diphasic milk fever, Diphtheria, Disseminated Intravascular Coagulation, Dog tapeworm, Donovanosis, Donovanosis (Granuloma inguinale), Dracontiasis, Dracunculosis, Duke's disease, Dum Dum Disease, Durand-Nicholas-Favre disease, Dwarf tapeworm, E.
  • Coli infection (Kcoli), Eastern equine encephalitis, Ebola Hemorrhagic Fever (Ebola virus disease EVD), Ectothrix, Ehrlichiosis (Sennetsu fever).
  • Encephalitis Endemic Relapsing fever, Endemic syphilis, Endophthalmitis, Endothrix, Enterobiasis (Pinworm infection), Enterotoxin - B Poisoning (Staph Food Poisoning), Enterovirus Infection, Epidemic Keratoconjunctivitis, Epidemic Relapsing fever, Epidemic typhus, Epiglottitis, Erysipelis, Erysipeloid (Erysipelothricosis), Erythema chronicum migrans, Erythema infectiosum, Erythema marginatum.
  • HUS Hemolytic Uremic Syndrome
  • Hepatitis A Hepatitis B, Hepatitis C, Hepatitis D, Hepatitis E, Herpangina, Herpes- genital, Herpes labialis, Herpes- neonatal, Hidradenitis, Histoplasmosis, Histoplasmosis infection (Histoplasmosis), His-Werner disease, HIV infection, Hookworm infections, Hordeola, Hordeola (Stye), HTLV, HTLV- associated
  • Leptospirosis Naukayami fever; Weil's disease), Listeriosis (Listeria), Liver fluke infection, Lobo's mycosis, Lockjaw, Loiasis, Louping 111, Ludwig's angina, Lung fluke infection, Lung fluke infection (Paragonimiasis), Lyme disease, Lymphogranuloma venereum infection (LGV), Machupo Cambodian hemorrhagic fever, Madura foot, Mai del pinto, Malaria, Malignant pustule, Malta fever, Marburg hemorrhagic fever, Masters disease, Maternal Sepsis (Puerperal fever), Measles, Mediterranean spotted fever, Melioidosis (Whitmore's disease), Meningitis,
  • MERS Meningococcal Disease
  • MERS Milker's nodule, Molluscum contagiosum
  • Moniliasis monkeypox
  • Mononucleosis Mononucleosis-like syndrome
  • Montezuma's Revenge Morbilli
  • MRSA methicillin-resistant Staphylococcus aureus
  • Mucormycosis- Zygomycosis Multiple Organ Dysfunction Syndrome or MODS
  • MSA Multiple-system atrophy
  • Mumps Murine typhus, Murray Valley Encephalitis(MVE), Mycoburuli ulcers, Mycoburuli ulcers- Buruli ulcers, Mycotic vulvovaginitis, Myositis, Nanukayami fever, Necrotizing fasciitis, Necrotizing fasciitis- Type 1, Necrotizing fasciitis- Type 2, Negishi, New world spotted fever, Nocardiosis, Nongonococcal urethritis, Non-Polio (Non-Pol
  • Pustular Rash diseases Small pox
  • Pyelonephritis Pylephlebitis
  • Q-Fever Quinsy
  • Quintana fever 5-day fever
  • Rabbit fever Rabies, Racoon roundworm infection
  • Rat bite fever Rat bite fever
  • Panencephalitis SSPE
  • Sudden Acute Respiratory Syndrome Sudden Rash
  • Swimmer's ear Swimmer's Itch
  • swimming Pool conjunctivitis Sylvatic yellow fever
  • Syphilis Systemic Inflammatory Response Syndrome (SIRS)
  • Tabes dorsalis tertiary syphilis
  • Taeniasis Taiga encephalitis, Tanner's disease
  • Tapeworm infections Temporal lobe encephalitis
  • Temporal lobe encephalitis Temporal lobe encephalitis
  • tetani Lock Jaw
  • Tetanus Infection Threadworm infections, Thrush, Tick, Tick typhus.
  • Trichinellosis Trichomoniasis, Trichomycosis axillaris, Trichuriasis, Tropical Spastic
  • TSP Trypanosomiasis
  • Tuberculosis TB
  • Tuberculosis Tularemia
  • Typhoid Fever Typhus fever, Ulcus molle
  • Undulant fever Urban yellow fever, Urethritis, Vaginitis, Vaginosis, Vancomycin Intermediate (VISA), Vancomycin Resistant (VRSA), Varicella, Venezuelan Equine encephalitis, Verruga peruana, Vibrio cholerae (Cholera), Vibriosis (Vibrio), Vincent's disease or Trench mouth, Viral conjunctivitis, Viral Meningitis, Viral
  • meningoencephalitis Viral rash, Visceral Larval Migrans, Vomito negro, Vulvovaginitis, Warts, Waterhouse, Weil's disease, West Nile Fever, Western equine encephalitis, Whipple's disease.
  • Respiratory syncytial virus (RSV), Herpes simplex virus 1 and 2, Human Cytomegalovirus, Epstein-Barr virus, Varicella zoster virus, Coronaviruses, Poxviruses, Enterovirus 71, Rubella virus, Human papilloma virus, Streptococcus pneumoniae, Streptococcus viridans.,
  • Staphylococcus aureus S. aureus
  • Methicillin-resistant Staphylococcus aureus MRSA
  • Vancomycin-intermediate Staphylococcus aureus VSA
  • Vancomycin-resistant Staphylococcus aureus VRSA
  • Staphylococcus epidermidis S. epidermidis
  • Clostridium Tetani Bordetella pertussis, Bordetella paratussis, Mycobacterium, Francisella Tularensis, Toxoplasma gondii, Candida (C. albicans, C. glabrata, C. parapsilosis, C. tropicalis, C. krusei and C. lusitaniae) and/or any other infectious diseases, disorders or syndromes.
  • toxins may be treated with pharmaceutical compositions, biocircuits, biocircuit components, effector modules including their SREs or payloads of the present invention.
  • Non- limited examples of toxins include Ricin, Bacillus anthracis, Shiga toxin and Shiga-like toxin, Botulinum toxins.
  • Various tropical diseases may be treated with pharmaceutical compositions, biocircuits, biocircuit components, effector modules including their SREs or payloads of the present invention.
  • Non-limited examples of tropical diseases include Chikungunya fever, Dengue fever, Chagas disease, Rabies, Malaria, Ebola virus, Marburg virus, West Nile Virus, Yellow Fever, Japanese encephalitis virus, St. Louis encephalitis virus.
  • fbodborne illnesses and gastroenteritis may be treated with pharmaceutical compositions, biocircuits, biocircuit components, effector modules including their SREs or payloads of the present invention.
  • gastroenteritis include Rotavirus, Norwalk virus (Noro virus), Campylobacter jejuni, Clostridium difficile, Entamoeba histolytica, Helicobacter pylori, Enterotoxin B of Staphylococcus aureus, Hepatitis A virus (HAV), Hepatitis E, Listeria monocytogenes, Salmonella, Clostridium perfringens, and Salmonella.
  • infectious agents may be treated with pharmaceutical compositions, biocircuits, biocircuit components, effector modules including their SREs or payloads of the present invention.
  • infectious agents include adenoviruses, Anaplasma phagocytophilium, Ascaris lumbricoides, Bacillus anthracis, Bacillus cereus, Bacteriodes sp, Barman Forest virus, Bartonella bacilliformis, Bartonella henselae, Bartonella quintana, beta- toxin of Clostridium perfringens, Bordetella pertussis, Bordetella parapertussis, Borrelia burgdorferi, Borrelia miyamotoi, Borrelia recurrentis, Borrelia sp., Botulinum toxin, Brucella sp., Burkholderia pseudomallei, California encephalitis virus, Campylobacter, Candida albicans, chikungunya
  • Clostridium difficile bacteria Clostridium tetani, Colorado tick fever virus, Corynebacterium diphtheriae, Corynebacterium minutissimum, Coxiella burnetii, coxsackie A, coxsackie B, Crimean-Congo hemorrhagic fever virus, cytomegalovirus, dengue virus, Eastern Equine encephalitis virus, Ebola viruses, echovirus, Ehrlichia chaffeensis., Ehrlichia equi., Ehrlichia sp., Entamoeba histolytica, Enterobacter sp., Enterococcus faecalis, Enterovirus 71, Epstein-Barr virus (EBV), Erysipelothrix rhusiopathiae, Escherichia coli, Flavivirus, Fusobacterium necrophorum, Gardnerella vaginalis, Group B streptococcus, Haemophilus ae
  • Streptococcus agalactiae Streptococcus group A-H, Streptococcus pneumoniae, Streptococcus pyogenes, Treponema pallidum subsp. Pallidum, Treponema pallidum var. carateum,
  • rare diseases may be treated with pharmaceutical compositions, biocircuits, biocircuit components, effector modules including their SREs or payloads of the present invention.
  • the term "rare disease” refers to any disease that affects a small percentage of the population.
  • the rare disease may be
  • Acrocephalosyndactylia Acrodermatitis, Addison Disease, Adie Syndrome, Alagille Syndrome, Amylose, Amyotrophic Lateral Sclerosis, Angelman Syndrome, Angiolymphoid Hyperplasia with Eosinophilia, Amold-Chiari Malformation, Arthritis, Juvenile Rheumatoid, Asperger Syndrome, Bardet-Biedl Syndrome, Barrett Esophagus, Beckwith-Wiedemann Syndrome, Behcet Syndrome, Bloom Syndrome, Bowen's Disease, Brachial Plexus Neuropathies, Brown- Sequard Syndrome, Budd-Chiari Syndrome, Burkitt Lymphoma, Carcinoma 256, Walker, Caroli Disease, Charcot-Marie-Tooth Disease, Chediak-Higashi Syndrome, Chiari-Frommel Syndrome, Chondrodysplasia Punctata, Colonic Pseudo-Obstruction, Colorectal Neoplasms, Hereditary Nonpolyposis, Craniofa
  • Hyperaldosteronism Hyperhidrosis, Hyperostosis, Diffuse Idiopathic Skeletal, Hypopituitarism, Inappropriate ADH Syndrome, Intestinal Polyps, Isaacs Syndrome, Kartagener Syndrome, Kearns-Sayre Syndrome, Klippel-Feil Syndrome, Klippel-Trenaunay-Weber Syndrome, Kluver- Bucy Syndrome, Korsakoff Syndrome, Lafora Disease, Lambert-Eaton Myasthenic Syndrome, Landau-Kleffher Syndrome, Langer-Giedion Syndrome, Leigh Disease, Lesch-Nyhan
  • autoimmune diseases and autoimmune-related diseases may be treated with pharmaceutical compositions, biocircuits, biocircuit components, effector modules including their SREs or payloads of the present invention.
  • the term "autoimmune disease” refers to a disease in which the body produces antibodies that attack its own tissues.
  • the autoimmune disease may be Acute Disseminated Encephalomyelitis (ADEM), Acute necrotizing hemorrhagic leukoencephalitis, Addison's disease,
  • Immunoregulatory lipoproteins Inclusion body myositis, Interstitial cystitis, Juvenile arthritis, Juvenile diabetes (Type 1 diabetes), Juvenile myositis, Kawasaki syndrome, Lambert-Eaton syndrome, Leukocytoclastic vasculitis, Lichen planus, Lichen sclerosus, Ligneous conjunctivitis, Linear IgA disease (LAD), Lupus (SLE), Lyme disease, chronic, Meniere's disease.
  • mice Microscopic polyangiitis, Mixed connective tissue disease (MCTD), Mooren's ulcer, Mucha-Habermann disease, Multiple sclerosis, Myasthenia gravis, Myositis, Narcolepsy, Neuromyelitis optica (Devic's), Neutropenia, Ocular cicatricial pemphigoid, Optic neuritis, Palindromic rheumatism, PANDAS (Pediatric Autoimmune Neuropsychiatric Disorders Associated with Streptococcus), Paraneoplastic cerebellar degeneration, Paroxysmal nocturnal hemoglobinuria (PNH), Parry Romberg syndrome, Parsonnage-Turner syndrome, Pars planitis (peripheral uveitis), Pemphigus, Peripheral neuropathy, Perivenous encephalomyelitis, Pernicious anemia, POEMS syndrome, Polyarteritis nodosa, Type I, ⁇ , & III autoimmune polyglandular syndromes,
  • Psoriasis Psoriatic arthritis, Idiopathic pulmonary fibrosis, Pyoderma gangrenosum. Pure red cell aplasia, Raynauds phenomenon, Reactive Arthritis, Reflex sympathetic dystrophy, Reiter's syndrome, Relapsing polychondritis, Restless legs syndrome, Retroperitoneal fibrosis, Rheumatic fever, Rheumatoid arthritis, Sarcoidosis, Schmidt syndrome, Scleritis, Scleroderma, Sjogren's syndrome, Sperm & testicular autoimmunity, Stiff person syndrome, Subacute bacterial endocarditis (SBE), Susac's syndrome, Sympathetic ophthalmia, Takayasu's arteritis, Temporal arteritis/Giant cell arteritis, Thrombocytopenic purpura (TTP), Tolosa-Hunt syndrome,
  • kidney diseases may be treated with pharmaceutical compositions, biocircuits, biocircuit components, effector modules including their SREs or payloads of the present invention.
  • the kidney disease Abderhalden-Kaufmann-Lignac syndrome (Nephropathic Cystinosis), Abdominal Compartment Syndrome, Acute Kidney Failure/Acute Kidney Injury, Acute Lobar Nephroma, Acute Phosphate Nephropathy, Acute Tubular Necrosis, Adenine Phosphoribosyltransferase Deficiency, Adenovirus Nephritis, Alport Syndrome, Amyloidosis, ANCA Vasculitis Related to Endocarditis and Other Infections, Angiomyolipoma, Analgesic Nephropathy, Anorexia Nervosa and Kidney Disease, Angiotensin Antibodies and Focal Segmental Glomerulosclerosis, Antiphospholipid Syndrome, Anti-TNF-a Therapy-related Glomerulonep
  • Glomerulopathy Collapsing Glomerulopathy, Collapsing Glomerulopathy Related to CMV, Congenital Nephrotic Syndrome, Conorenal syndrome (Mainzer- Saldino Syndrome or Saldino- Mainzer Disease), Contrast Nephropathy, Copper Sulpfate Intoxication, Cortical Necrosis, Crizotinib-related Acute Kidney Injury, Cryoglobuinemia, Crystalglobulin-Induced
  • Cystinuria Dasatinib-Induced Nephrotic-Range Proteinuria, Dense Deposit Disease (MPGN Type 2), Dent Disease (X-linked Recessive Nephrolithiasis), Dialysis Disequilibrium Syndrome, Diabetes and Diabetic Kidney Disease, Diabetes Insipidus, Dietary Supplements and Renal Failure, Drugs of Abuse and Kidney Disease, Duplicated Ureter, EAST syndrome, Ebola and the Kidney, Ectopic Kidney, Ectopic Ureter, Edema, Swelling, Erdheim-Chester Disease, Fabry's Disease, Familial Hypocalciuric Hypercalcemia, Fanconi Syndrome, Fraser syndrome,
  • Fibronectin Glomerulopathy Fibrillary Glomerulonephritis and Immunotactoid Glomerulopathy, Fraley syndrome, Focal Segmental Glomerulosclerosis, Focal Sclerosis, Focal
  • Glomerulosclerosis Galloway Mowat syndrome, Giant Cell (Temporal) Arteritis with Kidney Involvement, Gestational Hypertension, Gitelman Syndrome, Glomerular Diseases, Glomerular Tubular Reflux, Glycosuria, Goodpasture Syndrome, Hair Dye Ingestion and Acute Kidney Injury, Hantavirus Infection Podocytopathy, Hematuria (Blood in Urine), Hemolytic Uremic Syndrome (HUS), Atypical Hemolytic Uremic Syndrome (aHUS), Hemophagocytic Syndrome, Hemorrhagic Cystitis, Hemorrhagic Fever with Renal Syndrome (HFRS, Hantavirus Renal Disease, Korean Hemorrhagic Fever, Epidemic Hemorrhagic Fever, Nephropathis Epidemica), Hemosiderosis related to Paroxysmal Nocturnal Hemoglobinuria and Hemolytic Anemia, Hepatic Glomerulopathy, Hepatic Veno
  • Glomerulopathy Lithium Nephrotoxicity, LMX1B Mutations Cause Hereditary FSGS, Loin Pain Hematuria, Lupus, Systemic Lupus Erythematosis, Lupus Kidney Disease, Lupus Nephritis, Lupus Nephritis with Antineutrophil Cytoplasmic Antibody Seropositivity, Lyme Disease- Associated Glomerulonephritis, Malarial Nephropathy, Malignancy-Associated Renal Disease, Malignant Hypertension, Malakoplakia, Meatal Stenosis, Medullary' Cystic Kidney Disease, Medullary Sponge Kidney, Megaureter, Melamine Toxicity and the Kidney,
  • Membranoproliferative Glomerulonephritis Membranous Nephropathy, Me so American Nephropathy, Metabolic Acidosis, Metabolic Alkalosis, Methotrexate-related Renal Failure, Microscopic Polyangiitis, Milk-alkalai syndrome, Minimal Change Disease, MDMA (Molly; Ecstacy; 3,4-MethylenecUoxymethamphetamine) and Kidney Failure, Multicystic dysplastic kidney, Multiple Myeloma, Myeloproliferative Neoplasms and Glomerulopathy, Nail-patella Syndrome, Nephrocalcinosis, Nephrogenic Systemic Fibrosis, Nephroptosis (Floating Kidney, Renal Ptosis), Nephrotic Syndrome, Neurogenic Bladder, Nodular Glomerulosclerosis, Non- Gonococcal Urethritis, Nutcracker syndrome, Orofaciodigital Syndrome, Orotic Aciduria, Orthostatic Hypotension, Orthostatic Proteinuria, Osmotic
  • Pseudohypoparathyroidism Pulmonary-Renal Syndrome, Pyelonephritis (Kidney Infection), Pyonephrosis, Radiation Nephropathy, Ranolazine and the Kidney, Refeeding syndrome, Reflux Nephropathy, Rapidly Progressive Glomerulonephritis, Renal Abscess, Peripnephric Abscess, Renal Agenesis, Renal Arcuate Vein Microthrombi-Associated Acute Kidney Injury, Renal Artery Aneurysm, Renal Artery Stenosis, Renal Cell Cancer, Renal Cyst, Renal Hypouricemia with Exercise-induced Acute Renal Failure, Renal Infarction, Renal Osteodystrophy, Renal Tubular Acidosis, Renin Secreting Tumors (Juxtaglomerular Cell Tumor), Reset Osmostat, Retrocaval Ureter, Retroperitoneal Fibrosis, Rhabdomyolysis, Rhabdomyolysis related to Bariatric surgery
  • Membrane Disease Benign Familial Hematuria, Trigonitis, Tuberculosis, Genitourinary, Tuberous Sclerosis, Tubular Dysgenesis, Immune Complex Tubulointerstitial Nephritis Due to Autoantibodies to the Proximal Tubule Brush Border, Tumor Lysis Syndrome, Uremia, Uremic Optic Neuropathy, Ureteritis Cystica, Ureterocele, Urethral Caruncle, Urethral Stricture, Urinary Incontinence, Urinary Tract Infection, Urinary Tract Obstruction, Vesicointestinal Fistula, Vesicoureteral Reflux, Volatile Anesthetics and Acute Kidney Injury, Von Hippel-Lindau Disease, Waldenstrom's Macroglobulinemic Glomerulonephritis, Warfarin-Related Nephropathy, Wasp Stings and Acute Kidney Injury, Wegener's Granulomatosis,
  • cardiovascular diseases may be treated with pharmaceutical compositions, biocircuits, biocircuit components, effector modules including their SREs or payloads of the present invention.
  • the cardiovascular disease may be Ischemic heart disease also known as coronary artery disease, Cerebrovascular disease (Stroke), Peripheral vascular disease, Heart failure, Rheumatic heart disease, and Congenital heart disease.
  • the antibody deficiencies may be treated with pharmaceutical compositions, biocircuits, biocircuit components, effector modules including their SREs or payloads of the present invention.
  • the antibody deficiencies may be X-Linked Agammaglobulinemia (XLA), Autosomal Recessive Agammaglobulinemia (ARA), Common Variable Immune Deficiency (CVID), IgG (IgGl, IgG2, IgG3 and IgG4) Subclass Deficiency, Selective IgA Deficiency, Specific Antibody Deficiency (SAD), Transient
  • Immunoglobulins Selective IgM Deficiency, Immunodeficiency with Thymoma (Good's Syndrome), Transcobalamin ⁇ Deficiency, Warts, Hypogammaglobulinemia, Infection, Myelokathexis (WHIM) Syndrome, Drug-Induced Antibody Deficiency, Kappa Chain
  • ocular diseases may be treated with pharmaceutical compositions, biocircuits, biocircuit components, effector modules including their SREs or payloads of the present invention.
  • the ocular disease may be thyroid eye disease (TED), Graves' disease (GD) and orbitopathy, Retina Degeneration, Cataract, optic atrophy, macular degeneration, Leber congenital amaurosis, retinal degeneration, cone-rod dystrophy, Usher syndrome, leopard syndrome, photophobia, and photoaversion.
  • the neurological disease may be Absence of the Septum Pellucidum, Acid Lipase Disease, Acid Maltase Deficiency, Acquired Epileptiform Aphasia, Acute Disseminated Encephalomyelitis, Attention Deficit-Hyperactivity Disorder (ADHD), Adie's Pupil, Adie's Syndrome, Adrenoleukodystrophy, Agenesis of the Corpus Callosum, Agnosia, Aicardi Syndrome, Aicardi-Goutieres Syndrome Disorder, AIDS - Neurological Complications, Alexander Disease, Alpers' Disease, Alternating Hemiplegia, Alzheimer's Disease, Amyotrophic Lateral Sclerosis (ALS), Anencephaly, Aneurysm, Angelman Syndrome, Angiomatosis, Anoxia, Antiphospholipid Syndrome,
  • Atrial Fibrillation and Stroke Attention Deficit-Hype ractivity Disorder, Autism Spectrum Disorder, Autonomic Dysfunction, Back Pain, Barth Syndrome, Batten Disease, Becker's Myotonia, Behcet's Disease, Bell's Palsy, Benign Essential Blepharospasm, Benign Focal Amyotrophy, Benign Intracranial Hypertension, Bernhardt-Roth Syndrome, Binswanger's Disease, Blepharospasm, Bloch-Sulzberger Syndrome, Brachial Plexus Birth Injuries, Brachial Plexus Injuries, Bradbury-Eggleston Syndrome, Brain and Spinal Tumors, Brain Aneurysm, Brain Injury, Brown-Sequard Syndrome, Bulbospinal Muscular Atrophy, Cerebral Autosomal Dominant Arteriopathy with Sub-cortical Infarcts and Leukoencephalopathy (CADAS1L), Canavan Disease, Carpal Tunnel Syndrome, Causalgia, Cavernom
  • Leukoencephalopathy Progressive Sclerosing Poliodystrophy, Progressive Supranuclear Palsy, Prosopagnosia, Pseudo-Torch syndrome, Pseudotoxoplasmosis syndrome.
  • Pseudotumor Cerebri Psychigenic Movement, Ramsay Hunt Syndrome I, Ramsay Hunt Syndrome ⁇ , Rasmussen's Encephalitis, Reflex Sympathetic Dystrophy Syndrome, Refsum Disease, Refsum Disease - Infantile, Repetitive Motion Disorders, Repetitive Stress Injuries, Restless Legs Syndrome, Retrovirus-Associated Myelopathy, Rett Syndrome, Reye's Syndrome, Rheumatic Encephalitis, Riley-Day Syndrome, Sacral Nerve Root Cysts, Saint Vitus Dance, Salivary Gland Disease, Sandhoff Disease, Schilder's Disease, Schizencephaly, Seitelberger Disease, Seizure Disorder, Semantic Dementia, Septo-Optic Dysplasia, Severe Myoclonic Epilepsy of Infancy (SMEI), Shaken Baby Syndrome, Shingles, Shy-Drager Syndrome, Sjogren's Syndrome, Sleep Apnea, Sleeping Sickness, Sotos Syndrome, Spasticity
  • Panencephalitis Subcortical Arteriosclerotic Encephalopathy, Short-lasting, Unilateral, Neuralgiform (SUNCT) Headache, Swallowing Disorders, Sydenham Chorea, Syncope, Syphilitic Spinal Sclerosis, Syringohydromyelia, Syringomyelia, Systemic Lupus
  • VHL Von Economo's Disease
  • VHL Von Hippel-Lindau Disease
  • VHL Von Recklinghausen's Disease
  • Wallenberg's Syndrome Werdnig-Hoffman Disease
  • Wernicke- Korsakoff Syndrome West Syndrome
  • Whiplash Whipple's Disease
  • Williams Syndrome Wilson Disease
  • Wolman's Disease X-Linked Spinal and Bulbar Muscular Atrophy.
  • the psychological disorders may be Aboulia, Absence epilepsy, Acute stress Disorder, Adjustment Disorders, Adverse effects of medication NOS, Age related cognitive decline, Agoraphobia, Alcohol Addiction, Alzheimer's Disease, Amnesia (also known as Amnestic Disorder), Amphetamine Addiction, Anorexia Nervosa, Anterograde amnesia, Antisocial personality disorder (also known as Sociopathy), Anxiety Disorder (Also known as Generalized Anxiety Disorder), Anxiolytic related disorders,
  • Asperger's Syndrome (now part of Autism Spectrum Disorder), Attention Deficit Disorder (Also known as ADD), Attention Deficit Hyperactivity Disorder (Also known as ADHD), Autism Spectrum Disorder (also known as Autism), Autophagia, Avoidant Personality Disorder, Barbiturate related disorders, Benzodiazepine related disorders.
  • ADD Attention Deficit Disorder
  • ADHD Attention Deficit Hyperactivity Disorder
  • Autism Spectrum Disorder also known as Autism
  • Autophagia Avoidant Personality Disorder
  • Barbiturate related disorders Benzodiazepine related disorders.
  • Bibliomania also known as Manic Depression, includes Bipolar I and Bipolar II
  • Body Dysmorphic Disorder Borderline intellectual functioning
  • Borderline Personality Disorder Breathing-Related Sleep Disorder, Brief Psychotic Disorder, Bruxism
  • Bulimia Nervosa Caffeine Addiction
  • Cannabis Addiction Catatonic disorder
  • Catatonic schizophrenia Childhood amnesia, Childhood Disintegrative Disorder (now part of Autism Spectrum Disorder), Childhood Onset Fluency Disorder (formerly known as Stuttering), Circadian Rhythm Disorders, Claustrophobia, Cocaine related disorders, Communication disorder, Conduct Disorder, Conversion Disorder, Cotard delusion, Cyclothymia (also known as Cyclothymic Disorder), Delerium, Delusional Disorder, dementia, Dependent Personality Disorder (also known as Asthenic Personality Disorder), Depersonalization disorder (now known as Depersonalization / Derealization Disorder), Depression (also known as Major Depressive Disorder), Depressive personality disorder, Derealization disorder (now known as
  • Depersonalization / Derealization Disorder Dermotillomania, Desynchronosis, Developmental coordination disorder, Diogenes Syndrome, Disorder of written expression, Dispareunia, Dissocial Personality Disorder, Dissociative Amnesia, Dissociative Fugue, Dissociative Identity' Disorder (formerly known as Multiple Personality Disorder), Down syndrome, Dyslexia, Dyspareunia, Dysthymia (now known as Persistent Depressive Disorder), Eating disorder NOS, Ekbom's Syndrome (Delusional Parasitosis), Emotionally unstable personality disorder, Encopresis, Enuresis (bedwetting), Erotomania, Exhibitionistic Disorder, Expressive language disorder, Factitious Disorder, Female sexual Disorders, Fetishistic Disorder, Folie alons, Fregoli delusion, Frotteuristic Disorder, Fugue State, Ganser syndrome, Gambling Addiction, Gender Dysphoria (formerly known as Gender Identity Disorder), Generalized Anxiety Disorder, General adaptation syndrome.
  • Grandiose delusions, Hallucinogen Addiction Haltlose personality disorder, Histrionic Personality Disorder, Primary hypersomnia, Huntington's Disease, Hypoactive sexual desire disorder, Hypochondriasis, Hypomania, Hyperkinetic syndrome, Hypersomnia, Hysteria, Impulse control disorder, Impulse control disorder NOS, Inhalant Addiction, Insomnia, Intellectual Development Disorder, Intermittent Explosive Disorder, Joubert syndrome, Kleptomania, Korsakoff s syndrome, Lacunar amnesia. Language Disorder, Learning Disorders, Major Depression (also known as Major Depressive Disorder), major depressive disorder, Male sexual Disorders, Malingering, Mathematics disorder,
  • Medication-related disorder Melancholia, Mental Retardation (now known as Intellectual Development Disorder), Misophonia, Morbid MasterCardy, Multiple Personality Disorder (now known as Dissociative Identity Disorder), Munchausen Syndrome, Munchausen by Proxy, Narcissistic Personality Disorder, Narcolepsy, Neglect of child, Neurocognitive Disorder (formerly known as Dementia), Neuroleptic-related disorder, Nightmare Disorder, Non Rapid Eye Movement, Obsessive-Compulsive Disorder, Obsessive-Compulsive Personality Disorder (also known as Anankastic Personality Disorder), Oneirophrenia, Onychophagia, Opioid Addiction, Oppositional Defiant Disorder, Orthorexia (ON), Pain disorder, Panic attacks. Panic Disorder, Paranoid Personality Disorder, Parkinson's Disease, Partner relational problem, Passive-aggressive personality disorder, Pathological gambling, Pedophilic Disorder,
  • Schizophrenia Schizophreniform disorder, Schizotypal Personality Disorder, Seasonal Affective Disorder, Sedative, Hypnotic, or Anxiolytic Addiction, Selective Mutism, Self-defeating personality disorder, Separation Anxiety Disorder, sexual Disorders Female, sexual Disorders Male, sexual Addiction, Sexual Masochism Disorder, Sexual Sadism Disorder, Shared Psychotic Disorder, Sleep Arousal Disorders, Sleep Paralysis, Sleep Terror Disorder (now part of
  • Nightmare Disorder Social Anxiety Disorder, Somatization Disorder, Specific Phobias, Stendhal syndrome, Stereotypic movement disorder, Stimulant Addiction, Stuttering (now known as Childhood Onset Fluency Disorder), Substance related disorder, Tardive dyskinesia, Tobacco Addiction, Tourettes Syndrome, Transient tic disorder, Transient global amnesia, Transvestic Disorder, Trichotillomania, Undifferentiated Somatoform Disorder, Vaginismus, and Voyeuristic Disorder.
  • Various lung diseases may be treated with pharmaceutical compositions, biocircuits, biocircuit components, effector modules including their SREs or payloads of the present invention.
  • the lung diseases may be Asbestosis, Asthma,
  • Bronchiectasis Bronchitis, Chronic Cough, Chronic Obstructive Pulmonary Disease (COPD), Croup, Cystic Fibrosis, Hantavirus, Idiopathic Pulmonary Fibrosis, Pertussis, Pleurisy,
  • Pneumonia Pulmonary Embolism, Pulmonary Hypertension, Sarcoidosis, Sleep Apnea, Spirometry, Sudden Infant Death Syndrome (SIDS), Tuberculosis, Alagille Syndrome,
  • Nonalcoholic Steatohepatitis Porphyria, Primary Biliary Cirrhosis, Primary Sclerosing Cholangitis.
  • Various bone diseases may be treated with pharmaceutical compositions, biocircuits, biocircuit components, effector modules including their SREs or payloads of the present invention.
  • the bone diseases may be osteoporosis,
  • osteogenesis imperfecta OI
  • rickets osteosarcoma
  • achondroplasia fracture
  • osteomyelitis Ewing tumor of bone
  • osteomalacia hip dysplasia
  • Paget disease of bone marble bone disease, osteochondroma, bone cancer, bone disease, osteochondrosis, osteoma, fibrous dysplasia, cleidocranial dysostosis, osteoclastoma, bone cyst, metabolic bone disease, melorheostosis, callus, Caffey syndrome, and mandibulofacial dysostosis.
  • Various blood diseases may be treated with pharmaceutical compositions, biocircuits, biocircuit components, effector modules including their SREs or payloads of the present invention.
  • the blood diseases may be Anemia and CKD (for health care professionals), Aplastic Anemia and Myelodysplastic Syndromes, Deep Vein Thrombosis, Hemochromatosis, Hemophilia, Henoch-Schonlein Purpura, Idiopathic Thrombocytopenic Purpura, Iron-Deficiency Anemia, Pernicious Anemia, Pulmonary Embolism, Sickle Cell Anemia, Sickle Cell Trait and Other Hemoglobinopathies, Thalassemia, Thrombotic
  • the CRISPR-Cas9 system is a novel genome editing system which has been rapidly developed and implemented in a multitude of model organisms and cell types, and supplants other genome editing technologies, such as TALENs and ZFNs.
  • CRISPRs are sequence motifs are present in bacterial and archaeal genomes, and are composed of short (about 24-48 nucleotide) direct repeats separated by similarly sized, unique spacers (Grissa et al. BMC Bioinformatics 8, 172 (2007).
  • CRISPR-associated (Cas) protein-coding genes that are required for CRISPR maintenance and function
  • CRISPR-associated (Cas) protein-coding genes that are required for CRISPR maintenance and function
  • CRISPR-associated (Cas) protein-coding genes Barrangou et al., Science 315, 1709 (2007), Brouns et al., Science 321, 960 (2008), Haft et al. PLoS Comput Biol 1, e60 (2005).
  • CRISPR-Cas systems provide adaptive immunity against invasive genetic elements (e.g., viruses, phages and plasmids) (Horvath and Barrangou, Science, 2010, 327: 167- 170; Bhaya et al., Annu. Rev.
  • CRISPR-Cas small CRISPR RNAs (crRNAs) processed from the pre-repeat-spacer transcript (pre-crRNA) in the presence of a trans-activating RNA (tracrRNA)/ Cas9 can form a duplex with the tracrRNA/Cas9 complex.
  • pre-crRNA pre-repeat-spacer transcript
  • tracrRNA trans-activating RNA
  • the mature complex is recruited to a target double strand DNA sequence that is complementary to the spacer sequence in the tracrRNA: crRN A duplex to cleave the target DNA by Cas9 endonuclease (Garneau et al., Nature, 2010, 468: 67-71; Jinek et al., Science, 2012, 337: 816-821; Gasiunas et al., Proc. Natl Acad. Sci. USA., 109: E2579-2586; and Haurwitz et al., Science, 2010, 329: 1355-1358).
  • tracrRNA/Cas9 complex in the type ⁇ CRISPR-CAS system not only requires a sequence in the tracrRNA: crRNA duplex that is a complementary to the target sequence (also called “protospacer” sequence) but also requires a protospacer adjacent motif (PAM) sequence located 3 'end of the protospacer sequence of a target polynucleotide.
  • PAM protospacer adjacent motif
  • CRISPR-Cas9 systems have been developed and modified for use in genetic editing and prove to be a high effective and specific technology for editing a nucleic acid sequence even in eukaryotic cells.
  • Representative references include US Pat. NOs.
  • CRISPR-Cas system e.g., guide RNA and nuclease
  • biocircuits of the present invention and/or any of their components may be utilized in regulating or tuning the CRISPR/Cas9 system in order to optimize its utility.
  • the payloads of the effector modules of the invention may include alternative isoforms or orthologs of the Cas9 enzyme.
  • the most commonly used Cas9 is derived from Streptococcus pyogenes and the RuvC domain can be inactivated by a D10A mutation and the HNH domain can be inactivated by an H840A mutation.
  • Cas9 RNA guided endonucleases
  • RGEN RNA guided endonucleases
  • Cas9 sequences have been identified in more than 600 bacterial strains. Though Cas9 family shows high diversity of amino acid sequences and protein sizes. All Cas9 proteins share a common architecture with a central HNH nuclease domain and a split RuvC/RHase H domain. Examples of Cas9 orthologs from other bacterial strains including but not limited to, Cas proteins identified in Acaryochloris marina MBIC 11017; Acetohalobium arabaticum DSM 5501; Acidithiobacillus caldus;
  • Cas9 orthologs In addition to Cas9 orthologs, other Cas9 variants such as fusion proteins of inactive dCas9 and effector domains with different functions may be served as a platform for genetic modulation. Any of the foregoing enzymes may be useful in the present invention.
  • biocircuits of the present invention and/or any of their components may be utilized in the regulated reprogramming of cells, stem cell engraftment or other application where controlled or tunable expression of such reprogramming factors are useful.
  • the biocircuits of the present invention may be used in reprogramming cells including stem cells or induced stem cells.
  • Induction of induced pluripotent stem cells (iPSC) was first achieved by Takahashi and Yamanaka ⁇ Cell, 2006. 126(4):663-76; herein incorporated by reference in its entirety) using viral vectors to express KLF4, c-MYC, OCT4 and SOX2 otherwise collectively known as KMOS.
  • DNA-free methods to generate human iPSC has also been derived using serial protein transduction with recombinant proteins incorporating cell-penetrating peptide moieties (Kim, D, et al. Cell Stem Cell, 2009. 4(6): 472-476; Zhou, H, et al. Cell Stem Cell, 2009. 4(5):381-4; each of which is herein incorporated by reference in its entirety), and infectious transgene delivery using the Sendai virus (Fusaki, N, et al, Proc Jpn Acad Ser B Phys Biol Sci, 2009. 85(8): p. 348-62; herein incorporated by reference in its entirety).
  • the effector modules of the present invention may include a payload comprising any of the genes including, but not limited to, OCT such as OCT4, SOX such as SOX1, SOX2, SOX3, SOX15 and SOX18, NANOG, KLF such as KLFl, KLF2, KLF4 and KLF5, MYC such as c- MYC and n-MYC, REM2, TERT and LIN28 and variants thereof in support of reprogramming cells. Sequences of such reprogramming factors are taught in for example International
  • the present invention provides methods comprising administering any one or more compositions for immunotherapy to a subject in need thereof. These may be administered to a subject using any amount and any route of administration effective for preventing or treating a clinical condition such as cancer, infection diseases and other immunodeficient diseases.
  • compositions in accordance with the invention are typically formulated in dosage unit form for ease of administration and uniformity of dosage. It will be understood, however, that the total daily usage of the compositions of the present invention may be decided by the attending physician within the scope of sound medical judgment.
  • the specific therapeutically effective, or prophylactically effective dose level for any particular patient will depend upon a variety of factors including the disorder being treated and the severity of the disorder; the activity of the specific compound employed; the specific composition employed; the age, body weight, general health, sex and diet of the patient; the time of administration, route of administration, previous or concurrent therapeutic interventions and rate of excretion of the specific compound employed; the duration of the treatment; drugs used in combination or coincidental with the specific compound employed; and like factors well known in the medical arts.
  • Hie destabilizing domains (DDs), effector modules and biocircuit systems of the invention and compositions comprising the same may be administered by any route to achieve a therapeutically effective outcome.
  • enteral into the intestine
  • gastroenteral into the dura matter
  • oral by way of the mouth
  • transdermal peridural
  • intracerebral into the cerebrum
  • intracerebroventricular into the cerebral ventricles
  • epicutaneous application onto the skin
  • intradermal into the skin itself
  • subcutaneous under the skin
  • nasal administration through the nose
  • intravenous into a vein
  • intravenous bolus intravenous drip
  • intraarterial into an artery
  • intramuscular into a muscle
  • intracardiac into the heart
  • intraosseous infusion into the bone marrow
  • intrathecal into the spinal canal
  • intraperitoneal infusion or injection into the peritoneum
  • intravesical infusion intravitreal, (through the eye), intracavernous injection (into a pathologic cavity) intracavitary (into the base of the penis), intra
  • a dressing which occludes the area
  • ophthalmic to the external eye
  • oropharyngeal directly to the mouth and pharynx
  • parenteral percutaneous, periarticular, peridural, perineural, periodontal, rectal, respiratory (within the respiratory tract by inhaling orally or nasally for local or systemic effect), retrobulbar (behind the pons or behind the eyeball), intramyocardial (entering the myocardium), soft tissue, subarachnoid, subconjunctival, submucosal, topical, transplacental (through or across the placenta), transtracheal (through the wall of the trachea), transtympanic (across or through the tympanic cavity), ureteral (to the ureter), urethral (to the urethra), vaginal, caudal block, diagnostic, nerve block, biliary perfusion, cardiac perfusion, photop
  • compositions of the present invention may be administered by any of the methods of administration taught in the copending commonly owned U.S. Provisional Patent Application No. 62/320,864 filed on 4/11/2017 or in US Provisional Application No. 62/466,596 filed March 3, 2017 and the International Publication WO2017/180587, the contents of each of which are incorporated herein by reference in their entirety.
  • The also provides a kit comprising any of the polynucleotides or expression vectors described herein.
  • kits for conveniently and/or effectively carrying out methods of the present invention.
  • kits will comprise sufficient amounts and/or numbers of components to allow a user to perform one or multiple treatments of a subjects) and/or to perform one or multiple experiments.
  • kits for inhibiting genes in vitro or in vivo comprising a biocircuit of the present invention or a combination of biocircuits of the present invention, optionally in combination with any other suitable active agents.
  • the kit may further comprise packaging and instructions and/or a delivery agent to form a formulation composition.
  • the delivery agent may comprise, for example, saline, a buffered solution.
  • assay screening kits are provided.
  • the kit includes a container for the screening assay. An instruction for the use of the assay and the information about the screening method are to be included in the kit.
  • the DDs, effector modules and biocircuit system and compositions of the invention may be used as research tools to investigate protein activity in a biological system such a cell and a subject.
  • the DDs, effector modules and biocircuit system and compositions of the invention may be used for treating a disease such as a cancer and a genetic disorder.
  • the present invention also provides vectors that package polynucleotides of the invention encoding biocircuits, effector modules, SREs (DDs) and payload constructs, and combinations thereof.
  • Vectors of the present invention may also be used to deliver the packaged polynucleotides to a cell, a local tissue site or a subject.
  • These vectors may be of any kind, including DNA vectors, RNA vectors, plasmids, viral vectors and particles.
  • Viral vector technology is well known and described in Sambrook et al. (2001, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, New York).
  • Viruses which are useful as vectors include, but are not limited to lentiviral vectors, adenoviral vectors, adeno-associated viral (AAV) vectors, herpes simplex viral vectors, retroviral vectors, oncolytic viruses, and the like.
  • vectors contain an origin of replication functional in at least one organism, a promoter sequence and convenient restriction endonuclease site, and one or more selectable markers e.g. a drug resistance gene.
  • a promoter is defined as a DNA sequence recognized by transcription machinery of the cell, required to initiate specific transcription of the polynucleotide sequence of the present invention.
  • Vectors can comprise native or non-native promoters operably linked to the polynucleotides of the invention.
  • the promoters selected may be strong, weak, constitutive, inducible, tissue specific, development stage-specific, and/or organism specific.
  • One example of a suitable promoter is the immediate early cytomegalovirus (CMV) promoter sequence. This promoter sequence is a strong constitutive promoter sequence capable of driving high levels of expression of polynucleotide sequence that is operatively linked to it.
  • CMV immediate early cytomegalovirus
  • This promoter sequence is a strong constitutive promoter sequence capable of driving high levels of expression of polynucleotide sequence that is operatively linked to it.
  • Another example of a preferred promoter is Elongation Growth Factor-1.
  • EF-1. alpha Other constitutive promoters may also be used, including, but not limited to simian virus 40 (SV40), mouse mammary tumor virus (MMTV), human immunodeficiency virus (HIV), long terminal repeat (LTR), promoter, an avian leukemia virus promoter, an Epstein-Barr virus immediate early promoter, a Rous sarcoma virus promoter as well as human gene promoters including, but not limited to the phosphoglycerate kinase (PGK) promoter, actin promoter, the myosin promoter, the hemoglobin promoter, the Ubiquitin C (Ubc) promoter, the human U6 small nuclear protein promoter and the creatine kinase promoter.
  • PGK phosphoglycerate kinase
  • actin promoter actin promoter
  • the myosin promoter the hemoglobin promoter
  • Ubiquitin C (Ubc) promoter the human U6 small nuclear protein promoter and
  • inducible promoters such as but not limited to metallothionine promoter, glucocorticoid promoter, a progesterone promoter, and a tetracycline promoter may be used.
  • the promoter may be selected from the following a CMV promoter, comprising a nucleotide sequence of SEQ ID NO. 269, a PGK promoter, comprising a nucleotide sequence of SEQ ID NO. 270, and an EFla promoter, comprising a nucleotide sequence of SEQ ID NO. 271, or SEQ YD NO. 376.
  • the optimal promoter may be selected based on its ability to achieve minimal expression of the SREs and payloads of the invention in the absence of the ligand and detectable expression in the presence of the ligand.
  • Additional promoter elements e.g. enhancers may be used to regulate the frequency of transcriptional initiation. Such regions may be located 10-100 base pairs upstream or downstream of the start site. In some instances, two or more promoter elements may be used to cooperatively or independently activate transcription.
  • the recombinant expression vector may comprise regulatory sequences, such as transcription and translation initiation and termination codons, which are specific to the type of host cell into which the vector is to be introduced.
  • lentiviral vectors/particles may be used as vehicles and delivery modalities.
  • Lentiviruses are subgroup of the Retroviridae family of viruses, named because reverse transcription of viral RNA genomes to DNA is required before integration into the host genome. As such, the most important features of lentiviral vehicles/particles are the integration of their genetic material into the genome of a target/host cell.
  • Some examples of lentivirus include the Human Immunodeficiency Viruses: HIV-1 and HTV-2, the Simian
  • Immunodeficiency Virus (SIV), feline immunodeficiency virus (FIV), bovine immunodeficiency virus (BIV), Jembrana Disease Virus (JDV), equine infectious anemia virus (EIAV), equine infectious anemia virus, visna-maedi and caprine arthritis encephalitis virus (CAEV).
  • SIV feline immunodeficiency virus
  • BIV bovine immunodeficiency virus
  • JDV Jembrana Disease Virus
  • EIAV equine infectious anemia virus
  • CAEV visna-maedi and caprine arthritis encephalitis virus
  • lentiviral particles making up the gene delivery vehicle are replication defective on their own (also referred to as "self-inactivating"). Lentiviruses are able to infect both dividing and non-dividing cells by virtue of the entry mechanism through the intact host nuclear envelope (Naldini L et al., Curr. Opin. Biotechnol, 1998, 9: 457-463). Recombinant lentiviral vehicles/particles have been generated by multiply attenuating the HIV virulence genes, for example, the genes Env, Vif, Vpr, Vpu, Nef and Tat are deleted making the vector biologically safe.
  • lentiviral vehicles for example, derived from HTV-l/HIV-2 can mediate the efficient delivery, integration and long-term expression of transgenes into non- dividing cells.
  • the term "recombinant” refers to a vector or other nucleic acid containing both lentiviral sequences and non-lentiviral retroviral sequences.
  • Lentiviral particles may be generated by co-expressing the virus packaging elements and the vector genome itself in a producer cell such as human HEK293T cells. These elements are usually provided in three (in second generation lentiviral systems) or four separate plasmids (in third generation lentiviral systems).
  • the producer cells are co-transfected with plasmids that encode lentiviral components including the core (i.e. structural proteins) and enzymatic components of the virus, and the envelope protein(s) (referred to as the packaging systems), and a plasmid that encodes the genome including a foreign transgene, to be transferred to the target cell, the vehicle itself (also referred to as the transfer vector).
  • the plasmids or vectors are included in a producer cell line.
  • the plasmids/vectors are introduced via transfection, transduction or infection into the producer cell line. Methods for transfection, transduction or infection are well known by those of skill in the art.
  • the packaging and transfer constructs can be introduced into producer cell lines by calcium phosphate transfection, lipofection or electroporation, generally together with a dominant selectable marker, such as neo, DHFR, Gin synthetase or ADA, followed by selection in the presence of the appropriate drug and isolation of clones.
  • the producer cell produces recombinant viral particles that contain the foreign gene, for example, the effector module of the present invention.
  • the recombinant viral particles are recovered from the culture media and titrated by standard methods used by those of skill in the art.
  • the recombinant lentiviral vehicles can be used to infect target cells.
  • Cells that can be used to produce high-titer lentiviral particles may include, but are not limited to, HEK293T cells, 293G cells, STAR cells (Relander et al., Mol. Ther., 2005, 11: 452- 459), FreeStyleTM 293 Expression System (ThermoFisher, Waltham, MA), and other HEK293T- based producer cell lines (e.g., Stewart et al., Hum Gene Ther. lQl 1, 22(3):357-369; Lee et al., Biotechnol Bioeng, 2012, 10996): 1551-1560; Throm et al., iHoorf. 2009, 113(21): 5104-5110; the contents of each of which are incorporated herein by reference in their entirety).
  • HEK293T cells e.g., Stewart et al., Hum Gene Ther. lQl 1, 22(3):357-369; Lee et al., Biotechno
  • the envelope proteins may be heterologous envelop proteins from other viruses, such as the G protein of vesicular stomatitis virus (VSV G) or baculoviral gp64 envelop proteins.
  • VSV-G glycoprotein may especially be chosen among species classified in the vesiculovirus genus: Carajas virus (CJSV), Chandipura virus (CHPV), Cocal virus (COCV), Isfahan virus (ISFV), Maraba virus (MARA V), Pity virus (PIRYV), Vesicular stomatitis Alagoas virus (VSAV), Vesicular stomatitis Indiana virus (VSIV) and Vesicular stomatitis New Jersey virus (VSNJV) and/or stains provisionally classified in the vesiculovirus genus as Grass carp rhabdovirus, BeAn 157575 virus (BeAn 157575), Boteke virus (BTKV),
  • CJSV Cara
  • TUPV Ulcerative disease rhabdovirus
  • UDRV Ulcerative disease rhabdovirus
  • YBV Yug Bogdanovac virus
  • the gp64 or other baculoviral env protein can be derived from Autographa californica
  • AcMNPV Anagrapha falcifera nuclear polyhedrosis virus, Bombyx mori nuclear polyhedrosis virus, Choristoneura fiimiferana nucleopolyhedrovirus, Orgyia pseudotsugata single capsid nuclear polyhedrosis virus, Epiphyas postvittana
  • nucleopolyhedrovirus Hyphantria cunea nucleopolyhedrovirus, Galleria mellonella nuclear polyhedrosis virus, Dhori virus, Thogoto virus, Antheraea pemyi nucleopolyhedrovirus or Batken virus.
  • Additional elements provided in lentiviral particles may comprise retroviral LTR (long- terminal repeat) at either 5 ' or 3' terminus, a retroviral export element, optionally a lentiviral reverse response element (RRE), a promoter or active portion thereof, and a locus control region (LCR) or active portion thereof.
  • retroviral LTR long- terminal repeat
  • RRE lentiviral reverse response element
  • Other elements include central polypurine tract (cPPT) sequence to improve transduction efficiency in non-dividing cells, Woodchuck Hepatitis Virus (WHP) Posttranscriptional Regulatory Element (WPRE) which enhances the expression of the transgene, and increases titer.
  • WPRE Posttranscriptional Regulatory Element
  • Lenti virus vectors used may be selected from, but are not limited to pLVX, pLenti, pLenti6, pLJMl, FUGW, pWPXL, pWPI, pLenti CMV puro DEST, pLJMl-EGFP, pULTRA, plnducer20, pfflV-EGFP, pCW57.1, pTRPE, pELPS, pRRL, and pLionll.
  • Lentiviral vehicles known in the art may also be used (See, U.S. Pat. NOs. 9, 260, 725; 9,068,199; 9,023,646; 8,900,858; 8,748,169; 8,709,799; 8,420,104; 8,329,462; 8,076,106;
  • Retroviral vectors ( ⁇ -retroviral vectors)
  • retroviral vectors may be used to package and deliver the biocircuits, biocircuit components, effector modules, SREs or payload constructs of the present invention.
  • Retroviral vectors allow the permanent integration of a transgene in target cells.
  • retroviral vectors based on simple gam ma-retro viruses have been widely used to deliver therapeutic genes and demonstrated clinically as one of the most efficient and powerful gene delivery' systems capable of transducing a broad range of cell types.
  • Example species of Gamma retroviruses include the murine leukemia viruses (MLVs) and the feline leukemia viruses (FeLV).
  • gam ma-retro viral vectors derived from a mammalian gamma- retrovirus such as murine leukemia viruses (MLVs)
  • MLVs murine leukemia viruses
  • the MLV families of gamma retroviruses include the ecotropic, amphotropic, xenotropic and polytropic subfamilies.
  • Ecotropic viruses are able to infect only murine cells using mCAT-1 receptor. Examples of ecotropic viruses are Moloney MLV and AKV.
  • Amphotropic viruses infect murine, human and other species through the Pit-2 receptor.
  • An amphotropic virus is the 4070A virus.
  • Xenotropic and polytropic viruses utilize the same (Xprl) receptor, but differ in their species tropism. Xenotropic viruses such as NZB-9-1 infect human and other species but not murine species, whereas polytropic viruses such as focus-forming viruses (MCF) infect murine, human and other species.
  • MMF focus-forming viruses
  • Gamma-retro viral vectors may be produced in packaging cells by co-transfecting the cells with several plasmids including one encoding the retroviral structural and enzymatic (gag- pol) polyprotein, one encoding the envelope (env) protein, and one encoding the vector mRNA comprising polynucleotide encoding the compositions of the present invention that is to be packaged in newly formed viral particles.
  • several plasmids including one encoding the retroviral structural and enzymatic (gag- pol) polyprotein, one encoding the envelope (env) protein, and one encoding the vector mRNA comprising polynucleotide encoding the compositions of the present invention that is to be packaged in newly formed viral particles.
  • the recombinant gamma-retroviral vectors are pseudotyped with envelope proteins from other viruses.
  • Envelope glycoproteins are incorporated in the outer lipid layer of the viral particles which can increase/alter the cell tropism.
  • Exemplary envelop proteins include the gibbon ape leukemia virus envelope protein (GALV) or vesicular stomatitis virus G protein (VSV-G), or Simian endogenous retrovirus envelop protein, or Measles Virus H and F proteins, or Human immunodeficiency virus gpl20 envelope protein, or cocal vesiculovirus envelop protein (See, e.g., U.S. application publication NO.
  • envelope glycoproteins may be genetically modified to incorporate targeting/binding ligands into gamma-retroviral vectors, binding ligands including, but not limited to, peptide ligands, single chain antibodies and growth factors (Waehler et al., Nat. Rev. Genet. 2007, 8(8):573-587; the contents of which are incorporated herein by reference in its entirety)- These engineered glycoproteins can retarget vectors to cells expressing their corresponding target moieties.
  • a "molecular bridge" may be introduced to direct vectors to specific cells.
  • the molecular bridge has dual specificities: one end can recognize viral glycoproteins, and the other end can bind to the molecular determinant on the target cell.
  • Such molecular bridges for example ligand-receptor, avidin-biotin, and chemical conjugations, monoclonal antibodies and engineered fusogenic proteins, can direct the attachment of viral vectors to target cells for transduction (Y ang et al., Biotechnol. Bioeng., 2008, 101(2): 357-368; and Maetzig et al., Viruses, 2011, 3, 677-713; the contents of each of which are incorporated herein by reference in their entirety).
  • the recombinant gamma-re troviral vectors are self-inactivating (SIN) gammaretro viral vectors.
  • the vectors are replication incompetent.
  • SIN vectors may harbor a deletion within the 3' U3 region initially comprising enhancer/promoter activity.
  • the 5' U3 region may be replaced with strong promoters (needed in the packaging cell line) derived from Cytomegalovirus or RSV, or an internal promoter of choice, and/or an enhancer element.
  • the choice of the internal promoters may be made according to specific requirements of gene expression needed for a particular purpose of the invention.
  • polynucleotides encoding the biocircuit, biocircuit components, effector module, SRE are inserted within the recombinant viral genome.
  • the other components of the viral mRNA of a recombinant gamma-retro viral vector may be modified by insertion or removal of naturally occurring sequences (e.g., insertion of an IRES, insertion of a heterologous polynucleotide encoding a polypeptide or inhibitory nucleic acid of interest, shuffling of a more effective promoter from a different retrovirus or virus in place of the wild-type promoter and the like).
  • the recombinant gamma-retro viral vectors may comprise modified packaging signal, and/or primer binding site (PBS), and/or 5'-enhancer/promoter elements in the U3-region of the 5'- long terminal repeat (LTR), and/or 3 -SIN elements modified in the US- region of the 3 -LTR. These modifications may increase the titers and the ability of infection.
  • PBS primer binding site
  • LTR 5'-enhancer/promoter elements in the U3-region of the 5'- long terminal repeat
  • 3 -SIN elements modified in the US- region of the 3 -LTR.
  • Gamma retroviral vectors suitable for delivering biocircuit components, effector modules, SREs or payload constructs of the present invention may be selected from those disclosed in U.S. Pat. NOs. 8,828,718; 7,585,676; 7,351,585; U.S. application publication NO. 2007/048285; PCT application publication NOs. WO2010/113037; WO2014/121005;
  • Adeno-associated viral vectors AAV
  • polynucleotides of present invention may be packaged into recombinant adeno-associated viral (rAAV) vectors.
  • rAAV adeno-associated viral
  • Such vectors or viral particles may be designed to utilize any of the known serotype capsids or combinations of serotype capsids.
  • the serotype capsids may include capsids from any identified AAV serotypes and variants thereof, for example, AAV1, AAV2, AAV2G9, AAV3, AAV4, AAV4-4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11, AAV12 and AAVrhlO.
  • the AAV serotype may be or have a sequence as described in United States Publication No. US20030138772, herein incorporated by reference in its entirety, such as, but not limited to, AAV1 (SEQ ID NO. 6 and 64 of US20030138772), AAV2 (SEQ ID NO. 7 and 70 of US20030138772), AAV3 (SEQ ID NO. 8 and 71 of US20030138772), AAV4 (SEQ ID NO. 63 of US20030138772), AAV5 (SEQ ID NO. 114 of US20030138772), AAV6 (SEQ ID NO. 65 of US20030138772), AAV7 (SEQ ID NO. 1-3 of US20030138772), AAV8 (SEQ ID NO. 4 and 95 of US20030138772), AAV9 (SEQ ID NO. 5 and 100 of
  • US20030138772 AAV10 (SEQ ID NO. 117 of US20030138772), AAV11 (SEQ ID NO. 118 of US20030138772), AAV12 (SEQ ID NO. 119 of US20030138772), AAVrhlO (amino acids 1 to 738 of SEQ ID NO. 81 of US20030138772) or variants thereof.
  • variants include SEQ ID NOs. 9, 27-45, 47-62, 66-69, 73-81, 84-94, 96, 97, 99, 101-113 of US20030138772, the contents of which are herein incorporated by reference in their entirety.
  • the AAV serotype may have a sequence as described in Pulichla et al. (Molecular Therapy, 2011, 19(6): 1070-1078), U.S. Pat. NOs. 6,156,303; 7,198,951; U.S. Patent Publication NOs. US2015/0159173 and US2014/0359799; and International Patent Publication NOs. WO 1998/011244, WO2005/033321 and WO2014/14422; the contents of each of which are incorporated herein by reference in their entirety.
  • AAV vectors include not only single stranded vectors but self-complementary AAV vectors (scAAVs).
  • scAAV vectors contain DNA which anneals together to form double stranded vector genome. By skipping second strand synthesis, scAAVs allow for rapid expression in the cell.
  • the rAAV vectors may be manufactured by standard methods in the art such as by triple transfection, in sf9 insect cells or in suspension cell cultures of human cells such as HEK293 cells.
  • the biocircuits, biocircuit components, effector modules, SREs or payload constructs may be encoded in one or more viral genomes to be packaged in the AAV capsids taught herein.
  • Such vectors or viral genomes may also include, in addition to at least one or two ITRs (inverted terminal repeats), certain regulator ⁇ ' elements necessary for expression from the vector or viral genome.
  • ITRs inverted terminal repeats
  • regulator ⁇ ' elements necessary for expression from the vector or viral genome.
  • regulatory elements are well known in the art and include for example promoters, introns, spacers, stuffer sequences, and the like.
  • more than one effector module or SRE may be encoded in a viral genome.
  • polynucleotides of present invention may be packaged into oncolytic viruses, such as vaccine viruses.
  • Oncolytic vaccine viruses may include viral particles of a thymidine kinase (TK)-deficient, granulocyte macrophage (GM)-colony stimulating factor (CSF)-expressing, replication-competent vaccinia virus vector sufficient to induce oncolysis of cells in the tumor (e.g., US Pat. NO. 9,226,977).
  • TK thymidine kinase
  • GM granulocyte macrophage
  • CSF colony stimulating factor
  • the viral vector of the invention may comprise two or more immunotherapeutic agents taught herein, wherein the two or more immune-therapeutic agents may be included in one effector module under the regulation of the same DD. In this case, the two or more immunotherapeutic agents are tuned by the same stimulus simultaneously.
  • the viral vector of the invention may comprise two or more effector modules, wherein each effector module comprises a different immunotherapeutic agent. In this case, the two or more effector modules and immunotherapeutic agents are tuned by different stimuli, providing separately independent regulation of the two or more components.
  • the effector modules of the invention may be designed as a messenger RNA (mRNA).
  • mRNA messenger RNA
  • the term "messenger RNA” (mRNA) refers to any polynucleotide which encodes a polypeptide of interest and which is capable of being translated to produce the encoded polypeptide of interest in vitro, in vivo, in situ or ex vivo.
  • mRNA molecules may have the structural components or features of any of those taught in International Publication No. WO2018151666, the contents of which are incorporated herein by reference in its entirety.
  • Polynucleotides of the invention may also be designed as taught in, for example, Ribostem Limited in United Kingdom patent application serial number 0316089.2 filed on July 9, 2003 now abandoned, PCT application number PCT/GB2004/002981 filed on July 9, 2004 published as WO2005005622, United States patent application national phase entry serial number 10/563,897 filed on June 8, 2006 published as US20060247195 now abandoned, and European patent application national phase entry serial number EP2004743322 filed on July 9, 2004 published as EP 1646714 now withdrawn; Novozymes, Inc.
  • PCT/EP2008/03033 filed on April 16, 2008 published as WO2009127230
  • PCT/EP2006/004784 filed on May 19, 2005 published as WO2006122828
  • PCT/EP2008/00081 filed on January 9, 2007 published as WO2008083949
  • the effector modules may be designed as self-amplifying RNA.
  • Self-amplifjong RNA refers to RNA molecules that can replicate in the host resulting in the increase in the amount of the RNA and the protein encoded by the RNA.
  • Such self-amplifying RNA may have structural features or components of any of those taught in International Patent Application Publication No. WO2011005799 (the contents of which are incorporated herein by reference in their entirety).
  • compositions of the present disclosure are disclosed in groups or in ranges. It is specifically intended that the present disclosure include each and every individual subcombination of the members of such groups and ranges. The following is a non-limiting list of term definitions.
  • Activity refers to the condition in which things are happening or being done.
  • Compositions of the invention may have activity and this activity may involve one or more biological events.
  • biological events may include cell signaling events.
  • biological events may include cell signaling events associated protein interactions with one or more corresponding proteins, receptors, small molecules or any of the biocircuit components described herein.
  • Alkyl The terms “alkyl”, “alkoxy”, “hydroxyalkyl”, “alkoxy alkyl”, and “alkoxy carbonyl”, as used herein, include both straight and branched chains containing one to twelve carbon atoms, and/or which may or may not be substituted.
  • Alkenyl The terms “alkenyl” and “alkynyl” as used herein alone or as part of a larger moiety shall include both straight and branched chains containing two to twelve carbon atoms.
  • Aryl refers to monocyclic, bicyclic and tricyclic carbocyclic ring systems having a total of five to fourteen ring members, wherein at least one ring is aromatic and wherein each ring in the system contains 3 to 8 ring members.
  • aryl may be used interchangeably with the term “aryl ring.”
  • Aromatic refers to an unsaturated hydrocarbon ring structure with delocalized pi electrons. As used herein “aromatic” may refer to a monocyclic, bicyclic orpolycyclic aromatic compounds.
  • Aliphatic refers to a straight or branched C1-C8 hydrocarbon chain or a monocyclic C3-C8hydrocarbon or bicyclic C8- C12 hydrocarbon which are fully saturated or that contains one or more units of unsaturation, that is completely saturated or that contains one or more units of unsaturation, but which is not aromatic (also referred to herein as "carbocycle” or “cycloalkyl”), and that has a single point of attachment to the rest of the molecule wherein any individual ring in said bicyclic ring system has 3-7 members.
  • association when used with respect to two or more moieties, mean that the moieties are physically associated or connected with one another, either directly or via one or more additional moieties that serve as linking agents, to form a structure that is sufficiently stable so that the moieties remain physically associated under the conditions in which the structure is used, e.g., physiological conditions.
  • An “association” need not be strictly through direct covalent chemical bonding. It may also suggest ionic or hydrogen bonding or a hybridization based connectivity sufficiently stable such that the "associated" entities remain physically associated.
  • Biocircuit system As used herein, a “biocircuit” or “biocircuit system” is defined as a circuit within or useful in biologic systems comprising a stimulus and at least one effector module responsive to a stimulus, where the response to the stimulus produces at least one signal or outcome within, between, as an indicator of, or on a biologic system.
  • Biologic systems are generally understood to be any cell, tissue, organ, organ system or organism, whether animal, plant, fungi, bacterial, or viral.
  • biocircuits may be artificial circuits which employ the stimuli or effector modules taught by the present invention and effect signals or outcomes in acellular environments such as with diagnostic, reporter systems, devices, assays or kits.
  • the artificial circuits may be associated with one or more electronic, magnetic, or radioactive components or parts.
  • a biocircuit includes a destabilizing domain (DD) biocircuit system.
  • DD destabilizing domain
  • Conservative amino acid substitution is one in which an amino acid residue is substituted by another amino acid residue having a side chain (R group) with similar properties (e.g charge or hydrophobicity).
  • Destabilized As used herein, the term “destable,” “destabilize,” destabilizing region” or “destabilizing domain” means a region or molecule that is less stable than a starting, reference, wild-type or native form of the same region or molecule.
  • expression of a nucleic acid sequence refers to one or more of the following events: (1) production of an RNA template from a DNA sequence (e.g., by transcription); (2) processing of an RNA transcript (e.g., by splicing, editing, 5' cap formation, and/or 3' end processing); (3) translation of an RNA into a polypeptide or protein; (4) folding of a polypeptide or protein; and (5) post-translational modification of a polypeptide or protein.
  • Feature refers to a characteristic, a property, or a distinctive element.
  • Formulation includes at least a compound and/or composition of the present invention and a delivery agent.
  • fragments of proteins may comprise polypeptides obtained by digesting full-length protein.
  • a fragment of a protein includes at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 250 or more amino acids.
  • fragments of an antibody include portions of an antibody.
  • a "functional" biological molecule is a biological entity with a structure and in a form in which it exhibits a property and/or activity by which it is characterized.
  • Heterocycle refers to monocyclic, bicyclic or tricyclic ring systems having three to fourteen ring members in which one or more ring members is a heteroatom, wherein each ring in the system contains 3 to 7 ring members and is non-aromatic.
  • Hotspot As used herein, a "hotspot” or a “mutational hotspot” refers to an amino acid position in a protein coding gene that is mutated (by substitutions) more frequently relative to elsewhere within the same gene.
  • ICso- refers to the concentration of the ligand where the response or binding is reduced to half.
  • in vitro refers to events that occur in an artificial environment, e.g., in a test tube or reaction vessel, in cell culture, in a Petri dish, etc., rather than within an organism (e.g., animal, plant, or microbe).
  • in vivo refers to events that occur within an organism (e.g., animal, plant, or microbe or cell or tissue thereof).
  • Linker refers to a moiety that connects two or more domains, moieties or entities.
  • a linker may comprise 10 or more atoms.
  • a linker may comprise a group of atoms, e.g., 10-1,000 atoms, and can be comprised of the atoms or groups such as, but not limited to, carbon, amino, alkylamino, oxygen, sulfur, sulfoxide, sulfonyl, carbonyl, and imine.
  • a linker may comprise one or more nucleic acids comprising one or more nucleotides.
  • the linker may comprise an amino acid, peptide, polypeptide or protein.
  • a moiety bound by a linker may include, but is not limited to an atom, a chemical group, a nucleoside, a nucleotide, a nucleobase, a sugar, a nucleic acid, an amino acid, a peptide, a polypeptide, a protein, a protein complex, a payload (e.g., a therapeutic agent), or a marker (including, but not limited to a chemical, fluorescent, radioactive or bioluminescent marker).
  • the linker can be used for any useful purpose, such as to form multimers or conjugates, as well as to administer a payload, as described herein.
  • linker examples include, but are not limited to, alkyl, alkenyl, alkynyl, amido, amino, ether, thioether, ester, alkylene, heteroalkylene, aryl, or heterocyclyl, each of which can be optionally substituted, as described herein.
  • a disulfide bond e.g., ethylene or propylene glycol monomelic units, e.g., diethylene glycol, dipropylene glycol, triethylene glycol, tripropylene glycol, tetraethylene glycol, or tetraethylene glycol
  • dextran polymers Other examples include,
  • Non-limiting examples of a selectively cleavable bonds include an amido bond which may be cleaved for example by the use of tris(2- carboxyethyl) phosphine (TCEP), or other reducing agents, and/or photolysis, as well as an ester bond which may be cleaved for example by acidic or basic hydrolysis.
  • TCEP tris(2- carboxyethyl) phosphine
  • MOI refers to the multiplicity of infection which is defined as the average number of virus particles infecting a target cell.
  • Modified refers to a changed state or structure of a molecule or entity as compared with a parent or reference molecule or entity. Molecules may be modified in many ways including chemically, structurally, and functionally. In some
  • compounds and/or compositions of the present invention are modified by the introduction of non-natural amino acids.
  • mutations refers to a change and/or alteration.
  • mutations may be changes and/or alterations to proteins (including peptides and polypeptides) and/or nucleic acids (including polynucleic acids).
  • mutations comprise changes and/or alterations to a protein and/or nucleic acid sequence.
  • Such changes and/or alterations may comprise the addition, substitution and or deletion of one or more amino acids (in the case of proteins and/or peptides) and/or nucleotides (in the case of nucleic acids and or polynucleic acids, e.g., polynucleotides).
  • mutations comprise the addition and/or substitution of amino acids and/or nucleotides
  • such additions and/or substitutions may comprise 1 or more amino acid and/or nucleotide residues and may include modified amino acids and/or nucleotides.
  • the resulting construct, molecule or sequence of a mutation, change or alteration may be referred to herein as a mutant.
  • off target refers to any unintended effect on any one or more target, gene, cellular transcript, cell, and/or tissue.
  • Operably linked refers to a functional connection between two or more molecules, constructs, transcripts, entities, moieties or the like.
  • Protein of interest As used herein, the terms “proteins of interest” or “desired proteins” include those provided herein and fragments, mutants, variants, and alterations thereof.
  • Purine As used herein, “purine” refers to an aromatic heterocyclic structure, wherein one of the heterocycles is an imidazole ring and one of the heterocycles is a pyrimidine ring.
  • Pyrimidine refers to an aromatic heterocyclic structure similar to benzene, but wherein two of the carbon atoms are replaced by nitrogen atoms.
  • Pyridopyrimidine refers to an aromatic heterocyclic structure, wherein one of the heterocycles is a purine ring and one of the heterocycles is a pyrimidine ring.
  • Quinazoline refers to an aromatic heterocyclic structure, wherein one of the heterocycles is a benzene ring and one of the heterocycles is a pyrimidine ring.
  • Stable refers to a compound or entity that is sufficiently robust to survive isolation to a useful degree of purity from a reaction mixture, and preferably capable of formulation into an efficacious therapeutic agent.
  • Stabilized As used herein, the term “stabilize”, “stabilized,” “stabilized region” means to make or become stable. In some embodiments, stability is measured relative to an absolute value. In some embodiments, stability is measured relative to a secondary status or state or to a reference compound or entity.
  • Stimulus response element is a component of an effector module which is joined, attached, linked to or associated with one or more payloads of the effector module and in some instances, is responsible for the responsive nature of the effector module to one or more stimuli.
  • the "responsive" nature of an SRE to a stimulus may be characterized by a covalent or non-covalent interaction, a direct or indirect association or a structural or chemical reaction to the stimulus. Further, the response of any SRE to a stimulus may be a matter of degree or kind. The response may be a partial response. The response may be a reversible response.
  • the response may ultimately lead to a regulated signal or output.
  • Such output signal may be of a relative nature to the stimulus, e.g., producing a modulatory effect of between 1 and 100 or a factored increase or decrease such as 2- fold, 3-fold, 4-fold, 5-fold, 10-fold or more.
  • DD destabilizing domain
  • Subject refers to any organism to which a composition in accordance with the invention may be administered, e.g., for experimental, diagnostic, prophylactic, and/or therapeutic purposes. Typical subjects include animals (e.g., mammals such as mice, rats, rabbits, non-human primates, and humans) and/or plants.
  • Therapeutic Agent refers to any agent that, when administered to a subject, has a therapeutic, diagnostic, and/or prophylactic effect and/or elicits a desired biological and/or pharmacological effect.
  • Therapeutic agents of the present invention include any of the biocircuit components taught herein either alone or in combination with other therapeutic agents.
  • therapeutically effective amount means an amount of an agent to be delivered (e.g., nucleic acid, drug, therapeutic agent, diagnostic agent, prophylactic agent, etc.) that is sufficient, when administered to a subject suffering from or susceptible to an infection, disease, disorder, and/or condition, to treat, improve symptoms of, diagnose, prevent, and/or delay the onset of the infection, disease, disorder, and/or condition.
  • a therapeutically effective amount is provided in a single dose.
  • a therapeutically effective amount is administered in a dosage regimen comprising a plurality of doses.
  • a unit dosage form may be considered to comprise a therapeutically effective amount of a particular agent or entity if it comprises an amount that is effective when administered as part of such a dosage regimen.
  • Triazine is a class of nitrogen containing heterocycles with a structure similar to benzene, but wherein three carbon atoms are replaced by nitrogen atoms.
  • treatment or treating denote an approach for obtaining a beneficial or desired result including and preferably a beneficial or desired clinical result.
  • beneficial or desired clinical results include, but are not limited to, one or more of the following: reducing the proliferation of (or destroying) cancerous cells or other diseased, reducing metastasis of cancerous cells found in cancers, shrinking the size of the tumor, decreasing symptoms resulting from the disease, increasing the quality of life of those suffering from the disease, decreasing the dose of other medications required to treat the disease, delaying the progression of the disease, and/or prolonging survival of individuals.
  • Tune means to adjust, balance or adapt one thing in response to a stimulus or toward a particular outcome.
  • the SREs and/or DDs of the present invention adjust, balance or adapt the function or structure of compositions to which they are appended, attached or associated with in response to particular stimuli and/or environments.
  • variant refers to a first composition (e.g., a first DD or payload), that is related to a second composition (e.g., a second DD or payload, also termed a "parent" molecule).
  • the variant molecule can be derived from, isolated from, based on or homologous to the parent molecule.
  • variant can be used to describe either
  • articles such as “a,” “an,” and “the” may mean one or more than one unless indicated to the contrary or otherwise evident from the context. Claims or descriptions that include “or” between one or more members of a group are considered satisfied if one, more than one, or all of the group members are present in, employed in, or otherwise relevant to a given product or process unless indicated to the contrary or otherwise evident from the context.
  • the invention includes embodiments in which exactly one member of the group is present in, employed in, or otherwise relevant to a given product or process.
  • the invention includes embodiments in which more than one, or the entire group members are present in, employed in, or otherwise relevant to a given product or process.
  • any particular embodiment of the present invention that falls within the prior art may be explicitly excluded from any one or more of the claims. Since such embodiments are deemed to be known to one of ordinary skill in the art, they may be excluded even if the exclusion is not set forth explicitly herein. Any particular embodiment of the compositions of the invention (e.g., any antibiotic, therapeutic or active ingredient; any method of production; any method of use; etc.) can be excluded from any one or more claims, for any reason, whether or not related to the existence of prior art.
  • a candidate ligand binding domain (LBD) is selected and a cell-based screen using yellow fluorescent protein (YFP) as a reporter for protein stability is designed to identify mutants of the candidate LBD possessing the desired characteristics of a destabilizing domain: low protein levels in the absence of a ligand of the LBD, (i.e., low basal stability), large dynamic range, robust and predictable dose-response behavior, and rapid kinetics of degradation (Banaszynski, etal., (2006) Cell; 126(5): 995-1004).
  • YFP yellow fluorescent protein
  • the candidate LBD sequence (as a template) is first mutated using a combination of nucleotide analog mutagenesis and error-prone PCR, to generate libraries of mutants based on the template candidate domain sequence.
  • the libraries generated are cloned in-frame at either the 5'- or 3'-ends of the YFP gene, and a retroviral expression system is used to stably transduce the libraries of YFP fusions into NIH3T3 fibroblasts.
  • the transduced NIH3T3 cells are subjected to three to four rounds of sorting using fluorescence-activated cell sorting (FACS) to screen the libraries of candidate DDs.
  • FACS fluorescence-activated cell sorting
  • Transduced NIH3T3 cells are cultured in the absence of the high affinity ligand of the ligand binding domain (LBD), and cells that exhibit low levels of YFP expression are selected through FACS.
  • the selected cell population is cultured in the presence of the high affinity ligand of the ligand binding domain for a period of time (e.g., 24 hours), at which point cells are sorted again by FACS.
  • Cells that exhibit high levels of YFP expression are selected through FACS and the selected cell population is split into two groups and treated again with the high affinity ligand of the ligand binding domain at different concentrations; one group is treated with the lower concentration of the ligand and the other is treated with a high concentration of the ligand, for a period of time (e.g., 24 hours), at which point cells are sorted again by FACS.
  • Cells expressing mutants that are responsive to lower concentrations of the ligand are isolated.
  • the isolated cells responsive to the lower concentration of the ligand are treated with the ligand again and cells exhibiting low fluorescence levels are collected 4 hours following removal of the ligand from the media.
  • This fourth sorting is designed to enrich cells that exhibit fast kinetics of degradation (lwamoto etal, Cnem Biol. 2010 Sep 24; 17(9): 981-988).
  • Hie selected cell population is subject to additional one or more sorts by FACS in the absence of high affinity ligand of LBD and cells that exhibit low levels of YFP expression are selected for further analysis.
  • Cells are treated with high affinity ligand of the ligand binding domain, for a period of time (e.g. 24 hours), and sorted again by FACS.
  • Cells expressing high levels of YFP are selected for through FACS.
  • Cells with high expression of YFP are treated with ligand again and cells exhibiting low fluorescence levels are collected 4 hours following removal of the ligand from the media to enrich cells that exhibit fast kinetics of degradation. Any of the sorting steps may be repeated to identify DDs with ligand dependent stability.
  • the cells are recovered after sorting.
  • the identified candidate cells are harvested and the genomic DNA is extracted.
  • the candidate DDs are amplified by PCR and isolated.
  • the candidate DDs are sequenced and compared to the LBD template to identify the mutations in candidate DDs.
  • ecDHFR E. coli DHFR
  • hDHFR human DHFR
  • hDHFR mutants were then fused to a linker, GGSGGG of SEQ ID NO. 4 and a GFP reporter gene at the N terminus.
  • the stability of the mutants in response to TMP and MTX was tested.
  • the hDHFR N terminus mutant construct cloned into pLVX. IRES.
  • the reporter constructs were transfected into NTH 3T3 cells.
  • Transfected cells were incubated with either ⁇ MTX or 10uM TMP for 48 hours.
  • DMSO was used as control. Fluorescence signal was measured by FACS and median fluorescence signal intensity was calculated. Median fluorescence intensity following DMSO treatment are shown in Table 10.
  • the destabilizing mutation co-efficient was calculated as the fold change in GFP intensity in the hDHFR mutant constructs compared to the hDHFR (WT) in the absence of the ligand. Destabilizing mutation co-efficients less than 1 are desired in DDs.
  • hDHFR Y 1221 (OT-hDHFRN-002), hDHFR A125F, and Y122I (OT-hDHFRN-005) showed a fold change increase in GFP intensity with MTX and TMP, suggesting a MTX and TMP dependent stabilization of the DD.
  • the percentage of GFP positive cells in the hDHFR mutants was low with DMSO treatment and comparable to the control cells.
  • the wildtype hDHFR (OT- hDHFRN-001) showed a high percentage of GFP positive cells with DMSO treatment.
  • OT- hDHFRN-001 shows a high percentage of GFP positive cells with DMSO treatment.
  • stabilizing ligands i.e. luM MTX or ⁇ TMP.
  • OT- hDHFRN-002 (hDHFR Y122I), OT-hDHFRN-005 (hDHFR A125F, Y122I) and OT-hDHFRN- 021 (hDHFR V121A, Y122I) showed an increase in the percentage of GFP positive cells indicating a ligand dependent stabilization.
  • OT-DHFRN-003, OT-DHFRN-004, OT-DHFRN- 006 OT-DHFRN-007 and OT-DHFRN-008 showed MTX specific stabilization as indicated by the increase in the percentage of GFP positive cells following MTX treatment.
  • hDHFR WT and mutants were immunoblotted after TMP or MTX or DMSO treatment for 48 hours.
  • Anti-AcGFP antibody (Clonetech, Mountain View, CA) and anti-hDHFR antibody (GeneTex Cat. NO.
  • hDHFR mutants including OT-DHFRN-006 OT-DHFRN-007 and OT-DHFRN-008 showed stabilization exclusively with MTX. Wild type hDHFR showed enhanced stabilization upon addition of MTX and TMP. The results were consistent using both the AcGFP antibody as well as the hDHFR antibody.
  • the mutant library was ligated in frame with an AcGFP reporter at the C- terminus into pLVX-IRES-Puro vector and packaged into lentivirus.
  • the lentivirus library was then used to infect HEK293T cells at multiplicity of infection (MOI) of 0.3. Stably transduced cells wens selected with puromycin. Cells were then treated with 1 ⁇ Methotrexate or ⁇ Trimethoprim for 48 hrs.
  • Table 3 provides the sequence identity of the clones generated by error prone PCR based mutagenesis. The sequence confirmed clones were ligated in frame to AcGFP reporter at the C-terminus into pLVX-IRES-Puro and transformed into E. coli. Individual clones were sequenced and packaged into lentivirus. HEK293 cells were transduced with the lentivirus and stable integrants were selected with puromycin. Cells expressing individual clones were then incubated with vehicle, Dimethylsulfoxide (DMSO), 10 or SO uM Trimethoprim or 1 ⁇ Methotrexate. Median GFP fluorescence was quantified using FACS and the results from various experiments are presented in Tables 13-16.
  • DMSO Dimethylsulfoxide
  • the stabilization ratio was calculated as the fold change in GFP intensity in ligand treated samples compared to treatment with DMSO (i.e. in the absence of ligand) with the same construct.
  • the destabilizing mutation co-efficient was calculated as the fold change in GFP intensity in the DHFR mutant constructs in the absence of the ligand compared to the wildtype DHFR construct. Destabilizing mutation co-efficient less than 1 and stabilization ratios greater than 1 are desired in DDs.
  • the hDHFR mutants can be classified into four groups with reference to GFP intensity with DMSO or ligand treatment as compared to the wildtype as well as their stabilization and destabilizing mutation co-efficient s.
  • One group of hDHFR mutants showed low GFP intensity compared to WT with DMSO treatment and high GFP intensity with both MTX and TMP treatment suggesting that the mutants are destabilized in the absence of ligand, but are stabilized in the presence of both ligands.
  • Mutants that showed this behavior include Clone Cl-4(hDHFR(F59S)), Clone Cl-8 (hDHFR 017V)), Clone Cl-3 (hDHFR (A107V)), Clone Cl-14 (hDHFR (N127Y), Clone Cl-21(hDHFR (K185E)), Clone C2- 20 (hDHFR (N186D)), Clone Cl-24 (hDHFR (VI 10A, V136M, K177R)), Clone C2-25 (hDHFR (E162G, I176F)), Clone C3-3 (hDHFR (M140I)), and Clone C3-9 (hDHFR (H131R, E144G)). Among these mutants.
  • Mutants that showed MTX dependent stability include Clone Cl-18 (hDHFR (V9A, S93R, P150L)), Clone C2-21(hDHFR (A10V, H88Y)), Clone C2-8 (hDHFR (I8V, K133E, Y163Q), Clone C2-15 (hDHFR (K19E, F89L, E181G)), Clone C2-8 (hDHFR (I8V, K133E, Y163Q), Clone C2-15 (hDHFR (K19E, F89L, E181G)), Clone C3-l(hDHFR (Y178H, E181G)), Clone C3-22 (hDHFR (T57A, I72A)), Clone C3-10 (hDHFR (Y183H, K185E)), and Clone C4-3 (hDHFR (G21E, I72V, I176T)).
  • hDHFR mutants that were only destabilized include Clone C 1-10 (hDHFR (C7R, Y163Q), Clone Cl-25 (hDHFR (T137R, F143L)), Clone C2-22 (hDHFR (G54R, II 15L, M140V, S168Q), Clone C2-23 (hDHFR (L23S, V121A, Y157C)), and Clone C3-2(hDHFR (N49D, F59S, D153G)).
  • hDHFR mutants showed GFP expression levels with DMSO treatment that was comparable to the wildtype DHFR, with a further increase in GFP intensity with TMP and MTX treatment suggesting that these mutations were only capable of stabilizing hDHFR.
  • stabilizing mutants include Clone Cl-11 (hDHFR (N65D)), and Clone Cl-12 (hDHFR(K81R)).
  • DDs may be positioned upstream or downstream of the payload within an SRE.
  • hDHFR mutants generated by structure guided mutagenesis as discussed in example 2 were fused at the C -terminus of GFP to test if the hDHFR mutants can destabilize proteins of interest when fused to the C-terminus of the protein of interest.
  • a linker, GGSGGG SEQ ID NO. 4 was placed between GFP and hDHFR and cloned into pLVX.IRES. Puro.
  • HEK 293T cells stably expressing GFP-hDHFR -WT or GFP-hDHFR(mutant) constructs were incubated with ⁇ MTX or 50 ⁇ IMP or DMSO (control) for 48 hours. Following the incubation, median fluorescence intensity (MFI) was measured using FACS. All hDHFR(mutant)-GFP constructs demonstrated lower MFI intensities compared to hDHFR WT, suggesting a significant destabilization in the absence of the ligand (Figure 8A).
  • OT- hDHFRC-012 (hDHFR (Y 1221), OT-hDHFRC-015 (hDHFR (A125F, Y122I), OT-hDHFRC- 019 (hDHFR (Q36K, Y1221), and OT-hDHFRC-020, and (hDHFR (Q36F, N65F, Y122I) showed a several fold increase in MFI over DMSO with both MTX and TMP treatment suggesting that these constructs can be stabilized by both ligands.
  • hDHFR mutants The binding of hDHFR mutants to varying doses of ligands was characterized using DHFR mutants fused to N terminus of AcGFP.
  • HEK293 cells stably expressing OT-hDHFRN- 002 (hDHFR(Y122I)-GFP) construct were incubated with varying concentrations of MTX or DMSO in DMEM with 10%FBS for 48hrs. Median GFP fluorescence intensity was measured using FACS analysis.
  • hDHFR (Y122I) mutant showed a ligand dose dependent increase in GFP intensity (Figure 9A). This data suggests that hDHFR (Y122I) was stabilized by MTX in a dose dependent manner. Since MTX is also an inhibitor of DHFR, the IC50 was also calculated and an ICso of 108 nM was obtained.
  • HEK293 cells stably expressing OT-hDHFRN-002 (hDHFR(Y122I)-GFP), OT- hDHFRN-005 (hDHFR (A125F, Y122I)), OT-hDHFRN-008 (hDHFR (G21T, Y122I)) and OT- hDHFRN-021 (hDHFR (V121A, Y122I)) constructs were incubated with varying concentrations of TMP or DMSO in DMEM with 10%FBS for 48hrs. Mean GFP fluorescence intensity was measured using FACS analysis ( Figure 9B). All mutants showed ligand dose dependent increase in GFP intensity suggesting an increase in TMP dependent stabilization of the hDHFR mutants.
  • HEK293 cells stably expressing hDHFR- WT or hDHFR mutant constructs were incubated with 50 ⁇ TMP in DMLEM with 10% FBS for 48 hours. Following incubation, cells were washed with DMEM containing 10% FBS. DMEM containing ⁇ g/mL recombinant human DHFR protein was added to the cells and were further incubated for 2, 4, 6 or 24 hours. Median fluorescence intensity of the cells was measured using FACS and compared to the median fluorescence intensity of cells before incubation with the recombinant human DHFR (time 0). The results are depicted as the percentage of median fluorescence intensity (MFI) of GFP remaining after time 0 ( Figure 10).
  • MFI median fluorescence intensity
  • mice were dosed with one of three different concentrations of TMP 30 mg/kg, 100 mg/kg, or 300mg/kg TMP.
  • concentration of TMP in the plasma was measured at 0.083 hours, 0.2S hours,0.5 hours, 1 hour, 2 hours, 4 hours. 8 hours, 12 hours, 16 hours, 20 hours, and 24 hours after dosing.
  • the plasma TMP levels at different time points are presented in Table 18.
  • 100 mg/kg resulted in TMP concentrations in the plasma of 50-100 ⁇ at the early time points and 300 mg/kg dose resulted in 100-150 ⁇ plasma concertation of TMP at early time points. Virtually no TMP levels were detected in the plasma 4 hours after dosing. Thus 100 mg/kg represents the lowest dose that results in significant plasma concentrations of TMP that may be required for human DHFR stabilization in vivo.
  • Example 7 Human DHFR regulated expression of IL15-IL15Ra fusion molecule
  • a fusion molecule was generated by fusing membrane bound IL15, IL15 Receptor alpha subunit (IL15Ra) and human DHFR (DO). These fusion molecules were cloned into pLVX-EFla-IRES-Puro vector.
  • Membrane bound-IL15-IL15Ra constructs (OT-IL15-008 to OT IL-15-011) were transduced into human colorectal carcinoma cell line, HCT-116 and stable integrants were selected with 2 ⁇ g of puromycin. Stably integrated cells were incubated for 24 hours in the presence or absence of 10 ⁇ Trimethoprim or luM Methotrexate.
  • IL 15 -IL 15Ra fusion constructs were examined by staining with PE- conjugated IL15Ra antibody (Cat no. 330207, Biolegend, San Diego, CA).
  • the median fluorescence intensity obtained with the different constructs in the presence or absence of the corresponding ligand is presented in Table 19.
  • the stabilization ratio was calculated as the fold change in fluorescence intensity in ligand treated samples compared to treatment with DMSO (i.e. in the absence of ligand) with the same construct.
  • the destabilization ratio was calculated as the fold change in fluorescence intensity in the DD regulated constructs compared to the constitutive construct (OT-IL15-008) in the absence of the ligand. Destabilization ratios less than 1 and stabilization ratios greater than 1 are desired in DDs.
  • IL15-IL15Ra constructs (OT-IL15-008, OT-IL15-010, OT-IL15-011) in HCT-116, cells were incubated with lOuM Trimethoprim or luM Methotrexate or DMSO for 24 hours. Following incubation, cells were harvested and cell extracts were prepared. Cell extracts were run on SDS-PAGE and western blotted with anti-IL15 antibody (Catalog No. 7213, Abeam, Cambridge, UK).
  • the IL15/IL15Ra constitutive construct (OT-IL15-008) showed ligand independent IL15 expression while the DD regulated constructs (OT-IL15-0010 and OT-IL15-011) showed ligand dependent IL15 expression.
  • the identity of the IL 15 bands was also confirmed by immunoblotting with the anti-human DHFR antibody (Catalog No. 117705, Genetex, Irvine, CA).
  • Both IL15-IL15Ra fusion constructs (OT-IL15-010 and 011) showed ligand dependent expression of DHFR expression.
  • IL15-IL15Ra fusion constructs namely, OT-IL15-008, OT-IL15-010 (hDHFR (Y122I, A125F)), and OT-IL15-011 (hDHFR (Q36F, N65F, Y1221)) were stably transduced into HCT-116 cells and incubated with increasing concentrations of Trimethoprim for 24 hours.
  • Surface expression of IL15-IL15Ra fusion constructs was quantified by FACS using IL15Ra- PE antibody. The median fluorescence intensity with increasing doses of TMP is represented in Table 20.
  • Human DHFR mutants generated by site directed and random mutagenesis were compared with wildtype human DHFR protein sequence and analyzed for patterns. Exemplary alignments are shown in Figure 12A, and Figure 12B. The analysis of the sequences showed that many hDHFR DDs mutations match a vicinal amino acid, located up to 5 amino acids upstream or downstream of the mutation site. The human DHFR mutants that have been mutated to the immediately upstream or downstream wildtype amino acid are listed in Table 21.
  • Thermal shift assays can be used to measure the thermal denatu ration temperature of a protein as an indicator of its stability in response to different conditions such as pH, ions, salts, additives, drugs, and/or mutations. It can also be used to determine conditions under which protein stabilization or destabilization can be maximized.
  • Human DHFR mutants are mixed with a thermal assay dye, thermal assay buffer, and ligand (or DMSO control). Samples are also treated with varying concentrations of factors such as drugs, salts, ions, or other parameters.
  • the samples are loaded into an instrument such as a real-time PCR instrument and the temperature ramp rates is set within a range of approximately 0.1-10 degrees Celsius per minute. The fluorescence in each condition is measured at regular intervals, over a temperature range spanning the typical protein unfolding temperatures of 25-95 degrees Celsius.
  • DHFR (DD)-IL12 constructs are packaged into pLVX-IRES-Puro lentiviral vectors with CMV, EFla, PGK or without a promoter.
  • hDHFR Q36F, Y122I, Al 25F (OT-IL12-008) or the constitutive construct (OT-IL12-006) and cloned into a pLVX-CMV-IRES- Puro.
  • a p40 signal sequence was inserted at the N terminus of the construct and a furin protease cleavage site or a modified furin site was also included (see Table 8).
  • HEK293T cells are transiently or stably transfected, or stably transduced with IL12 constructs (OT-IL12-006, and OT-IL12-008), and subsequently treated with Trimethoprim, or Methotrexate, or left untreated for 6 hours.
  • Culture media is collected from transfected cells and diluted 1:50 to measure IL12 levels using p40 ELISA. Treatment with ligand is expected to result in a significant increase in IL12 over untreated control.
  • ligand (MTX or TMP) dependent 1L12 induction 2 million cells e.g. HEK 293T cells are plated in growth medium and incubated overnight in the presence of TMP or MTX, or left untreated. Cells are then incubated for additional time ranging from 2 to 72 hours and growth media is collected from the cells at all time points. Growth media is diluted 400-fold and IL12 levels are measured using IL12 p40 ELISA. IL12 expression in ligand treated cells is expected to increase over time.
  • DP regulated CD19 CAR 2 million cells e.g. HEK 293T cells are plated in growth medium and incubated overnight in the presence of TMP or MTX, or left untreated. Cells are then incubated for additional time ranging from 2 to 72 hours and growth media is collected from the cells at all time points. Growth media is diluted 400-fold and IL12 levels are measured using IL12 p40 ELISA. IL12 expression in ligand treated cells is expected to increase over
  • a CD 19 CAR fusion polypeptide was linked to the N terminus of human DHFR derived DDs (as shown in Table 6) and the constructs are cloned into pLVX-IRES-Puro vector.
  • HEK 293T cells are cultured in growth medium containing DMEM and 10% FBS and transfected with CAR constructs using Lipofectamine 2000. 48 hours after transaction, cells are treated 1 ⁇ Trimethoprim or vehicle control and incubated further for another 24 hours. Cells are then harvested, lysed and immunoblotted for CD3 Zeta using anti-CD247 (BD Pharmingen, Franklin Lanes, NJ) and Alexa 555-conjugated-goat-anti mouse antibody (red) (Li-Cor, Lincoln, NE).
  • anti-CD247 BD Pharmingen, Franklin Lanes, NJ
  • red Alexa 555-conjugated-goat-anti mouse antibody
  • Lysates are also immunoblotted for Actin with Alexa 488-conjugated secondary antibody (green) to confirm even protein loading across all samples.
  • TMP treated human DHFR mutant CD19 CAR constructs (OT-CD19C-008 to OT-CD19C-011) are expected to show an increase in CD3 Zeta protein levels in the presence of TMP indicating the stabilization of the CD 19 CAR.
  • CD 19 CAR-hDHFR constructs in HEK 293T cells is measured using FACS with Protein L-Biotin-Streptavidin-Allophycocyanin which binds to the kappa light chain of the CAR (ThermoFisher Scientific, Waltham, MA). Cells are treated with 10 ⁇ Trimethoprim or 1 ⁇ MTX, or vehicle control for 24 hours and subject to FACS analysis. Surface expression of CD 19 CAR-hDHFR constructs is expected to be detected only in the presence of ligand.
  • Clone Cl-3 (hDHFR (A107V)) mutant showed higher fluoresce intensity values man hDHFR (WT) at multiple doses of MTX.
  • Clone Cl-4 (hDHFR (F59S)) showed an increase in fluorescence intensity at 33.3 and 11 ⁇ doses of MTX.
  • Clone Cl-8 (hDHFR (I17V)), hDHFR (N127Y), and hDHFR (K185E) mutants showed fluorescence intensities that were less than hDHFR (WT).
  • Clone Cl-3 (hDHFR (A107V)) mutant showed higher fluorescence intensity values than hDHFR (WT) at multiple doses of TMP.
  • Clone Cl-8(hDHFR (117V)) an increase in fluorescence intensity at 3.704 ⁇ dose of TMP.
  • Clone Cl-8 (hDHFR (I17V)), Clone Cl-14 (hDHFR (N127Y)), and Clone Cl-25 (hDHFR (K185E)) mutants showed fluorescence intensities that were less than hDHFR (WT).
  • TMP ratio or MTX ratio was defined as the ratio of % Normalized Response of a mutant at a particular dose of the ligand (TMP or MTX) to the % Normalized Response of hDHFR (WT) at the same dose of the same ligand.
  • the ratios are presented in Table 25.
  • Clone Cl-8 (hDHFR (I17V)) and Clone Cl-14 (hDHFR (N127Y)) mutants can bind to and be stabilized by TMP, but cannot be stabilized by MTX.
  • Clone Cl-3 (hDHFR (A107V)) preserves TMP and MTX stabilization
  • Clone Cl-4 (hDHFR (F59S)) selectively disrupts TMP stabilization while Clone Cl-14 (hDHFR (N127Y)) and Clone Cl-8 (hDHFR (I17V)) affect MTX stabilization.
  • Clone Cl-3(hDHFR (A107V)) maybe a better substrate for combination mutants and in the search for better TMP binders.
  • E. coli DHFR amino acid 2-187 of WT
  • R12Y, Y100I amino acid 2-187 of WT
  • GFP amino acid sequence
  • Transfected cells were incubated with varying concentrations of TMP ranging from 0.001 to 1 ⁇ TMP.
  • DMSO was used as control.
  • Fluorescence signal was measured by FACS and median fluorescence signal intensity (MFI) was calculated. The results are shown in Table 26. Relative MFI was calculated relative to untreated control.
  • Example 15 TMP dose responsive expression of IL15-IL15Ra
  • IL15-IL15Ra fusion constructs, OT-IL15-008, and OT-IL15-010 were stably expressed in HCT116 cells are treated with increasing doses of TMP ranging from ⁇ , and ⁇ TMP for 24 hours. Cell lysates were obtained and immunoblotted with anti IL15Ra antibody. As shown in Figure 13, an increase in IL15Ra expression was observed with OT-IL15- 010 construct with the addition of TMP. As expected, the constitutive construct, OT-IL15-008 showed strong expression of IL15Ra both in the presence and absence of ligand.
  • a CD 19 CAR fusion polypeptide was linked to human DHFR- DD and the constructs were cloned into pLVX-IRES-Puro vector.
  • [0048 ⁇ hDHFR DDs were positioned at the C terminus of the construct (OT-CD19C-008, OT- CD19C-009, OT-CD19C-010, OT-CD19C-011). In some instances, a furin cleavage site was added between the DD and the CD 19 scFv. A constitutively expressed CAR construct, OT- CD19C-001 was used as a positive control.
  • HEK 293T cells were cultured in growth medium containing DMEM and 10 FBS and transfected with CAR constructs using Lipofectamine 2000. 48 hours after transfection, cells were treated with ⁇ orlOuM Shield-1, 10 ⁇ Trimethoprim, ⁇ Methotrexate, or vehicle control and incubated for 24 hours. Cells were harvested, lysed and immunoblotted for CD3 Zeta, a component of the CAR, using anti-CD247 (BD Phaimingen, Franklin Lanes, NJ) and Alexa 555- conj ugated-goat-anti mouse antibody (red) (Li-Cor, Lincoln, NE). Lysates were also
  • CD19C-009 showed modest increase in CD3 Zeta levels in the presence of Methotrexate, indicating a modest ligand-dependent stabilization of CD 19 CAR
  • Lysates from cells expressing CD 19 CAR constructs were also immunoblotted for 4 1- BB, a component of the CAR.
  • OT-CD19C-008, OT-CD19C-009, OT- CD19C-010 and OT-CD19C-011 showed low levels of 4-1 BB in the absence of ligand and high levels of 4-1 BB in the presence of the ligand, Methotrexate, indicating a strong ligand dependent stabilization of CD 19 CAR using these constructs.
  • Constructs OT-CD19N-014 and OT-CD19N-015, which contain a furin cleavage site showed an additional, smaller 4 IBB protein product upon treatment with MTX. This smaller 4-1BB protein band was only seen with the addition of the ligand and its molecular weight is consistent with the size of the CD 19 C AR.
  • the mean fluorescence intensities are presented in Table 28.
  • MFI represents mean fluorescence intensity.
  • the stabilization ratio was calculated as the fold change in GFP intensity in ligand treated samples compared to treatment with DMSO (i.e. in the absence of ligand) with the same construct.
  • the destabilization ratio was calculated as the fold change in GFP intensity in the DD regulated constructs compared to the constitutive construct (OT- CD19C-001) in the absence of the ligand. Destabilization ratios less than 1 and stabilization ratios greater than 1 are desired.
  • a destabilization ration less than 1 was observed with all constructs indicating that all DD regulated constructs are destabilized in the absence of ligand.
  • a stabilization ratio of greater than 1 was observed with OT-CD19C-008, OT-CD19C-009, OT-CD19C-010, OT-CD19C-011, OT-CD19C-014 and OT-CD19C-015.
  • these constructs were also destabilized in the absence of ligand and therefore represent suitable CD19-DD constructs.
  • DHFR mutants generated by random mutagenesis were fused to GFP, transfected into HEK293 cells and treated with increasing doses of Trimethoprim and Methotrexate for 48 hours. Cell lysates were harvested and immunoblotted using Anti-AcGFP antibody (Clonetech, Mountain View, CA) by western blotting.
  • hDHFR H131R, E144G
  • DMSO treatment DMSO treatment
  • TMP dose dependent stabilization was observed with the mutant Clone Cl-8 (hDHFR (I17V)) and hDHFR (Wildtype), although the basal expression in the absence of ligand was still detectable.
  • Figure 15B represents ligand dependent stabilization observed with MTX.
  • Clone Cl-8 hDHFR (I17V)
  • hDHFR H131R, E144G
  • MFI mean fluorescence intensity
  • constructs, Cl-8, clone 1-14, clone 2-25, clone 3-3 and C3-9 showed robust ligand dependent stabilization over a range of TMP doses demonstrating the tunability of these constructs.
  • Constructs CI -3 and C2-20 showed modest ligand dependent stabilization even at the highest doses of TMP.
  • Further even in the absence of ligand CI -3 and C2-20 showed high basal expression compared to the other constructs tested, indicating that Cl-8, clone 1-14, clone 2-25, clone 3-3 and C3-9 may be suitable DDs for further analysis.
  • DHFR mutants were analyzed at a fixed dose over 0- 48 hours and analyzed by FACS. The mean fluorescence intensity and destabilizing mutation co-efficient s are shown in Tables 30A and 30B respectively.
  • Mutations identified by random mutagenesis and analyzed by FACS were mapped onto the H2W3A structure of hDHFR from the protein data bank. Both inhibitors of DHFR, namely Trimethoprim and Methotrexate as well as co-factor, NADP were modelled into the structure of DHFR. The positions of the destabilizing mutations, relative to the ligand and co-factor were visualized. Only constructs that showed destabilization in the absence of ligand and ligand dependent stabilization were chosen for the analysis were chosen.
  • the constructs tested include Cl-14 (hDHFR (N127Y)), Cl-18 (hDHFR (V9A, S93R, P150L)), Cl-21 hDHFR (K185E)), Cl- 24 (hDHFR (VI 10A, V136M, K177R)), Cl-4 (hDHFR (F59S)), Cl-8 (hDHFR (I17V)), C2-15 (hDHFR (K19E, F89L, E181G)), C2-21 (hDHFR (A10V, H88Y)), C2-23 (hDHFR (L23S, V121A, Y157Q), C2-25 (hDHFR (E162G, I176F)), C3-1 (hDHFR (Y178H, E181G)), C3-10 (hDHFR (Y183H, K185E)), C3-22 (hDHFR (T57A, I72A)), C3-3 (hDHFR (M140I)), C3-9 (hDHFR (H131R, E144G)),
  • mutants generated by site directed and random mutagenesis identified amino acid hotspots whose mutation confers destabilization and ligand dependent stabilization properties to DHFR.
  • the amino acid at the hotspot position is mutated to any of the known amino acids, including, but not limited to lysine, aspartic acid, glutamic acid, glutamine, asparagine, histidine, serine, threonine, tyrosine, cysteine, methionine, tryptophan, alanine, isoleucine, leucine, phenylalanine, valine, proline, and glycine.
  • a library of hotspot mutations is generated by site directed mutagenesis and each of the mutants in the library is fused to a reporter protein e.g. AcGFP via a linker.
  • the properties of the DDs are analyzed in the presence and absence of ligands via western blot and FACS as previously described.
  • Ligands evaluated include, but are not limited TMP and MTX.
  • Example 21 Destabilizing flomains with improved ligand binding
  • DHFR bound trimethoprim key DHFR residues required for binding to TMP were identified. These include aspartic acid at position 22 which contributes to loop charge, glutamic acid at position 31, phenylalanine at position 32 which is in the ligand binding pocket, arginine at position 33 which plays a role in helix orientation, glutamine at position 36 which plays a role in helix orientation, asparagine at position 65 which lines the binding pocket and valine at position 116.
  • OT-hDHFRC-027 and OT-hDHFRC-028 are generated.
  • Constructs are introduced by transfection or transduction into cell lines such as HEK293T cells and HCT116 cells.
  • Ligand dependent stabilization of expression is measured by comparing the expression of the constructs in the presence of varying doses of the ligand to the expression of the construct in the absence of the ligand.
  • the kinetics of the ligand dose responsive behavior of OT-DHFRC- 027 and OT-DHFRC-028 are compared to other DD constructs described.
  • OT-DHFRC-027 and OT-DHFRC-028 are expected to demonstrate better binding to TMP at lower concentrations of TMP, when compared to wildtype and other DHFR-DD constructs.
  • the biocircuits of the invention comprise multiple modules which can be optimized. Libraries of each of the components is generated to allow for the rapid generation of new constructs with desired behaviors.
  • Ligand pharmacokinetics is a powerful tool for payload specific tuning in vivo, which can be used to shift the ligand response curve of the effector module to the left or right depending on the modulating factors. Several modulating factors are tested, including, but not limited to the ligand dose, concentrations, magnitude, duration, and route of administration.
  • Destabilizing domains can also be modified to improve biocircuit behavior. The destabilizing domain is the core determinant of the dynamic range of the biocircuit. Depending on the DD selected, the ligand response curve of the effector module can be shifted up or down.
  • DD selection is also altered depending on its degradation kinetics desired. Promoters that transcriptionally control the expression of the SREs are optimized. Choice of promoter impacts the basal -off state and affects the dynamic range of stabilization. Further, promoter choice contributes to the extent of stabilized payload produced. Other optimizable elements of the biocircuits include vector, translational elements, leader sequence, placement of the components within the SRE, codon selection, protease sites, linkers, and mRNA stability.
  • a caspase 9 polypeptide was linked to the N or C-terminus of FKBP, ecDHFR and hDHFR DDs and cloned into pLVX.IRES. Puro vectors.
  • 1 million HEK-293T cells are plated in a 6-well plate in growth media containing DMEM and 10 FBS and incubated overnight at 37°C, 5% C02. Cells are transiently transfected with lOOng of DD-Caspase 9 constructs using Lipofectamine 2000 and incubated for 48 hrs. Following the incubation, growth media is exchanged for media containing ligands
  • Luciferase tagged DHFR DD constructs allows the in vivo tracking of DHFR DDs and evaluation of in vivo kinetics of destabilization and ligand dependent stabilization.
  • OT-DHFR- 023 to OT-DHFR-028 were generated by appending DHFR DDs described herein to luciferase.
  • the constructs were stably transduced into HCT116 cells and seeded into 96-well plates at 2000/well. The cells were incubated with 50 ⁇ TMP or without TMP i.e. vehicle control, for 48hrs. The cells were lysed, and the luciferase activity was measured. The results are shown in Table 32.
  • the stabilization ratio which is defined as the stabilization ratio was calculated as the fold change in GFP intensity in ligand treated samples compared to treatment with vehicle control (i.e. in the absence of ligand) with the same construct.
  • the parental untransduced HCT116 cells were included in the experiment as a negative control. Table 32; Luciferase activity
  • OT-DHFR-024, OT-DHFR-025 and OT-DHFR-026 showed stabilization ratios greater than 2, which is greater than the ratio observed with the parental cells.
  • OT- DHFR-023 show a stabilization ratio comparable to the parent cells, indicating that the luciferase expression observed with this construct is not significantly higher than background luciferase expression detected with the assay.
  • a mutant library is generated using DHFR (Y122I) as the template.
  • the DDs are tagged to reporter proteins such as GFP.
  • Mutant libraries are generated by error-prone PCR and/or commercially available kits such as
  • GeneMorph ⁇ (Agilent, Santa Clara, CA).
  • the libraries arc packaged in lentivirus vectors such as pLVX-IRES-puro and are screened for GFP expression in the presence or absence of TMP. Clones from the library that show higher GFP expression than the template, in the presence of TMP, as well as little to no GFP in the absence of ligand.

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Abstract

La présente invention concerne des compositions et des méthodes pour l'expression régulée et contrôlée de protéines.
PCT/US2018/020718 2017-03-03 2018-03-02 Régulation de protéine modulable dhfr WO2018161000A1 (fr)

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WO2020086742A1 (fr) * 2018-10-24 2020-04-30 Obsidian Therapeutics, Inc. Régulation de protéine accordable par er
WO2020185628A1 (fr) 2019-03-08 2020-09-17 Obsidian Therapeutics, Inc. Compositions de cd40l et procédés de régulation accordable
WO2021040736A1 (fr) * 2019-08-30 2021-03-04 Obsidian Therapeutics, Inc. Compositions à base de car cd19 tandem et méthodes d'immunothérapie
WO2021046451A1 (fr) 2019-09-06 2021-03-11 Obsidian Therapeutics, Inc. Compositions et méthodes de régulation de protéine accordable dhfr
US11058725B2 (en) 2019-09-10 2021-07-13 Obsidian Therapeutics, Inc. CA2 compositions and methods for tunable regulation
WO2021142376A1 (fr) 2020-01-08 2021-07-15 Obsidian Therapeutics, Inc. Compositions et procédés pour la régulation accordable de la transcription
WO2021262773A1 (fr) 2020-06-22 2021-12-30 Obsidian Therapeutics, Inc. Compositions et méthodes de régulation accordable de nucléases de cas
WO2022159939A1 (fr) 2021-01-19 2022-07-28 Obsidian Therapeutics, Inc. Lymphocytes infiltrant les tumeurs avec interleukine 15 liée à la membrane et leurs utilisations
WO2022261475A1 (fr) * 2021-06-11 2022-12-15 Spark Therapeutics, Inc. Méthodes de régulation de la production de virus adénoassociés
US11629340B2 (en) 2017-03-03 2023-04-18 Obsidian Therapeutics, Inc. DHFR tunable protein regulation
WO2023069418A2 (fr) 2021-10-18 2023-04-27 Obsidian Therapeutics, Inc. Compositions et systèmes pour la régulation de la fonction/abondance et de l'administration de charges utiles polypeptidiques
WO2023141436A1 (fr) 2022-01-18 2023-07-27 Obsidian Therapeutics, Inc. Procédés d'identification et d'utilisation de lymphocytes infiltrant les tumeurs allogéniques pour traiter le cancer

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Cited By (13)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US11629340B2 (en) 2017-03-03 2023-04-18 Obsidian Therapeutics, Inc. DHFR tunable protein regulation
WO2020086742A1 (fr) * 2018-10-24 2020-04-30 Obsidian Therapeutics, Inc. Régulation de protéine accordable par er
WO2020185628A1 (fr) 2019-03-08 2020-09-17 Obsidian Therapeutics, Inc. Compositions de cd40l et procédés de régulation accordable
WO2021040736A1 (fr) * 2019-08-30 2021-03-04 Obsidian Therapeutics, Inc. Compositions à base de car cd19 tandem et méthodes d'immunothérapie
WO2021046451A1 (fr) 2019-09-06 2021-03-11 Obsidian Therapeutics, Inc. Compositions et méthodes de régulation de protéine accordable dhfr
US11058725B2 (en) 2019-09-10 2021-07-13 Obsidian Therapeutics, Inc. CA2 compositions and methods for tunable regulation
WO2021142376A1 (fr) 2020-01-08 2021-07-15 Obsidian Therapeutics, Inc. Compositions et procédés pour la régulation accordable de la transcription
WO2021262773A1 (fr) 2020-06-22 2021-12-30 Obsidian Therapeutics, Inc. Compositions et méthodes de régulation accordable de nucléases de cas
WO2022159935A1 (fr) 2021-01-19 2022-07-28 Obsidian Therapeutics, Inc. Compositions et procédés pour l'expansion de lymphocytes t et de lymphocytes infiltrant les tumeurs
WO2022159939A1 (fr) 2021-01-19 2022-07-28 Obsidian Therapeutics, Inc. Lymphocytes infiltrant les tumeurs avec interleukine 15 liée à la membrane et leurs utilisations
WO2022261475A1 (fr) * 2021-06-11 2022-12-15 Spark Therapeutics, Inc. Méthodes de régulation de la production de virus adénoassociés
WO2023069418A2 (fr) 2021-10-18 2023-04-27 Obsidian Therapeutics, Inc. Compositions et systèmes pour la régulation de la fonction/abondance et de l'administration de charges utiles polypeptidiques
WO2023141436A1 (fr) 2022-01-18 2023-07-27 Obsidian Therapeutics, Inc. Procédés d'identification et d'utilisation de lymphocytes infiltrant les tumeurs allogéniques pour traiter le cancer

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